Analysis scripts: K. pneumoniae complex genomics
analysis-kleb.Rmd
library(tidytree)
#> If you use the ggtree package suite in published research,
#> please cite the appropriate paper(s):
#>
#> Guangchuang Yu. Data Integration, Manipulation and Visualization of
#> Phylogenetic Trees (1st edition). Chapman and Hall/CRC. 2022,
#> doi:10.1201/9781003279242
#>
#> G Yu. Data Integration, Manipulation and Visualization of Phylogenetic
#> Trees (1st ed.). Chapman and Hall/CRC. 2022. ISBN: 9781032233574
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library(rstatix)
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library(phytools)
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library(ggtree)
#> ggtree v3.9.1 For help: https://yulab-smu.top/treedata-book/
#>
#> If you use the ggtree package suite in published research, please cite
#> the appropriate paper(s):
#>
#> Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
#> ggtree: an R package for visualization and annotation of phylogenetic
#> trees with their covariates and other associated data. Methods in
#> Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
#>
#> LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR
#> Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package
#> for phylogenetic tree input and output with richly annotated and
#> associated data. Molecular Biology and Evolution. 2020, 37(2):599-603.
#> doi: 10.1093/molbev/msz240
#>
#> S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
#> Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
#> visualization of richly annotated phylogenetic data. Molecular Biology
#> and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166
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library(ape)
library(cowplot)
library(ggpubr)
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library(dplyr)
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library(forcats)
library(tidyr)
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library(here)
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library(kableExtra)
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#> group_rows
library(patchwork)
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#> align_plots
library(scales)
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library(viridis)
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library(pheatmap)
library(ggplotify)
library(blantyreESBL)
library(stringr)
library(ggnewscale)
library(vegan)
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#> scores
# helper to reliably round numbers
sp_dc <- function(x, k) {
trimws(format(round(x, k), nsmall = k))
}
# flag - save figs to file?
write_figs <- FALSE
if (write_figs) {
if (!dir.exists(here("figures"))) {
dir.create(here("figures"))
}
if (!dir.exists(here("tables"))) {
dir.create(here("tables"))
}
if (!dir.exists(here("figures/kleb-genomics"))) {
dir.create(here("figures/kleb-genomics"))
}
if (!dir.exists(here("tables/kleb-genomics"))) {
dir.create(here("tables/kleb-genomics"))
}
}Introduction
This document generates the tables and figures for the manuscript:
Genomic and antigenic diversity of colonising Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi
Joseph M Lewis1,2,3,4, , Madalitso Mphasa1, Rachel Banda1, Matthew Beale4, Jane Mallewa5, Eva Heinz2, Nicholas Thomson4,6, Nicholas A Feasey1,2
- Malawi Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
- Wellcome Sanger Institute, Hinxton, UK
- College of Medicine, University of Malawi, Malawi
- London School of Tropical Medicine and Hygiene, London, UK
Look at within-participant correlation of STs
btESBL_sequence_sample_metadata %>%
mutate(ST = if_else(is.na(ST), NA_character_, ST)) ->
btESBL_sequence_sample_metadata
# plot ST distribution; then exclude all samples that are
# 1) within one participant
# 2) have same ST
# and plot
bind_rows(
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
group_by(ST, pid) %>%
mutate(
ST = paste0("ST", ST),
group = "All samples"
) %>%
arrange(pid, ST),
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
group_by(ST, pid) %>%
mutate(
ST = paste0("ST", ST),
group = "Within-participant\nDuplicate STs exlcuded"
) %>%
arrange(pid, ST) %>%
slice(1)
) %>%
select(pid, ST, group, kleb_k_locus, kleb_o_locus) %>%
rename_with(~ gsub("kleb_", "", .x)) %>%
rename_with(~ gsub("k_locus", "K locus", .x)) %>%
rename_with(~ gsub("o_locus", "O locus", .x)) %>%
pivot_longer(-c(pid, group)) %>%
ggplot(aes(fct_infreq(value), fill = group)) +
geom_bar(position = "dodge") +
facet_wrap(~name, scales = "free", ncol = 1) +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
labs(fill = "", x = "", y = "Number of samples") ->
ST_K_O_within_pt_sens_ax_plot
bind_rows(
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
group_by(ST, pid) %>%
mutate(
ST = paste0("ST", ST),
group = "All samples"
) %>%
arrange(pid, ST),
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
group_by(ST, pid) %>%
mutate(
ST = paste0("ST", ST),
group = "Within-participant\nDuplicate STs exlcuded"
) %>%
arrange(pid, ST) %>%
slice(1)
) %>%
select(pid, ST, group, kleb_k_locus, kleb_o_locus) %>%
rename_with(~ gsub("kleb_", "", .x)) %>%
rename_with(~ gsub("k_locus", "K locus", .x)) %>%
rename_with(~ gsub("o_locus", "O locus", .x)) %>%
pivot_longer(-c(pid, group)) %>%
ungroup() %>%
group_by(name) %>%
summarise(chi = fisher.test(table(group, value), simulate.p.value = TRUE)$p.value)
#> # A tibble: 3 × 2
#> name chi
#> <chr> <dbl>
#> 1 K locus 1
#> 2 O locus 1
#> 3 ST 1
# median number of STs per participant
btESBL_sequence_sample_metadata %>%
filter(grepl("Kleb", species)) %>%
select(pid, ST) %>%
group_by(pid) %>%
mutate(n = length(unique(ST))) %>%
ungroup() %>%
summarise(med_STs_per_participant = median(n), lq = quantile(n, 0.25), uq = quantile(n, 0.75))
#> # A tibble: 1 × 3
#> med_STs_per_participant lq uq
#> <int> <dbl> <dbl>
#> 1 1 1 2
# Functions to calculate % of within- and between- participants samples
# that have same
prop_same_ST_within <- function(df) {
full_join(
df %>%
filter(grepl("Kleb", species)) %>%
select(pid, ST) %>%
mutate(key = 1:nrow(.)),
df %>%
filter(grepl("Kleb", species)) %>%
select(pid, ST) %>%
mutate(key = 1:nrow(.)),
by = character()
) %>%
filter(key.x != key.y) -> d
d[!duplicated(apply(d[c(3,6)], 1, sort), MARGIN = 2), ] -> d
outdf <-
data.frame(
n_same_ST = sum(d$pid.x == d$pid.y & d$ST.x == d$ST.y, na.rm = TRUE),
n_total_comparisons = sum(d$pid.x == d$pid.y, na.rm = TRUE)) %>%
rowwise() %>%
mutate(prop = n_same_ST / n_total_comparisons,
lci = binom.test(n_same_ST,
n_total_comparisons)$conf.int[1],
uci = binom.test(n_same_ST,
n_total_comparisons)$conf.int[2] )
return(outdf)
}
prop_same_ST_between <- function(df) {
full_join(
df %>%
filter(grepl("Kleb", species)) %>%
select(pid, ST) %>%
mutate(key = 1:nrow(.)),
df %>%
filter(grepl("Kleb", species)) %>%
select(pid, ST) %>%
mutate(key = 1:nrow(.)),
by = character()
) %>%
filter(key.x != key.y) -> d
d[!duplicated(apply(d[c(3,6)], 1, sort), MARGIN = 2), ] -> d
outdf <-
data.frame(
n_same_ST = sum(d$ST.x == d$ST.y & d$pid.x != d$pid.y, na.rm = TRUE),
n_total_comparisons = sum(d$pid.x != d$pid.y, na.rm = TRUE)) %>%
rowwise() %>%
mutate(prop = n_same_ST / n_total_comparisons,
lci = binom.test(n_same_ST,
n_total_comparisons)$conf.int[1],
uci = binom.test(n_same_ST,
n_total_comparisons)$conf.int[2] )
return(outdf)
}
# calculate
prop_same_ST_between(btESBL_sequence_sample_metadata)
#> Warning: Using `by = character()` to perform a cross join was deprecated in dplyr 1.1.0.
#> ℹ Please use `cross_join()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> # A tibble: 1 × 5
#> # Rowwise:
#> n_same_ST n_total_comparisons prop lci uci
#> <int> <int> <dbl> <dbl> <dbl>
#> 1 550 20225 0.0272 0.0250 0.0295
prop_same_ST_within(btESBL_sequence_sample_metadata)
#> # A tibble: 1 × 5
#> # Rowwise:
#> n_same_ST n_total_comparisons prop lci uci
#> <int> <int> <dbl> <dbl> <dbl>
#> 1 20 76 0.263 0.169 0.377
# if we sdample one of each duplicated within-particpant ST how many left
btESBL_sequence_sample_metadata %>%
filter(grepl("Kleb", species)) %>%
group_by(pid, ST) %>%
slice(1) %>%
nrow()
#> [1] 184
ST_K_O_within_pt_sens_ax_plot
Distribution of ST, O- and K- loci for all samples, and excluding all but one sample in cases where a participant has two samples where the same ST was identified.
if (write_figs) {
ggsave(
filename = here("figures/kleb-genomics/SUP_F_st_o_k_sensax_plot.svg"),
plot = ST_K_O_within_pt_sens_ax_plot,
width = 12,
height = 8
)
ggsave(
filename = here("figures/kleb-genomics/SUP_F_st_o_k_sensax_plot.pdf"),
plot = ST_K_O_within_pt_sens_ax_plot,
width = 12,
height = 8
)
}MLST, K and O loci
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
rename_with(~ gsub("kleb_", "", .x)) %>%
rename_with(~ gsub("k_locus", "K_locus", .x)) %>%
rename_with(~ gsub("o_locus", "O_locus", .x)) ->
dassimKleb_BTKleb.diversity
dassimKleb_BTKleb.diversity %>%
group_by(ST) %>%
mutate(n = n(),
ST = paste0("ST", ST)) %>%
filter(n > 1, ST != "STNovel") %>%
ggplot(aes(fct_infreq(ST))) +
geom_bar(fill = viridis_pal()(4)[3]) +
coord_flip() +
labs(y = "Number", x = element_blank()) +
theme_bw() -> a
dassimKleb_BTKleb.diversity %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ "Unknown")) %>%
group_by(K_locus) %>%
mutate(n = n()) %>%
filter(n > 1) %>%
ggplot(aes(fct_infreq(K_locus))) +
geom_bar(fill = viridis_pal()(4)[2]) +
coord_flip() +
labs(y = "Number", x = element_blank()) +
theme_bw() -> b
dassimKleb_BTKleb.diversity %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown")) %>%
group_by(O_locus) %>%
mutate(n = n()) %>%
# filter(n > 1) %>%
ggplot(aes(fct_infreq(O_locus))) +
geom_bar(fill = viridis_pal()(4)[1]) +
coord_flip() +
labs(y = "Number", x = element_blank()) +
theme_bw() -> c
# cum K and O serotypes
bind_rows(
dassimKleb_BTKleb.diversity %>%
group_by(K_locus) %>%
summarise(n = n()) %>%
ungroup() %>%
arrange(desc(n)) %>%
mutate(
n_loci = 1:n(),
cum_n = cumsum(n),
cum_prop = cum_n / (max(cum_n) + 9),
type = "K-type"
) %>%
rename(Locus = K_locus),
dassimKleb_BTKleb.diversity %>%
group_by(O_locus) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c(
"Good",
"High",
"Very high"
) ~ O_locus,
TRUE ~ "Unknown"
)) %>%
filter(O_locus != "Unknown") %>%
summarise(n = n()) %>%
ungroup() %>%
arrange(desc(n)) %>%
mutate(
n_loci = 1:n(),
cum_n = cumsum(n),
cum_prop = cum_n / (max(cum_n) + 6), # fudge for unknown O tyoe
type = "O-type"
) %>%
rename(Locus = O_locus),
dassimKleb_BTKleb.diversity %>%
filter(ST != "Novel") %>%
group_by(ST) %>%
summarise(n = n()) %>%
ungroup() %>%
arrange(desc(n)) %>%
mutate(
n_loci = 1:n(),
cum_n = cumsum(n),
cum_prop = cum_n / max(cum_n),
type = "ST"
) %>%
rename(Locus = ST)
) %>%
mutate(type = factor(type,
levels =
c(
"O-type",
"K-type",
"ST"
)
)) %>%
ggplot(aes(n_loci, cum_prop, color = type)) +
geom_line() +
theme_bw() +
scale_color_manual(values = viridis_pal()(4)[1:3]) +
labs(x = "Number of K/O-type/ST", y = "Cum. prevalence") +
theme(legend.title = element_blank()) -> d
dassimKleb_BTKleb.diversity %>%
mutate(
O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown"
),
ST = paste0("ST", ST)
) %>%
filter(ST != "STNovel") %>%
group_by(ST) %>%
mutate(n = n()) %>%
filter(n > 1) %>%
ungroup() %>%
mutate(O_locus = fct_infreq(O_locus),
ST = fct_infreq(ST)) %>%
group_by(O_locus, ST) %>%
summarise(n = n()) %>%
ggplot(aes(ST, O_locus, size = n)) +
geom_point(color = viridis_pal()(4)[1]) +
theme_bw() +
labs(y = "O-type") +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
legend.title = element_blank()) -> e
#> `summarise()` has grouped output by 'O_locus'. You can override using the
#> `.groups` argument.
dassimKleb_BTKleb.diversity %>%
mutate(
K_locus = case_when(
K_locus_confidence %in%
c(
"Good",
"High",
"Very high"
) ~ K_locus,
TRUE ~ "Unknown"
),
ST = paste0("ST", ST)
) %>%
filter(ST != "STNovel") %>%
group_by(ST) %>%
mutate(n = n()) %>%
filter(n > 1) %>%
ungroup() %>%
mutate(
K_locus = fct_infreq(K_locus),
ST = fct_infreq(ST)
) %>%
group_by(K_locus, ST) %>%
summarise(n = n()) %>%
ggplot(aes(ST, K_locus, size = n)) +
geom_point(color = viridis_pal()(4)[2]) +
theme_bw() +
labs(y = "K-type") +
theme(
axis.text.x = element_text(angle = 45, hjust = 1),
legend.title = element_blank()
) +
scale_size(breaks = c(5, 10, 15)) -> f
#> `summarise()` has grouped output by 'K_locus'. You can override using the
#> `.groups` argument.
((a + b + (c / d)) / e / f) +
plot_layout(heights = c(2, 1, 2)) +
plot_annotation(tag_levels = "A") -> stplot
stplot
FIGURE X: Diversity of Klebsiella chromasomal sequence type (ST, A), K-type (B) and O-type (C). (D) shows cumulative prevalence for ST, K-type and O-types for all isolates in the collection as a function of the number of K-types, O-types, or STs, with each category ordered in size from largest to smallest. (E) and (F) show ST association of O-type and K-type respectively, where area of point is proportional to number of samples in the study. STs with only a single representative in the collection are excluded from plots A, B, C,E, F.
if (write_figs) {
ggsave(
filename = here("figures/kleb-genomics/F1_stplot.svg"),
plot = stplot,
width = 8,
height = 11
)
ggsave(
filename = here("figures/kleb-genomics/F1_stplot.pdf"),
plot = stplot,
width = 8,
height = 11
)
}
dassimKleb_BTKleb.diversity %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c(
"Good",
"High",
"Very high"
) ~ O_locus,
TRUE ~ "Unknown"
)) %>%
group_by(O_locus) %>%
summarise(n = n()) %>%
arrange(desc(n)) %>%
mutate(csum = cumsum(n)) %>%
mutate(n = paste0(n, " (", sp_dc(100 * n / max(csum), 1), "%)")) %>%
mutate(prop = paste0(csum, " (", sp_dc(100 * csum / max(csum), 1), "%)")) %>%
select(O_locus, n, prop) %>%
kbl(
caption = "O-types of carriage isolates",
col.names = c(
"O-type",
"n (%)",
"Cumulative n (%)"
)
) %>%
kable_classic(full_width = FALSE)| O-type | n (%) | Cumulative n (%) |
|---|---|---|
| O1v1 | 60 (29.6%) | 60 (29.6%) |
| O2v2 | 30 (14.8%) | 90 (44.3%) |
| O1v2 | 29 (14.3%) | 119 (58.6%) |
| O4 | 29 (14.3%) | 148 (72.9%) |
| O3b | 16 (7.9%) | 164 (80.8%) |
| O2v1 | 13 (6.4%) | 177 (87.2%) |
| O5 | 6 (3.0%) | 183 (90.1%) |
| OL101 | 6 (3.0%) | 189 (93.1%) |
| OL103 | 6 (3.0%) | 195 (96.1%) |
| Unknown | 6 (3.0%) | 201 (99.0%) |
| O12 | 1 (0.5%) | 202 (99.5%) |
| OL104 | 1 (0.5%) | 203 (100.0%) |
dassimKleb_BTKleb.diversity %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c(
"Good",
"High",
"Very high"
) ~ K_locus,
TRUE ~ "Unknown"
)) %>%
group_by(K_locus) %>%
summarise(n = n()) %>%
arrange(desc(n)) %>%
mutate(csum = cumsum(n)) %>%
mutate(n = paste0(n, " (", sp_dc(100 * n / max(csum), 1), "%)")) %>%
mutate(prop = paste0(csum, " (", sp_dc(100 * csum / max(csum), 1), "%)")) %>%
select(K_locus, n, prop) %>%
kbl(
caption = "K-types of carriage isolates",
col.names = c(
"K-type",
"n (%)",
"Cumulative n (%)"
)
) %>%
kable_classic(full_width = FALSE)| K-type | n (%) | Cumulative n (%) |
|---|---|---|
| KL2 | 23 (11.3%) | 23 (11.3%) |
| KL102 | 19 (9.4%) | 42 (20.7%) |
| KL15 | 13 (6.4%) | 55 (27.1%) |
| KL25 | 12 (5.9%) | 67 (33.0%) |
| KL111 | 11 (5.4%) | 78 (38.4%) |
| Unknown | 9 (4.4%) | 87 (42.9%) |
| KL149 | 8 (3.9%) | 95 (46.8%) |
| KL30 | 8 (3.9%) | 103 (50.7%) |
| KL16 | 7 (3.4%) | 110 (54.2%) |
| KL24 | 7 (3.4%) | 117 (57.6%) |
| KL10 | 6 (3.0%) | 123 (60.6%) |
| KL17 | 6 (3.0%) | 129 (63.5%) |
| KL57 | 6 (3.0%) | 135 (66.5%) |
| KL112 | 5 (2.5%) | 140 (69.0%) |
| KL23 | 5 (2.5%) | 145 (71.4%) |
| KL27 | 5 (2.5%) | 150 (73.9%) |
| KL110 | 4 (2.0%) | 154 (75.9%) |
| KL48 | 4 (2.0%) | 158 (77.8%) |
| KL137 | 3 (1.5%) | 161 (79.3%) |
| KL18 | 3 (1.5%) | 164 (80.8%) |
| KL39 | 3 (1.5%) | 167 (82.3%) |
| KL108 | 2 (1.0%) | 169 (83.3%) |
| KL13 | 2 (1.0%) | 171 (84.2%) |
| KL136 | 2 (1.0%) | 173 (85.2%) |
| KL151 | 2 (1.0%) | 175 (86.2%) |
| KL155 | 2 (1.0%) | 177 (87.2%) |
| KL21 | 2 (1.0%) | 179 (88.2%) |
| KL54 | 2 (1.0%) | 181 (89.2%) |
| KL63 | 2 (1.0%) | 183 (90.1%) |
| KL67 | 2 (1.0%) | 185 (91.1%) |
| KL8 | 2 (1.0%) | 187 (92.1%) |
| KL103 | 1 (0.5%) | 188 (92.6%) |
| KL105 | 1 (0.5%) | 189 (93.1%) |
| KL114 | 1 (0.5%) | 190 (93.6%) |
| KL115 | 1 (0.5%) | 191 (94.1%) |
| KL12 | 1 (0.5%) | 192 (94.6%) |
| KL123 | 1 (0.5%) | 193 (95.1%) |
| KL14 | 1 (0.5%) | 194 (95.6%) |
| KL145 | 1 (0.5%) | 195 (96.1%) |
| KL157 | 1 (0.5%) | 196 (96.6%) |
| KL19 | 1 (0.5%) | 197 (97.0%) |
| KL52 | 1 (0.5%) | 198 (97.5%) |
| KL59 | 1 (0.5%) | 199 (98.0%) |
| KL62 | 1 (0.5%) | 200 (98.5%) |
| KL64 | 1 (0.5%) | 201 (99.0%) |
| KL74 | 1 (0.5%) | 202 (99.5%) |
| KL9 | 1 (0.5%) | 203 (100.0%) |
Species and population structure
# what species from kleborate
table(dassimKleb_BTKleb.diversity$species)
#>
#> Klebsiella pneumoniae
#> 190
#> Klebsiella quasipneumoniae subsp. quasipneumoniae
#> 2
#> Klebsiella quasipneumoniae subsp. similipneumoniae
#> 7
#> Klebsiella quasivariicola
#> 1
#> Klebsiella variicola subsp. variicola
#> 3
dassimKleb_trees.BTcarriage <- btESBL_coregene_tree_kleb
dassimKleb_BTKleb.diversity %>%
select(ST, lane) %>%
mutate(ST = if_else(ST == "Novel",
"Novel",
paste0("ST", ST))) %>%
pivot_wider(
id_cols = lane,
names_from = ST,
values_from = ST,
values_fn = length,
values_fill = 0
) %>%
mutate(lane = gsub("#", "_", lane)) %>%
as.data.frame() ->
mlst.onehot
mlst.onehot[, c(
"lane",
names(sort(apply(mlst.onehot[-1], 2, sum),
decreasing = TRUE
))
)] -> mlst.onehot
mlst.onehot[-1] <- lapply(mlst.onehot[-1], as.factor)
rownames(mlst.onehot) <- mlst.onehot$lane
dassimKleb_BTKleb.diversity %>%
rename(strain = lane) %>%
mutate(strain = gsub("#", "_", strain)) %>%
select(strain, species) %>%
as.data.frame() ->
spec_hm
rownames(spec_hm) <- spec_hm$strain
get_legend(
ggtree(btESBL_coregene_tree_kleb) %>%
gheatmap(
select(spec_hm, species),
width = 0.05,
color = NA,
font.size = 3,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 10,
offset = 0.006 ) +
theme(legend.position = "bottom", legend.title = element_blank()) +
ylim(NA, 220) +
scale_fill_manual(values = viridis(n = 5)[c(2:5,1)])
) -> leg
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
ggtree(btESBL_coregene_tree_kleb) %>%
gheatmap(
select(spec_hm, species) %>%
rename(Species = species),
width = 0.05,
color = NA,
font.size = 3,
colnames_angle = 90,
colnames_position = "top",
hjust = 0,
colnames_offset_y = 0,
offset = 0 ) %>%
gheatmap(
select(mlst.onehot,-lane),
width = 3,
color = NA,
font.size = 3,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 0,
hjust = 0,
offset = 0.008
) +
theme(legend.position = "none") +
ylim(NA, 220) +
scale_fill_manual(values = c("lightgrey", "black", viridis(n = 5)[c(2:5,1)])) +
geom_treescale(x = 0.05, y = 180, offset = 2) ->
p1
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
ggtree(tree_subset(btESBL_coregene_tree_kleb, 210,
levels_back = 0)) %>%
gheatmap(
select(mlst.onehot,-lane),
width = 2,
color = NA,
font.size = 3,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 0,
hjust = 0,
offset = 0
) + ylim(NA, 205) +
theme(legend.position = "none") +
scale_fill_manual(values = c("lightgrey", "black")) +
geom_treescale(x = 0.002, y = 180, offset = 2) -> p2
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
((p1 + labs(tag = "A")) / leg / (p2 + labs(tag = "B"))) +
plot_layout(heights = c(1, 0.1,1)) -> dassim_trees
dassim_trees
Midpoint-rooted maximum likelihood core gene phylogeny for all samples in collection (A) and restricted to K. pneumoniae sensu stricto (B) showing chromasomal sequence types where black indicates presence and grey absence.
AMR determinents
# add class ro which resistnce is conferred --------------------------------
quinolone <- "Par|Gyr|Par|Qnr|Qep|Nor|GyrA|GyrB|ParC|ParE"
tetracycline <- "Tet"
sulphonamide <- "Sul"
aminoglycoside <- "Str|Aad|Aac|Aph|Rmt|APH"
streptothricin <- "Sat"
macrolide <- "Mph|Mdf|Erm|Ere"
fosfomycin <- "Fos"
chloramphenicol <- "Cat|FloR|Cml"
trimethoprim <- "Dfr"
rifampicin <- "Arr"
ESBL <- "SHV_12"
penicillinase <- "OKP|SCO|LEN|LAP|AmpC|AmpH"
ampc <- "CMY"
btESBL_amrgenes %>%
semi_join(dassimKleb_BTKleb.diversity,
by = c( "lane")) %>%
select(-genus) %>%
rename(gene = ref_seq) %>%
# add in QRDR mutations
bind_rows(
btESBL_qrdr_mutations %>%
filter(genus == "K. pneumoniae complex") %>%
select(-genus) %>%
semi_join(
btESBL_CARD_qrdr_mutations,
by = c("variant" = "variant",
"gene" = "gene")
) %>%
select(gene, lane) %>%
unique() %>%
mutate(gene =
gsub("(^.{1})", '\\U\\1',
gene,
perl = TRUE))
) %>%
filter(!grepl("MrdA|MefB", gene)) %>% # AmpH|AMPH|AmpC|
# add in beta-lactamases
left_join(
select(btESBL_NCBI_phenotypic_bl, allele_name, class),
by = c("gene" = "allele_name")) %>%
mutate(class = case_when(
str_detect(gene, quinolone) ~ "Quinolone",
str_detect(gene, tetracycline) ~ "Tetracycline",
str_detect(gene, sulphonamide) ~ "Sulphonamide",
str_detect(gene, aminoglycoside) ~ "Aminoglycoside",
str_detect(gene, streptothricin) ~ "Streptothricin",
str_detect(gene, macrolide) ~ "Macrolide",
str_detect(gene, fosfomycin) ~ "Fosfomycin",
str_detect(gene, chloramphenicol) ~ "Chloramphenicol",
str_detect(gene, rifampicin) ~ "Rifampicin",
str_detect(gene,trimethoprim) ~ "Trimethoprim",
str_detect(gene,ESBL) ~ "ESBL",
str_detect(gene,penicillinase) ~ "Penicillinase",
str_detect(gene,ampc) ~ "AmpC",
TRUE ~ class
)) %>%
mutate(gene = if_else(gene == "TEM_95",
"TEM_1",
gene)) ->
dassimKleb_BTKleb.amr
# how many genes per sample
dassimKleb_BTKleb.amr %>%
group_by(lane) %>%
mutate(n = n()) %>%
ungroup() %>%
select(lane, n) %>%
unique() %>%
summarise(
min = min(n),
lq = quantile(n, 0.25),
med = median(n),
uq = quantile(n, 0.75),
max = max(n)
)
#> # A tibble: 1 × 5
#> min lq med uq max
#> <int> <dbl> <int> <dbl> <int>
#> 1 6 11.5 15 17 25
### Plot overall prevalence
dassimKleb_BTKleb.amr %>%
filter(!grepl("Oqx", gene)) %>% # remove efflux and intrinsic K pnemo
group_by(class) %>% # penicillinase
mutate(n_class = length(class),
n_genes_in_class = n_distinct(gene)) %>%
select(class, n_class, n_genes_in_class) %>%
unique() %>%
arrange(n_class) %>%
ungroup() %>%
mutate(
end = cumsum(n_genes_in_class),
start = lag(end, default = 0),
textpos = start + 0.5 * (end - start)
) -> annotate.df
dassimKleb_BTKleb.amr %>%
filter(!grepl("Oqx", gene)) %>%
group_by(class) %>%
mutate(
n_class = length(class),
n_genes_in_class = n_distinct(gene),
gene = gsub("_", "-", gene)
) %>%
ggplot(aes(fct_reorder(fct_rev(fct_infreq(
gene
)), n_class),
fill = class)) +
geom_bar() +
theme_bw() +
coord_flip(ylim = c(-5, 210),
clip = "off",
expand = FALSE) +
annotate(
geom = "segment",
x = annotate.df$start + 0.5 + 0.2,
xend = annotate.df$end + 0.5 - 0.2,
y = -60,
yend = -60
) +
annotate(
geom = "text",
y = -70,
x = annotate.df$textpos,
label = annotate.df$class,
size = 3,
hjust = 1
) +
labs(y = "Number") +
theme(
plot.margin = unit(c(0.2, 0.5, 0.2, 4), "cm"),
axis.title.y = element_blank(),
legend.position = "none"
) -> amrplot
amrplot
FIGURE X: Prevalence of AMR gene grouped by class
Clustering of AMR genes
# jaccard distance
dassimKleb_BTKleb.amr %>%
filter(!grepl("AmpH|Oqx|ParC|GyrA", gene)) %>%
select(-class) %>%
pivot_wider(id_cols = lane ,
names_from = gene,
values_from = gene,
values_fn = length,
values_fill = 0) -> amr.ariba.onehot
names(amr.ariba.onehot) <- gsub("_","-",names(amr.ariba.onehot))
as.data.frame(
1 - as.matrix(
dist(t(amr.ariba.onehot[-1]), method = "binary")
)
) -> clust.amr
ggplotify::as.ggplot(
pheatmap(clust.amr,
color = viridis_pal()(100),
fontsize = 6)
) -> amr.heatmap
SUPPLEMENTARY FIGURE X: Jaccard-distance heatmap of presence of ARIBA-identified AMR genes, clustered with a hierarchical clustering algorithm. Several AMR-gene clusters are apparent. Excluded from this matrix are the chromasomally-integrated gyrA, parC (quinolone resistance genes) and the ampH penicillinase.
if (write_figs) {
ggsave(
filename = here("figures/kleb-genomics/SUP_F_amr_heatmap.svg"),
plot = amr.heatmap,
width = 9,
height = 8
)
ggsave(
filename = here("figures/kleb-genomics/SUP_F_amr_heatmap.pdf"),
plot = amr.heatmap,
width = 9,
height = 8
)
}
dassimKleb_BTKleb.amr %>%
filter(!gene %in% c("OqxA", "OqxB", "FosA")) %>%
# remove FosA as not in KpI which we are plottingh
mutate(lane = gsub("#", "_", lane),
gene = gsub("_","-", gene)) %>%
group_by(class) %>%
mutate(n_class = length(class)) %>%
ungroup() %>%
group_by(gene) %>%
mutate(n_gene = length(gene)) %>%
arrange(desc(n_class), desc(n_gene)) %>%
select(-n_class, -n_gene) %>%
pivot_wider(id_cols = lane,
values_from = class,
names_from = gene) %>%
as.data.frame() ->
amr.ariba.maptotree
dassimKleb_BTKleb.amr %>%
filter(!gene %in% c("OqxA", "OqxB", "FosA")) %>%
mutate(lane = gsub("#", "_", lane),
gene = gsub("_","-", gene)) %>%
group_by(class) %>%
mutate(n_class = length(class)) %>%
ungroup() %>%
group_by(gene) %>%
mutate(n_gene = length(gene)) %>%
arrange(desc(n_class), desc(n_gene)) %>% pull(class) %>%
unique() -> class_order
rownames(amr.ariba.maptotree) <- amr.ariba.maptotree$lane
colz = hue_pal()(11)
names(colz) <- sort(unique(dassimKleb_BTKleb.amr %>%
# filter(class != "Fosfomycin") %>%
pull(class)))
ggtree(tree_subset(btESBL_coregene_tree_kleb, 210,
levels_back = 0)) %>%
#ggtree(tree) %>%
gheatmap(
select(amr.ariba.maptotree,-lane),
width = 5,
color = NA,
font.size = 3,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 0,
hjust = 0,
offset = 0
) +
ylim(NA, 210) +
scale_fill_manual(name = "Class", values = colz,
breaks = class_order,
na.translate = FALSE) ->
malawi_tree_with_amr_kp1
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
ggtree(btESBL_coregene_tree_kleb) %>%
#ggtree(tree) %>%
gheatmap(
select(amr.ariba.maptotree,-lane),
width = 5,
color = NA,
font.size = 3,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 0,
hjust = 0,
offset = 0
) +
ylim(NA, 220) +
scale_fill_manual(name = "Class", values = colz,
breaks = class_order,
na.translate = FALSE) ->
malawi_tree_with_amr_all
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
(malawi_tree_with_amr_kp1 / malawi_tree_with_amr_all) + plot_annotation(tag_levels = "A") + plot_layout(guides = "collect") -> tree_amr_plt
tree_amr_plt
Presence of ARIBA-identified AMR genes mapped back to phylogeny for (A) KPI isolates only (B) all samples. Some lineage association of AMR genes is apparent.
Diversity of Malawian carriage isolates in a global context
Plot table of metadata across studies
# function to boostrap confidence intervals for diversity indices from
# vegan package
bootstrap_diveristy_cis <-
function(df,
n_reps = 100,
diversity_measure = "shannon",
output = "string") {
outlist <- list()
if (all(is.na(df$ST))) {
if (output == "string") {
out <- "NA"
} else {
out <- data.frame(mid = NA,
lci = NA,
uci = NA)
}
} else {
for (i in 1:n_reps) {
df_resample <-
df %>%
ungroup() %>%
slice_sample(n = nrow(df), replace = TRUE) %>%
select(ST) %>%
filter(!is.na(ST)) %>%
pivot_wider(
names_from = ST,
values_from = ST,
values_fn = length,
values_fill = 0
)
outlist[[i]] <-
vegan::diversity(df_resample, index = diversity_measure)
}
results <- unlist(outlist)
outdf <- data.frame(mid = median(results, na.rm = TRUE),
lci = quantile(results, 0.025, na.rm = TRUE),
uci = quantile(results, 0.975, na.rm = TRUE))
outstr = paste0(
sp_dc(median(results, na.rm = TRUE),2),
" 95% CI (",
sp_dc(quantile(results, 0.025, na.rm = TRUE), 2),
"-",
sp_dc(quantile(results, 0.975, na.rm = TRUE), 2),
")"
)
rownames(outdf) <- NULL
if (output == "string") {
out <- outstr
} else {
out <- outdf
}
}
return(out)
}
# by group
left_join(
btESBL_kleb_global_metadata %>%
filter(name %in% btESBL_kleb_globaltree$tip.label) %>%
mutate(
`Isolate Type` = case_when(
`Isolate Type` == "Carriage" ~ "Colonising",
`Isolate Type` == "Infection" ~ "Invasive",
TRUE ~ `Isolate Type`
)
) %>%
group_by(study) %>%
summarise(
n = n(),
invasive = paste0(
sum(`Isolate Type` == "Invasive", na.rm = TRUE),
"/",
sum(!is.na(`Isolate Type`)),
" (",
sp_dc(100 * (
sum(`Isolate Type` == "Invasive", na.rm = TRUE) /
sum(!is.na(`Isolate Type`))
),
0),
" %)"
),
esbl = paste0(
sum(ESBL == "ESBL", na.rm = TRUE),
"/",
sum(!is.na(ESBL)),
" (",
sp_dc(100 * (
sum(ESBL == "ESBL", na.rm = TRUE) /
sum(!is.na(ESBL))
),
0),
" %)"
),
),
btESBL_kleb_global_metadata %>%
filter(name %in% btESBL_kleb_globaltree$tip.label) %>%
mutate(
`Isolate Type` = case_when(
`Isolate Type` == "Carriage" ~ "Colonising",
`Isolate Type` == "Infection" ~ "Invasive",
TRUE ~ `Isolate Type`
)
) %>%
group_by(study) %>%
group_modify(
~ bootstrap_diveristy_cis(
.x,
diversity_measure = "shannon",
output = "df",
n_reps = 1000
)
) %>%
mutate(st_diversity =
if_else(
is.na(mid),
"-",
paste0(sp_dc(mid, 2),
" 95% CI (",
sp_dc(lci, 2),
"-",
sp_dc(uci, 2),
")")
)) %>%
select(study, st_diversity),
by = c("study")
) %>%
mutate(
study = case_when(
study == "cornick" ~ "Cornick et al 2021",
study == "DASSIM" ~ "This study",
study == "global" ~ "Holt et al 2015",
study == "kenya" ~ "Henson et el 2017",
study == "musciha" ~ "Musicha et al 2019"
)
) %>%
kbl(
col.names = c(
"Study",
"Included genomes",
"Invasive",
"ESBL",
"Shannon diversity in ST (95% CI)"
),
caption = "Characteristics of included genomes"
) %>%
add_header_above(c(
" " = 2,
"Proportion of samples that are" = 2,
" " = 1
)) %>%
kable_classic(full_width = FALSE) %>%
footnote(
general = c(
"Invasive is defined as cultured from a sterile site",
"ESBL is defined as presence of any recognised ESBL gene"
)
)| Study | Included genomes | Invasive | ESBL | Shannon diversity in ST (95% CI) |
|---|---|---|---|---|
| This study | 203 | 0/203 (0 %) | 200/203 (99 %) | 3.57 95% CI (3.43-3.69) |
| Cornick et al 2021 | 79 | 79/79 (100 %) | 66/79 (84 %) | 2.74 95% CI (2.46-2.99) |
| Holt et al 2015 | 264 | 142/187 (76 %) | 104/264 (39 %) |
|
| Henson et el 2017 | 65 | 65/65 (100 %) | 43/65 (66 %) |
|
| Musicha et al 2019 | 71 | 60/71 (85 %) | 40/71 (56 %) | 3.17 95% CI (2.92-3.37) |
| Note: | ||||
| Invasive is defined as cultured from a sterile site | ||||
| ESBL is defined as presence of any recognised ESBL gene |
btESBL_kleb_global_metadata %>%
select(study, ST, `Isolate Type`) %>%
mutate(ST = if_else(grepl("Novel|Unknown", ST), NA_character_, ST)) %>%
filter(!is.na(ST)) %>%
mutate(`Isolate Type` = case_when(
`Isolate Type` == "Carriage" ~ "Colonising",
`Isolate Type` == "Infection" ~ "Invasive",
TRUE ~ `Isolate Type`)) %>%
mutate(
study = case_when(
study == "cornick" ~ "Cornick et al 2021",
study == "DASSIM" ~ "This study",
study == "global" ~ "Holt et al 2015",
study == "kenya" ~ "Henson et el 2017",
study == "musciha" ~ "Musicha et al 2019"
)) %>%
ggplot(aes(fct_infreq(ST), fill = `Isolate Type`)) +
geom_bar() +
facet_wrap(~ study, ncol = 1, scales = "free_y") +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 4)) +
labs(x = "ST", y = "Number of samples") ->
st_dist_plot_malawi
st_dist_plot_malawi
ST distribution stratified by Malawian samples
if (write_figs) {
ggsave(
filename = here("figures/kleb-genomics/SUP_F_malawi_st_by_study.pdf"),
plot = st_dist_plot_malawi,
width = 9,
height = 5
)
ggsave(
filename = here("figures/kleb-genomics/SUP_F_malawi_st_by_study.svg"),
plot = st_dist_plot_malawi,
width = 9,
height = 5
)
}
btESBL_kleb_global_metadata %>%
mutate(`Isolate Type` = case_when(
`Isolate Type` == "Carriage" ~ "Colonising",
`Isolate Type` == "Infection" ~ "Invasive",
TRUE ~ `Isolate Type`)) ->
dassimKleb_globalKleb.metadata
col <-
c("white",
"grey30",
brewer_pal(palette = "Set3")(6))
names(col) <-
c("0",
"1",
"Human",
"Animal",
"Environmental",
"Invasive",
"Colonising",
"ESBL")
(
(
(
(
ggtree(
tree_subset(btESBL_kleb_globaltree, 734, levels_back = 0),
size = 0.3
) %>%
gheatmap(
select(dassimKleb_globalKleb.metadata, Malawi) %>%
mutate(Malawi =
case_when(
Malawi == "1" ~ "Malawi",
Malawi == "0" ~ "Not Malawi"
)),
width = 0.03,
color = NA,
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0
) +
scale_fill_manual(
values = c("Not Malawi" = "white", "Malawi" = "grey30"),
name = "Country",
na.translate = FALSE,
guide = guide_legend(order = 1)
) +
new_scale_fill()
) %>%
gheatmap(
select(dassimKleb_globalKleb.metadata, `Sample Source`),
width = 0.03,
color = NA,
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0,
offset = 0.00022
) +
scale_fill_manual(
values =
c(
"Human" = brewer_pal(palette = "Set3")(6)[1],
"Animal" = brewer_pal(palette = "Set3")(6)[2],
"Environmental" = brewer_pal(palette = "Set3")(6)[3]
),
na.translate = FALSE,
name = "Sample\nSource",
guide = guide_legend(order = 2)
) +
new_scale_fill()
) %>%
gheatmap(
select(dassimKleb_globalKleb.metadata, `Isolate Type`),
width = 0.03,
color = NA,
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0,
offset = 0.00044
) +
scale_fill_manual(
values =
c(
"Invasive" = brewer_pal(palette = "Set3")(6)[4],
"Colonising" = brewer_pal(palette = "Set3")(6)[5]
),
na.translate = FALSE,
name = "Isolate\nType",
guide = guide_legend(order = 3)
) +
new_scale_fill()
) %>% gheatmap(
select(dassimKleb_globalKleb.metadata, ESBL) %>%
mutate(ESBL = if_else(ESBL == "ESBL", "Present", NA_character_)),
width = 0.03,
color = NA,
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0,
offset = 0.00066
) +
scale_fill_manual(
values =
c("Present" = brewer_pal(palette = "Set3")(6)[6]),
na.translate = FALSE,
name = "ESBL",
guide = guide_legend(order = 4)
) +
new_scale_fill()
) +
ylim(NA, 680) +
geom_cladelabel(
node = 759,
label = "ST14",
align = TRUE,
offset = -0.0008,
barsize = 0.3
) +
geom_cladelabel(
node = 801,
label = "ST15",
align = TRUE,
offset = -0.0008,
barsize = 0.3
) +
geom_cladelabel(
node = 1059,
label = "ST340",
align = TRUE,
offset = -0.002,
barsize = 0.3
) +
geom_cladelabel(
node = 1145,
label = "ST307",
align = TRUE,
offset = -0.002,
barsize = 0.3
) +
geom_treescale(x = 0.001, y = 550, offset = 5,width = 0.001,
linesize =0.3) ->
globaltree_plot
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
globaltree_plot
#> Warning: The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
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#> the data.
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#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
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#> the data.
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#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
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#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
Malawian isolates: comparing carriage and infection
(
(
ggtree(
tree_subset(
btESBL_kleb_malawi_allisolate_core_gene_tree,
372,
levels_back = 0
)
) %>%
gheatmap(
select(dassimKleb_globalKleb.metadata, `Isolate Type`),
width = 0.03,
color = NA,
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0,
offset = 0.0002
) +
scale_fill_manual(
values =
c(
"Invasive" = brewer_pal(palette = "Set3")(6)[4],
"Colonising" = brewer_pal(palette = "Set3")(6)[5]
),
na.translate = FALSE,
name = "Isolate\nType",
guide = guide_legend(order = 2)
) +
new_scale_fill()
) %>% gheatmap(
select(dassimKleb_globalKleb.metadata, ESBL) %>%
mutate(ESBL = if_else(ESBL == "ESBL", "Present", NA_character_)),
width = 0.03,
color = NA,
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0,
offset = 0
) +
scale_fill_manual(
values =
c("Present" = brewer_pal(palette = "Set3")(6)[6]),
na.translate = FALSE,
name = "ESBL",
guide = guide_legend(order = 1)
) +
new_scale_fill()
) %>% gheatmap(
select(dassimKleb_globalKleb.metadata, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
mutate(across(
everything(), ~
if_else(.x == "1", "Present", NA_character_)
)),
width = 0.18,
color = "lightgrey",
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0,
offset = 0.0005
) +
scale_fill_manual(
values = c("Present" = "grey30"),
name = "Virulence\nLocus",
na.translate = FALSE,
guide = guide_legend(order = 3)
) +
ylim(NA, 370) +
geom_cladelabel(
node = 516,
label = "ST268",
align = TRUE,
offset = -0.0011,
fontsize = 3
) +
geom_cladelabel(
node = 629,
label = "ST218",
align = TRUE,
offset = -0.00163,
fontsize = 3
) +
geom_cladelabel(
node = 376,
label = "ST14",
align = TRUE,
offset = -0.00062,
fontsize = 3
) +
geom_cladelabel(
node = 412,
label = "ST15",
align = TRUE,
offset = -0.00074,
fontsize = 3
) +
geom_cladelabel(
node = 585,
label = "ST340",
align = TRUE,
offset = -0.00158,
fontsize = 3
) +
geom_cladelabel(
node = 523,
label = "ST307",
align = TRUE,
offset = -0.0013,
fontsize = 3
) +
geom_treescale(
x = 0.0003,
y = 330,
offset = 2,
width = 0.001,
fontsize = 3
) -> malawi_tree_plot_final
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
malawi_tree_plot_final
#> Warning: The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
#> The following aesthetics were dropped during statistical transformation: node,
#> parent
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#> the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#> variable into a factor?
Midpoint rooted core gene maximum likelihood phylogenetic tree of Malawian isolates.
if (write_figs) {
ggsave(
filename = here("figures/kleb-genomics/F4_malawitree.pdf"),
plot = malawi_tree_plot_final,
width = 8,
height = 10
)
ggsave(
filename = here("figures/kleb-genomics/F4_malawitree.svg"),
plot = malawi_tree_plot_final,
width = 8,
height = 10
)
}
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi") %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(`Isolate Type`, ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
pivot_longer(-c(`Isolate Type`, ESBL)) %>%
mutate(value = if_else(value == 1, "Present", "Absent")) %>%
filter(!is.na(value)) %>%
ggplot(aes(name, fill = value)) + geom_bar(position = "fill") +
facet_grid( ~ `Isolate Type`) +
theme_bw() +
scale_fill_viridis_d() +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
legend.title = element_blank()) +
labs(y = "Proportion", x = "") -> a
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi",!is.na(ESBL)) %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(`Isolate Type`, ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
pivot_longer(-c(`Isolate Type`, ESBL)) %>%
mutate(value = if_else(value == 1, "Present", "Absent")) %>%
filter(!is.na(value)) %>%
ggplot(aes(name, fill = value)) + geom_bar(position = "fill") +
facet_grid( ~ ESBL) +
theme_bw() +
scale_fill_viridis_d() +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
legend.title = element_blank()) +
labs(y = "Proportion", x = "") -> b
(a / b) +
plot_layout(guides = "collect") +
plot_annotation(tag_levels = "A") -> virplot
virplot
O types infection vs carriage
dassimKleb_globalKleb.metadata %>%
filter(study %in% c("cornick", "DASSIM","musciha"),
!is.na(O_locus)) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown")) %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ "Unknown")) %>%
group_by(`Isolate Type`) %>%
mutate(total = length(O_locus)) %>%
group_by(O_locus, `Isolate Type`) %>%
summarise(prop = length(O_locus)/unique(total),
lci = binom.test(length(O_locus), unique(total))$conf.int[1],
uci = binom.test(length(O_locus), unique(total))$conf.int[2]) %>%
ggplot(aes(fct_rev(fct_reorder(O_locus,prop)),
prop,
color = `Isolate Type`,
shape = `Isolate Type`,
ymin = lci,
ymax = uci)) +
geom_point(position = position_dodge(width = 0.5)) +
geom_errorbar(width = 0, position = position_dodge(width = 0.5)) +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
labs(x = "O-type", y = "Proportion of samples") +
scale_color_manual(values = hue_pal()(2)[c(2,1)]) ->
o_type_distn_plot
#> `summarise()` has grouped output by 'O_locus'. You can override using the
#> `.groups` argument.
dassimKleb_globalKleb.metadata %>%
filter(study %in% c("cornick", "DASSIM", "musciha"),!is.na(O_locus)) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown"
)) %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ "Unknown"
)) %>%
mutate(K_locus = as.factor(K_locus),
`Isolate Type` = as.factor(`Isolate Type`)) %>%
count(K_locus, `Isolate Type`, .drop = FALSE) %>%
group_by(`Isolate Type`) %>%
mutate(total = sum(n)) %>%
group_by(K_locus) %>%
filter(sum(n) > 2) %>%
group_by(K_locus, `Isolate Type`) %>%
summarise(
prop = n / unique(total),
lci = binom.test(n, unique(total))$conf.int[1],
uci = binom.test(n, unique(total))$conf.int[2]
) %>%
ggplot(aes(
fct_rev(fct_reorder(K_locus, prop)),
prop,
color = `Isolate Type`,
shape = `Isolate Type`,
ymin = lci,
ymax = uci
)) +
geom_point(position = position_dodge(width = 0.5)) +
geom_errorbar(width = 0, position = position_dodge(width = 0.5)) +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
labs(x = "K-type", y = "Proportion of samples") +
scale_color_manual(values = hue_pal()(2)[c(2, 1)]) ->
k_type_distn_plot
#> `summarise()` has grouped output by 'K_locus'. You can override using the
#> `.groups` argument.
o_type_distn_plot + k_type_distn_plot +
plot_annotation(tag_levels = "A") +
plot_layout(widths = c(1,1.8), guides = 'collect') &
theme(legend.position = "bottom") -> o_ktype_distn_plot
o_ktype_distn_plot
Testing independence of distributions of K- and O-types
dassimKleb_globalKleb.metadata %>%
filter(study %in% c("cornick", "DASSIM","musciha"),
!is.na(O_locus)) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown")) %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ "Unknown")) -> df
row_wise_fisher_test(
table(df$K_locus, df$`Isolate Type`),
simulate.p.value = TRUE,
p.adjust.method = "fdr") %>%
select(-c(n,p.adj.signif)) ->
tab
tab %>%
kbl(
caption = "Benjamini-Hochberg corrected p values testing equal distribution of K-types across invasive and carriage isolates",
col.names = c(
"K-type",
"Uncorrected p-value",
"Benjamini-Hochberg corrected p-values"
)
) %>%
kable_classic(full_width = FALSE) %>%
row_spec(which(tab$p.adj < 0.05), bold = TRUE)| K-type | Uncorrected p-value | Benjamini-Hochberg corrected p-values |
|---|---|---|
| KL10 | 0.154000 | 0.6640 |
| KL102 | 0.054300 | 0.5120 |
| KL103 | 1.000000 | 1.0000 |
| KL104 | 0.394000 | 0.8390 |
| KL105 | 1.000000 | 1.0000 |
| KL106 | 1.000000 | 1.0000 |
| KL108 | 0.521000 | 0.8820 |
| KL109 | 0.394000 | 0.8390 |
| KL110 | 0.157000 | 0.6640 |
| KL111 | 0.032300 | 0.3550 |
| KL112 | 0.161000 | 0.6640 |
| KL114 | 1.000000 | 1.0000 |
| KL115 | 1.000000 | 1.0000 |
| KL12 | 1.000000 | 1.0000 |
| KL122 | 0.394000 | 0.8390 |
| KL123 | 1.000000 | 1.0000 |
| KL125 | 0.394000 | 0.8390 |
| KL127 | 0.394000 | 0.8390 |
| KL13 | 1.000000 | 1.0000 |
| KL132 | 1.000000 | 1.0000 |
| KL134 | 0.394000 | 0.8390 |
| KL136 | 0.521000 | 0.8820 |
| KL137 | 0.282000 | 0.8390 |
| KL14 | 0.564000 | 0.9080 |
| KL142 | 0.394000 | 0.8390 |
| KL145 | 1.000000 | 1.0000 |
| KL149 | 0.094500 | 0.6640 |
| KL15 | 0.013900 | 0.2290 |
| KL151 | 0.521000 | 0.8820 |
| KL155 | 0.521000 | 0.8820 |
| KL157 | 1.000000 | 1.0000 |
| KL158 | 0.394000 | 0.8390 |
| KL16 | 0.774000 | 1.0000 |
| KL165 | 0.394000 | 0.8390 |
| KL17 | 1.000000 | 1.0000 |
| KL18 | 0.282000 | 0.8390 |
| KL19 | 1.000000 | 1.0000 |
| KL2 | 0.865000 | 1.0000 |
| KL20 | 0.003490 | 0.0768 |
| KL21 | 0.521000 | 0.8820 |
| KL23 | 0.252000 | 0.8390 |
| KL24 | 0.538000 | 0.8880 |
| KL25 | 0.176000 | 0.6830 |
| KL27 | 0.085200 | 0.6640 |
| KL3 | 0.154000 | 0.6640 |
| KL30 | 0.770000 | 1.0000 |
| KL39 | 0.652000 | 1.0000 |
| KL43 | 0.000194 | 0.0128 |
| KL45 | 0.154000 | 0.6640 |
| KL48 | 0.652000 | 1.0000 |
| KL5 | 0.394000 | 0.8390 |
| KL51 | 0.154000 | 0.6640 |
| KL52 | 1.000000 | 1.0000 |
| KL53 | 0.394000 | 0.8390 |
| KL54 | 0.521000 | 0.8820 |
| KL55 | 0.154000 | 0.6640 |
| KL57 | 1.000000 | 1.0000 |
| KL59 | 1.000000 | 1.0000 |
| KL62 | 0.001280 | 0.0422 |
| KL63 | 1.000000 | 1.0000 |
| KL64 | 1.000000 | 1.0000 |
| KL67 | 0.521000 | 0.8820 |
| KL74 | 1.000000 | 1.0000 |
| KL8 | 0.521000 | 0.8820 |
| KL9 | 1.000000 | 1.0000 |
| Unknown | 0.028400 | 0.3550 |
row_wise_fisher_test(
table(df$O_locus, df$`Isolate Type`),
simulate.p.value = TRUE,
p.adjust.method = "fdr") %>%
select(-c(n,p.adj.signif)) ->
tab
tab %>%
kbl(caption = "Benjamini-Hochberg corrected p values testing equal distribution of O-types across invasive and carriage isolates",
col.names = c(
"O-type",
"Uncorrected p-value",
"Benjamini-Hochberg corrected p-values"
)) %>%
kable_classic(full_width = FALSE) %>%
row_spec(which(tab$p.adj < 0.05), bold = TRUE)| O-type | Uncorrected p-value | Benjamini-Hochberg corrected p-values |
|---|---|---|
| O1/O2v1 | 0.15400 | 0.431 |
| O12 | 1.00000 | 1.000 |
| O1v1 | 0.20300 | 0.474 |
| O1v2 | 0.04140 | 0.290 |
| O2v1 | 0.29800 | 0.596 |
| O2v2 | 0.53000 | 0.824 |
| O3/O3a | 0.00906 | 0.127 |
| O3b | 0.09730 | 0.341 |
| O4 | 0.75500 | 0.903 |
| O5 | 0.77400 | 0.903 |
| OL101 | 0.48800 | 0.824 |
| OL103 | 0.08520 | 0.341 |
| OL104 | 1.00000 | 1.000 |
| Unknown | 0.75800 | 0.903 |
Sensitivity analyses
K- and O-type distributions
K- and O- type distributions in a sub population defined by:
- Restricted to ESBL
- Exclude all but one samples from within one participant where there is a repeated ST
- Exclude ST340 from Cornick et al - the outbreak clone
dassimKleb_globalKleb.metadata %>%
filter(study %in% c("cornick", "DASSIM","musciha"),
!is.na(O_locus),
ESBL == "ESBL") %>%
anti_join(
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
group_by(pid,ST) %>%
mutate(n = 1:n()) %>%
filter(n > 1),
by = c("name" = "lane")) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown")) %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ "Unknown")) %>%
filter(!(study == "cornick" & ST == "ST340")) %>%
group_by(`Isolate Type`) %>%
mutate(total = length(O_locus)) %>%
group_by(O_locus, `Isolate Type`) %>%
summarise(prop = length(O_locus)/unique(total),
lci = binom.test(length(O_locus), unique(total))$conf.int[1],
uci = binom.test(length(O_locus), unique(total))$conf.int[2]) %>%
ggplot(aes(fct_rev(fct_reorder(O_locus,prop)),
prop,
color = `Isolate Type`,
shape = `Isolate Type`,
ymin = lci,
ymax = uci)) +
geom_point(position = position_dodge(width = 0.5)) +
geom_errorbar(width = 0, position = position_dodge(width = 0.5)) +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
labs(x = "O-type", y = "Proportion of samples") +
scale_color_manual(values = hue_pal()(2)[c(2,1)]) ->
o_type_distn_plot_sensax
#> `summarise()` has grouped output by 'O_locus'. You can override using the
#> `.groups` argument.
dassimKleb_globalKleb.metadata %>%
filter(study %in% c("cornick", "DASSIM", "musciha"),
!is.na(O_locus),
ESBL == "ESBL") %>%
anti_join(
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
group_by(pid,ST) %>%
mutate(n = 1:n()) %>%
filter(n > 1),
by = c("name" = "lane")) %>%
filter(!(study == "cornick" & ST == "ST340")) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown"
)) %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ "Unknown"
)) %>%
mutate(K_locus = as.factor(K_locus),
`Isolate Type` = as.factor(`Isolate Type`)) %>%
count(K_locus, `Isolate Type`, .drop = FALSE) %>%
group_by(`Isolate Type`) %>%
mutate(total = sum(n)) %>%
group_by(K_locus) %>%
filter(sum(n) > 2) %>%
group_by(K_locus, `Isolate Type`) %>%
summarise(
prop = n / unique(total),
lci = binom.test(n, unique(total))$conf.int[1],
uci = binom.test(n, unique(total))$conf.int[2]
) %>%
ggplot(aes(
fct_rev(fct_reorder(K_locus, prop)),
prop,
color = `Isolate Type`,
shape = `Isolate Type`,
ymin = lci,
ymax = uci
)) +
geom_point(position = position_dodge(width = 0.5)) +
geom_errorbar(width = 0, position = position_dodge(width = 0.5)) +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
labs(x = "K-type", y = "Proportion of samples") +
scale_color_manual(values = hue_pal()(2)[c(2, 1)]) ->
k_type_distn_plot_sensax
#> `summarise()` has grouped output by 'K_locus'. You can override using the
#> `.groups` argument.
o_type_distn_plot_sensax + k_type_distn_plot_sensax +
plot_annotation(tag_levels = "A") +
plot_layout(widths = c(1,1.8), guides = 'collect') &
theme(legend.position = "bottom") -> o_ktype_distn_plot_sensax
o_ktype_distn_plot_sensax
Testing independence of distributions of K- and O-types
dassimKleb_globalKleb.metadata %>%
filter(study %in% c("cornick", "DASSIM","musciha"),
!is.na(O_locus),
ESBL == "ESBL") %>%
anti_join(
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
group_by(pid,ST) %>%
mutate(n = 1:n()) %>%
filter(n > 1),
by = c("name" = "lane")) %>%
filter(!(study == "cornick" & ST == "ST340")) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown")) %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ "Unknown")) -> df
row_wise_fisher_test(
table(df$K_locus, df$`Isolate Type`),
simulate.p.value = TRUE,
p.adjust.method = "fdr") %>%
select(-c(n,p.adj.signif)) ->
tab
tab %>%
kbl(
caption = "Benjamini-Hochberg corrected p values testing equal distribution of K-types across invasive and carriage isolates in the sensitivity analysis subpopulation",
col.names = c(
"K-type",
"Uncorrected p-value",
"Benjamini-Hochberg corrected p-values"
)
) %>%
kable_classic(full_width = FALSE) %>%
row_spec(which(tab$p.adj < 0.05), bold = TRUE)| K-type | Uncorrected p-value | Benjamini-Hochberg corrected p-values |
|---|---|---|
| KL10 | 3.26e-01 | 0.964000 |
| KL102 | 4.81e-01 | 1.000000 |
| KL103 | 1.00e+00 | 1.000000 |
| KL105 | 1.00e+00 | 1.000000 |
| KL106 | 1.00e+00 | 1.000000 |
| KL108 | 1.00e+00 | 1.000000 |
| KL109 | 2.90e-01 | 0.964000 |
| KL110 | 3.27e-01 | 0.964000 |
| KL111 | 6.78e-02 | 0.666000 |
| KL112 | 3.26e-01 | 0.964000 |
| KL114 | 1.00e+00 | 1.000000 |
| KL115 | 1.00e+00 | 1.000000 |
| KL12 | 1.00e+00 | 1.000000 |
| KL123 | 1.00e+00 | 1.000000 |
| KL125 | 2.90e-01 | 0.964000 |
| KL13 | 1.00e+00 | 1.000000 |
| KL136 | 1.00e+00 | 1.000000 |
| KL137 | 5.59e-01 | 1.000000 |
| KL14 | 4.97e-01 | 1.000000 |
| KL142 | 2.90e-01 | 0.964000 |
| KL145 | 1.00e+00 | 1.000000 |
| KL149 | 6.77e-01 | 1.000000 |
| KL15 | 1.17e-01 | 0.819000 |
| KL151 | 1.00e+00 | 1.000000 |
| KL155 | 1.00e+00 | 1.000000 |
| KL16 | 2.88e-01 | 0.964000 |
| KL17 | 4.82e-01 | 1.000000 |
| KL18 | 1.00e+00 | 1.000000 |
| KL19 | 1.00e+00 | 1.000000 |
| KL2 | 4.05e-01 | 1.000000 |
| KL20 | 1.87e-03 | 0.052400 |
| KL21 | 1.00e+00 | 1.000000 |
| KL23 | 1.86e-01 | 0.964000 |
| KL24 | 1.00e+00 | 1.000000 |
| KL25 | 3.58e-01 | 1.000000 |
| KL27 | 3.26e-01 | 0.964000 |
| KL3 | 8.33e-02 | 0.666000 |
| KL30 | 7.49e-01 | 1.000000 |
| KL39 | 1.00e+00 | 1.000000 |
| KL43 | 1.03e-05 | 0.000577 |
| KL45 | 8.33e-02 | 0.666000 |
| KL48 | 1.00e+00 | 1.000000 |
| KL51 | 8.33e-02 | 0.666000 |
| KL52 | 1.00e+00 | 1.000000 |
| KL54 | 1.00e+00 | 1.000000 |
| KL55 | 2.90e-01 | 0.964000 |
| KL57 | 7.22e-01 | 1.000000 |
| KL59 | 1.00e+00 | 1.000000 |
| KL62 | 2.03e-01 | 0.964000 |
| KL63 | 1.00e+00 | 1.000000 |
| KL64 | 4.97e-01 | 1.000000 |
| KL67 | 1.00e+00 | 1.000000 |
| KL74 | 1.00e+00 | 1.000000 |
| KL8 | 1.00e+00 | 1.000000 |
| KL9 | 1.00e+00 | 1.000000 |
| Unknown | 4.86e-02 | 0.666000 |
row_wise_fisher_test(
table(df$O_locus, df$`Isolate Type`),
simulate.p.value = TRUE,
p.adjust.method = "fdr") %>%
select(-c(n,p.adj.signif)) ->
tab
tab %>%
kbl(caption = "Benjamini-Hochberg corrected p values testing equal distribution of O-types across invasive and carriage isolates in the sensitivity analysis subpopulation",
col.names = c(
"O-type",
"Uncorrected p-value",
"Benjamini-Hochberg corrected p-values"
)) %>%
kable_classic(full_width = FALSE) %>%
row_spec(which(tab$p.adj < 0.05), bold = TRUE)| O-type | Uncorrected p-value | Benjamini-Hochberg corrected p-values |
|---|---|---|
| O1/O2v1 | 0.08330 | 0.2170 |
| O12 | 0.49700 | 0.5870 |
| O1v1 | 0.06190 | 0.2010 |
| O1v2 | 0.11200 | 0.2430 |
| O2v1 | 0.00809 | 0.0728 |
| O2v2 | 1.00000 | 1.0000 |
| O3b | 0.04530 | 0.1960 |
| O4 | 0.01120 | 0.0728 |
| O5 | 0.72200 | 0.7820 |
| OL101 | 0.18600 | 0.3020 |
| OL103 | 0.18600 | 0.3020 |
| OL104 | 0.49700 | 0.5870 |
| Unknown | 0.48200 | 0.5870 |
Virulence determinents in sensitivity analysis subpopulation
df %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(`Isolate Type`, ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
pivot_longer(-c(`Isolate Type`, ESBL)) %>%
mutate(value = if_else(value == 1, "Present", "Absent")) %>%
filter(!is.na(value)) %>%
ggplot(aes(name, fill = value)) + geom_bar(position = "fill") +
facet_grid( ~ `Isolate Type`) +
theme_bw() +
scale_fill_viridis_d() +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
legend.title = element_blank()) +
labs(y = "Proportion", x = "") -> a
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi") %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(`Isolate Type`, ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
pivot_longer(-c(`Isolate Type`, ESBL)) %>%
mutate(value = if_else(value == 1, "Present", "Absent")) %>%
filter(!is.na(value)) %>%
ggplot(aes(name, fill = value)) + geom_bar(position = "fill") +
facet_grid( ~ `Isolate Type`) +
theme_bw() +
scale_fill_viridis_d() +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
legend.title = element_blank()) +
labs(y = "Proportion", x = "") -> b
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi",!is.na(ESBL)) %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(`Isolate Type`, ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
pivot_longer(-c(`Isolate Type`, ESBL)) %>%
mutate(value = if_else(value == 1, "Present", "Absent")) %>%
filter(!is.na(value)) %>%
ggplot(aes(name, fill = value)) + geom_bar(position = "fill") +
facet_grid( ~ ESBL) +
theme_bw() +
scale_fill_viridis_d() +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
legend.title = element_blank()) +
labs(y = "Proportion", x = "") -> c
(b / c / a) + plot_annotation(tag_levels = "A") +
plot_layout(guides = "collect") -> virulence_sensax_plot
virulence_sensax_plot
Virulence determinents comparing in colonising and invasive isolates (A), ESBL and non ESBL isolates (B), both considering all isolates, and colonising and infecting isolates only in the sensitivity analysis population.
if (write_figs) {
ggsave(
filename = here("figures/kleb-genomics/SUP_F_virulence_sens_ax.pdf"),
plot = virulence_sensax_plot,
width = 5,
height = 7.5
)
ggsave(
filename = here("figures/kleb-genomics/SUP_F_virulence_sens_ax.svg"),
plot = o_ktype_distn_plot_sensax,
width = 5,
height = 7.5
)
}
bind_rows(
dassimKleb_globalKleb.metadata %>%
filter(
location == "Malawi",
!is.na(`Isolate Type`)
) %>%
select(`Isolate Type`, ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(`Isolate Type`, ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
pivot_longer(-c(`Isolate Type`, ESBL)) %>%
mutate(value = as.factor(if_else(value == 1, "Present", "Absent"))) %>%
ungroup() %>%
group_by(name) %>%
mutate(p = fisher.test(table(`Isolate Type`, value),
simulate.p.value = TRUE
)$p.value) %>%
summarise(
population = "all",
invasive = paste0(
sum(value == "Present" & `Isolate Type` == "Invasive", na.rm = TRUE),
"/",
sum(`Isolate Type` == "Invasive", na.rm = TRUE),
" (",
sp_dc(
100 * sum(value == "Present" & `Isolate Type` == "Invasive", na.rm = TRUE) /
sum(`Isolate Type` == "Invasive", na.rm = TRUE), 0
),
"%)"
),
colonising = paste0(
sum(value == "Present" & `Isolate Type` == "Colonising"),
"/",
sum(`Isolate Type` == "Colonising"),
" (",
sp_dc(
100 * sum(value == "Present" & `Isolate Type` == "Colonising") /
sum(`Isolate Type` == "Colonising"), 0
),
"%)"
),
p = unique(p)
),
df %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(`Isolate Type`, ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
pivot_longer(-c(`Isolate Type`, ESBL)) %>%
mutate(value = as.factor(if_else(value == 1, "Present", "Absent"))) %>%
ungroup() %>%
group_by(name) %>%
mutate(p = fisher.test(table(`Isolate Type`, value),
simulate.p.value = TRUE
)$p.value) %>%
summarise(
population = "sensitivity",
invasive = paste0(
sum(value == "Present" & `Isolate Type` == "Invasive"),
"/",
sum(`Isolate Type` == "Invasive"),
" (",
sp_dc(
100 * sum(value == "Present" & `Isolate Type` == "Invasive") /
sum(`Isolate Type` == "Invasive"), 0
),
"%)"
),
colonising = paste0(
sum(value == "Present" & `Isolate Type` == "Colonising"),
"/",
sum(`Isolate Type` == "Colonising"),
" (",
sp_dc(
100 * sum(value == "Present" & `Isolate Type` == "Colonising") /
sum(`Isolate Type` == "Colonising"), 0
),
"%)"
),
p = unique(p)
)
) %>%
select(-population) %>%
mutate(
p = sp_dc(p, 3),
p = if_else(p == "0.000", "<0.001", p)
) %>%
kbl(col.names = c(
"Virulence gene",
"Invasive Isolates",
"Colonising Isolates",
"p value"
),
caption = "Distribution of virulence determinents stratified by whether sample is invasive or colonising") %>%
kable_classic(full_width = FALSE) %>%
pack_rows("All samples", 1, 6) %>%
pack_rows("Sensitivity analysis population", 7, 12) %>%
add_header_above(c(" ",
"Gene present in" = 2,
" "
))|
Gene present in
|
|||
|---|---|---|---|
| Virulence gene | Invasive Isolates | Colonising Isolates | p value |
| All samples | |||
| clb | 4/139 (3%) | 0/214 (0%) | 0.023 |
| iro | 8/139 (6%) | 1/214 (0%) | 0.003 |
| iuc | 18/139 (13%) | 1/214 (0%) | <0.001 |
| rmpA | 3/139 (2%) | 1/214 (0%) | 0.304 |
| rmpA2 | 18/139 (13%) | 1/214 (0%) | <0.001 |
| ybt | 26/139 (19%) | 68/214 (32%) | 0.007 |
| Sensitivity analysis population | |||
| clb | 4/78 (5%) | 0/191 (0%) | 0.007 |
| iro | 7/78 (9%) | 1/191 (1%) | 0.001 |
| iuc | 7/78 (9%) | 1/191 (1%) | 0.001 |
| rmpA | 3/78 (4%) | 1/191 (1%) | 0.075 |
| rmpA2 | 7/78 (9%) | 1/191 (1%) | 0.001 |
| ybt | 21/78 (27%) | 61/191 (32%) | 0.467 |
df %>%
select(K_locus, O_locus,ST) %>%
mutate(type = "Sensitivity\nAnalysis",
ST = gsub("STNovel", "Novel", ST)) %>%
bind_rows(
dassimKleb_globalKleb.metadata %>%
filter(
location == "Malawi",
!is.na(`Isolate Type`)
) %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ "Unknown")) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown")) %>%
select(K_locus, O_locus,ST) %>%
mutate(type = "All samples")
) %>%
pivot_longer(-type) %>%
filter(!value %in% c("Unknown", "Novel", "STNovel")) %>%
mutate(value = fct_infreq(value)) %>%
ungroup() %>%
count(name,type, value, .drop = FALSE) %>%
filter(
!(name == "K_locus" & !grepl("K", value)),
!(name == "O_locus" & !grepl("O", value)),
!(name == "ST" & !grepl("ST", value))) %>%
group_by(name,type) %>%
mutate(tot = sum(n)) %>%
rowwise() %>%
mutate(
prop = n / tot,
lci = binom.test(n, tot)$conf.int[1],
uci = binom.test(n, tot)$conf.int[2],
name = gsub("_"," ", name)
) %>%
ggplot(aes(value, prop,
color = type,
ymin = lci,
ymax = uci)) +
geom_point(position = position_dodge(width = 0.3)) +
geom_errorbar(width = 0, position = position_dodge(width = 0.3)) +
facet_wrap(~ name, scales = "free", ncol = 1) +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 6),
legend.position = "top") +
labs(x = "", y = "Number of samples", color = "") -> st_k_o_plot_sensax
st_k_o_plot_sensax
K- and O-tyep and ST distribution comparing all sampes and sensitivity analsyis population
VFDB Analaysis
bind_rows(
left_join(
btESBL_kleb_global_metadata %>%
filter(location == "Malawi") %>%
select(name, `Isolate Type`),
btESBL_kleb_malawi_vfdb_output %>%
filter(
vf != "VF0560", # capsule
vf != "VF0561", # O type
vf != "VF0564", # yersinabactin
vf != "VF0562", # enterobactin
vf != "VF0228", # enterobactin
vf != "VF0564", # enterobactin
vf != "VF0136", # yresiniabactin
vf != "VF0565",
!grepl("rmpA|rmpA2|ybt|iuc|iro|clb", gene)
) %>%
mutate(
VF_Name = if_else(
!is.na(VF_FullName), VF_FullName,
VF_Name
),
VF_Name = case_when(
VF_Name == "Type I fimbriae" ~ "Type 1 fimbriae",
TRUE ~ VF_Name
)
) %>%
select(name, VF_Name) %>%
unique() %>%
filter(!is.na(VF_Name)) %>%
pivot_wider(
id_cols = name,
names_from = VF_Name,
values_from = VF_Name,
values_fn = length,
values_fill = 0
)
) %>%
mutate(across(is.numeric, ~ if_else(is.na(.x),
as.integer(0),
.x
))) %>%
pivot_longer(-c(name, `Isolate Type`), names_to = "gene") %>%
group_by(gene) %>%
mutate(p = fisher.test(`Isolate Type`, value)$p.value) %>%
summarise(
total = paste0(
sum(value),
"/",
length(value),
" (",
sp_dc(100 * sum(value) / length(value), 0),
"%)"
),
sorter = sum(value),
invasive = paste0(
sum(value == 1 & `Isolate Type` == "Infection"),
"/",
sum(`Isolate Type` == "Infection"),
" (",
sp_dc(100 *
sum(value == 1 & `Isolate Type` == "Infection") /
sum(`Isolate Type` == "Infection"), 0),
"%)"
),
carriage = paste0(
sum(value == 1 & `Isolate Type` == "Carriage"),
"/",
sum(`Isolate Type` == "Carriage"),
" (",
sp_dc(100 *
sum(value == 1 & `Isolate Type` == "Carriage") /
sum(`Isolate Type` == "Carriage"), 0),
"%)"
),
p = unique(p)
) %>%
arrange(-sorter) %>%
select(-sorter) %>%
left_join(
btESBL_kleb_malawi_vfdb_output %>% mutate(VF_Name = if_else(
!is.na(VF_FullName), VF_FullName,
VF_Name
)) %>% group_by(VF_Name) %>%
summarise(genes = paste(sort(unique(gene)), collapse = ", ")),
by = c("gene" = "VF_Name")
) %>%
transmute(
"Virulence Factor" = gene,
Genes = genes,
"All isolates" = total,
"Invasive isolates" = invasive,
"Colonising Isolates" = carriage,
"p-value" = p,
type = "all"
),
left_join(
btESBL_kleb_global_metadata %>%
filter(
study %in% c("cornick", "DASSIM", "musciha"),
!is.na(O_locus),
ESBL == "ESBL"
) %>%
anti_join(
btESBL_sequence_sample_metadata %>%
filter(grepl("Klebsiella", species)) %>%
group_by(pid, ST) %>%
mutate(n = 1:n()) %>%
filter(n > 1),
by = c("name" = "lane")
) %>%
filter(!(study == "cornick" & ST == "ST340")) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c(
"Good",
"High",
"Very high"
) ~ O_locus,
TRUE ~ "Unknown"
)) %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c(
"Good",
"High",
"Very high"
) ~ K_locus,
TRUE ~ "Unknown"
)) %>%
filter(location == "Malawi") %>%
select(name, `Isolate Type`),
btESBL_kleb_malawi_vfdb_output %>%
filter(
vf != "VF0560", # capsule
vf != "VF0561", # O type
vf != "VF0564", # yersinabactin
vf != "VF0562", # enterobactin
vf != "VF0228", # enterobactin
vf != "VF0564", # enterobactin
vf != "VF0136", # yresiniabactin
vf != "VF0565",
!grepl("rmpA|rmpA2|ybt|iuc|iro|clb", gene)
) %>%
mutate(
VF_Name = if_else(
!is.na(VF_FullName), VF_FullName,
VF_Name
),
VF_Name = case_when(
VF_Name == "Type I fimbriae" ~ "Type 1 fimbriae",
TRUE ~ VF_Name
)
) %>%
select(name, VF_Name) %>%
unique() %>%
filter(!is.na(VF_Name)) %>%
pivot_wider(
id_cols = name,
names_from = VF_Name,
values_from = VF_Name,
values_fn = length,
values_fill = 0
)
) %>%
mutate(across(is.numeric, ~ if_else(is.na(.x),
as.integer(0),
.x
))) %>%
pivot_longer(-c(name, `Isolate Type`), names_to = "gene") %>%
group_by(gene) %>%
mutate(
value2 = as.factor(value),
p = fisher.test(`Isolate Type`, value2)$p.value
) %>%
summarise(
total = paste0(
sum(value),
"/",
length(value),
" (",
sp_dc(100 * sum(value) / length(value), 0),
"%)"
),
sorter = sum(value),
invasive = paste0(
sum(value == 1 & `Isolate Type` == "Infection"),
"/",
sum(`Isolate Type` == "Infection"),
" (",
sp_dc(100 *
sum(value == 1 & `Isolate Type` == "Infection") /
sum(`Isolate Type` == "Infection"), 0),
"%)"
),
carriage = paste0(
sum(value == 1 & `Isolate Type` == "Carriage"),
"/",
sum(`Isolate Type` == "Carriage"),
" (",
sp_dc(100 *
sum(value == 1 & `Isolate Type` == "Carriage") /
sum(`Isolate Type` == "Carriage"), 0),
"%)"
),
p = unique(p)
) %>%
arrange(-sorter) %>%
select(-sorter) %>%
left_join(
btESBL_kleb_malawi_vfdb_output %>% mutate(VF_Name = if_else(
!is.na(VF_FullName), VF_FullName,
VF_Name
)) %>% group_by(VF_Name) %>%
summarise(genes = paste(sort(unique(gene)), collapse = ", ")),
by = c("gene" = "VF_Name")
) %>%
transmute(
"Virulence Factor" = gene,
Genes = genes,
"All isolates" = total,
"Invasive isolates" = invasive,
"Colonising Isolates" = carriage,
"p-value" = p,
type = "sens"
)
) %>%
mutate(
`p-value` = sp_dc(`p-value`, 3),
`p-value` = if_else(`p-value` == "0.000", "<0.001", `p-value`),
Genes = gsub("VFG048736", "tle1", Genes),
Genes = gsub("_(?![0-9])", "\\/", Genes, perl = TRUE),
`Virulence Factor` = gsub(
"K1 capsule", "E. coli K1 capsule",
`Virulence Factor`
)
) %>%
as.data.frame() %>%
select(-type) %>%
kbl() %>%
kable_classic(full_width = FALSE) %>%
pack_rows("All samples", 1, 17) %>%
pack_rows("Sensitivity analysis population", 18, 34)
#> Joining with `by = join_by(name)`
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(is.numeric, ~if_else(is.na(.x), as.integer(0), .x))`.
#> Caused by warning:
#> ! Use of bare predicate functions was deprecated in tidyselect 1.1.0.
#> ℹ Please use wrap predicates in `where()` instead.
#> # Was:
#> data %>% select(is.numeric)
#>
#> # Now:
#> data %>% select(where(is.numeric))
#> Joining with `by = join_by(name)`| Virulence Factor | Genes | All isolates | Invasive isolates | Colonising Isolates | p-value |
|---|---|---|---|---|---|
| All samples | |||||
| AcrAB | acrA, acrB | 350/353 (99%) | 136/139 (98%) | 214/214 (100%) | 0.060 |
| Regulation of capsule synthesis | rcsA, rcsB | 350/353 (99%) | 136/139 (98%) | 214/214 (100%) | 0.060 |
| Type 1 fimbriae | fimA, fimB, fimC, fimE, fimH, fimI | 348/353 (99%) | 137/139 (99%) | 211/214 (99%) | 1.000 |
| Type 3 fimbriae | mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ | 347/353 (98%) | 135/139 (97%) | 212/214 (99%) | 0.217 |
| T6SS | clpV/tssH, dotU/tssL, hcp/tssD, icmF/tssM, impA/tssA, KPHS_23120, sciN/tssJ, tli1, tssF, tssG, vasE/tssK, tle1, vgrG/tssI, vipA/tssB, vipB/tssC | 338/353 (96%) | 134/139 (96%) | 204/214 (95%) | 0.789 |
| E. coli common pilus | yagW/ecpD, yagY/ecpB, yagZ/ecpA, ykgK/ecpR | 32/353 (9%) | 2/139 (1%) | 30/214 (14%) | <0.001 |
| Allantion utilization | allA, allB, allC, allD, allR, allS | 12/353 (3%) | 4/139 (3%) | 8/214 (4%) | 0.770 |
| E. coli K1 capsule | kpsD, kpsE, kpsF | 2/353 (1%) | 2/139 (1%) | 0/214 (0%) | 0.154 |
| P fimbriae | papI | 2/353 (1%) | 2/139 (1%) | 0/214 (0%) | 0.154 |
| Afa/Dr family | afaE-I | 1/353 (0%) | 1/139 (1%) | 0/214 (0%) | 0.394 |
| Dr adhesins | draP | 1/353 (0%) | 1/139 (1%) | 0/214 (0%) | 0.394 |
| E. coli heme uptake | chuA, chuS, chuT, chuU, chuV, chuW, chuX, chuY | 1/353 (0%) | 1/139 (1%) | 0/214 (0%) | 0.394 |
| Flagella | fliJ | 1/353 (0%) | 1/139 (1%) | 0/214 (0%) | 0.394 |
| Invasion of brain endothelial cells | ibeA | 1/353 (0%) | 1/139 (1%) | 0/214 (0%) | 0.394 |
| Secreted autotransporter toxin | sat | 1/353 (0%) | 1/139 (1%) | 0/214 (0%) | 0.394 |
| Shigella enterotoxin 2 | senB | 1/353 (0%) | 1/139 (1%) | 0/214 (0%) | 0.394 |
| Type II secretion system | gspD, gspK | 1/353 (0%) | 1/139 (1%) | 0/214 (0%) | 0.394 |
| Sensitivity analysis population | |||||
| AcrAB | acrA, acrB | 269/269 (100%) | 78/78 (100%) | 191/191 (100%) | 1.000 |
| Regulation of capsule synthesis | rcsA, rcsB | 269/269 (100%) | 78/78 (100%) | 191/191 (100%) | 1.000 |
| Type 1 fimbriae | fimA, fimB, fimC, fimE, fimH, fimI | 266/269 (99%) | 78/78 (100%) | 188/191 (98%) | 0.559 |
| Type 3 fimbriae | mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ | 266/269 (99%) | 77/78 (99%) | 189/191 (99%) | 1.000 |
| T6SS | clpV/tssH, dotU/tssL, hcp/tssD, icmF/tssM, impA/tssA, KPHS_23120, sciN/tssJ, tli1, tssF, tssG, vasE/tssK, tle1, vgrG/tssI, vipA/tssB, vipB/tssC | 258/269 (96%) | 76/78 (97%) | 182/191 (95%) | 0.519 |
| E. coli common pilus | yagW/ecpD, yagY/ecpB, yagZ/ecpA, ykgK/ecpR | 27/269 (10%) | 2/78 (3%) | 25/191 (13%) | 0.007 |
| Allantion utilization | allA, allB, allC, allD, allR, allS | 11/269 (4%) | 3/78 (4%) | 8/191 (4%) | 1.000 |
| Afa/Dr family | afaE-I | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| Dr adhesins | draP | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| E. coli heme uptake | chuA, chuS, chuT, chuU, chuV, chuW, chuX, chuY | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| Invasion of brain endothelial cells | ibeA | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| E. coli K1 capsule | kpsD, kpsE, kpsF | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| P fimbriae | papI | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| Secreted autotransporter toxin | sat | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| Shigella enterotoxin 2 | senB | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| Type II secretion system | gspD, gspK | 1/269 (0%) | 1/78 (1%) | 0/191 (0%) | 0.290 |
| Flagella | fliJ | 0/269 (0%) | 0/78 (0%) | 0/191 (0%) | 1.000 |
left_join(
btESBL_kleb_global_metadata %>%
filter(location == "Malawi") %>%
select(name, `Isolate Type`, ESBL),
btESBL_kleb_malawi_vfdb_output %>%
filter(
vf != "VF0560", # capsule
vf != "VF0561", # O type
vf != "VF0564", # yersinabactin
vf != "VF0562", # enterobactin
vf != "VF0228", # enterobactin
vf != "VF0564", # enterobactin
vf != "VF0136", # yresiniabactin
vf != "VF0565",
!grepl("rmpA|rmpA2|ybt|iuc|iro|clb", gene)
) %>%
select(name, VF_Name) %>%
unique() %>%
filter(!is.na(VF_Name)) %>%
group_by(VF_Name) %>%
mutate(n = n()) %>%
filter(n > 5) %>%
select(-n) %>%
pivot_wider(
id_cols = name,
names_from = VF_Name,
values_from = VF_Name,
values_fn = length,
values_fill = 0
)
) %>%
mutate(across(is.numeric, ~ case_when(
.x == 0 ~ NA_character_,
.x == 1 ~ "Present",
TRUE ~ NA_character_
))) %>%
mutate(
`Isolate Type` =
case_when(
`Isolate Type` == "Infection" ~ "Invasive",
`Isolate Type` == "Carriage" ~ "Colonising",
TRUE ~ NA_character_
),
ESBL = if_else(ESBL == 0,
NA_character_,
ESBL
)
) %>%
relocate(matches("ECP|Allanti")) %>%
as.data.frame() -> vfdb_onehot
#> Joining with `by = join_by(name)`
rownames(vfdb_onehot) <- vfdb_onehot$name
(
(ggtree(
tree_subset(
btESBL_kleb_malawi_allisolate_core_gene_tree,
372,
levels_back = 0
)
) %>%
gheatmap(
select(vfdb_onehot, c(`Isolate Type`)),
width = 0.03,
color = NA,
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0,
offset = 0.0002
) +
scale_fill_manual(
values =
c(
"Invasive" = brewer_pal(palette = "Set3")(6)[4],
"Colonising" = brewer_pal(palette = "Set3")(6)[5]
),
na.translate = FALSE,
name = "Isolate\nType",
guide = guide_legend(order = 2)
) +
new_scale_fill()
) %>% gheatmap(
select(vfdb_onehot, ESBL) %>%
mutate(ESBL = if_else(ESBL == "ESBL", "Present", NA_character_)),
width = 0.03,
color = NA,
font.size = 4,
colnames_angle = 90,
colnames_position = "top",
colnames_offset_y = 5,
hjust = 0,
offset = 0
) +
scale_fill_manual(
values =
c("Present" = brewer_pal(palette = "Set3")(6)[6]),
na.translate = FALSE,
name = "ESBL",
guide = guide_legend(order = 1)
) +
new_scale_fill()
) %>%
gheatmap(
select(vfdb_onehot, -c(name, `Isolate Type`, ESBL)),
colnames_position = "top",
colnames_angle = 90,
offset = 0.0004,
colnames_offset_y = 5,
hjust = 0,
width = 0.21,
color = "lightgrey"
) +
scale_fill_manual(values = c("Present" = "grey30"),
na.translate = FALSE,
name = "Virulence\nLocus") +
ylim(NA, 370) ->
vfdb_malawi_tree_plot
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
vfdb_malawi_tree_plot
Midpoint rooted core gene maximum likelihood phylogenetic tree of Malawian isolates, showing VFDB virulence determinants.
Odds and ends to calculate for manuscript
length(unique(dassimKleb_BTKleb.diversity$ST))
#> [1] 62
dassimKleb_BTKleb.diversity %>%
group_by(ST) %>%
summarise(n = n()) %>%
ungroup() %>%
summarise(
median = median(n),
lqi = quantile(n, 0.25),
uqi = quantile(n, 0.75),
n_singletons = sum(n == 1)
)
#> # A tibble: 1 × 4
#> median lqi uqi n_singletons
#> <dbl> <dbl> <dbl> <int>
#> 1 2 1 4 26
length(unique(dassimKleb_BTKleb.diversity$K_locus))
#> [1] 49
dassimKleb_BTKleb.diversity %>%
group_by(K_locus) %>%
summarise(n = length(unique(ST))) %>%
ungroup() %>%
summarise(median = median(n),
lqi = quantile(n, 0.25),
uqi = quantile(n, 0.75))
#> # A tibble: 1 × 3
#> median lqi uqi
#> <int> <dbl> <dbl>
#> 1 1 1 2
length(unique(dassimKleb_BTKleb.diversity$O_locus))
#> [1] 12
dassimKleb_BTKleb.diversity %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ "Unknown")) %>%
mutate(O_locus =
case_when(
grepl("O1", O_locus) ~ "O1",
grepl("O2", O_locus) ~ "O2",
TRUE ~ O_locus)
) %>%
filter(O_locus != "Unknown") %>%
group_by(O_locus) %>%
summarise(n = length(unique(ST))) %>%
ungroup() %>%
summarise(median = median(n),
lqi = quantile(n, 0.25),
uqi = quantile(n, 0.75))
#> # A tibble: 1 × 3
#> median lqi uqi
#> <dbl> <dbl> <dbl>
#> 1 6 2.5 11.8
dassimKleb_BTKleb.amr %>%
filter(!gene %in% c("OqxA", "OqxB", "AmpH")) %>%
group_by(lane, class) %>%
ungroup() %>%
select(lane, class) %>%
unique() %>%
filter(!is.na(class)) %>%
group_by(class) %>%
summarise(n = n(), prop = n /203) %>%
as.data.frame()
#> class n prop
#> 1 Aminoglycoside 198 0.975369458
#> 2 Chloramphenicol 140 0.689655172
#> 3 ESBL 200 0.985221675
#> 4 Fosfomycin 1 0.004926108
#> 5 Macrolide 34 0.167487685
#> 6 Penicillinase 200 0.985221675
#> 7 Quinolone 76 0.374384236
#> 8 Rifampicin 52 0.256157635
#> 9 Sulphonamide 201 0.990147783
#> 10 Tetracycline 120 0.591133005
#> 11 Trimethoprim 198 0.975369458
btESBL_qrdr_mutations %>%
filter(genus == "K. pneumoniae complex") %>%
select(-genus) %>%
semi_join(
btESBL_CARD_qrdr_mutations,
by = c("variant" = "variant",
"gene" = "gene")) %>%
unique() %>% count(gene,variant)
#> # A tibble: 2 × 3
#> gene variant n
#> <chr> <chr> <int>
#> 1 gyrA S83F 10
#> 2 parC S80I 1
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi") %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(ybt, clb, iuc, iro, rmpA, rmpA2) %>%
summarise(across(everything(), ~ sum(as.numeric(.x), na.rm = TRUE)))
#> ybt clb iuc iro rmpA rmpA2
#> 1 94 4 19 9 4 19
# virulence by carriage vs infection
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi") %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(`Isolate Type`, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
group_by(`Isolate Type`) %>%
summarise(across(everything(), ~ sum(as.numeric(.x), na.rm = TRUE)))
#> # A tibble: 2 × 7
#> `Isolate Type` ybt clb iuc iro rmpA rmpA2
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Colonising 68 0 1 1 1 1
#> 2 Invasive 26 4 18 8 3 18
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi") %>%
group_by(`Isolate Type`) %>%
tally()
#> # A tibble: 2 × 2
#> `Isolate Type` n
#> <chr> <int>
#> 1 Colonising 214
#> 2 Invasive 139
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi") %>%
group_by(ESBL) %>%
tally()
#> # A tibble: 2 × 2
#> ESBL n
#> <chr> <int>
#> 1 0 47
#> 2 ESBL 306
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi") %>%
mutate(ESBL = if_else(ESBL == "ESBL", "ESBL", "Not ESBL")) %>%
select(ESBL, ybt, clb, iuc, iro, rmpA, rmpA2) %>%
group_by(ESBL) %>%
summarise(across(everything(), ~ sum(as.numeric(.x), na.rm = TRUE)))
#> # A tibble: 2 × 7
#> ESBL ybt clb iuc iro rmpA rmpA2
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 ESBL 89 4 8 8 4 8
#> 2 Not ESBL 5 0 11 1 0 11
dassimKleb_globalKleb.metadata %>%
filter(ST %in% c("ST218", "ST268"))
#> name ESBL Sample accession Lane accession study
#> 16228_1_61 16228_1_61 0 ERS669098 ERR972007 musciha
#> 16228_1_64 16228_1_64 ESBL ERS669104 ERR972010 musciha
#> 16228_1_77 16228_1_77 ESBL ERS669129 ERR972023 musciha
#> 16228_1_83 16228_1_83 ESBL ERS669139 ERR972029 musciha
#> 22036_8_82 22036_8_82 ESBL ERS1545129 ERR2397672 cornick
#> 22072_1_143 22072_1_143 ESBL ERS1531011 ERR2497284 cornick
#> 22072_1_151 22072_1_151 ESBL ERS1531021 ERR2497292 cornick
#> 22072_1_163 22072_1_163 ESBL ERS1531039 ERR2497304 cornick
#> 22072_1_241 22072_1_241 ESBL ERS1531130 ERR2497382 cornick
#> Sample Source Isolate Type Year location ST YbST CbST AbST
#> 16228_1_61 Human Invasive 1999 Malawi ST218 0 0 1
#> 16228_1_64 Human Invasive 2004 Malawi ST268 234-3LV 13-1LV 1-1LV
#> 16228_1_77 Human Invasive 2006 Malawi ST268 234-3LV 13-1LV 1-1LV
#> 16228_1_83 Human Invasive 2010 Malawi ST218 0 0 1-1LV
#> 22036_8_82 Human Invasive NA Malawi ST218 0 0 1-1LV
#> 22072_1_143 Human Invasive NA Malawi ST268 234-3LV 13-1LV 1-1LV
#> 22072_1_151 Human Invasive NA Malawi ST268 234-3LV 13-1LV 1-1LV
#> 22072_1_163 Human Invasive NA Malawi ST268 120-6LV 0 0
#> 22072_1_241 Human Invasive NA Malawi ST218 0 0 1-1LV
#> SmST rmpA rmpA2 O_locus K_locus K_locus_confidence
#> 16228_1_61 1 0 1 O2v2 KL57 Very high
#> 16228_1_64 1-1LV 0 1 O2v1 KL20 Very high
#> 16228_1_77 1 0 1 O2v1 KL20 Very high
#> 16228_1_83 1-1LV 0 1 O2v2 KL57 Very high
#> 22036_8_82 1-1LV 1 1 O2v2 KL57 Very high
#> 22072_1_143 1 0 1 O2v1 KL20 Very high
#> 22072_1_151 1 1 1 O2v1 KL20 Very high
#> 22072_1_163 0 0 0 O2v1 KL20 Very high
#> 22072_1_241 1-1LV 1 1 O2v2 KL57 High
#> O_locus_confidence ybt clb iuc iro year_dassim Malawi
#> 16228_1_61 Very high 0 0 1 1 NA 1
#> 16228_1_64 Very high 1 1 1 1 NA 1
#> 16228_1_77 Very high 1 1 1 1 NA 1
#> 16228_1_83 Very high 0 0 1 1 NA 1
#> 22036_8_82 Very high 0 0 1 1 NA 1
#> 22072_1_143 Very high 1 1 1 1 NA 1
#> 22072_1_151 Very high 1 1 1 1 NA 1
#> 22072_1_163 Very high 1 0 0 0 NA 1
#> 22072_1_241 Very high 0 0 1 1 NA 1
dassimKleb_globalKleb.metadata %>%
filter(location == "Malawi") %>%
mutate(vir = clb == 1 |
iuc == 1 | iro == 1 | rmpA == 1 | rmpA2 == 1) %>%
filter(ESBL == "ESBL" & vir == TRUE)
#> name ESBL Sample accession Lane accession study
#> 16228_1_64 16228_1_64 ESBL ERS669104 ERR972010 musciha
#> 16228_1_77 16228_1_77 ESBL ERS669129 ERR972023 musciha
#> 16228_1_83 16228_1_83 ESBL ERS669139 ERR972029 musciha
#> 22036_8_82 22036_8_82 ESBL ERS1545129 ERR2397672 cornick
#> 22072_1_143 22072_1_143 ESBL ERS1531011 ERR2497284 cornick
#> 22072_1_151 22072_1_151 ESBL ERS1531021 ERR2497292 cornick
#> 22072_1_241 22072_1_241 ESBL ERS1531130 ERR2497382 cornick
#> 34154_7_87 34154_7_87 ESBL DASSIM38743801 ERR6057939 DASSIM
#> Sample Source Isolate Type Year location ST YbST CbST AbST
#> 16228_1_64 Human Invasive 2004 Malawi ST268 234-3LV 13-1LV 1-1LV
#> 16228_1_77 Human Invasive 2006 Malawi ST268 234-3LV 13-1LV 1-1LV
#> 16228_1_83 Human Invasive 2010 Malawi ST218 0 0 1-1LV
#> 22036_8_82 Human Invasive NA Malawi ST218 0 0 1-1LV
#> 22072_1_143 Human Invasive NA Malawi ST268 234-3LV 13-1LV 1-1LV
#> 22072_1_151 Human Invasive NA Malawi ST268 234-3LV 13-1LV 1-1LV
#> 22072_1_241 Human Invasive NA Malawi ST218 0 0 1-1LV
#> 34154_7_87 Human Colonising 2018 Malawi ST25 0 0 1
#> SmST rmpA rmpA2 O_locus K_locus K_locus_confidence
#> 16228_1_64 1-1LV 0 1 O2v1 KL20 Very high
#> 16228_1_77 1 0 1 O2v1 KL20 Very high
#> 16228_1_83 1-1LV 0 1 O2v2 KL57 Very high
#> 22036_8_82 1-1LV 1 1 O2v2 KL57 Very high
#> 22072_1_143 1 0 1 O2v1 KL20 Very high
#> 22072_1_151 1 1 1 O2v1 KL20 Very high
#> 22072_1_241 1-1LV 1 1 O2v2 KL57 High
#> 34154_7_87 1 1 1 O1v2 KL2 Very high
#> O_locus_confidence ybt clb iuc iro year_dassim Malawi vir
#> 16228_1_64 Very high 1 1 1 1 NA 1 TRUE
#> 16228_1_77 Very high 1 1 1 1 NA 1 TRUE
#> 16228_1_83 Very high 0 0 1 1 NA 1 TRUE
#> 22036_8_82 Very high 0 0 1 1 NA 1 TRUE
#> 22072_1_143 Very high 1 1 1 1 NA 1 TRUE
#> 22072_1_151 Very high 1 1 1 1 NA 1 TRUE
#> 22072_1_241 Very high 0 0 1 1 NA 1 TRUE
#> 34154_7_87 Very high 0 0 1 1 2018 1 TRUE
# simpsons diversity
dassimKleb_BTKleb.diversity %>%
mutate(K_locus = case_when(
K_locus_confidence %in%
c("Good",
"High",
"Very high") ~ K_locus,
TRUE ~ NA_character_)) %>%
mutate(O_locus = case_when(
O_locus_confidence %in%
c("Good",
"High",
"Very high") ~ O_locus,
TRUE ~ NA_character_)) -> dfMetadata table
# load accessions and assembly stats
btESBL_kleb_global_metadata %>%
transmute(
name,
Sample_accession = `Sample accession`,
Run_accession = `Lane accession`,
Year = if_else(is.na(Year), "Unknown", as.character(Year)),
Study = case_when(
study == "kenya" ~ "Henson et al",
study == "musciha" ~ "Musicha et al",
study == "global" ~ "Holt et al",
study == "DASSIM" ~ "This study",
study == "cornick" ~ "Cornick et al"
),
Sample_source = `Sample Source`,
Isolate_type = case_when(
`Isolate Type` == "Infection" ~ "Invasive",
`Isolate Type` == "Carriage" ~ "Colonising",
TRUE ~ "Unknown"
),
ST = ST,
O_locus = O_locus,
O_locus_confidence = O_locus_confidence,
K_locus = K_locus,
K_locus_confidence = K_locus_confidence,
ybt = ybt,
clb = clb,
iuc = iuc,
iro = iro,
rmpA = rmpA,
rmpA2 = rmpA2,
ESBL = if_else(ESBL == "ESBL", 1, 0)
) %>%
mutate(across(
matches("O_locus|K_locus|ST|ybt|clb|iuc|iro|rmpA"),
~ if_else(is.na(.x), "-", as.character(.x))
)) %>%
mutate(Study = factor(
Study,
c(
"This study",
"Cornick et al",
"Musicha et al",
"Henson et al",
"Holt et al"
)
)) %>%
arrange(Study) %>%
left_join(
btESBL_kleb_malawi_vfdb_output %>% group_by(name) %>% summarise(vfdb_genes = paste(sort(unique(gene)), collapse = ", ")),
by = "name"
) %>%
left_join(
btESBL_amrgenes %>% group_by(lane) %>% summarise(amr_genes = paste(sort(unique(ref_seq)), collapse = ", ")),
by = c("name" = "lane")
) -> metadata_table
metadata_table %>%
kbl(caption = "Accession numbers and metadata for included samples") %>%
kable_classic(full_width = FALSE)| name | Sample_accession | Run_accession | Year | Study | Sample_source | Isolate_type | ST | O_locus | O_locus_confidence | K_locus | K_locus_confidence | ybt | clb | iuc | iro | rmpA | rmpA2 | ESBL | vfdb_genes | amr_genes |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 34154_7_10 | DASSIM38743590 | ERR6057881 | 2017 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, AadA1_pm, AadA2, AmpH, Aph3, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, MphA, OqxA, OqxB, OXA_10, SHV_11, SulI, SulII, TEM_1 |
| 34154_7_100 | DASSIM38743612 | ERR6057949 | 2017 | This study | Human | Colonising | ST45 | O2v1 | Very high | KL24 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac6Ib_cr, AadA1_pm, AmpH, Arr2, CatA2, CatB4, CmlA5, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, OXA_10, SHV_27, StrA, StrB, SulII, TEM_1 |
| 34154_7_102 | DASSIM38743613 | ERR6057950 | 2017 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, AadA1_pm, AadA2, AmpH, Aph3, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, MphA, OqxA, OqxB, OXA_10, SHV_11, SulI, SulII, TEM_1 |
| 34154_7_103 | DASSIM38743805 | ERR6057951 | 2018 | This study | Human | Colonising | ST101 | O1v1 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_104 | DASSIM38743709 | ERR6057952 | 2017 | This study | Human | Colonising | ST152 | O4 | Very high | KL149 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA1, CatB4, CTX_M_15, DfrA27, OqxA, OqxB, OXA_1, SHV_1, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_105 | DASSIM38743710 | ERR6057953 | 2017 | This study | Human | Colonising | ST34 | O2v2 | Very high | KL23 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, galF, glf, gnd, iroE, kfoC, rcsA, rcsB, ugd, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_26, SulII, TEM_1 |
| 34154_7_106 | DASSIM38743806 | ERR6057954 | 2018 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA1_pm, AmpH, Arr2, CatA2, CatB4, CmlA5, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, OXA_10, SHV_28, StrA, StrB, SulII, TEM_1 |
| 34154_7_108 | DASSIM38743614 | ERR6057955 | 2017 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, SHV_65, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_11 | DASSIM38743782 | ERR6057882 | 2018 | This study | Human | Colonising | ST35 | O1v1 | Very high | KL16 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_33, SulII, TEM_1 |
| 34154_7_110 | DASSIM38743615 | ERR6057956 | 2017 | This study | Human | Colonising | ST736 | O5 | High | KL115 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fimA, fimC, fimG, fimH, galF, gnd, hcp_tssD, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkH, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, ybdA | Aac3_IIa, AadA1, AmpH, Arr2, CatA2, CmlA5, CTX_M_15, DfrA1, DfrA14, OKP_B_4, OqxA, OqxB, OXA_10, SulI, SulII |
| 34154_7_112 | DASSIM38743807 | ERR6057958 | 2018 | This study | Human | Colonising | ST1427 | OL101 | Good | KL67 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_116 | DASSIM38743616 | ERR6057961 | 2017 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_11, StrA, StrB, SulII, TEM_1, TetD |
| 34154_7_118 | DASSIM38743617 | ERR6057962 | 2017 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_28, SulII, TEM_1 |
| 34154_7_119 | DASSIM38743713 | ERR6057963 | 2017 | This study | Human | Colonising | ST54 | O3b | Good | KL14 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IId, AmpH, CatA1, CTX_M_15, DfrA30, OqxA, OqxB, SHV_80, SulII, TEM_1, TetD |
| 34154_7_12 | DASSIM38743686 | ERR6057883 | 2017 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, AadA1_pm, AadA2, AmpH, Aph3, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, MphA, OqxA, OqxB, OXA_10, SHV_11, SulI, SulII, TEM_1 |
| 34154_7_122 | DASSIM38743618 | ERR6057965 | 2017 | This study | Human | Colonising | ST219 | O1v1 | Very high | KL114 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA | AadA17, AadA2, AmpH, Aph3, CatA2, CTX_M_15, DfrA12, MphA, OqxA, OqxB, Qnr_S1, SHV_98, StrA, StrB, SulI, SulII, TetA |
| 34154_7_123 | DASSIM38743714 | ERR6057966 | 2018 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AadA1_pm, AmpH, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, OqxA, OqxB, OXA_10, SHV_11, SulII |
| 34154_7_125 | DASSIM38743619 | ERR6057968 | 2017 | This study | Human | Colonising | Novel | O1v2 | Very high | KL57 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac6Ib_cr, AadA16, AmpH, Arr3, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_75, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_13 | DASSIM38743783 | ERR6057884 | 2018 | This study | Human | Colonising | ST1193 | O2v1 | Very high | KL22 | Low | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AadA17, AadA2, AmpH, CatA2, CatB4, CTX_M_15, DfrA12, MphA, OqxA, OqxB, OXA_1, Qnr_S1, SHV_75, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_130 | DASSIM38743620 | ERR6057971 | 2017 | This study | Human | Colonising | ST152 | O4 | Very high | KL149 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA1, CatB4, CTX_M_15, DfrA27, MphA, OqxA, OqxB, OXA_1, QnrB6, SHV_187, SHV_38, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_131 | DASSIM38743716 | ERR6057972 | 2017 | This study | Human | Colonising | ST392 | O4 | Very high | KL27 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, yagZ_ecpA, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_67, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_134 | DASSIM38743717 | ERR6057975 | 2017 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA | Aac3_IId, AmpH, CTX_M_15, DfrA30, DfrA7, OqxA, OqxB, SHV_1, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_136 | DASSIM38743621 | ERR6057976 | 2017 | This study | Human | Colonising | ST152 | O4 | Very high | KL149 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA1, CatB4, CTX_M_15, DfrA27, MphA, OqxA, OqxB, OXA_1, QnrB6, SHV_187, SHV_38, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_138 | DASSIM38743622 | ERR6057977 | 2017 | This study | Human | Colonising | ST152 | O4 | Very high | KL149 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA1, CatB4, CTX_M_15, DfrA27, MphA, OqxA, OqxB, OXA_1, QnrB6, SHV_187, SHV_38, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_14 | DASSIM38743687 | ERR6057885 | 2017 | This study | Human | Colonising | ST716 | O2v1 | Very high | KL110 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_27, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_140 | DASSIM38743718 | ERR6057979 | 2017 | This study | Human | Colonising | ST17 | OL104 | Very high | KL107 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac6_Ib, AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_98, TEM_90 |
| 34154_7_142 | DASSIM38743719 | ERR6057981 | 2017 | This study | Human | Colonising | ST45 | O2v1 | Very high | KL24 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_27, StrA, StrB, SulII, TEM_1 |
| 34154_7_144 | DASSIM38743623 | ERR6057982 | 2017 | This study | Human | Colonising | ST25 | O2v2 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, Aph3, CatB4, CTX_M_15, DfrA14, MphA, OXA_1, SHV_81, StrA, StrB, SulII, TEM_1 |
| 34154_7_146 | DASSIM38743624 | ERR6057983 | 2018 | This study | Human | Colonising | ST3717 | O1v2 | Very high | KL57 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, yagZ_ecpA, ybdA | Aac6Ib_cr, AadA16, AmpH, Arr3, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_75, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_148 | DASSIM38743720 | ERR6057985 | 2017 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_150 | DASSIM38743625 | ERR6057986 | 2018 | This study | Human | Colonising | ST340 | O4 | Very high | KL39 | None | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, impA_tssA, iroE, irp1, irp2, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_11, StrA, StrB, SulII, TEM_1, TetA, TetD |
| 34154_7_152 | DASSIM38743721 | ERR6057988 | 2017 | This study | Human | Colonising | ST1777 | O3b | Very high | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, yagZ_ecpA, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SCO_1, SHV_80, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_153 | DASSIM38743626 | ERR6057989 | 2018 | This study | Human | Colonising | ST1582 | O5 | Very high | KL123 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IId, Aac6Ib_cr, AadA17, AadA2, AmpH, Aph3, CatA2, CatB4, CTX_M_15, DfrA12, LEN_22, MphA, OqxA, OqxB, OXA_1, StrA, StrB, SulI, SulII, TEM_1, TetB |
| 34154_7_155 | DASSIM38743722 | ERR6057991 | 2018 | This study | Human | Colonising | ST2176 | O3b | Very high | KL151 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IId, AmpH, CatA1, DfrA5, LAP_2, OqxA, OqxB, Qnr_S1, SHV_41, StrA, StrB, SulII, TetD |
| 34154_7_158 | DASSIM38743627 | ERR6057992 | 2018 | This study | Human | Colonising | ST392 | O4 | Very high | KL27 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_67, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_16 | DASSIM38743591 | ERR6057886 | 2017 | This study | Human | Colonising | ST432 | O2v1 | Very high | KL62 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_14, DfrA1, LAP_2, OqxA, OqxB, Qnr_S1, SHV_60, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_160 | DASSIM38743723 | ERR6057994 | 2018 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL112 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1 |
| 34154_7_162 | DASSIM38743724 | ERR6057996 | 2018 | This study | Human | Colonising | ST789 | O1v1 | Very high | KL18 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, DfrA5, OqxA, OqxB, SHV_12, StrA, StrB, SulII |
| 34154_7_164 | DASSIM38743628 | ERR6057997 | 2017 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL48 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA15, OqxA, OqxB, OXA_1, QnrB2, SCO_1, SHV_28, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_166 | DASSIM38743629 | ERR6057998 | 2017 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, AadA1_pm, AadA2, AmpH, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, MphA, OqxA, OqxB, OXA_10, SHV_11, SulI, SulII, TEM_1 |
| 34154_7_168 | DASSIM38743725 | ERR6058000 | 2018 | This study | Human | Colonising | ST280 | O2v2 | Good | KL23 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA14, DfrA30, OqxA, OqxB, SHV_27, SulII, TEM_1 |
| 34154_7_172 | DASSIM38743630 | ERR6058003 | 2017 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA30, OqxA, OqxB, SHV_28, SulII |
| 34154_7_174 | DASSIM38743631 | ERR6058004 | 2017 | This study | Human | Colonising | ST25 | O1v2 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, Aph3, CatB4, CTX_M_15, DfrA14, MphA, OXA_1, SHV_81, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_176 | DASSIM38743727 | ERR6058006 | 2017 | This study | Human | Colonising | ST45 | O2v1 | Very high | KL24 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, hcp_tssD, icmF_tssM, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CatB4, CTX_M_15, DfrA14, DfrA27, OqxA, OqxB, OXA_1, SCO_1, SHV_27, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_178 | DASSIM38743728 | ERR6058008 | 2018 | This study | Human | Colonising | ST1777 | O3b | Very high | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, yagZ_ecpA, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SCO_1, SHV_80, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_179 | DASSIM38743632 | ERR6058009 | 2017 | This study | Human | Colonising | ST1079 | O1v2 | Very high | KL10 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, Aac6Ib_cr, AadA17, AadA2, AmpH, CatB4, CTX_M_15, DfrA12, MphA, OqxA, OqxB, OXA_1, SHV_1, StrA, StrB, SulI, SulII, TEM_1, TetB |
| 34154_7_18 | DASSIM38743592 | ERR6057887 | 2017 | This study | Human | Colonising | ST39 | O1v1 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroD, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_183 | DASSIM38743729 | ERR6058011 | 2018 | This study | Human | Colonising | ST34 | O2v2 | Very high | KL57 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsB, ugd, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_14, DfrA1, LAP_2, OqxA, OqxB, Qnr_S1, SHV_26, StrA, StrB, SulI, SulII, TetA, TetD |
| 34154_7_184 | DASSIM38743633 | ERR6058012 | 2017 | This study | Human | Colonising | ST70 | O1v2 | Very high | KL136 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_32, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_185 | DASSIM38743634 | ERR6058013 | 2017 | This study | Human | Colonising | ST1427 | OL101 | Good | KL155 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1 |
| 34154_7_189 | DASSIM38743731 | ERR6058016 | 2017 | This study | Human | Colonising | ST5013 | OL101 | Very high | KL137 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimG, galF, gnd, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, rcsA, rcsB, ugd, yagZ_ecpA, ybdA | Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA14, DfrA15, OKP_B_2, OqxA, OqxB, OXA_1, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_19 | DASSIM38743784 | ERR6057888 | 2017 | This study | Human | Colonising | ST5013 | OL101 | None | KL137 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimG, fimH, galF, gnd, manC, mrkA, mrkB, mrkC, mrkD, mrkH, mrkJ, rcsA, rcsB, ugd, ybdA | Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA14, DfrA15, OKP_B_2, OqxA, OqxB, OXA_1, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_191 | DASSIM38743635 | ERR6058018 | 2018 | This study | Human | Colonising | ST2668 | OL103 | High | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_33, StrA, StrB, SulII, TEM_1 |
| 34154_7_194 | DASSIM38743732 | ERR6058019 | 2018 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL16 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatA1, CatB4, CTX_M_15, DfrA14, DfrA5, OqxA, OqxB, OXA_1, SHV_70, StrA, StrB, SulII, TetD |
| 34154_7_197 | DASSIM38743733 | ERR6058022 | 2018 | This study | Human | Colonising | ST29 | O1v2 | Good | KL19 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_187, StrA, StrB, SulII, TEM_1 |
| 34154_7_199 | DASSIM38743637 | ERR6058024 | 2018 | This study | Human | Colonising | ST1035 | O1v2 | Very high | KL57 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA | AadA17, AadA2, AmpH, CTX_M_3, DfrA16, OqxA, OqxB, SHV_185, SulI, SulII, TEM_1 |
| 34154_7_20 | DASSIM38743688 | ERR6057889 | 2018 | This study | Human | Colonising | Novel | O4 | Very high | KL149 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA1, CatB4, CTX_M_15, DfrA27, MphA, OqxA, OqxB, OXA_1, QnrB6, SHV_187, SHV_38, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_202 | DASSIM38743734 | ERR6058025 | 2018 | This study | Human | Colonising | ST1916 | O1v1 | Very high | KL27 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IId, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, OqxA, OqxB, OXA_1, SHV_98, StrA, StrB, SulII, TEM_1, TetA, TetB |
| 34154_7_204 | DASSIM38743638 | ERR6058027 | 2018 | This study | Human | Colonising | ST584 | O2v2 | Very high | KL9 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_72, StrA, StrB, SulII, TEM_1 |
| 34154_7_205 | DASSIM38743735 | ERR6058028 | 2017 | This study | Human | Colonising | Novel | O4 | None | KL107 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, cpsACP, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimF, fimG, fimH, fimI, fimK, mrkA, mrkB, mrkC, mrkD, rcsB, ybdA | AadA17, AadA2, AmpH, CatA1, CatA2, DfrA14, SHV_12, StrB, SulI, SulII, TEM_1, TetA, TetC |
| 34154_7_207 | DASSIM38743639 | ERR6058030 | 2018 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL48 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA15, OqxA, OqxB, OXA_1, QnrB2, SCO_1, SHV_28, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_210 | DASSIM38743736 | ERR6058031 | 2017 | This study | Human | Colonising | ST39 | O1v1 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_212 | DASSIM38743640 | ERR6058033 | 2018 | This study | Human | Colonising | ST5028 | O3b | Very high | KL11 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimD, fimG, fimH, galF, gnd, hcp_tssD, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkH, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, DfrA27, OKP_B_3, OqxA, OqxB, Qnr_S1, SHV_12, SulI, TetA, TetD |
| 34154_7_213 | DASSIM38743641 | ERR6058034 | 2018 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA | Aac3_IId, AmpH, CTX_M_15, EreA2, OqxA, OqxB, SHV_28, SulI, SulII, TEM_1 |
| 34154_7_216 | DASSIM38743737 | ERR6058036 | 2017 | This study | Human | Colonising | ST280 | O2v2 | Good | KL23 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, yagZ_ecpA, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_27, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_218 | DASSIM38743738 | ERR6058038 | 2017 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SCO_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_219 | DASSIM38743642 | ERR6058039 | 2018 | This study | Human | Colonising | ST391 | O1v2 | Very high | KL30 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA14, DfrA30, MphA, OqxA, OqxB, SHV_89, SulII, TEM_1 |
| 34154_7_22 | DASSIM38743593 | ERR6057890 | 2017 | This study | Human | Colonising | ST152 | O4 | Very high | KL149 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA1, CatB4, CTX_M_15, DfrA27, MphA, OqxA, OqxB, OXA_1, QnrB6, SHV_187, SHV_38, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_221 | DASSIM38743643 | ERR6058040 | 2018 | This study | Human | Colonising | ST2668 | OL103 | High | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_33, StrA, StrB, SulII, TEM_1 |
| 34154_7_224 | DASSIM38743739 | ERR6058042 | 2017 | This study | Human | Colonising | ST551 | O1v1 | Very high | KL10 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_172, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_226 | DASSIM38743740 | ERR6058044 | 2017 | This study | Human | Colonising | ST101 | O1v1 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_227 | DASSIM38743644 | ERR6058045 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_23 | DASSIM38743689 | ERR6057891 | 2018 | This study | Human | Colonising | ST716 | O2v1 | Very high | KL110 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_27, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_231 | DASSIM38743741 | ERR6058047 | 2017 | This study | Human | Colonising | ST1414 | O1v1 | Very high | KL8 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IId, Aac6Ib_cr, AadA5, AmpH, Arr3, CTX_M_15, DfrA14, DfrA17, MphA, OqxA, OqxB, SHV_101, SHV_187, StrB, SulI, SulII, TEM_1 |
| 34154_7_232 | DASSIM38743645 | ERR6058048 | 2018 | This study | Human | Colonising | ST789 | O1v1 | Very high | KL18 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CatA1, DfrA5, OqxA, OqxB, SHV_73, StrA, StrB, SulII |
| 34154_7_234 | DASSIM38743742 | ERR6058050 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_235 | DASSIM38743646 | ERR6058051 | 2018 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IId, AadA1_pm, AadA2, AmpH, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, DfrA30, LAP_2, MphA, OqxA, OqxB, OXA_10, Qnr_S1, SHV_11, SulI, SulII, TEM_1, TetD |
| 34154_7_239 | DASSIM38743743 | ERR6058053 | 2018 | This study | Human | Colonising | ST152 | O4 | Very high | KL149 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA1, CatB4, CTX_M_15, DfrA27, MphA, OqxA, OqxB, OXA_1, QnrB6, SHV_187, SHV_38, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_24 | DASSIM38743785 | ERR6057892 | Unknown | This study | Human | Colonising | ST280 | O2v2 | Good | KL23 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_27, SulII, TEM_1 |
| 34154_7_240 | DASSIM38743647 | ERR6058054 | 2018 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IId, AadA1_pm, AadA2, AmpH, Aph3, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, LAP_2, MphA, OqxA, OqxB, OXA_10, Qnr_S1, SHV_11, SulI, SulII, TEM_1, TetD |
| 34154_7_242 | DASSIM38743744 | ERR6058056 | 2018 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL24 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA1, AmpH, CatA1, CatB4, CTX_M_15, DfrA14, DfrA15, MphA, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_247 | DASSIM38743745 | ERR6058059 | 2018 | This study | Human | Colonising | ST3477 | O2v2 | Good | KL39 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, galF, glf, gnd, hcp_tssD, icmF_tssM, kfoC, KPHS_23120, manB, manC, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | AmpH, DfrA14, SHV_12, StrA, StrB, SulII, TEM_1, TetD |
| 34154_7_248 | DASSIM38743649 | ERR6058060 | 2018 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_65, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_249 | DASSIM38743650 | ERR6058061 | 2018 | This study | Human | Colonising | Novel | OL102 | None | KL17 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimC, fimG, fimH, galF, hcp_tssD, icmF_tssM, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkH, mrkJ, rcsB, sciN_tssJ, tssF, vasE_tssK, vgrG_tssI, vipA_tssB, ybdA | AadA17, AadA2, AmpH, CTX_M_65, DfrA12, FosA, OKP_A_3, OqxA, OqxB, RmtB, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_25 | DASSIM38743594 | ERR6057893 | 2017 | This study | Human | Colonising | ST2665 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IId, AmpH, CTX_M_15, DfrA30, OqxA, OqxB, SHV_98, SulII, TEM_1 |
| 34154_7_252 | DASSIM38743746 | ERR6058063 | 2018 | This study | Human | Colonising | ST5013 | OL101 | None | KL137 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimG, gnd, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, rcsA, rcsB, ugd, ybdA | Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA14, DfrA15, OKP_B_2, OqxA, OqxB, OXA_1, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_254 | DASSIM38743747 | ERR6058065 | 2018 | This study | Human | Colonising | ST985 | O1v2 | Very high | KL39 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_187, StrA, StrB, SulII, TEM_1 |
| 34154_7_255 | DASSIM38743651 | ERR6058066 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_259 | DASSIM38743748 | ERR6058068 | 2018 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL24 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | AmpH, Arr2, CatA1, CatB4, CmlA5, CTX_M_15, DfrA14, DfrA15, OqxA, OqxB, OXA_1, OXA_10, SHV_28, SulI, TEM_1, TetA |
| 34154_7_26 | DASSIM38743690 | ERR6057894 | 2017 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL112 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_260 | DASSIM38743652 | ERR6058069 | 2018 | This study | Human | Colonising | ST3717 | O1v2 | Very high | KL57 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, yagZ_ecpA, ybdA | Aac6Ib_cr, AadA16, AmpH, Arr3, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_75, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_262 | DASSIM38743749 | ERR6058071 | 2018 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL48 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA15, OqxA, OqxB, OXA_1, QnrB2, SCO_1, SHV_28, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_263 | DASSIM38743653 | ERR6058072 | 2017 | This study | Human | Colonising | ST45 | OL101 | High | KL52 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA14, LAP_2, MphA, OqxA, OqxB, OXA_1, Qnr_S1, SHV_98, StrA, StrB, SulII, TEM_1 |
| 34154_7_267 | DASSIM38743750 | ERR6058074 | 2018 | This study | Human | Colonising | ST101 | O1v1 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_268 | DASSIM38743654 | ERR6058075 | 2017 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL112 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_269 | DASSIM38743751 | ERR6058076 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, SHV_28, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_27 | DASSIM38743786 | ERR6057895 | 2017 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_65, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_271 | DASSIM38743655 | ERR6058078 | 2017 | This study | Human | Colonising | ST403 | O3b | Very high | KL105 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_80, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_274 | DASSIM38743752 | ERR6058079 | 2018 | This study | Human | Colonising | ST1799 | O1v1 | Very high | KL16 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatA1, CTX_M_15, DfrA14, DfrA7, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_276 | DASSIM38743656 | ERR6058081 | 2017 | This study | Human | Colonising | ST391 | O1v2 | Very high | KL30 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1 |
| 34154_7_277 | DASSIM38743657 | ERR6058082 | 2017 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL157 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, glf, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IId, Aac6Ib_cr, AadA16, AmpH, Arr3, DfrA27, OqxA, OqxB, QnrB6, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_279 | DASSIM38743753 | ERR6058083 | 2018 | This study | Human | Colonising | ST1427 | OL101 | Good | KL67 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_281 | DASSIM38743754 | ERR6058085 | 2018 | This study | Human | Colonising | ST1799 | O1v1 | Very high | KL16 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatA1, CTX_M_15, DfrA14, DfrA7, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_283 | DASSIM38743658 | ERR6058087 | 2018 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL112 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1 |
| 34154_7_287 | DASSIM38743755 | ERR6058089 | 2018 | This study | Human | Colonising | Novel | O1v2 | Very high | KL108 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssG, ugd, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_89, StrB, SulII, TEM_1, TetA |
| 34154_7_289 | DASSIM38743756 | ERR6058091 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_291 | DASSIM38743660 | ERR6058093 | 2018 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_28, SulII, TEM_1 |
| 34154_7_294 | DASSIM38743757 | ERR6058094 | 2018 | This study | Human | Colonising | ST147 | O2v1 | Very high | KL64 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_67, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_296 | DASSIM38743661 | ERR6058096 | 2018 | This study | Human | Colonising | ST39 | O1v1 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroD, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_298 | DASSIM38743758 | ERR6058098 | 2018 | This study | Human | Colonising | ST2668 | OL103 | High | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_33, StrA, StrB, SulII, TEM_1 |
| 34154_7_299 | DASSIM38743662 | ERR6058099 | 2017 | This study | Human | Colonising | ST25 | O1v2 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, Aph3, CatB4, CTX_M_15, DfrA14, MphA, OXA_1, SHV_81, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_3 | DASSIM38743780 | ERR6057876 | 2018 | This study | Human | Colonising | ST1193 | O2v1 | Very high | KL22 | Low | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA | Aac3_IIa, Aac6Ib_cr, AadA17, AadA2, AmpH, CatA2, CatB4, CTX_M_15, DfrA12, MphA, OqxA, OqxB, OXA_1, Qnr_S1, SHV_75, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_30 | DASSIM38743595 | ERR6057896 | 2017 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_28, SulII, TEM_1 |
| 34154_7_303 | DASSIM38743759 | ERR6058101 | 2018 | This study | Human | Colonising | ST985 | O1v2 | Very high | KL39 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_187, StrA, StrB, SulII, TEM_1 |
| 34154_7_304 | DASSIM38743663 | ERR6058102 | 2017 | This study | Human | Colonising | ST711 | O1v2 | Very high | KL54 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_187, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_306 | DASSIM38743760 | ERR6058103 | 2018 | This study | Human | Colonising | Novel | O1v2 | Very high | KL63 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CTX_M_15, DfrA30, OqxA, OqxB, SHV_40, SulII, TEM_1 |
| 34154_7_307 | DASSIM38743664 | ERR6058104 | 2017 | This study | Human | Colonising | ST25 | O1v2 | Very high | KL2 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, Aph3, CatB4, CTX_M_15, DfrA14, MphA, OXA_1, SHV_81, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_31 | DASSIM38743691 | ERR6057897 | 2017 | This study | Human | Colonising | ST17 | O5 | High | KL25 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_96, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_312 | DASSIM38743665 | ERR6058106 | 2017 | This study | Human | Colonising | ST3717 | O1v2 | Very high | KL57 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac6Ib_cr, AadA16, AmpH, Arr3, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_75, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_313 | DASSIM38743666 | ERR6058107 | 2017 | This study | Human | Colonising | Novel | O2v2 | Very high | KL136 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, galF, glf, gnd, hcp_tssD, icmF_tssM, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkJ, rcsB, tli1, tssF, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, AadA17, AadA2, AmpH, Arr2, CatA2, CatB4, CmlA5, CTX_M_15, DfrA12, DfrA14, LAP_2, LEN_26, MphA, OqxA, OqxB, OXA_1, OXA_10, Qnr_S1, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_316 | DASSIM38743762 | ERR6058108 | 2018 | This study | Human | Colonising | ST17 | O5 | Good | KL25 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_96, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_317 | DASSIM38743763 | ERR6058109 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_28, StrA, StrB, SulII, TEM_1 |
| 34154_7_318 | DASSIM38743667 | ERR6058110 | 2017 | This study | Human | Colonising | Novel | O4 | Very high | KL149 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA1, CatB4, CTX_M_15, DfrA27, MphA, OqxA, OqxB, OXA_1, QnrB6, SHV_187, SHV_38, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_32 | DASSIM38743787 | ERR6057898 | 2018 | This study | Human | Colonising | ST37 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_322 | DASSIM38743764 | ERR6058111 | 2018 | This study | Human | Colonising | ST789 | O1v1 | Very high | KL18 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CatA1, DfrA5, OqxA, OqxB, SHV_12, StrA, StrB, SulII, TetD |
| 34154_7_323 | DASSIM38743668 | ERR6058112 | 2018 | This study | Human | Colonising | ST4283 | O4 | Very high | KL145 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_32, StrA, StrB, SulII, TEM_1 |
| 34154_7_324 | DASSIM38743765 | ERR6058113 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, SHV_28, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_325 | DASSIM38743669 | ERR6058114 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, SHV_28, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_33 | DASSIM38743692 | ERR6057899 | 2017 | This study | Human | Colonising | ST307 | O1v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, manB, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrB, SulII, TEM_1, TetA |
| 34154_7_330 | DASSIM38743766 | ERR6058115 | 2018 | This study | Human | Colonising | ST2136 | O2v2 | Very high | KL2 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | AadA17, AadA2, AmpH, CatA2, CTX_M_15, DfrA12, MphA, OqxA, OqxB, Qnr_S1, SHV_27, StrB, SulI, SulII, TEM_135, TetD |
| 34154_7_331 | DASSIM38743670 | ERR6058116 | 2018 | This study | Human | Colonising | ST20 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CTX_M_15, DfrA30, OqxA, OqxB, SHV_98, SulII, TEM_1 |
| 34154_7_332 | DASSIM38743767 | ERR6058117 | 2018 | This study | Human | Colonising | ST3559 | O4 | Very high | KL27 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_80, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_333 | DASSIM38743671 | ERR6058118 | 2018 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL48 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA15, OqxA, OqxB, OXA_1, QnrB2, SCO_1, SHV_28, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_338 | DASSIM38743768 | ERR6058119 | 2018 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fyuA, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, irp1, irp2, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, AadA1_pm, AadA2, AmpH, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, OqxA, OqxB, OXA_10, Qnr_S1, SHV_11, SulII, TEM_1, TetD |
| 34154_7_339 | DASSIM38743672 | ERR6058120 | 2018 | This study | Human | Colonising | ST3586 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, impA_tssA, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | AmpH, DfrA14, OqxA, OqxB, Qnr_S1, SHV_70, StrA, StrB, SulII, TEM_1, TetD |
| 34154_7_340 | DASSIM38743673 | ERR6058121 | 2018 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_65, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_343 | DASSIM38743769 | ERR6058122 | 2018 | This study | Human | Colonising | ST39 | O1v1 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroD, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_89, StrA, StrB, SulII, TEM_1 |
| 34154_7_344 | DASSIM38743770 | ERR6058123 | 2018 | This study | Human | Colonising | ST39 | O1v1 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroD, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_345 | DASSIM38743674 | ERR6058124 | 2018 | This study | Human | Colonising | ST2668 | OL103 | High | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, yagZ_ecpA, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_33, StrA, StrB, SulII, TEM_1 |
| 34154_7_348 | DASSIM38743675 | ERR6058125 | 2018 | This study | Human | Colonising | ST35 | O1v1 | Very high | KL16 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | AmpH, CTX_M_15, DfrA30, OqxA, OqxB, SHV_33 |
| 34154_7_351 | DASSIM38743771 | ERR6058126 | 2018 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL16 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, DfrA14, LAP_2, OqxA, OqxB, OXA_1, Qnr_S1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_352 | DASSIM38743772 | ERR6058127 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, AmpH, CTX_M_15, OqxA, OqxB, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_353 | DASSIM38743676 | ERR6058128 | 2017 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA30, OqxA, OqxB, SHV_28, SulII |
| 34154_7_359 | DASSIM38743677 | ERR6058130 | 2017 | This study | Human | Colonising | ST391 | O1v2 | Very high | KL30 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA14, DfrA30, MphA, OqxA, OqxB, SHV_89, SulII, TEM_1 |
| 34154_7_36 | DASSIM38743596 | ERR6057901 | 2017 | This study | Human | Colonising | ST37 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_360 | DASSIM38743774 | ERR6058131 | 2018 | This study | Human | Colonising | ST323 | O3b | Good | KL21 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_99, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_361 | DASSIM38743678 | ERR6058132 | 2017 | This study | Human | Colonising | ST716 | O2v1 | Very high | KL110 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_27, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_366 | DASSIM38743775 | ERR6058133 | 2018 | This study | Human | Colonising | ST273 | O3b | Good | KL74 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IId, AadA5, AmpH, CatA1, CTX_M_15, DfrA17, MphA, OqxA, OqxB, SHV_67, StrA, StrB, SulI, SulII, TetD |
| 34154_7_367 | DASSIM38743679 | ERR6058134 | 2017 | This study | Human | Colonising | ST551 | O1v1 | Very high | KL10 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, yagZ_ecpA, ybdA | Aac3_IIa, AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_172, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_368 | DASSIM38743776 | ERR6058135 | 2018 | This study | Human | Colonising | ST35 | O1v1 | Very high | KL30 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IId, AmpH, Aph3, CatA2, CTX_M_15, DfrA14, DfrA30, MphA, OqxA, OqxB, SHV_33, StrA, StrB, SulII, TEM_1 |
| 34154_7_369 | DASSIM38743680 | ERR6058136 | 2017 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, SHV_65, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_374 | DASSIM38743777 | ERR6058137 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1 |
| 34154_7_375 | DASSIM38743681 | ERR6058138 | 2018 | This study | Human | Colonising | Novel | O1v2 | Very high | KL63 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, yagZ_ecpA, ybdA | Aac3_IId, AmpH, CTX_M_15, DfrA30, OqxA, OqxB, SHV_40, SulII, TEM_1 |
| 34154_7_376 | DASSIM38743682 | ERR6058139 | 2018 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_28, SulII, TEM_1 |
| 34154_7_378 | DASSIM38743778 | ERR6058140 | 2018 | This study | Human | Colonising | ST45 | O2v1 | Very high | KL24 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_27, StrA, StrB, SulII, TEM_1 |
| 34154_7_379 | DASSIM38743779 | ERR6058141 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, AadA1, AmpH, CTX_M_15, DfrA15, OqxA, OqxB, SHV_28, SulI, TEM_1, TetA |
| 34154_7_38 | DASSIM38743597 | ERR6057902 | 2017 | This study | Human | Colonising | ST2601 | O4 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | AmpH, DfrA14, OqxA, OqxB, SHV_12, StrA, StrB, SulII, TEM_1 |
| 34154_7_380 | DASSIM38743683 | ERR6058142 | 2018 | This study | Human | Colonising | ST2126 | O2v2 | Very high | KL54 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AadA1, AmpH, CatB4, CTX_M_15, OqxA, OqxB, OXA_1, Qnr_S1, SCO_1, SHV_89, SulI, TEM_1 |
| 34154_7_39 | DASSIM38743693 | ERR6057903 | 2017 | This study | Human | Colonising | ST323 | O3b | Good | KL21 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_99, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_4 | DASSIM38743684 | ERR6057877 | 2018 | This study | Human | Colonising | ST280 | O2v2 | Good | KL23 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, yagZ_ecpA, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_27, SulII, TEM_1 |
| 34154_7_40 | DASSIM38743789 | ERR6057904 | 2018 | This study | Human | Colonising | ST1427 | OL101 | Good | KL155 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1 |
| 34154_7_41 | DASSIM38743694 | ERR6057905 | 2017 | This study | Human | Colonising | ST334 | O5 | High | KL103 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimG, fimH, galF, manC, mrkA, mrkB, mrkC, mrkD, mrkH, rcsA, rcsB, ugd, ybdA | Aac3_IId, AmpH, DfrA14, OKP_B_4, QnrB1, SHV_12, StrA, StrB, SulII, TEM_90, TetD |
| 34154_7_42 | DASSIM38743790 | ERR6057906 | 2018 | This study | Human | Colonising | ST1777 | O3b | Very high | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SCO_1, SHV_80, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_44 | DASSIM38743598 | ERR6057907 | 2017 | This study | Human | Colonising | ST2668 | OL103 | High | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_33, StrA, StrB, SulII, TEM_1 |
| 34154_7_46 | DASSIM38743599 | ERR6057908 | 2018 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL16 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_47 | DASSIM38743695 | ERR6057909 | 2017 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_65, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_48 | DASSIM38743791 | ERR6057910 | 2018 | This study | Human | Colonising | ST2668 | OL103 | High | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_33, StrA, StrB, SulII, TEM_1 |
| 34154_7_49 | DASSIM38743792 | ERR6057911 | 2018 | This study | Human | Colonising | ST17 | O5 | High | KL25 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_96, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_5 | DASSIM38743781 | ERR6057878 | 2018 | This study | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1 |
| 34154_7_50 | DASSIM38743696 | ERR6057912 | 2017 | This study | Human | Colonising | ST1418 | O3b | Good | KL13 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, hcp_tssD, iroE, irp1, irp2, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, AmpH, CatA2, CTX_M_15, DfrA14, OqxA, OqxB, SHV_98, StrA, StrB, SulII, TEM_1, TetD |
| 34154_7_52 | DASSIM38743600 | ERR6057913 | 2018 | This study | Human | Colonising | ST2176 | O3b | Very high | KL151 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IId, AmpH, CatA1, DfrA5, LAP_2, OqxA, OqxB, Qnr_S1, SHV_41, StrA, StrB, SulII |
| 34154_7_54 | DASSIM38743601 | ERR6057914 | 2018 | This study | Human | Colonising | ST1418 | O3b | Very high | KL13 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, hcp_tssD, iroE, irp1, irp2, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_98, StrA, StrB, SulII, TEM_1 |
| 34154_7_55 | DASSIM38743793 | ERR6057915 | 2018 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_65, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_56 | DASSIM38743697 | ERR6057916 | 2017 | This study | Human | Colonising | ST1414 | O1v1 | Very high | KL8 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IId, Aac6Ib_cr, AadA5, AmpH, Arr3, CTX_M_15, DfrA14, DfrA17, MphA, OqxA, OqxB, SHV_101, SHV_187, StrA, StrB, SulI, SulII, TEM_1 |
| 34154_7_58 | DASSIM38743602 | ERR6057917 | 2017 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_59 | DASSIM38743794 | ERR6057918 | 2018 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_65, StrA, StrB, SulI, SulII, TetD |
| 34154_7_6 | DASSIM38743685 | ERR6057879 | 2017 | This study | Human | Colonising | ST101 | O1v1 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_60 | DASSIM38743698 | ERR6057919 | 2018 | This study | Human | Colonising | ST551 | O1v1 | Very high | KL10 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | Aac3_IIa, AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_172, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_62 | DASSIM38743795 | ERR6057921 | 2018 | This study | Human | Colonising | ST35 | O1v1 | Very high | KL30 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | AadA1, AmpH, CatB4, CTX_M_15, DfrA30, OqxA, OqxB, OXA_1, SHV_33, SulII, TEM_1 |
| 34154_7_63 | DASSIM38743699 | ERR6057922 | 2018 | This study | Human | Colonising | ST551 | O1v1 | Good | KL10 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbN, wzm, wzt, ybdA | Aac3_IIa, AmpH, CTX_M_15, DfrA14, OqxA, OqxB, SHV_172, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_68 | DASSIM38743700 | ERR6057925 | 2018 | This study | Human | Colonising | ST1416 | O12 | Good | KL59 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimG, fimH, hcp_tssD, mrkA, mrkB, mrkC, mrkD, mrkF, rcsA, rcsB, sciN_tssJ, tssF, vasE_tssK, ybdA | AmpH, CTX_M_15, DfrA14, DfrA15, OKP_A_8, OqxA, OqxB, Qnr_S1, StrA, StrB, SulI, SulII, TEM_1, TetA |
| 34154_7_69 | DASSIM38743797 | ERR6057926 | 2018 | This study | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_70 | DASSIM38743701 | ERR6057927 | 2018 | This study | Human | Colonising | Novel | O1v2 | Very high | KL108 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssG, ugd, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, yagZ_ecpA, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_89, StrB, SulII, TEM_1, TetA |
| 34154_7_74 | DASSIM38743606 | ERR6057929 | 2017 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, AadA1_pm, AadA2, AmpH, Arr2, CmlA5, CTX_M_15, DfrA14, OqxA, OqxB, OXA_10, SHV_11, SulI, SulII, TEM_1, TetD |
| 34154_7_75 | DASSIM38743798 | ERR6057930 | 2018 | This study | Human | Colonising | ST45 | O2v1 | Very high | KL24 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac6Ib_cr, AadA16, AmpH, Arr3, CTX_M_15, DfrA14, DfrA27, OqxA, OqxB, Qnr_S1, SHV_27, StrA, StrB, SulI, SulII, TEM_135 |
| 34154_7_76 | DASSIM38743702 | ERR6057931 | 2017 | This study | Human | Colonising | ST392 | O4 | Very high | KL27 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_67, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_77 | DASSIM38743799 | ERR6057932 | 2018 | This study | Human | Colonising | ST34 | O3b | Very high | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, yagZ_ecpA, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_26, SulII |
| 34154_7_78 | DASSIM38743703 | ERR6057933 | 2017 | This study | Human | Colonising | ST736 | O1v1 | None | KL107 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimH, galF, hcp_tssD, KPHS_23120, mrkA, mrkB, mrkC, mrkD, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | AmpH, CTX_M_15, DfrA14, OKP_B_4, OqxA, OqxB, Qnr_S1, StrA, StrB, SulII |
| 34154_7_8 | DASSIM38743589 | ERR6057880 | 2017 | This study | Human | Colonising | ST1079 | O1v2 | Very high | KL10 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, Aac6Ib_cr, AadA17, AadA2, AmpH, CatA2, CatB4, CTX_M_15, DfrA12, MphA, OqxA, OqxB, OXA_1, SHV_1, StrA, StrB, SulI, SulII, TEM_1, TetB |
| 34154_7_80 | DASSIM38743607 | ERR6057934 | 2017 | This study | Human | Colonising | ST607 | O1v1 | Very high | KL25 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, QnrB6, SHV_65, StrA, StrB, SulI, SulII, TEM_1, TetD |
| 34154_7_83 | DASSIM38743800 | ERR6057936 | 2018 | This study | Human | Colonising | ST391 | O1v2 | Very high | KL30 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_89, SulII, TEM_1 |
| 34154_7_84 | DASSIM38743704 | ERR6057937 | 2017 | This study | Human | Colonising | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, AadA1_pm, AmpH, Arr2, CatA2, CmlA5, CTX_M_15, DfrA14, OqxA, OqxB, OXA_10, SHV_11, SulII, TEM_1 |
| 34154_7_86 | DASSIM38743609 | ERR6057938 | 2017 | This study | Human | Colonising | ST231 | O1v2 | Very high | KL30 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, Aac6Ib_cr, AadA16, AmpH, Arr3, CatA2, CTX_M_15, DfrA27, OqxA, OqxB, SHV_28, StrA, StrB, SulI, SulII, TEM_90, TetD |
| 34154_7_87 | DASSIM38743801 | ERR6057939 | 2018 | This study | Human | Colonising | ST25 | O1v2 | Very high | KL2 | Very high | 0 | 0 | 1 | 1 | 1 | 1 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, iroN, iucA, iucB, iucC, iucD, iutA, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, yagZ_ecpA, ybdA | Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_89, StrA, StrB, SulII, TEM_1 |
| 34154_7_88 | DASSIM38743705 | ERR6057940 | 2017 | This study | Human | Colonising | ST34 | O3b | Very high | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, yagZ_ecpA, ybdA | Aac3_IId, AmpH, CTX_M_15, DfrA30, OqxA, OqxB, SHV_26, SulII, TEM_1 |
| 34154_7_89 | DASSIM38743610 | ERR6057941 | 2017 | This study | Human | Colonising | ST37 | OL103 | None | KL12 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | AmpH, CTX_M_15, DfrA1, OqxA, OqxB, Qnr_S1, SHV_81, SulI, TEM_1, TetA |
| 34154_7_90 | DASSIM38743802 | ERR6057942 | 2018 | This study | Human | Colonising | ST391 | O1v2 | Very high | KL30 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | Aac3_IId, AmpH, CatA2, CTX_M_15, DfrA30, OqxA, OqxB, SHV_89, SulII, TEM_1 |
| 34154_7_91 | DASSIM38743706 | ERR6057943 | 2017 | This study | Human | Colonising | ST101 | O1v2 | Very high | KL2 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_94 | DASSIM38743611 | ERR6057944 | 2017 | This study | Human | Colonising | ST15 | O1v1 | Very high | KL112 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, DfrA14, OqxA, OqxB, OXA_1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 34154_7_95 | DASSIM38743803 | ERR6057945 | 2018 | This study | Human | Colonising | ST716 | O2v1 | Very high | KL110 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_27, StrA, StrB, SulII, TEM_1 |
| 34154_7_96 | DASSIM38743707 | ERR6057946 | 2017 | This study | Human | Colonising | ST2601 | O4 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | AmpH, DfrA14, OqxA, OqxB, SHV_89, StrA, StrB, SulII, TEM_1 |
| 34154_7_97 | DASSIM38743804 | ERR6057947 | 2018 | This study | Human | Colonising | ST5153 | O3b | Very high | KL22 | Low | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | Aac3_IIa, Aac6Ib_cr, AmpH, CatB4, CTX_M_15, OqxA, OqxB, OXA_1, SHV_89, StrB, SulII, TEM_1, TetA |
| 34154_7_98 | DASSIM38743708 | ERR6057948 | 2018 | This study | Human | Colonising | ST101 | O1v2 | Very high | KL2 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA | AmpH, CTX_M_15, DfrA14, OqxA, OqxB, Qnr_S1, SHV_28, StrA, StrB, SulII, TEM_1, TetA |
| 22036_8_82 | ERS1545129 | ERR2397672 | Unknown | Cornick et al | Human | Invasive | ST218 | O2v2 | Very high | KL57 | Very high | 0 | 0 | 1 | 1 | 1 | 1 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, iroN, iucA, iucB, iucC, iucD, iutA, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_101 | ERS1530960 | ERR2497242 | Unknown | Cornick et al | Human | Invasive | ST372 | O2v1 | Very high | KL43 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_102 | ERS1530961 | ERR2497243 | Unknown | Cornick et al | Human | Invasive | ST372 | O2v1 | Very high | KL43 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_103 | ERS1530962 | ERR2497244 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_104 | ERS1530963 | ERR2497245 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL16 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_105 | ERS1530964 | ERR2497246 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_106 | ERS1530965 | ERR2497247 | Unknown | Cornick et al | Human | Invasive | ST702 | O2v2 | Very high | KL109 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_107 | ERS1530966 | ERR2497248 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_108 | ERS1530967 | ERR2497249 | Unknown | Cornick et al | Human | Invasive | Unknown | O5 | High | KL68 | Low | 0 | 0 | 0 | 0 | 0 | 0 | 0 | fimF | NA |
| 22072_1_110 | ERS1530969 | ERR2497251 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acpC, acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_111 | ERS1530970 | ERR2497252 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_112 | ERS1530971 | ERR2497253 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_113 | ERS1530972 | ERR2497254 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL16 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_114 | ERS1530973 | ERR2497255 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_117 | ERS1530976 | ERR2497258 | Unknown | Cornick et al | Human | Invasive | ST985 | O1v2 | Very high | KL39 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_119 | ERS1530978 | ERR2497260 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_120 | ERS1530980 | ERR2497261 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_121 | ERS1530981 | ERR2497262 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_122 | ERS1530982 | ERR2497263 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_123 | ERS1530983 | ERR2497264 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_124 | ERS1530984 | ERR2497265 | Unknown | Cornick et al | Human | Invasive | ST1208 | O3/O3a | Good | KL16 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, dotU_tssL, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimC, fimD, fimF, fimG, fimH, fimK, hcp_tssD, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkI, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, ybdA | NA |
| 22072_1_125 | ERS1530985 | ERR2497266 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_126 | ERS1530986 | ERR2497267 | Unknown | Cornick et al | Human | Invasive | ST391 | O1v2 | Very high | KL30 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_127 | ERS1530987 | ERR2497268 | Unknown | Cornick et al | Human | Invasive | ST391 | O1v2 | Very high | KL30 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_128 | ERS1530988 | ERR2497269 | Unknown | Cornick et al | Human | Invasive | ST2439 | O1v1 | Very high | KL3 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_129 | ERS1530989 | ERR2497270 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_130 | ERS1530990 | ERR2497271 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_131 | ERS1530992 | ERR2497272 | Unknown | Cornick et al | Human | Invasive | ST14 | O1/O2v1 | None | KL2 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_132 | ERS1530995 | ERR2497273 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_134 | ERS1530997 | ERR2497275 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_135 | ERS1530998 | ERR2497276 | Unknown | Cornick et al | Human | Invasive | ST17 | O5 | High | KL25 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, ugd, ybdA | NA |
| 22072_1_136 | ERS1531000 | ERR2497277 | Unknown | Cornick et al | Human | Invasive | ST2793 | O2v2 | Very high | KL55 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_137 | ERS1531001 | ERR2497278 | Unknown | Cornick et al | Human | Invasive | ST17 | O5 | High | KL25 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, hcp_tssD, iroE, irp1, irp2, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_138 | ERS1531002 | ERR2497279 | Unknown | Cornick et al | Human | Invasive | ST36 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_139 | ERS1531003 | ERR2497280 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_140 | ERS1531007 | ERR2497281 | Unknown | Cornick et al | Human | Invasive | ST2824 | O3/O3a | Very high | KL55 | High | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepC, fepD, fepG, fes, fimA, fimC, fimG, fimH, galF, gnd, hcp_tssD, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkJ, rcsB, sciN_tssJ, tssF, tssG, ugd, vipA_tssB, ybdA | NA |
| 22072_1_142 | ERS1531009 | ERR2497283 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_143 | ERS1531011 | ERR2497284 | Unknown | Cornick et al | Human | Invasive | ST268 | O2v1 | Very high | KL20 | Very high | 1 | 1 | 1 | 1 | 0 | 1 | 1 | acrA, acrB, clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbI, clbJ, clbL, clbM, clbN, clbO, clbP, clbQ, clbS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, iroN, irp1, irp2, iucA, iucB, iucC, iucD, iutA, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, rmpA2, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_144 | ERS1531012 | ERR2497285 | Unknown | Cornick et al | Human | Invasive | ST70 | O4 | Very high | KL15 | Very high | 0 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, hcp_tssD, icmF_tssM, iroE, iucA, iucB, iucC, iucD, iutA, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, ybdA | NA |
| 22072_1_145 | ERS1531014 | ERR2497286 | Unknown | Cornick et al | Human | Invasive | ST4 | O1v1 | Very high | KL62 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_146 | ERS1531015 | ERR2497287 | Unknown | Cornick et al | Human | Invasive | ST348 | O1v1 | Very high | KL62 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_147 | ERS1531017 | ERR2497288 | Unknown | Cornick et al | Human | Invasive | ST14 | O1/O2v1 | Very high | KL2 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_148 | ERS1531018 | ERR2497289 | Unknown | Cornick et al | Human | Invasive | ST101 | O1v1 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_149 | ERS1531019 | ERR2497290 | Unknown | Cornick et al | Human | Invasive | ST1552 | O1/O2v1 | Very high | KL25 | None | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_150 | ERS1531020 | ERR2497291 | Unknown | Cornick et al | Human | Invasive | ST25 | O2v2 | Very high | KL2 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_151 | ERS1531021 | ERR2497292 | Unknown | Cornick et al | Human | Invasive | ST268 | O2v1 | Very high | KL20 | Very high | 1 | 1 | 1 | 1 | 1 | 1 | 1 | acrA, acrB, clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbI, clbK, clbL, clbM, clbN, clbO, clbP, clbQ, clbS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, irp1, irp2, iucA, iucB, iucC, iucD, iutA, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_153 | ERS1531024 | ERR2497294 | Unknown | Cornick et al | Human | Invasive | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_154 | ERS1531027 | ERR2497295 | Unknown | Cornick et al | Human | Invasive | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_155 | ERS1531028 | ERR2497296 | Unknown | Cornick et al | Human | Invasive | ST54 | O3b | Very high | KL14 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, ugd, vasE_tssK, vipA_tssB, vipB_tssC, yagZ_ecpA, ybdA | NA |
| 22072_1_157 | ERS1531033 | ERR2497298 | Unknown | Cornick et al | Human | Invasive | ST307 | O2v2 | Very high | KL102 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_159 | ERS1531035 | ERR2497300 | Unknown | Cornick et al | Human | Invasive | Unknown | O5 | High | KL68 | Low | 0 | 0 | 0 | 0 | 0 | 0 | 0 | NA | NA |
| 22072_1_160 | ERS1531036 | ERR2497301 | Unknown | Cornick et al | Human | Invasive | ST297 | O1v1 | Very high | KL158 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_161 | ERS1531037 | ERR2497302 | Unknown | Cornick et al | Human | Invasive | ST2144 | O12 | Good | KL64 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, allA, allB, allC, allD, allR, allS, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimC, fimF, fimG, galF, gnd, manC, rcsA, rcsB, ybdA | NA |
| 22072_1_162 | ERS1531038 | ERR2497303 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_163 | ERS1531039 | ERR2497304 | Unknown | Cornick et al | Human | Invasive | ST268 | O2v1 | Very high | KL20 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_164 | ERS1531040 | ERR2497305 | Unknown | Cornick et al | Human | Invasive | ST874 | O1v2 | Very high | KL45 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_165 | ERS1531041 | ERR2497306 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL16 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_166 | ERS1531042 | ERR2497307 | Unknown | Cornick et al | Human | Invasive | ST372 | O2v1 | Very high | KL43 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_167 | ERS1531043 | ERR2497308 | Unknown | Cornick et al | Human | Invasive | ST372 | O2v1 | Very high | KL43 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_168 | ERS1531044 | ERR2497309 | Unknown | Cornick et al | Human | Invasive | ST36 | O2v1 | Very high | KL51 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_169 | ERS1531045 | ERR2497310 | Unknown | Cornick et al | Human | Invasive | ST499 | OL102 | None | KL70 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_237 | ERS1531126 | ERR2497378 | Unknown | Cornick et al | Human | Invasive | ST17 | O3b | Very high | KL134 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_238 | ERS1531127 | ERR2497379 | Unknown | Cornick et al | Human | Invasive | Unknown | O5 | None | KL25 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_239 | ERS1531128 | ERR2497380 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_240 | ERS1531129 | ERR2497381 | Unknown | Cornick et al | Human | Invasive | ST152 | O4 | Very high | KL149 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, iroE, irp1, irp2, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_241 | ERS1531130 | ERR2497382 | Unknown | Cornick et al | Human | Invasive | ST218 | O2v2 | Very high | KL57 | High | 0 | 0 | 1 | 1 | 1 | 1 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, iroN, iucA, iucB, iucC, iucD, iutA, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_243 | ERS1531132 | ERR2497384 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_245 | ERS1531134 | ERR2497386 | Unknown | Cornick et al | Human | Invasive | Unknown | O1v1 | Good | KL145 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | fliJ | NA |
| 22072_1_246 | ERS1531135 | ERR2497387 | Unknown | Cornick et al | Human | Invasive | ST4151 | O3/O3a | Good | KL53 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, cpsACP, dotU_tssL, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimF, fimG, fimH, fimI, fimK, fyuA, gnd, hcp_tssD, irp1, irp2, manC, mrkA, mrkB, mrkC, mrkD, mrkF, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 22072_1_247 | ERS1531136 | ERR2497388 | Unknown | Cornick et al | Human | Invasive | ST1799 | O1v1 | Very high | KL16 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_248 | ERS1531137 | ERR2497389 | Unknown | Cornick et al | Human | Invasive | ST499 | OL102 | None | KL70 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_249 | ERS1531138 | ERR2497390 | Unknown | Cornick et al | Human | Invasive | ST111 | O1v2 | Very high | KL104 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 22072_1_250 | ERS1531140 | ERR2497391 | Unknown | Cornick et al | Human | Invasive | ST4314 | O5 | Very high | KL165 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkH, mrkI, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_94 | ERS1521635 | ERR2497235 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_95 | ERS1530953 | ERR2497236 | Unknown | Cornick et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_96 | ERS1530954 | ERR2497237 | Unknown | Cornick et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 22072_1_97 | ERS1530955 | ERR2497238 | Unknown | Cornick et al | Human | Invasive | ST1801 | O1v1 | Good | KL35 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_98 | ERS1530956 | ERR2497239 | Unknown | Cornick et al | Human | Invasive | ST106 | O1v1 | Very high | KL43 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 22072_1_99 | ERS1530957 | ERR2497240 | Unknown | Cornick et al | Human | Invasive | ST372 | O2v1 | Very high | KL43 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 15966_8_21 | ERS668986 | ERR926371 | 2013 | Musicha et al | Human | Invasive | ST609 | O1v1 | Very high | KL114 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 15966_8_57 | ERS669023 | ERR926407 | 1997 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, iucA, iucB, iucC, iucD, iutA, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 15966_8_86 | ERS669059 | ERR926436 | 2012 | Musicha et al | Human | Invasive | ST37 | O3b | Good | KL14 | High | 1 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, gnd, hcp_tssD, iroE, irp1, irp2, kpsF, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, papI, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 15966_8_87 | ERS669060 | ERR926437 | 1996 | Musicha et al | Human | Invasive | ST17 | O2v2 | Very high | KL122 | Very high | 0 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, hcp_tssD, iroE, iucA, iucB, iucC, iucD, iutA, kfoC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 15966_8_88 | ERS669061 | ERR926438 | 1999 | Musicha et al | Human | Invasive | ST1139 | O3/O3a | Good | KL49 | Low | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entB, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 15966_8_89 | ERS669062 | ERR926439 | 2011 | Musicha et al | Human | Invasive | ST4073 | O1v1 | Very high | KL5 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 15966_8_91 | ERS669064 | ERR926441 | 2014 | Musicha et al | Human | Invasive | ST348 | O1v1 | Very high | KL62 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 15966_8_93 | ERS669066 | ERR926443 | 2012 | Musicha et al | Human | Invasive | ST106 | O1v1 | Very high | KL43 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 15966_8_95 | ERS669068 | ERR926445 | 2013 | Musicha et al | Human | Invasive | ST874 | O1v2 | Very high | KL45 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_11 | ERS669081 | ERR971957 | 2009 | Musicha et al | Human | Colonising | ST1907 | O12 | Very high | KL132 | High | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimG, fimH, galF, gnd, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, rcsA, rcsB, ugd, ybdA | NA |
| 16228_1_13 | ERS669084 | ERR971959 | 2004 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, iucA, iucB, iucC, iucD, iutA, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_14 | ERS669085 | ERR971960 | 1997 | Musicha et al | Human | Invasive | ST48 | O1v1 | Very high | KL62 | Good | 0 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, iucA, iucB, iucC, iucD, iutA, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_15 | ERS669086 | ERR971961 | 1998 | Musicha et al | Human | Invasive | ST1425 | OL101 | Good | KL118 | None | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, galF, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | NA |
| 16228_1_18 | ERS669090 | ERR971964 | 1998 | Musicha et al | Human | Invasive | ST664 | O1v1 | Very high | KL62 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_19 | ERS669099 | ERR971965 | 2005 | Musicha et al | Human | Invasive | ST45 | O2v1 | Very high | KL24 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_2 | ERS669070 | ERR971948 | 2006 | Musicha et al | Human | Invasive | ST664 | O1v1 | Very high | KL62 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_21 | ERS669103 | ERR971967 | 2007 | Musicha et al | Human | Invasive | ST161 | OL101 | Good | KL127 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | NA |
| 16228_1_23 | ERS669113 | ERR971969 | 2009 | Musicha et al | Human | Invasive | ST198 | O1v1 | Very high | KL30 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_26 | ERS669116 | ERR971972 | 2008 | Musicha et al | Human | Invasive | ST4228 | O1v1 | Very high | KL103 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_28 | ERS669120 | ERR971974 | 2009 | Musicha et al | Human | Colonising | ST101 | O1v2 | Very high | KL106 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_29 | ERS669123 | ERR971975 | 2009 | Musicha et al | Human | Colonising | ST3119 | O2v2 | Good | KL39 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, ugd, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_3 | ERS669071 | ERR971949 | 2007 | Musicha et al | Human | Invasive | ST478 | O5 | High | KL125 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimE, fimF, fimG, fimH, fimI, fimK, galF, hcp_tssD, iroE, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | NA |
| 16228_1_30 | ERS669124 | ERR971976 | 2009 | Musicha et al | Human | Colonising | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_31 | ERS669126 | ERR971977 | 2009 | Musicha et al | Human | Colonising | ST39 | O1v2 | Very high | KL23 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_32 | ERS669127 | ERR971978 | 2009 | Musicha et al | Human | Colonising | ST107 | O1v1 | Very high | KL10 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, ugd, vasE_tssK, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_34 | ERS669131 | ERR971980 | 2010 | Musicha et al | Human | Invasive | ST15 | O1v1 | Very high | KL48 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_36 | ERS669134 | ERR971982 | 2011 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_38 | ERS669141 | ERR971984 | 2012 | Musicha et al | Human | Invasive | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_39 | ERS669143 | ERR971985 | 2009 | Musicha et al | Human | Invasive | ST198 | O1v1 | Very high | KL30 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_4 | ERS669072 | ERR971950 | 2014 | Musicha et al | Human | Invasive | ST1023 | O3/O3a | Very high | KL20 | High | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, dotU_tssL, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, ybdA | NA |
| 16228_1_40 | ERS669145 | ERR971986 | 2004 | Musicha et al | Human | Invasive | ST15 | O1v1 | Very high | KL24 | High | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_47 | ERS669056 | ERR971993 | Unknown | Musicha et al | Human | Colonising | ST307 | O2v2 | Very high | KL102 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_5 | ERS669073 | ERR971951 | 2013 | Musicha et al | Human | Invasive | ST340 | O4 | Very high | KL15 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, galF, hcp_tssD, icmF_tssM, impA_tssA, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, vasE_tssK, VFG048736, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 16228_1_50 | ERS669078 | ERR971996 | 2009 | Musicha et al | Human | Colonising | ST101 | O1v1 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_51 | ERS669080 | ERR971997 | 1997 | Musicha et al | Human | Invasive | ST48 | O1v1 | Very high | KL62 | High | 1 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, irp1, irp2, iucA, iucB, iucC, iucD, iutA, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_52 | ERS669082 | ERR971998 | 2000 | Musicha et al | Human | Invasive | ST73 | O1v1 | Very high | KL25 | High | 1 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp2, iucA, iucB, iucC, iucD, iutA, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA2, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_53 | ERS669088 | ERR971999 | 2006 | Musicha et al | Human | Invasive | ST297 | O1v1 | Very high | KL10 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_54 | ERS669091 | ERR972000 | 2000 | Musicha et al | Human | Invasive | ST2558 | O4 | None | KL107 | None | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, allA, allB, allC, allD, allR, allS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimD, fimG, fimH, galF, hcp_tssD, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, rcsA, rcsB, sciN_tssJ, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 16228_1_55 | ERS669092 | ERR972001 | 2004 | Musicha et al | Human | Invasive | ST3132 | O1v1 | Very high | KL142 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, cpsACP, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, ugd, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_56 | ERS669093 | ERR972002 | 1998 | Musicha et al | Human | Invasive | ST14 | O1v1 | Good | KL2 | Very high | 0 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, iucA, iucB, iucC, iucD, iutA, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_57 | ERS669094 | ERR972003 | 2007 | Musicha et al | Human | Invasive | ST231 | O1v2 | Very high | KL51 | High | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_58 | ERS669095 | ERR972004 | 2000 | Musicha et al | Human | Invasive | ST25 | O1v2 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_59 | ERS669096 | ERR972005 | 2005 | Musicha et al | Human | Invasive | ST664 | O1v1 | Very high | KL62 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_6 | ERS669074 | ERR971952 | 2006 | Musicha et al | Human | Invasive | ST101 | O1v1 | Very high | KL17 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, afaA, afaE-I, chuA, chuS, chuT, chuU, chuV, chuW, chuX, chuY, clpV_tssH, cpsACP, daaF, dotU_tssL, draP, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, gspD, gspK, hcp_tssD, ibeA, iroD, iroE, irp1, irp2, iucA, iucB, iucC, iutA, kpsD, kpsE, kpsF, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, papI, papX, rcsA, rcsB, sat, sciN_tssJ, senB, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wzm, wzt, yagW_ecpD, yagY_ecpB, yagZ_ecpA, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX, ykgK_ecpR | NA |
| 16228_1_61 | ERS669098 | ERR972007 | 1999 | Musicha et al | Human | Invasive | ST218 | O2v2 | Very high | KL57 | Very high | 0 | 0 | 1 | 1 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, iucA, iucB, iucC, iucD, iutA, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_63 | ERS669102 | ERR972009 | 2008 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_64 | ERS669104 | ERR972010 | 2004 | Musicha et al | Human | Invasive | ST268 | O2v1 | Very high | KL20 | Very high | 1 | 1 | 1 | 1 | 0 | 1 | 1 | acrA, acrB, clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbI, clbK, clbL, clbM, clbN, clbO, clbP, clbQ, clbS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, iroN, irp1, irp2, iucA, iucB, iucC, iucD, iutA, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_65 | ERS669105 | ERR972011 | 2005 | Musicha et al | Human | Invasive | ST560 | O2v2 | Very high | KL9 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_66 | ERS669106 | ERR972012 | 2008 | Musicha et al | Human | Invasive | ST4 | O1v1 | Very high | KL13 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_67 | ERS669108 | ERR972013 | 2006 | Musicha et al | Human | Invasive | ST664 | O1v2 | Very high | KL133 | None | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_68 | ERS669109 | ERR972014 | 2007 | Musicha et al | Human | Invasive | ST1128 | OL104 | Good | KL107 | None | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 16228_1_69 | ERS669110 | ERR972015 | 2006 | Musicha et al | Human | Invasive | ST34 | O3b | Very high | KL111 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, ybdA | NA |
| 16228_1_7 | ERS669075 | ERR971953 | 1996 | Musicha et al | Human | Invasive | ST111 | O1v2 | Very high | KL63 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_70 | ERS669111 | ERR972016 | 1999 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, iucA, iucB, iucC, iucD, iutA, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_71 | ERS669112 | ERR972017 | 2005 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 1 | 0 | 0 | 1 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, iucA, iucB, iucC, iucD, iutA, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_72 | ERS669117 | ERR972018 | 2008 | Musicha et al | Human | Invasive | ST276 | O2v2 | Very high | KL43 | Good | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_73 | ERS669118 | ERR972019 | 2009 | Musicha et al | Human | Invasive | ST101 | O1v1 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_74 | ERS669121 | ERR972020 | 2009 | Musicha et al | Human | Colonising | ST15 | O1v1 | Very high | KL24 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_75 | ERS669122 | ERR972021 | 2009 | Musicha et al | Human | Colonising | ST334 | O5 | High | KL103 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fimA, fimC, fimF, fimG, galF, gnd, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, rcsA, rcsB, ugd, ybdA | NA |
| 16228_1_76 | ERS669125 | ERR972022 | 2009 | Musicha et al | Human | Colonising | ST1916 | O1v1 | Very high | KL27 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroE, KPHS_23120, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_77 | ERS669129 | ERR972023 | 2006 | Musicha et al | Human | Invasive | ST268 | O2v1 | Very high | KL20 | Very high | 1 | 1 | 1 | 1 | 0 | 1 | 1 | acrA, acrB, clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbI, clbJ, clbK, clbL, clbM, clbN, clbO, clbP, clbQ, clbS, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, iroN, irp1, irp2, iucA, iucB, iucC, iucD, iutA, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_78 | ERS669130 | ERR972024 | 2009 | Musicha et al | Human | Invasive | ST101 | O1v1 | Very high | KL17 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_79 | ERS669132 | ERR972025 | 2011 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_8 | ERS669076 | ERR971954 | 2014 | Musicha et al | Human | Invasive | ST372 | O2v1 | Very high | KL43 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_80 | ERS669135 | ERR972026 | 2006 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL2 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_81 | ERS669136 | ERR972027 | 2008 | Musicha et al | Human | Invasive | ST48 | O1v1 | Very high | KL62 | Good | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tli1, tssF, tssG, ugd, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_82 | ERS669137 | ERR972028 | 2005 | Musicha et al | Human | Invasive | ST20 | O1v1 | Very high | KL24 | High | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkF, mrkH, mrkI, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_83 | ERS669139 | ERR972029 | 2010 | Musicha et al | Human | Invasive | ST218 | O2v2 | Very high | KL57 | Very high | 0 | 0 | 1 | 1 | 0 | 1 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, icmF_tssM, iroB, iroC, iroD, iroE, iroN, iucA, iucB, iucC, iucD, iutA, kfoC, KPHS_23120, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, rmpA, sciN_tssJ, tli1, tssF, tssG, vasE_tssK, vgrG_tssI, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 16228_1_84 | ERS669140 | ERR972030 | 2009 | Musicha et al | Human | Invasive | ST14 | O1v1 | Very high | KL16 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wzm, wzt, ybdA | NA |
| 16228_1_85 | ERS669142 | ERR972031 | 2012 | Musicha et al | Human | Invasive | ST896 | O2v2 | Very high | KL3 | Very high | 1 | 0 | 0 | 0 | 0 | 0 | 1 | acrA, acrB, clpV_tssH, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, fyuA, galF, glf, gnd, hcp_tssD, iroE, irp1, irp2, kfoC, manB, manC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX | NA |
| 16228_1_9 | ERS669077 | ERR971955 | 2007 | Musicha et al | Human | Invasive | ST18 | O2v2 | Very high | KL23 | Very high | 0 | 0 | 0 | 0 | 0 | 0 | 0 | acrA, acrB, clpV_tssH, cpsACP, dotU_tssL, entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK, galF, glf, gnd, hcp_tssD, iroE, kfoC, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ, rcsA, rcsB, sciN_tssJ, tssF, tssG, ugd, vasE_tssK, vipA_tssB, vipB_tssC, wbbM, wbbN, wbbO, wzm, wzt, ybdA | NA |
| 10026_1_50 | ERS246996 | ERR323219 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 10026_1_53 | ERS246999 | ERR323222 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 10026_1_56 | ERS247002 | ERR323225 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_10 | ERS214292 | ERR315112 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9776_6_13 | ERS214295 | ERR315115 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9776_6_16 | ERS214298 | ERR315118 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_19 | ERS214301 | ERR315121 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9776_6_21 | ERS214303 | ERR315123 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9776_6_24 | ERS214306 | ERR315126 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9776_6_27 | ERS214309 | ERR315129 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9776_6_3 | ERS214285 | ERR315105 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_32 | ERS214314 | ERR315134 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_35 | ERS214317 | ERR315137 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_38 | ERS214320 | ERR315140 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_40 | ERS214322 | ERR315142 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_43 | ERS214325 | ERR315145 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_46 | ERS214328 | ERR315148 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_49 | ERS214331 | ERR315151 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_51 | ERS214333 | ERR315153 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9776_6_54 | ERS214336 | ERR315156 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9776_6_57 | ERS214339 | ERR315159 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_6 | ERS214288 | ERR315108 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_62 | ERS214344 | ERR315164 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_65 | ERS214347 | ERR315167 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_68 | ERS214350 | ERR315170 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_70 | ERS214352 | ERR315172 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_73 | ERS214355 | ERR315175 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_76 | ERS214358 | ERR315178 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_79 | ERS214361 | ERR315181 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_84 | ERS214366 | ERR315186 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_87 | ERS214369 | ERR315189 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_9 | ERS214291 | ERR315111 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_92 | ERS214374 | ERR315194 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9776_6_95 | ERS214377 | ERR315197 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_11 | ERS219111 | ERR319508 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_14 | ERS219114 | ERR319511 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_17 | ERS219117 | ERR319514 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_2 | ERS219102 | ERR319499 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_22 | ERS219122 | ERR319519 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_25 | ERS219125 | ERR319522 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_28 | ERS219128 | ERR319525 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_30 | ERS219130 | ERR319527 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_33 | ERS219133 | ERR319530 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_36 | ERS219136 | ERR319533 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_39 | ERS219139 | ERR319536 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_41 | ERS219141 | ERR319538 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_44 | ERS219144 | ERR319541 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_47 | ERS219147 | ERR319544 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_5 | ERS219105 | ERR319502 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_52 | ERS219152 | ERR319549 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_55 | ERS219155 | ERR319552 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_58 | ERS219158 | ERR319555 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_60 | ERS219160 | ERR319557 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_63 | ERS219100 | ERR319560 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_66 | ERS219165 | ERR319563 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_69 | ERS219168 | ERR319566 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_71 | ERS219170 | ERR319568 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 9870_4_74 | ERS219173 | ERR319571 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_77 | ERS219176 | ERR319574 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_8 | ERS219108 | ERR319505 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_82 | ERS219181 | ERR319579 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_85 | ERS219184 | ERR319582 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_88 | ERS219187 | ERR319585 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_90 | ERS219189 | ERR319587 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 9870_4_93 | ERS219192 | ERR319590 | Unknown | Henson et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_1_10 | ERS005750 | ERR024818 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_1_11 | ERS005751 | ERR024819 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_1_2 | ERS005742 | ERR024821 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_1_3 | ERS005743 | ERR024822 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_1_4 | ERS005744 | ERR024823 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_1_5 | ERS005745 | ERR024824 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_1_7 | ERS005747 | ERR024826 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_1_8 | ERS005748 | ERR024827 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_1_9 | ERS005749 | ERR024828 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_2_1 | ERS005752 | ERR024830 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_2_10 | ERS005762 | ERR024831 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_2_11 | ERS005763 | ERR024832 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_2_2 | ERS005754 | ERR024834 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_2_3 | ERS005756 | ERR024835 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_2_4 | ERS005755 | ERR024836 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_2_5 | ERS005757 | ERR024837 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_2_6 | ERS005758 | ERR024838 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_2_7 | ERS005759 | ERR024839 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_2_8 | ERS005760 | ERR024840 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_3_1 | ERS005765 | ERR024843 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_3_10 | ERS005774 | ERR024844 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_3_11 | ERS005775 | ERR024845 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_3_2 | ERS005766 | ERR024847 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_3_3 | ERS005767 | ERR024848 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_3_5 | ERS005768 | ERR024850 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_3_6 | ERS005770 | ERR024851 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_3_8 | ERS005771 | ERR024853 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_3_9 | ERS005773 | ERR024854 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_5_1 | ERS005777 | ERR025098 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_5_10 | ERS005786 | ERR025099 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_5_11 | ERS005787 | ERR025100 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_5_2 | ERS005778 | ERR025102 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_5_3 | ERS005779 | ERR025103 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_5_4 | ERS005780 | ERR025104 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_5_5 | ERS005781 | ERR025105 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_5_7 | ERS005783 | ERR025107 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5150_5_8 | ERS005784 | ERR025108 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5150_5_9 | ERS005785 | ERR025109 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_2_1 | ERS011914 | ERR025111 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_2_10 | ERS011923 | ERR025112 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_2_11 | ERS011924 | ERR025113 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_2_12 | ERS011925 | ERR025114 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_2_2 | ERS011915 | ERR025115 | 2003 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_2_3 | ERS011916 | ERR025116 | 2004 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_2_4 | ERS011917 | ERR025117 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_2_5 | ERS011918 | ERR025118 | 2004 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_2_6 | ERS011919 | ERR025119 | 2004 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_2_7 | ERS011920 | ERR025120 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_2_8 | ERS011921 | ERR025121 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_2_9 | ERS011922 | ERR025122 | 2008 | Holt et al | Environmental | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_3_1 | ERS011926 | ERR025124 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_3_10 | ERS011935 | ERR025125 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_3_2 | ERS011927 | ERR025128 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_3_8 | ERS011933 | ERR025134 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_3_9 | ERS011934 | ERR025135 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_5_1 | ERS011938 | ERR025137 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_10 | ERS011947 | ERR025138 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_11 | ERS011948 | ERR025139 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_12 | ERS011949 | ERR025140 | 2006 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_2 | ERS011939 | ERR025141 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_3 | ERS011940 | ERR025142 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_4 | ERS011941 | ERR025143 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_5 | ERS011942 | ERR025144 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_6 | ERS011943 | ERR025145 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_7 | ERS011944 | ERR025146 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_8 | ERS011945 | ERR025147 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_5_9 | ERS011946 | ERR025148 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_6_1 | ERS011950 | ERR025150 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_6_10 | ERS011959 | ERR025151 | 2005 | Holt et al | Environmental | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_6_11 | ERS011960 | ERR025152 | 2005 | Holt et al | Environmental | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_6_12 | ERS011961 | ERR025153 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_6_2 | ERS011951 | ERR025154 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_6_3 | ERS011952 | ERR025155 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_6_4 | ERS011953 | ERR025156 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5151_6_5 | ERS011954 | ERR025157 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_6_6 | ERS011955 | ERR025158 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_6_7 | ERS011956 | ERR025159 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_6_8 | ERS011957 | ERR025160 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5151_6_9 | ERS011958 | ERR025161 | 2005 | Holt et al | Environmental | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_1_1 | ERS011794 | ERR025462 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_1_10 | ERS011803 | ERR025463 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_1_11 | ERS011804 | ERR025464 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_1_12 | ERS011805 | ERR025465 | 2003 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_1_4 | ERS011797 | ERR025468 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_1_5 | ERS011798 | ERR025469 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_1_6 | ERS011799 | ERR025470 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_1_7 | ERS011800 | ERR025471 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_1_8 | ERS011801 | ERR025472 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_1_9 | ERS011802 | ERR025473 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_1 | ERS011806 | ERR025475 | 2004 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_10 | ERS011815 | ERR025476 | 2004 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_2_11 | ERS011816 | ERR025477 | 2004 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_12 | ERS011817 | ERR025478 | 2004 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_2 | ERS011807 | ERR025479 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_3 | ERS011808 | ERR025480 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_4 | ERS011809 | ERR025481 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_5 | ERS011810 | ERR025482 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_6 | ERS011811 | ERR025483 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_7 | ERS011812 | ERR025484 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_2_8 | ERS011813 | ERR025485 | 2004 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_2_9 | ERS011814 | ERR025486 | 2004 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_3_1 | ERS011830 | ERR025488 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_3_10 | ERS011839 | ERR025489 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_3_11 | ERS011840 | ERR025490 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_3_12 | ERS011841 | ERR025491 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_3_4 | ERS011833 | ERR025494 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_3_5 | ERS011834 | ERR025495 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_3_6 | ERS011835 | ERR025496 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_3_7 | ERS011836 | ERR025497 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_3_8 | ERS011837 | ERR025498 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_3_9 | ERS011838 | ERR025499 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_5_1 | ERS011842 | ERR025501 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_5_10 | ERS011851 | ERR025502 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_5_11 | ERS011852 | ERR025503 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_5_12 | ERS011853 | ERR025504 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_5_2 | ERS011843 | ERR025505 | 2007 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_5_4 | ERS011845 | ERR025507 | 2007 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_5_6 | ERS011847 | ERR025509 | 2007 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_5_7 | ERS011848 | ERR025510 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_5_8 | ERS011849 | ERR025511 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_5_9 | ERS011850 | ERR025512 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_6_1 | ERS011854 | ERR025514 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_6_10 | ERS011863 | ERR025515 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_6_11 | ERS011864 | ERR025516 | 2008 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_6_12 | ERS011865 | ERR025517 | 2008 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_6_2 | ERS011855 | ERR025518 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_6_3 | ERS011856 | ERR025519 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_6_4 | ERS011857 | ERR025520 | 2006 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_6_5 | ERS011858 | ERR025521 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_6_6 | ERS011859 | ERR025522 | 2008 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_6_7 | ERS011860 | ERR025523 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_6_8 | ERS011861 | ERR025524 | 2008 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_6_9 | ERS011862 | ERR025525 | 2009 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_7_1 | ERS011878 | ERR025527 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_7_10 | ERS011887 | ERR025528 | 2003 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_7_2 | ERS011879 | ERR025531 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_7_3 | ERS011880 | ERR025532 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_7_5 | ERS011882 | ERR025534 | 2000 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_7_6 | ERS011883 | ERR025535 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_7_7 | ERS011884 | ERR025536 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_7_8 | ERS011885 | ERR025537 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_7_9 | ERS011886 | ERR025538 | 2003 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_8_1 | ERS011902 | ERR025540 | 2004 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_8_10 | ERS011911 | ERR025541 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_8_11 | ERS011912 | ERR025542 | 2001 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_8_12 | ERS011913 | ERR025543 | 2002 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_8_2 | ERS011903 | ERR025544 | 1996 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_8_3 | ERS011904 | ERR025545 | 2004 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_8_4 | ERS011905 | ERR025546 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_8_5 | ERS011906 | ERR025547 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_8_6 | ERS011907 | ERR025548 | 2004 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_8_7 | ERS011908 | ERR025549 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5193_8_8 | ERS011909 | ERR025550 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5193_8_9 | ERS011910 | ERR025551 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_1 | ERS011818 | ERR025553 | 2004 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_10 | ERS011827 | ERR025554 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_11 | ERS011828 | ERR025555 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_12 | ERS011829 | ERR025556 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_2 | ERS011819 | ERR025557 | 2004 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_2_3 | ERS011820 | ERR025558 | 2004 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_4 | ERS011821 | ERR025559 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_5 | ERS011822 | ERR025560 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_6 | ERS011823 | ERR025561 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_2_7 | ERS011825 | ERR025562 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_2_8 | ERS011824 | ERR025563 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_2_9 | ERS011826 | ERR025564 | 2005 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_7_1 | ERS011866 | ERR025566 | 2006 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_7_2 | ERS011867 | ERR025570 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_7_3 | ERS011868 | ERR025571 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_7_4 | ERS011869 | ERR025572 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_7_5 | ERS011870 | ERR025573 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_7_6 | ERS011871 | ERR025574 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_7_7 | ERS011872 | ERR025575 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_7_8 | ERS011873 | ERR025576 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_8_11 | ERS011900 | ERR025581 | Unknown | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5197_8_2 | ERS011891 | ERR025583 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_8_3 | ERS011892 | ERR025584 | 2006 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_8_4 | ERS011893 | ERR025585 | 2006 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_8_5 | ERS011894 | ERR025586 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_8_6 | ERS011895 | ERR025587 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_8_7 | ERS011896 | ERR025588 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5197_8_8 | ERS011897 | ERR025589 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_1_10 | ERS011983 | ERR025593 | 2007 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_11 | ERS011984 | ERR025594 | 2007 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_2 | ERS011975 | ERR025596 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_3 | ERS011976 | ERR025597 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_4 | ERS011977 | ERR025598 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_5 | ERS011978 | ERR025599 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_6 | ERS011979 | ERR025600 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_7 | ERS011980 | ERR025601 | 2007 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_8 | ERS011981 | ERR025602 | 2007 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_1_9 | ERS011982 | ERR025603 | 2007 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_2_1 | ERS011986 | ERR025605 | 2007 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_2_11 | ERS011996 | ERR025607 | 2005 | Holt et al | Environmental | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_2_12 | ERS011997 | ERR025608 | 2005 | Holt et al | Environmental | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_2_2 | ERS011987 | ERR025609 | 2007 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_2_3 | ERS011988 | ERR025610 | 2007 | Holt et al | Human | Colonising |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_2_4 | ERS011989 | ERR025611 | 2007 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_2_5 | ERS011990 | ERR025612 | 2007 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_2_6 | ERS011991 | ERR025613 | 2005 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_2_7 | ERS011992 | ERR025614 | 2005 | Holt et al | Environmental | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_2_8 | ERS011993 | ERR025615 | 2007 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_3_1 | ERS011998 | ERR025618 | 2007 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_3_11 | ERS012008 | ERR025620 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_3_12 | ERS012009 | ERR025621 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_3_2 | ERS011999 | ERR025622 | 2007 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_3_4 | ERS012001 | ERR025624 | 2007 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_3_5 | ERS012002 | ERR025625 | 2006 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_3_7 | ERS012004 | ERR025627 | 2007 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_3_8 | ERS012005 | ERR025628 | 2006 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_5_11 | ERS012020 | ERR025633 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_5_2 | ERS012011 | ERR025635 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_5_3 | ERS012012 | ERR025636 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_5_5 | ERS012014 | ERR025638 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_5_8 | ERS012017 | ERR025641 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_6_1 | ERS012022 | ERR025644 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_6_10 | ERS012031 | ERR025645 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_6_11 | ERS012032 | ERR025646 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_6_12 | ERS012033 | ERR025647 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_6_2 | ERS012023 | ERR025648 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_6_3 | ERS012024 | ERR025649 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_6_5 | ERS012026 | ERR025651 | 2008 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_6_6 | ERS012027 | ERR025652 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_6_8 | ERS012029 | ERR025654 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_6_9 | ERS012030 | ERR025655 | 2009 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_7_1 | ERS012034 | ERR025657 | 2005 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_7_10 | ERS012043 | ERR025658 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_7_11 | ERS012044 | ERR025659 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_7_12 | ERS012045 | ERR025660 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_7_2 | ERS012035 | ERR025661 | 2005 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_7_3 | ERS012036 | ERR025662 | 2005 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_7_4 | ERS012037 | ERR025663 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_7_5 | ERS012038 | ERR025664 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_7_8 | ERS012041 | ERR025667 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_7_9 | ERS012042 | ERR025668 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_8_10 | ERS011792 | ERR025671 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_8_2 | ERS011784 | ERR025673 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_8_3 | ERS011785 | ERR025674 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_8_4 | ERS011786 | ERR025675 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_8_5 | ERS011787 | ERR025676 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_8_6 | ERS011788 | ERR025677 | 2008 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_8_7 | ERS011789 | ERR025678 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5235_8_8 | ERS011790 | ERR025679 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5235_8_9 | ERS011791 | ERR025680 | 2009 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5299_1_1 | ERS011962 | ERR025979 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_1_10 | ERS011971 | ERR025980 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_1_11 | ERS011972 | ERR025981 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_1_12 | ERS011973 | ERR025982 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_1_2 | ERS011963 | ERR025983 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_1_3 | ERS011964 | ERR025984 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_1_4 | ERS011965 | ERR025985 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_1_7 | ERS011968 | ERR025988 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5299_1_8 | ERS011969 | ERR025989 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_1_9 | ERS011970 | ERR025990 | 2007 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5299_7_1 | ERS012046 | ERR025992 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_7_10 | ERS012055 | ERR025993 | 2009 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5299_7_2 | ERS012047 | ERR025994 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_7_3 | ERS012048 | ERR025995 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5299_7_4 | ERS012049 | ERR025996 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5299_7_5 | ERS012050 | ERR025997 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5299_7_6 | ERS012051 | ERR025998 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
| 5299_7_7 | ERS012052 | ERR025999 | 2006 | Holt et al | Animal | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_7_8 | ERS012053 | ERR026000 | 2005 | Holt et al | Human | Unknown |
|
|
|
|
|
|
|
|
|
|
|
0 | NA | NA |
| 5299_7_9 | ERS012054 | ERR026001 | 2005 | Holt et al | Human | Invasive |
|
|
|
|
|
|
|
|
|
|
|
1 | NA | NA |
if (write_figs) {
write.csv(metadata_table,
here("tables/kleb-genomics/metadata_table.csv"),
row.names = FALSE
)
}Reproducability, session info
sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Sonoma 14.0
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
#>
#> locale:
#> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
#>
#> time zone: Europe/London
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] vegan_2.6-4 lattice_0.21-8 permute_0.9-7 ggnewscale_0.4.9
#> [5] stringr_1.5.0 blantyreESBL_1.4.1 ggplotify_0.1.2 pheatmap_1.0.12
#> [9] viridis_0.6.4 viridisLite_0.4.2 scales_1.2.1 patchwork_1.1.3
#> [13] kableExtra_1.3.4 here_1.0.1 tidyr_1.3.0 forcats_1.0.0
#> [17] dplyr_1.1.3 ggpubr_0.6.0 ggplot2_3.4.3 cowplot_1.1.1
#> [21] ggtree_3.9.1 phytools_1.9-16 maps_3.4.1 ape_5.7-1
#> [25] rstatix_0.7.2 tidytree_0.4.5
#>
#> loaded via a namespace (and not attached):
#> [1] mnormt_2.1.1 gridExtra_2.3 phangorn_2.11.1
#> [4] rlang_1.1.1 magrittr_2.0.3 compiler_4.3.1
#> [7] mgcv_1.8-42 systemfonts_1.0.4 vctrs_0.6.3
#> [10] combinat_0.0-8 quadprog_1.5-8 rvest_1.0.3
#> [13] crayon_1.5.2 pkgconfig_2.0.3 fastmap_1.1.1
#> [16] backports_1.4.1 labeling_0.4.3 utf8_1.2.3
#> [19] rmarkdown_2.25 ragg_1.2.5 purrr_1.0.2
#> [22] xfun_0.40 cachem_1.0.8 aplot_0.2.2
#> [25] clusterGeneration_1.3.8 jsonlite_1.8.7 highr_0.10
#> [28] cluster_2.1.4 broom_1.0.5 parallel_4.3.1
#> [31] R6_2.5.1 bslib_0.5.1 stringi_1.7.12
#> [34] RColorBrewer_1.1-3 car_3.1-2 jquerylib_0.1.4
#> [37] numDeriv_2016.8-1.1 Rcpp_1.0.11 iterators_1.0.14
#> [40] knitr_1.44 optimParallel_1.0-2 splines_4.3.1
#> [43] Matrix_1.6-1.1 igraph_1.5.1 tidyselect_1.2.0
#> [46] rstudioapi_0.15.0 abind_1.4-5 yaml_2.3.7
#> [49] doParallel_1.0.17 codetools_0.2-19 tibble_3.2.1
#> [52] treeio_1.26.0 withr_2.5.1 coda_0.19-4
#> [55] evaluate_0.22 gridGraphics_0.5-1 desc_1.4.2
#> [58] xml2_1.3.5 pillar_1.9.0 carData_3.0-5
#> [61] foreach_1.5.2 ggfun_0.1.3 generics_0.1.3
#> [64] rprojroot_2.0.3 munsell_0.5.0 glue_1.6.2
#> [67] scatterplot3d_0.3-44 lazyeval_0.2.2 tools_4.3.1
#> [70] webshot_0.5.5 ggsignif_0.6.4 fs_1.6.3
#> [73] fastmatch_1.1-4 grid_4.3.1 plotrix_3.8-2
#> [76] colorspace_2.1-0 nlme_3.1-162 cli_3.6.1
#> [79] textshaping_0.3.6 fansi_1.0.5 expm_0.999-7
#> [82] svglite_2.1.2 gtable_0.3.4 yulab.utils_0.1.0
#> [85] sass_0.4.7 digest_0.6.33 farver_2.1.1
#> [88] memoise_2.0.1 htmltools_0.5.6.1 pkgdown_2.0.7
#> [91] lifecycle_1.0.3 httr_1.4.7 MASS_7.3-60