Data: Accession numbers and metadata of isolates sequenced for this study

Metadata of all sequenced isolates

btESBL_sequence_sample_metadata

Format

A tidy data frame with 676 rows and 12 variables:

accession

Sample NCBI accession number

lane

Unique sample-sequencing run ID

supplier_name

Unique sample id

pid

Unique participant identifier

arm

Arm of study 1=sepsis, 2=inpatient, no abx, 3=community

visit

Study visit: 0 = baseline, 1 = d7, 2 = d28, 3 = d90, 4 = d180

data_date

Date of sample collection

enroll_date

Date of patient enrolment to study

assess_type

Number of days post-enrolment that sample was collected

hosp_assoc

Is sample community. hospital associated, or recent dc (see manuscript for details)

hospoutcomedate

Date of discharge from hospital. NA = never admittted

Cluster

PopPUNK cluster assignment. Prefix K = K. pneumo, E = E. coli

number_of_contigs

Number of contigs in assembly

N50

N50 of assembly

ecoli_phylogroup

E. coli phylogroup from in silico PCR

ecoli_pathogroup

E. coli pathogroup (see manuscript for details)

species

Isolate species either from API (E. coli) or Kleborate

kleb_k_locus

K. pnemo complex inferred K locus from Kleborate

kleb_k_locus_confidence

Kleborate defined K locus confidence

kleb_o_locus

K. pnemo complex inferred O locus from Kleborate

kleb_o_locus_confidence

Kleborate defined O locus confidence

kleb_YbST

Klebsiella YbST allele as per Kleborate

kleb_CbST

Klebsiella CbST allele as per Kleborate

kleb_AbST

Klebsiella AbST allele as per Kleborate

kleb_SmST

Klebsiella SmST allele as per Kleborate

kleb_rmpA

Klebsiella rmpA allele as per Kleborate

kleb_rmpA2

Klebsiella rmpA2 allele as per Kleborate