Reference

Participant data

Characteristics and exposures of study participants

btESBL_participants

Data: Characteristics of study participants.

btESBL_exposures

Data: Exposures of included participants

btESBL_stanmodeldata

Data: Covariate data to pass to Stan longitudinal carriage model in list format

btESBL_modeldata

Data: Covariate data to pass to Stan longitudinal carriage model in dataframe format

Stool culture data

Results of selective stool culture for ESBL

btESBL_stoolESBL

Data: Results of stool culture for ESBL

btESBL_stoolorgs

Data: Species of bacteria isolated from stool culture for ESBL

btESBL_AST

Data: Antimicrobial sensitivity testing for a suvet of isolates

Whole genome sequence metadata and analysis

Accession numbers of isolates and results of sequencing analysis

btESBL_sequence_sample_metadata

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

btESBL_amrgenes

Data: AMR genes identified in sequenced isolates (excluding QRDR mutations)

btESBL_qrdr_mutations

Data: Identified QRDR mutations

btESBL_plasmidreplicons

Data: Plasmid replicons identified in sequenced isolates

btESBL_contigclusters

Data: Contig cluster membership

btESBL_contigclusters_sensax

Data: Contig cluster assignment in sensitivity analyses

btESBL_contigclusters_msa_blastoutput

Data: Contig clusters BLASTed against ISFinder, PLasmidFinder, SRST2 databases

btESBL_contigclusters_msa_alignments

Data: Contig cluster multiple sequence alignments as PopGenome GENOME objects

btESBL_contigclusters_msa_paf_files

Data: Contig cluster multiple sequence alignment .paf files

btESBL_coregene_tree_esco

Data: E. coli core gene tree

btESBL_coregene_tree_kleb

Data: K. pneumoniae complex core gene tree

btESBL_snpdists_esco

Data: Pairwise SNP-distance matrix for all E. coli genomes

btESBL_snpdists_kleb

Data: Pairwise SNP-distance matrix for all K. pneumoniae complex genomes

btESBL_NCBI_phenotypic_bl

Data: NCBI phenotypic beta-lactamase classifications

btESBL_CARD_qrdr_mutations

Data: CARD described QRDR mutations

Results of modelling and simulations

Outputs from longituinal modelling of ESBL carriage

btESBL_model1posterior

Data: Posterior of fitted carriage model (constant antimicrobial effect)

btESBL_model2posterior

Data: Posterior of fitted carriage model (decaying antimicrobial effect)

btESBL_model3posterior

Data: Posterior of fitted carriage model (seperate ceftriaxone effect)

btESBL_model2simulations

Data: Results of simulations from the model posterior

btESBL_model2simulations_2

Data: Summary of results of simulations from model2 posterior to compare antimicrobials and hospitalisation

Global contextual analyses

Metadata of context genomes and results of clustering study isolates with global isolates

btESBL_ecoli_horesh_metadata

Data: metadata of 10,146 global E. coli genomes from Horesh et al

btESBL_ecoli_musicha_metadata

Data: Accession numbers and metadata of 97 E. coli genomes from Malawi from Musciha et al

btESBL_ecoli_global_popPUNK_clusters

Data: popPUNK cluster assignment of study E. coli isolates using global database

btESBL_ecoli_globaltree

Data: E.coli global context tree

btESBL_kleb_global_metadata

Data: Accession numbers and metadata of 682 global K. pneumoniae complex genomes

btESBL_kleb_globaltree

Data: K. pneumoniae complex global context phylogeny

btESBL_kleb_malawi_allisolate_core_gene_tree

Data: K. pneumoniae complex core gene tree of Malawian carriage and invasive isolates

Global E. coli ST410 contextual analysis

Metadata of global ST410 isolates and results of contextual genomic analysis

btESBL_ecoli_globalst167_tree

Data: E. coli ST167 global phylogeny

btESBL_ecoli_st167_metadata

Data: metadata of global E. coli ST167 isolates

btESBL_ecoli_st167_amr

Data: AMR genes identified in global ST167 isolates

btESBL_ecoli_st167_plasmids

Data: Plasmid replicons identified in global ST167 isolates

Global E. coli ST167 contextual analysis

Metadata of global ST167 isolates and results of contextual genomic analysis

btESBL_ecoli_globalst410_tree

Data: E. coli ST410 global phylogeny

btESBL_ecoli_st410_metadata

Data: metadata of global E. coli ST410 isolates

btESBL_ecoli_st410_amr

Data: AMR genes identified in global ST410 isolates

btESBL_ecoli_st410_plasmids

Data: Plasmid replicons identified in global ST410 isolates

Global E. coli ST131 contextual analysis

Metadata of global ST131 isolates and results of contextual genomic analysis

btESBL_ecoli_globalst131_tree

Data: E. coli ST131 global phylogeny

btESBL_ecoli_st131_metadata

Data: metadata of global E. coli ST131 isolates

btESBL_ecoli_st131_amr

Data: AMR genes identified in global ST131 isolates

btESBL_ecoli_st131_plasmids

Data: Plasmid replicons identified in global ST131 isolates