Genomic data and metadata from Extended-Spectrum Beta-Lactamase producing Escherichia coli

Summary Table for 2,507 Extended Spectrum Beta-Lactamase-producing Escherichia coli (ESBL-Ec) genomes This Supplementary Table contains the metadata associated with each genome analyzed, including: Genome accession (Strain); Lineage characteristics (Phylogroup, Clonal Complex, Sequence Type, Sequence Type 131 clade, Serotype); Carbapenemase production status (Carbapenemase-producing strain) ; Epidemic lineage assignment (Epidemic strain); Chromosomal (Chromosomal variant) and plasmidic (Plasmidic variant) blaCTX-M variants with copy number; Antimicrobial Resistance Genes (ARGs) barcodes associated to chromosomally-inserted blaCTX-M variant (ARGs barcode); Associated genomes accessions metadata (Assembly submitter, BioSample accession, BioProject accession) Available source metadata (Source type, Source niche, Source details, Collection year, Continent, Country, Region, District, and City). For genomes carrying multiple chromosomal or plasmidic blaCTX-M genes, variants are reported as a semicolon-separated list with the corresponding copy number (e.g., blaCTX-M-15 (n=2); blaCTX-M-14 (n=1)). Missing or unavailable (meta)data are reported as “Undefined”. Note: Although metadata are provided for all 2,507 ESBL-Ec genomes, only 2,269 non-duplicate genomes were included in the final analyses and the 238 excluded epidemic genomes ARGs barcodes were not evaluated. The Epidemic strain variable identifies the 2,269 genomes retained after duplicate removal. Duplicates were defined as genomes that i) belonged to the same 10-allele hierarchical clonal cluster (HierCC10), ii) originated from the same BioProject, and iii) shared an identical antimicrobial resistance gene content.