Chemical Resistome Evolution in Escherichia coli 1917-2023
Description
This dataset contains the curated master analytical matrix supporting the study “A Century of Chemical Resistome Evolution in Escherichia coli: Global Dynamics of Antibiotic and Biocide Resistance Genes from 1917 to 2023.” The dataset integrates genomic, epidemiological, population-structure, antimicrobial-resistance, biocide-associated, plasmid, genetic-location, and genome-quality information for 743 complete human-derived Escherichia coli genomes collected between 1917 and 2023. Genome assemblies were retrieved from the NCBI Assembly database and linked through assembly accession identifiers. The integrated matrix includes temporal and geographic metadata, Clermont phylogroup assignments, Achtman multilocus sequence types (MLST), antimicrobial resistance determinants identified using ResFinder and CARD, and curated functional information derived from BacMet. To maintain a conservative functional definition, the biocide-associated category was restricted to qac- and oqx-family determinants, whereas broader multidrug-efflux and stress-response functions were retained as separate annotations. The dataset additionally incorporates plasmid replicon information and MOB-suite-derived genetic-location assignments, allowing resistance determinants to be classified according to their predicted genomic context as Plasmid, Chromosome, Both, or Unassigned. Genome-quality information generated during quality-control analyses is also integrated into the analytical framework. This master matrix constitutes the common data structure used for the study's prevalence, temporal, population-structure, genetic-localization, and antibiotic resistance–biocide-associated determinant co-occurrence analyses. It is provided to facilitate transparency, reproducibility, independent reanalysis, and comparative genomic surveillance of antimicrobial resistance from a One Health perspective.
Files
Steps to reproduce
The reproducible analysis scripts associated with this dataset are available through the accompanying GitHub repository.