Profile of Genes Encoding Antimicrobial Resistance and Virulence in 3963 Escherichia coli Isolates

The prevalence and spread of antimicrobial resistance genes (ARGs) and virulence‐associated genes (VAGs) in bacterial pathogens is a major public health burden. Escherichia coli is an opportunistic pathogen that has garnered significant attention because of the emergence and dissemination of resistance to antibiotics of human and veterinary importance. The objective of this study was to characterize ARGs and VAGs in 3963 E. coli genomes released in complete level by the NCBI from 2006 to 2025. A total of 293 distinct ARGs and 351 distinct VAGs were identified from the genomes of E. coli isolates. Among the 293 ARGs, presence of 41 were found in the genomes of E. coli strains submitted since 2006, and the remaining 252 ARGs were identified in the genomes submitted in subsequent years. The genomes were enriched with ARGs corresponding to the drug classes fluoroquinolones, penam, tetracyclines, cephalosporins, and macrolides. The analysis identified that in 2037 (51.4%) isolates ARGs represented at least 1.29% of the genome, and in 1987 (50.13%) isolates accounted for at least 1.35% of their genome for virulence genes. Analysis of the distinct ARGs showed that 123 of them were found only on plasmids and 141 were shared between chromosomes and plasmids, whereas VAGs showed a greater tendency for chromosomal localization. Single‐copy occurrences of crp and cpxA were commonly found across all 3963 isolates, whereas multiple‐copy variants (≥ 2 copies) of sul1 , tet(A) , and bla _TEM-1 were detected in approximately 5% of the isolates. Sequence type analysis showed that ST10 was most frequently represented sequence type in higher level ARG Group III and IV, whereas almost all the strain in ST11 and ST73 were harbouring higher level of Group IV virulence. Weighted linear regression indicated an increase of 0.00292 percentage points per year in the genomic proportion encoding ARGs in E. coli . The results suggest a need for continuous genomic surveillance to tackle AMR, and the development of alternative approaches to overcome the burden of AMR and virulence.