Genetic comparison of virulence and resistance factors in phylogenetically diverse Escherichia coli from dairy cattle

Antimicrobial resistance (AMR) in livestock represents a significant and growing One Health concern, with Escherichia coli acting as a major reservoir of resistance and virulence determinants. The present study analysed the whole-genome sequences of 172 E. coli strains of dairy cattle origin from 7 countries, which included ESBL (Extended-Spectrum β-Lactamase) (n = 63) and non-ESBL (n = 109) strains. The isolates showed high genetic diversity across 64 sequence types (STs) and seven phylogroups, with A (34.88 %) and B1 (34.30 %) being the most prevalent. The STs, ST10 (14.53 %) and ST224 (9.30 %), were the most dominant. Among the 86 distinct antimicrobial resistance genes (ARGs) identified, ESBL genes were prevalent, with bla_CTX-M-1 (15.86 %) and bla_CTX-M-15 (11.71 %) being most common. ESBL strains showed enriched ARG profiles, whereas non-ESBL strains exhibited greater ARG diversity. Among the 163 virulence-associated genes identified, terC (7.39 %, Tellurium ion resistance protein) and fdeC (6.18 %, intimin-like adhesin FdeC) were the most widespread, with phylogroups C and D exhibiting the highest cumulative virulence scores. Notably, ESBL-producing E. coli strains showed marginally higher virulence gene frequencies than their non-ESBL counterparts. The accessory genome was enriched with mobile genetic elements (MGEs), notably IS26 and IS5075 (linked to 26 and 13 ARGs), Tn2 (bla_TEM variants), Tn1721/Tn6303 (tetA), and Tn801 (β-lactams). IncQ1 and IncF were the predominant plasmid vectors, with IncQ1 accounting for over 60 % of ARG-plasmid linkages. These findings provide important genomic associations of E. coli in dairy animals, highlighting the interplay of AMR gene mobility and virulence, and the importance of genomic surveillance in the dairy environment to prevent E. coli pathogen transmission into the human food chain.