Genomic Analyses of Antibiotic-Resistant Escherichia coli From Extensive Beef Cattle and Sheep Farms Identifies Inter-Species and Farm-Farm Sharing as Clonal Dissemination Pathways

Abstract

SynopsisO_ST_ABSBackgroundC_ST_ABSGlobally, there is a large gap in our understanding of the prevalence, ecology and transmission dynamics of antibiotic resistance (ABR) in extensively reared ruminants, despite these animals contributing to the food chain and frequently sharing land with humans. MethodsFive hundred and seventy one visits to 33 Welsh beef cattle and/or sheep farms resulted in 1874 samples being collected at faecally contaminated sites from April 2022 to March 2023 (ADGC1) and September 2023 to December 2024 (ADGC2). Samples were tested for resistant Escherichia coli using amoxicillin, streptomycin, spectinomycin, cefotaxime and ciprofloxacin. WGS used Illumina technology. Clonal relationships were determined following core-genome alignment. ResultsA significant reduction in positivity for spectinomycin-resistant E. coli in sheep samples from ADGC1 to ADGC2 was observed, coincident with market withdrawal of a spectinomycin-containing preparation widely used in sheep. Reductions were seen in 19/22 sheep flocks with nine seeing a >50% reduction. Resistance to other tested antibiotics was unchanged. Phenotypic analysis and WGS for 713 E. coli showed that resistance to antibacterials important for human medicine was rare and genetically diverse. We identified 77 E. coli clones (<100 SNP cutoff) circulating among study farms with mixed farms contributing most; clones were also shared between animal species on mixed farms. ConclusionsFor extensively reared ruminants, ABR-reducing efforts can have significant impacts on antibiotic resistance on farms. Focusing these efforts onto farms contributing to the most animal movement and mixing events may generate the greatest reductions in overall on-farm ABR prevalence at regional and national levels.