Genomic Epidemiology to Investigate the Origins and Zoonotic Implications of Antibiotic-Resistant Escherichia coli on Beef and Lamb Meat Sold by Independent Butchers in Wales

Many studies have identified antibiotic resistant (ABR) Escherichia coli on meat. Appropriate hand hygiene and cooking practices should minimise the risk of gastrointestinal colonisation with ABR E. coli found on meat, and the subsequent chance of causing resistant opportunistic extraintestinal infection. There are large gaps in our understanding of the prevalence, origins and zoonotic potential of ABR E. coli found on meat, however, and particularly for meat reared in extensive farming systems. Wales is a devolved nation within the United Kingdom having large populations of extensively-reared sheep and beef cattle. To help address knowledge gaps around ABR E. coli on extensively reared meat, therefore, beef mince and lamb loin/leg steaks/chops were purchased from 50 (beef) and 46 (lamb) independent butchers across Wales. Following enrichment culture, 200 g meat samples were found to be positive for E. coli resistant to amoxicillin (31% positivity), streptomycin (28%), spectinomycin (29%), amoxicillin-clavulanate (11%), 3rd generation cephalosporins (2%) and fluoroquinolones (5%). Phylogenetic analysis confirmed that Welsh lamb meat ABR E. coli isolates (n=79) are more closely related to those found in faecal samples collected around sheep (n=352) than around beef cattle (n=361) on Welsh farms. This suggests that faecal contamination at or around slaughter is their primary origin. We found no closely related meat/infection clones (<20 SNPs distant and the same antibiotic resistance genes) when comparing ABR E. coli from Welsh meat (n=92) and those causing extraintestinal infections in people (n=2387) in an English region bordering Wales. We conclude, therefore, that the wider zoonotic implications of finding ABR E coli on beef and lamb meat sold at independent butchers in Wales are small.