Genomic surveillance of extended spectrum cephalosporin resistant Escherichia coli isolated from poultry in the UK from 2016-2020.
Surveillance is vital for monitoring the increasing risk of antimicrobial resistance (AMR) in bacteria leading to failures in humans and animals to treat infections. In a One-Health context, AMR bacteria from livestock and food can transfer through the food chain to humans, and vice versa, which can be characterised in detail through genomics. In this study we performed whole genome sequencing for genomic characterisation of 761 extended spectrum cephalosporinase (ESC) harbouring Escherichia coli isolated from poultry caeca and meat through EU harmonised monitoring of AMR in zoonotic and commensal bacteria from 2016 and 2018 and UK national monitoring in 2020. The most common ESC in 2016 and 2018 was blaCTX-M-1, however 2020 had greater diversity with blaCTX-M-55 dominant in chickens and blaCTX-M-15 more prevalent in turkeys. Co-resistance to sulphonamides, tetracycline and trimethoprim was widespread and there were several positive correlations between the sequence types (STs) and ESC genes. We identified certain AMR genotypes and STs that were frequent each year but not as successful in subsequent years, e.g., ST350 harbouring blaCTX-M-1, sul2 and tetA-v4. Phylogenetic comparison of isolates prevalent in our panel with global ones from the same STs available in public databases showed that isolates from UK generally clustered together, suggesting greater within than between country transmission. We conclude that future genomic surveillance of indicator organisms will be invaluable as it will enable detailed comparisons of AMR between and within neighbouring countries, potentially identifying the most successful sequence types, plasmids, or emerging threats