Diversity of antimicrobial resistance and virulence genes of pathogenic Escherichia coli recovered from pigs from England

Samuel Alf Maurice Connelly^1*Manal AbuOun²Nicholas Duggett^2,3Miranda Kirchner²Indre Navickaite²Javier NunezGarcia²Susanna Williamson⁴Kelly Vaughan⁵Christopher Teale⁶Muna Anjum^2*

• ¹Animal and Plant Health Agency (United Kingdom), Addlestone, United Kingdom
• ²Animal and Plant Health Agency, Addlestone, United Kingdom
• ³Animal Health and Veterinary Laboratories Agency Veterinary Investigation Centre Thirsk, Thirsk, United Kingdom
• ⁴Animal and Plant Health Agency Veterinary Investigation Centre Bury Saint Edmunds, Bury Saint Edmunds, United Kingdom
• ⁵Animal and Plant Health Agency Veterinary Investigation Centre Starcross, Exeter, United Kingdom
• ⁶Animal and Plant Health Agency Veterinary Investigation Centre Shrewsbury, Shrewsbury, United Kingdom

The genomes of 208 pathogenic E. coli isolated from pigs with enteric colibacillosis (EC), bowel oedema (BO) or colisepticaemia (CS), in England and Wales between 2016-2020 were investigated for their virulence associated genes (VAGs) and antimicrobial resistance (AMR). The EC associated E. coli contained ETEC VAGs with the most common fimbriae and toxin genes being faeG (F4, 33%) and stb (STb, 48%). In the BO associated E. coli, 29% were identified as STEC with the fedF (F18, 38%) and stx2e-AB (Stx2e, 38%) genes the most prevalent. The CS group were more homogenous based on their VAGs; >70% of isolates contained genes corresponding with the curli fibre (csgABGFE), haemolysin, iss, sitABCD (iron transport), aerobactin (iucABCD) and salmochelin (iroBCDEN) siderophore genes. 62% of isolates were multidrug resistant (MDR). The ETEC showed the highest median antimicrobial class resistances (n = 6) and MDR prevalence (73%). Enteric E. coli were most resistant to gentamicin (17%) and uniquely to azithromycin (10%). Quinolone resistance mutations were only identified in enteric-associated E. coli. Single nucleotide polymorphism (SNP) and K-mer based phylogenetic methods identified that ST90 (n = 13) and ST772 (n = 14) are recently diverged groups of MDR ETEC, distinctly found to cause disease in juvenile pigs, suggesting that these lineages could be of concern to the pig industry. We elucidated the plasmids of a small subset of ETECs from these STs to highlight the carriage of several large MDR plasmids. One key feature of some of these plasmids showed the possible co-linkage of AMR with metal and disinfectant resistance genes. This study sheds light on the predominant AMR and VAGs present in clinical E. coli from diseased pre-and post-weaned pigs in England. We highlight the differences between the AMR in commensal and clinical E. coli isolated from adult and juvenile pigs, respectively, and presents data on mobile genetic elements (MGEs) that may contribute to these differences. Further work will need to be performed to characterise pathogenic E. coli that cause infections in pigs to facilitate appropriate treatment and control of disease outbreaks on farms.