Long read data on E. coli genomes
Three Escherichia coli-induced disease manifestations affecting pigs pre- and post-weaning include enteric colibacillosis (EC), bowel oedema (BO), and colisepticaemia (CS). These principally arise from the three E. coli pathotypes: enterotoxigenic E. coli (ETEC), Shiga-toxin producing E. coli (STEC), and extraintestinal pathogenic E. coli (ExPEC), respectively. ETEC and STEC utilize antigenically diverse fimbriae to colonise the gut epithelium, secreting toxins causing diarrhoea. STEC also secrete Shiga toxin Stx2e, causing vascular damage and inducing oedema in host tissues. ExPEC differ from the previous two pathotypes, possessing a heterogenous combination of virulence factors that aid in their escape from the gut and invasion of various tissues in the host. Here, the focus is on colisepticaemia which is seen mainly in young pre-weaned pigs. E. coli infections can have significant effects on the health and welfare of affected pigs and the productivity of affected farms. Antimicrobials are commonly used to treat clinical disease, but antimicrobial use can select for antimicrobial resistance (AMR) in bacteria, making treatment of outbreaks of pathogenic E. coli more challenging. To understand the landscape of AMR amongst pathogenic E. coli from pigs in England and Wales, the genomes of 208 E. coli were investigated for their AMR and virulence associated genes (VAGs). These E. coli were cultured from porcine diagnostic submissions to the Animal and Plant Health Agency's scanning surveillance network between 2016-2020 in which enteric colibacillosis (n = 122), bowel oedema (n = 34), and colisepticaemia (n = 52) cases were diagnosed. Approximately 71% of isolates had at least one detectable virulence factor and overall, 62% of isolates were multidrug resistant (MDR). The isolates with a ETEC pathotype exhibited the highest levels of MDR (73%). Two of the more common multi-locus sequence types (MLST) identified in the E. coli associated with enteric disease were ST90 (n = 13) and ST772 (n = 14), which were identified as ETEC. We identified 62% (n = 8/13) of ST90 and 93% (n = 13/14) of ST772 isolates with a MDR genotype and carried out long-read sequencing from both these STs to confirm the co-carriage of virulence and large MDR plasmids. These mobile genetic elements may provide a selective advantage, maintaining pathogenic lineages in the farming environment. This study sheds light on AMR and VAGs present in pathogenic E. coli in diseased pigs in England and Wales. The findings emphasise the benefit of appropriate diagnostic investigation of E. coli infections in pigs to identify the responsible pathogenic isolates, their antimicrobial sensitivity and virulence gene complement, to facilitate control of disease outbreaks.