Genomic epidemiology of multidrug resistant porcine commensal Escherichia coli

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Swine production is one of the largest agricultural industries in the world. The use of antimicrobials for treatment of disease outbreaks and as growth promoters drives the evolution of antimicrobial resistance in commensal populations of 𝘌𝘴𝘤𝘩𝘦𝘳𝘪𝘤𝘩𝘪𝘢 𝘤𝘰𝘭𝘪 in the pig gut. Therefore, the billions of tonnes of pig faeces generated by production every year are a serious environmental contaminant. Despite the status of 𝘌. 𝘤𝘰𝘭𝘪as an important commensal and pathogen of both animals and humans, little is known about the genomic characteristics of porcine commensal 𝘌. 𝘤𝘰𝘭𝘪 in Australia. The clonal groups, antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs) and virulence-associated genes (VAGs) they harbour remain poorly characterised. In order to address this, we characterised 103 multidrug resistant commensal 𝘌. 𝘤𝘰𝘭𝘪 from two Australian farms with a history of antimicrobial use using whole genome sequencing. Phylogroup A and clonal complex 10 strains with global origins and a variety of virulence genotypes associated with extra-intestinal pathogenic 𝘌. 𝘤𝘰𝘭𝘪 (ExPEC) dominated the collection. Multiple class 1 integrons augmented by IS26, an important driver of evolution in antimicrobial resistance loci were observed in multiple sequence types. Whilst no resistance to critically important human antimicrobials was observed, this suggests swine production is a reservoir for the evolution of novel drug resistance characteristics that may transfer to human populations and rapidly acquire resistance to critically important antimicrobials. We also identified an ST131 strain carrying an IncHI2 plasmid with multiple ARGs and a ColV plasmid conferring virulence traits. This strain was highly related to an ST131 strain isolated from a human infection. Remarkably, the human strain carried near identical plasmids. The apparent presence of the IncHI2 plasmid in multiple porcine strains, carriage of metal resistance and identical integrons strongly suggests the human pathogen originated from swine production. Whilst there is a need to increase the number of porcine commensal 𝘌. 𝘤𝘰𝘭𝘪 whole genome sequences from multiple farms and states in Australia, our findings support swine production as a reservoir of multiple drug resistance determinants. Furthermore, a proportion of porcine commensal 𝘌. 𝘤𝘰𝘭𝘪 are known or potential human pathogens. Genomic surveillance in swine and other intensively reared food production animals is critical to the ongoing management of the global issue of antimicrobial resistance.
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