Whole Genome Sequencing demonstrates that Rodents are a Reservoir of Antimicrobial Resistant Escherichia coli and Salmonella on Pig Farms

Background: Rodents can carry bacteria acquired from other animals and the environment, and can represent a reservoir of infection between batches of livestock on farm. The aim of this study was to investigate the role of wild mice in harbouring antimicrobial resistant (AMR) bacteria in three pig farms. Methods: Pooled faecal samples were obtained from one cohort of pigs on each of three finisher farms. Contemporaneous fresh mice carcases (n=2, 3 and 16 in farms 1, 2 and 3, respectively) were also collected at these farms. E. coli and Salmonella isolates were obtained from the pig faecal samples and the mice internal organs including intestine by plating on CHROMagar ECC (with and without the addition of antibiotics). The Minimum Inhibitory Concentration of 93 representative isolates was determined against a panel of 14 antibiotics. Selected isolates were also whole genome sequenced (WGS) using an Illumina platform and the presence of AMR genes, plasmid markers, multilocus sequence type and phylogeny were investigated. Results: The majority of isolates tested (83/93) showed reduced susceptibility to one or more antimicrobials. All but one mouse yielded resistant bacteria. Of the 61 colonies from mice samples subjected to MIC, 9 were sensitive to all 14 antimicrobials. All pig samples yielded resistant bacteria. Of the 32 colonies from mice samples subjected to MIC, 1 was sensitive to all 14 antimicrobials. Two mice caught on Farm 1 harboured the same multidrug resistant Salmonella, with multiple AMR genes apparently residing on an IncHI1 plasmid. On Farm 2, WGS identified a conserved IncQ plasmid carrying three AMR genes in E. coli from pigs and in Salmonella from pigs and mice. On Farm 3, six E. coli harbouring ESBL genes were detected: two different mice harboured a clone of E. coli with a blaCTX-M-1 on an IncI1 plasmid; and the blaCMY2 gene was present in a ST23 E. coli from a pig and a mouse. Conclusion: This study confirms that mice can carry AMR E.coli and Salmonella and shows that transfer of resistance genes occurred between these bacterial species which were present in mice and pigs on the same farm. The role of pests is important for the maintenance of resistant bacteria and resistance genes in the farm environment.