An epidemiological analysis of antimicrobial resistance in Escherichia coli of porcine agricultural origin

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The bacterial mobilome, a collection of plasmids, bacteriophages, transposons, and insertion sequences that capture, replicate, and share genes, is responsible for hosting and distributing antimicrobial resistance and virulence genes. Selective pressures generated by antimicrobial use promotes the acquisition of antimicrobial resistance mechanisms. Animal agriculture is one of the primary consumers of antimicrobials globally for the treatment of infection. The impacts of antimicrobial pressures are apparent through the analysis of 𝘌𝘴𝘤𝘩𝘦𝘳𝘪𝘤𝘩𝘪𝘢 𝘤𝘰𝘭𝘪. Porcine agriculture is especially pertinent, as enterotoxigenic 𝘌. 𝘤𝘰𝘭𝘪 represent a significant burden of disease in weaning piglets. For this project, a collection of one hundred and sixty-three 𝘌. 𝘤𝘰𝘭𝘪 isolates were sourced from a commercial piggery in 2007, and a selection of forty-eight multiple-drug resistant strains from this underwent short-read whole genome sequencing. Additionally, four enterotoxigenic 𝘌. 𝘤𝘰𝘭𝘪 pathogens were also sequenced. Genomes were assembled, and data characterised to determine the nature of these strains, including comparisons to isolates from a second facility in NSW during the same period. Whole genome sequence analysis provides a universal toolset to mine information from genomic data, including identifying genes and assessing diversity. Phylogenetics revealed antimicrobial resistance hosted in representatives across the known subclades of 𝘌. 𝘤𝘰𝘭𝘪. Sequence type 10 was most prevalent, and numerous subclades belonging to this clonal complex were identified. Plasmid replicons were identified amongst the strains, with IncF, IncI, IncY, IncHI2 and IncX most prominent. Genes encoding antimicrobial resistance matched known antibiotic use, including tetracycline, ampicillin, aminoglycosides, and sulphonamides. Resistance genes were frequently associated with class 1 integrons and the sulphonamide resistance genes s 𝘴𝘶𝘭1, 𝘴𝘶𝘭2 and 𝘴𝘶𝘭3. Numerous strains appeared to host IS26 transposon Tn6026 (𝘴𝘶𝘭2 associated) at a known insertion site. Identification of 𝘴𝘶𝘭3 was novel in Australian porcine data, associated with two novel IS26 mediated 𝘮𝘦𝘧𝘉 truncations. Two pathogens sequenced were serotype O157:H19 - related strains evolutionarily distinct from known O157 pathogens. Belonging to clonal complex 23, these strains hosted various resistance and porcine virulence factors, particularly O157 SvETEC which encoded the three 𝘴𝘶𝘭 genes and numerous large extrachromosomal elements. The remaining pathogens were of known ETEC serotype and had homologues among strains identified in the commensal populations. Long-read sequencing revealed that 𝘮𝘦𝘧𝘉_111bp was hosted on IncHI2:ST3 plasmids with evolutionary origins in Asia. These plasmids were identified in 𝘚𝘢𝘭𝘮𝘰𝘯𝘦𝘭𝘭𝘢 Typhimurium of Australian porcine origin in 2013, and comparative analyses revealed evolutionary events that shaped the plasmids and complex resistance structures.
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