Version 3: Genotypic and Phenotypic screening of agriculturally based antimicrobial resistant E. coli.

Antimicrobial resistance is undoubtedly one of the most significant threats to human health. Whilst finding alternative antimicrobials proves valuable, understanding how resistance is spread remains a necessity. The link between antimicrobial resistance in agriculture and the effect on human medicine is unclear, however the contribution and dissemination of resistance should not be overlooked. Escherichia coli (E. coli) are of particular concern for human health as the most common Gram-negative pathogen and are often used as a representative indicator of antimicrobial resistance. Sheep hold a unique role in agriculture, as large numbers are often transported between multiple farms to make use of seasonal grazing. We present a robust analysis of multi-antimicrobial resistance profiles, using short read metagenomics and long read sequencing, to identify plasmid borne resistance as well as chromosomal and mutational resistances. The analysis of these data highlighted putative plasmids in 85% of the isolates with putative plasmid borne resistance genes against the most commonly used antimicrobials, such as streptomycin, tetracycline, sulphonamide, licosamide, betalactam, macrolide, kanamycin, fosfomycin, chloramphenicaol, cephalosporin and aminoglycoside.