IPAP_Antimicrobial_resistant_Enterococcus_faecium_in_the_One_Health_context_in_the_UK_and_Canada_
Enterococcus faecium is a gut commensal of humans and animals and one of the most important opportunistic pathogens in hospitalised patients. Our previous work on E. faecium isolates of hospital, wastewater and livestock origin, demonstrated host adaptation at the core genome level, with strains causing infection belonging to a  ifferent clade compared to those found in livestock. Examining the wider resistome, there was further evidence of niche adaptation in terms of frequency and composition of genes reflecting distinct selective pressures in the animal and human reservoirs. However, identical antimicrobial resistance genes (ARGs) mediating resistance to aminoglycosides, macrolides and tetracyclines were found in both reservoirs, reflecting the prominent roles these antibiotics hold in both veterinary and human medicine. Additionally, there were rare instances of introgression of genes of animal origin into human isolates. The first aim of this project is to use long-read sequencing to better characterise and quantify the degree of sharing of mobile genetic elements and ARGs between E. faecium isolates of human and animal source. Antibiotic susceptibility testing (AST) is crucial to guide the right antibiotic treatment. Whole-genome sequencing has emerged as an attractive technology to characterise the full antibiogram of infecting strains, but a complete understanding of the genetics governing susceptibility to antibiotics is required before it can be adopted to inform prescribing. Our previous work has shown very accurate genotypic resistance predictions for most antibiotics but sensitivity gaps in achieving complete genotype-phenotype agreement for the important last-resort antibiotics daptomycin, tigecycline, and linezolid. Here, we aim to improve predictions of phenotypic susceptibility to these antibiotics by performing additional AST and sequencing on resistant isolates and applying state-of-the art approaches in population genomics.