Canada_IPAP Antimicrobial-resistant Enterococcus faecium in the One Health context in the UK and Canada

Antimicrobial resistance is one of the greatest public health threats spanning the One Health continuum (humans, animals and the environment). Antibiotics are of invaluable public health importance and are used on a daily basis worldwide to save and ease the suffering of millions of human and animal lives. However, their extensive and often uncontrolled use has led to the global spread of resistance in bacteria of medical and veterinary importance to an unprecedented level. This is threatening the ways we practice medicine and our ability to care for the sickest patients including those in need of life-saving treatments such as organ transplantation or cancer chemotherapy, and those in intensive care units. Antibiotic resistance is now recognised by the WHO as one of the greatest threats to human health and is increasingly topical within medical, veterinary and lay organisations of national and global reach.

Enterococcus faecium, a bacterium carried harmlessly in the gut of humans and animals, has emerged as a leading cause of infections in critically ill and severely immunocompromised patients in hospitals. It has a propensity to accumulate and disseminate multiple antibiotic resistance determinants. Our previous work using a bacterial DNA fingerprinting technique called short-read whole-genome sequencing (WGS) established that E. faecium causing infections in hospital belongs to distinct strains from those found in livestock. In addition, we found different types of antibiotic resistance genes predominating in the two reservoirs. However, we also found instances of identical resistance genes, including to classes of antibiotics that are important in human medicine. Short-read WGS has limitations when trying to reconstruct the hierarchical levels of transmission units responsible for the spread of antibiotic resistance, which range from the whole bacterial strains, to consecutively smaller layers of mobile genetic elements known as plasmids and transposons down to the gene level. In order to decipher this "Russian doll" model, a different technique known as long-read WGS is required. Here, we propose to carefully select isolates for long-read WGS to allow us to quantify and understand the architectural context of shared antibiotic resistance genes between human and animal strains of E. faecium.

Antibiotic susceptibility testing is a technique used daily in laboratories around the world to establish if antibiotics are still effective at treating bacterial strains of interest (i.e. ensuring the strains have not developed resistance). Resistance to antibiotics is mediated by genetic changes, hence whole genome sequencing has emerged as an attractive technology to characterise the full repertoire of known genetic changes that cause resistance and predict from the bacterial DNA if antibiotics are still effective. However, a complete understanding of the genetics governing resistance to antibiotics is required before WGS can be adopted to inform antibiotic prescribing. Our previous research has shown that WGS is very good at predicting the effectiveness of most antibiotics in E.faecium, except for 3 last-resort antibiotics used against the most resistant strains: daptomycin, tigecycline and linezolid. Here, we aim to redress this shortcoming by generating additional laboratory tests and sequencing data and to apply state-of-the art population genomic methods to improve predictions.

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 different 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.