| Abstract |
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. |
