Prediction of antibiotic resistance phenotypes using the genomes of carbapenem-resistant pathogens

Carbapenems are broad-spectrum β-lactam antibiotics that are resilient to most known β-lactamases, and, therefore, are used as drugs of last resort. However, certain β-lactamases – known as carbapenemases – that break down carbapenems and often most other β-lactam antibiotics. This makes carbapenemases a great threat to the ability to treat refractory bacterial infections. It is, therefore, important to understand how carbapenemase genes are mobilized and spread horizontally between bacteria. The aim of this study is to determine the genetic context of the carbapenemase genes and any additional acquired resistance genes, in clinical isolates. We also want to study the potential of using whole genome sequencing (WGS) to determine the antibiotic resistance phenotype of multi-resistant clinical isolates.