Tackling carbapenem resistance in the Australian setting: using genomics to understand the spread of deadly superbugs

Multi-drug resistance in Gram-negative bacteria (MDR-GNB) is a global health challenge that threatens many medical advances. Infections caused by MDR-GNB such as carbapenem-resistant Enterobacterales (CRE) have a high morbidity and mortality that exceeds 50%. CRE are increasingly prevalent in Australia and have been implicated in several outbreaks. This project aims to use innovative genomic technologies to dissect the rise of CRE in the Australian hospital setting. Using a collection of bacterial isolates dating back >15 years, we will study how carbapenem resistance has evolved, in particular through close analysis of plasmid dynamics and interspecies spread. This genomic data will be linked to clinical data to better understand the risk factors for CRE colonisation and infection, as well as analyse spread of CRE in the hospital setting. Finally, we will put Australian CRE data in a global context by comparing and contrasting CRE genomic settings from Australia with publicly available global data. Students would be expected to develop skills in computational biology approaches (including command-line programs) to analyse and interpret large datasets. Prior experience using the Unix operating system and the R and Python programming languages is preferred but not essential.