Development of a rapid diagnostic assay against antimicrobial resistant pathogens

--------------------------------------------- Background: --------------------------------------------- Antimicrobial resistance is a key global issue, with resistance to important antibiotics increasing yearly, resulting in 1.14 million deaths in 2021 alone. We treat bacterial infections with antimicrobials. However, pathogens rapidly develop resistance to antimicrobials by acquiring resistance genes, reducing treatment efficacy. In particular, resistance to carbapenems is concerning as these are last-line antibiotics. Accurate, rapid diagnostics are necessary to prevent the spread of carbapenem-resistant organisms. When patients get infections, they are swabbed and diagnosed via bacterial culture. This method is slow, taking 2-5 days and suffers from reduced sensitivity, where the pathogen is present but may not grow. This causes significant delays in patient diagnosis, treatment and outcomes. Loop-mediated isothermal AMPlification (LAMP) is a direct application of PCR which instead uses a consistent ~60°C temperature – requiring only a heat block, with unparalleled sensitivity. Importantly, this culture-free assay can return clinical results within ½ a day. We have identified LAMP targets against all known carbapenemases, but this requires laboratory validation. --------------------------------------------- In this project, you will: --------------------------------------------- ‎ ‎ 1) Design LAMP primers using computational software against all known carbapenemases and key bacterial pathogens we’ve previously identified ‎ ‎ 2) Validate the LAMP assay against clinical pathogens --------------------------------------------- Outcomes for you as a student on this project: --------------------------------------------- ‎ ‎ 1) Gain experience with molecular techniques and microbiology ‎ ‎ 2) Gain experience with command line, bioinformatics and genomics ‎ ‎ ‎ ‎ • Bioinformatics is an essential skill for modern biological research ‎ 3) Contribute to the development of a rapid diagnostic tool to identify carbapenem resistant organisms ‎ 4) Opportunity to contribute as a co-author to a publication --------------------------------------------- Resources you will be supported by: --------------------------------------------- ‎ • Global experts in bioinformatics and infectious diseases: Dr. Ben Vezina and Dr. Nenad Macesic (clinician-researcher) ‎ • Professional microbiology laboratories situated at The Department of Infectious Diseases, with close ties to Alfred Health ‎ • Handling a globally-unique collection of clinical isolates ‎ • Access to a high-performance supercomputer --------------------------------------------- Skills and interests you will bring --------------------------------------------- ‎ • Required ‎ ‎ ‎ o Interest in bioinformatic skill development ‎ ‎ ‎ o Interest in microbiology ‎ • Ideal but not required ‎ ‎ ‎ o Experience with command line or any coding language