Building a genomics framework for emerging hospital superbugs

--------------------------------------------- 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. Hospital-acquired infections are becoming more common, with many bacterial pathogens able to spread and cause outbreaks within hospitals. In particular, Proteus mirabilis, Citrobacter spp. and Providencia spp. are overlooked and understudied enteric pathogens that cause alarming numbers of bloodstream infections. These pathogens also carry worryingly high levels of antimicrobial resistance. We have DNA sequenced >70 clinical isolates from these species, along with an additional >560 in collaboration with the Microbial Diagnostic Unit Public Health Laboratory, which requires in-depth genomic analysis. --------------------------------------------- In this project, you will: --------------------------------------------- ‎ ‎1) Obtain and assemble genomes for 3 bacterial pathogens to identify genomic trends ‎ 2) Use genomics to analyse their antimicrobial resistance, plasmids and virulence gene patterns ‎ 3) Use genomics to understand their population structure and sequence diversity --------------------------------------------- Outcomes for you as a student on this project: --------------------------------------------- ‎ 1) Gain experience with command line, coding, bioinformatics and genomics ‎ ‎ ‎ ‎ • Bioinformatics is an essential skill for modern biological research ‎ ‎ ‎ ‎ • High performance computing ‎ 2) Contribute to knowledge for clinically-relevant but neglected enteric pathogens ‎ 3) Opportunity to contribute as a co-author to two publications --------------------------------------------- Resources you will be supported by: --------------------------------------------- ‎ • Global experts in bioinformatics and infectious diseases: Dr. Ben Vezina, Dr. Nenad Macesic (clinician-researcher) and Dr. Jake Lacey (University of Melbourne) ‎ • Professional microbiology laboratories situated at The Department of Infectious Diseases, with close ties to Alfred Health ‎ • The Microbiological Diagnostic Unit Public Health Laboratory at University of Melbourne ‎ • Handling a globally-unique collection of clinical genomes ‎ • 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