A translational genomic framework for addressing transmission and resistance in Stenotrophomonas maltophilia

Healthcare-associated infections impose a substantial and growing burden on healthcare systems, primarily targeting our most vulnerable groups undergoing life-saving therapies. This includes patients with lung disease, cancer, patients who are immunosuppressed, or organ transplant recipients. Stenotrophomonas maltophilia is a critical pathogen in these patients, yet effective treatment is hampered by intrinsic antibiotic resistance, the inability of clinical laboratories to differentiate between species, and a paucity of clinical data linking species to transmission risk or treatment outcomes. Recent genomic studies have revealed that S. maltophilia comprises a complex of over 24 distinct species, yet in clinical practice these are treated as a single entity, disregarding potentially significant differences in antibiotic resistance profiles and virulence. This project aims to provide the first species-specific framework for S. maltophilia, by improving identification of this pathogen and exploring variations in transmission potential. During this project, you will: • Develop a genomic framework to accurately identify species, sub-species, and lineages • Investigate transmission dynamics to determine whether specific lineages drive human-to-human transmission versus remaining purely environmental • Investigate the types of biofilms S. maltophilia can be found in: aqueous versus dry biofilms, and differences in biofilm properties by species or lineage You will gain interdisciplinary training throughout this project, spanning computational biology and its intersection with the clinic by developing skills in: • Analysis of large-scale microbial genomic datasets • Experimental biology approaches, including evaluating biofilms and resistance to disinfectants and antibiotics • Bridging the gap between basic discovery science and clinical microbiology and infection prevention You will be supervised by a multidisciplinary team that spans the spectrum of genomics, microbiology, and infection prevention, with direct clinical links at Alfred Health and Monash Health. This project will include collaborations with international partners in Asia, Africa and the UK. Eligibility Criteria: Applications are open to domestic candidates only. Funding and Scholarship: This is a fully funded PhD position which includes a PhD scholarship. Applicants should have: • An academic background in one or more of genomics, bioinformatics, computational biology, microbiology • A strong interest or beginner skills in programming (Python, R or bash) and/or wet lab microbiology techniques Please include the following information in your application: • Cover letter (max 1 page) highlighting your research background and interest in the topic • CV including academic achievements and relevant skills, and any publications or presentations • Official academic transcript • Details of 1-2 academic references Informal inquiries prior to applying are welcome via email. Application Deadline: September 25th, 2026