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Infectious Diseases and Microbiology Research

The Department conducts research into various aspects of clinical infectious diseases and microbiology with a focus on: multidrug-resistant bacteria and healthcare-associated infections they cause; pathogen genomics; infections in immunocompromised individuals; invasive bacterial infections, such as infections in the blood stream, deep tissues, and bones or joints; and respiratory infections in hospitalised patients including COVID-19.

Multidrug-resistant bacteria, and the hospital acquired infections they cause, are one of the most significant future threats to human health both in Australia and globally. Effective antibiotics are essential for the safe provision of life-saving interventions such as solid organ and bone marrow transplantation, cancer chemotherapy and surgery. These interventions are now under threat, due to rapidly expanding antimicrobial resistance and a lack of novel antimicrobial drug classes.

A major focus of the Department's research is understanding how these multidrug-resistant bacteria spread across the community and the hospital and how they adapt to specific niches, using pathogen genomics and state-of-the-art molecular epidemiological methods. This research is accomplished by patient screening, surveillance and use of whole genome sequencing for high-consequence and high-prevalence micro-organisms. The Department participates in national surveillance programs for bacterial resistance, reporting to the Australian Group for Antimicrobial Resistance (AGAR), OrgTrx and CARalerts.

The Department has led the state in developing highly specialised and locally optimised in-house bioinformatics pipelines and automated reporting systems. This has facilitated studies which have provided important insights into the transmission dynamics of healthcare-associated pathogens, particularly vancomycin-resistant enterococcus (VRE) and carbapenem-resistant Enterobacterales (CPE), and more recently SARS-CoV-2. Research findings have been rapidly translated into the implementation of targeted measures to optimise control of these multi-drug resistant organisms as well as COVID-19.

Our research in immunocompromised individuals includes liver, renal and allogeneic transplant recipients, as well as people with HIV. The Department participates in mycology studies evaluating fungal resistance rates, which have enabled refinement of local antifungal prophylaxis strategies for the numerous immunocompromised individuals cared for at Royal Prince Alfred Hospital. Ongoing studies in transplant recipients include evaluations of surgical site infections and colonisation and invasive infections with multidrug resistant infections. HIV drug resistance surveillance is another area of interest of the Department, through involvement in the implementation of a state-wide HIV drug resistance database and participation in national surveillance reports. Additional studies planned to start in 2024 in people with HIV include an observational study on women with HIV and a randomised clinical trial evaluating an intervention to improve cardiovascular health in people with HIV. 

We have several studies that are ongoing or planned to start in 2024 in the area of invasive bacterial infections including: an ongoing randomised clinical trial evaluating the management of Staphylococcus aureus blood stream infections; an observational study evaluating outcomes in people who inject drugs and are hospitalised with invasive infections; and a randomised clinical trial evaluating the optimal management of prosthetic joint infections. An additional study planned to start in 2024 is an international randomised clinical trial evaluating different medications for the treatment of respiratory infections in hospitalised patients including COVID-19.

Selected Grants

Amount awarded Grant and project details
$2,971,764 Medical Research Future Fund (MRFF) Clinical Trials Activity, 2023-2025
Modulating stem cell differentiation in individuals with high risk clonal haematopoiesis: the MOSAIC trial.
RPA Investigator: Dharan NJ (CIL)
$1,993,166 Medical Research Future Fund (MRFF) International Clinical Trials Collaboration, 2023-2025
Strategies and treatments for respiratory infections and viral emergencies (STRIVE).
RPA Investigator: Dharan NJ (CIB)
$983,939 NHMRC Clinical Trials and Cohorts Grant, 2023-2027
Improving the long-term health in people living with HIV: the RESPOND study. 
Investigators: Dharan NJ (CIG)
$655,150 NHMRC Investigator Grant, 2022-2025
The impact of chronic viral infections on molecular ageing processes and associated clinical outcomes.
RPA Investigator: Dharan NJ (CIA)

Our Publications


Burdon RM, Atefi D, Rana J, Parasuraman A, Lee AS, Nield B. Sustained Mpox Proctitis with Primary Syphilis and HIV Seroconversion, Australia. Emerg Infect Dis. 2023 Mar;29(3):647-649. doi: 10.3201/eid2903.221845. Epub 2023 Jan 26.
Coussement J, Heath CH, Roberts MB, Lane RJ, Spelman T, Smibert OC, Longhitano A, Morrissey O, Nield B, Tripathy M, Davis JS, Kennedy KJ, Lynar SA, Crawford LC, Crawford SJ, Smith BJ, Gador-Whyte AP, Haywood R, Mahony AA, Howard JC, Walls GB, O'Kane GM, Broom MT, Keighley CL, Bupha-Intr O, Cooley L, O'Hern JA, Jackson JD, Morris AJ, Bartolo C, Tramontana AR, Grimwade KC, Au Yeung V, Chean R, Woolnough E, Teh BW, Chen SCA, Slavin MA; Australian and New Zealand Study Group for Cryptococcosis in Patients Without HIV Infection. Current Epidemiology and Clinical Features of Cryptococcus Infection in Patients Without Human Immunodeficiency Virus: A Multicenter Study in 46 Hospitals in Australia and New Zealand. Clin Infect Dis. 2023 Oct 5;77(7):976-986. doi: 10.1093/cid/ciad321.
Dharan NJ, Sasson SC, Ahlenstiel G, Andersen CR, Bloch M, Buckland G, Hamad N, Han WM, Kelleher AD, Long GV, Matthews GV, Mina MM, Papot E, Petoumenos K, Swaminathan S, Withers B, Yun J, Polizzotto MN; CORIA Study Group. Clinical and laboratory features of COVID-19 illness and outcomes in immunocompromised individuals during the first pandemic wave in Sydney, Australia. PLoS One. 2023 Nov 1;18(11):e0289907. doi: 10.1371/journal.pone.0289907.
Foster CSP, Bull RA, Tedla N, Santiago F, Agapiou D, Adhikari A, Walker GJ, Shrestha LB, Van Hal SJ, Kim KW, Rawlinson WD. Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak. Viruses. 2023 Feb 13;15(2):522. doi: 10.3390/v15020522.
Georgevsky D, Ying L, Krishnan S, Laurence J, Robinson D, Campbell N, Wyburn K, Marinelli T, Davis R, Narayan R, Lutz T, Chan A, Heaney SA, Kitzing YX, Anderson L, Liyanagama K, Robson J, Carter J, Testa G, Johannesson L, Marren A. First uterine transplant case at the Royal Prince Alfred Hospital. Aust N Z J Obstet Gynaecol. 2023 Aug;63(4):599-602. doi: 10.1111/ajo.13700. Epub 2023 May 18.
Henderson A, Cheng MP, Chew KL, Coombs GW, Davis JS, Grant JM, Gregson D, Giulieri SG, Howden BP, Lee TC, Nguyen V, Mora JM, Morpeth SC, Robinson JO, Tong SYC, Van Hal SJ; Microbiology Working Group of the Staphylococcus aureus Network Adaptive Platform (SNAP) Trial Group. A multi-site, international laboratory study to assess the performance of penicillin susceptibility testing of Staphylococcus aureus. J Antimicrob Chemother. 2023 Jun 1;78(6):1499-1504. doi: 10.1093/jac/dkad116.
Lahra MM, Hurley SM, Van Hal S, Hogan TR. Australian Gonococcal Surveillance Programme, 1 October to 31 December 2022. Commun Dis Intell (2018). 2023 May 25;47. doi: 10.33321/cdi.2023.47.30.
Lau C, Marriott D, Bui J, Figtree M, Gould M, Chubaty A, Su Y, Adhikari S, Konecny P, Kozierowski K, Holland T, Milliken E, Akram A, Mcnamara A, Sun Y, Van Hal S, Patanwala AE, Shahabi-Sirjani A, Gray T, Yeo CY, Netluch A, Halena S, Appay M, Alameddine R, Yin F, Nguyen Q, So MY, Sandaradura I, Kim HY, Galimam S, Cerruto N, Lai T, Gilbey T, Daveson K, Reuter SE, Penm J, Alffenaar JW. LInezolid Monitoring to MInimise Toxicity (LIMMIT1): A multicentre retrospective review of patients receiving linezolid therapy and the impact of therapeutic drug monitoring. Int J Antimicrob Agents. 2023 May;61(5):106783. doi: 10.1016/j.ijantimicag.2023.106783. Epub 2023 Mar 14.
Lau NS, Ly M, Dennis C, Toomath S, Huang JL, Huang J, Ly H, Chanda S, Marinelli T, Davis R, Liu K, McCaughan G, Crawford M, Pulitano C. Microbial Contamination During Long-term Ex Vivo Normothermic Machine Perfusion of Human Livers. Transplantation. 2024 Jan 1;108(1):198-203. doi: 10.1097/TP.0000000000004653. Epub 2023 Dec 13.
Marinelli TM, Dolan L, Jenkins F, Lee A, Davis RJ, Crawford S, Nield B, Ronnachit A, Van Hal SJ. The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19). Infect Control Hosp Epidemiol. 2023 Jul;44(7):1116-1120. doi: 10.1017/ice.2022.220. Epub 2022 Sep 9.
O'Toole RF, Leong KWC, Cumming V, Van Hal SJ. Vancomycin-resistant Enterococcus faecium and the emergence of new sequence types associated with hospital infection. Res Microbiol. 2023 May;174(4):104046. doi: 10.1016/j.resmic.2023.104046. Epub 2023 Feb 27.
Pupune P, Puana I, Allen J, Kelly D, Ronnachit A; Antimicrobial resistance threatening animal-human health in Papua New Guinea. 2023 Australian Zoologist; doi: https://doi.org/10.7882/AZ.2023.040.
Stoler S, van Hal SJ, Chadban S, Le T, Torzillo P, Scarlato RM, Wyburn K, Perkins GB, Marinelli T. Protracted COVID-19 pneumonitis early post-ABO incompatible kidney transplantation: Management considerations and the role of whole genome sequencing. Nephrology (Carlton). 2023 Nov;28(11):639-643. doi: 10.1111/nep.14235. Epub 2023 Aug 27.
Van Dort BA, Penm J, Ritchie A, Gray TJ, Ronnachit A, Baysari MT. Antimicrobial Stewardship (AMS) During COVID-19: Eyes and Ears on the AMS Team. Stud Health Technol Inform. 2023 Jun 22;304:62-66. doi: 10.3233/SHTI230370.
van Hal SJ, Whiley DM, Le T, Ray S, Kundu RL, Kerr E, Lahra MM. Rapid expansion of Neisseria gonorrhoeae ST7827 clone in Australia, with variable ceftriaxone phenotype unexplained by genotype. J Antimicrob Chemother. 2023 Sep 5;78(9):2203-2208. doi: 10.1093/jac/dkad221.
Whiley DM, Tickner JA, Kundu RL, Hogan TR, van Hal SJ, Lahra MM. Selection of Neisseria gonorrhoeae ceftriaxone resistance using doxycycline post-exposure prophylaxis. Lancet Infect Dis. 2023 Aug;23(8):e268-e269. doi: 10.1016/S1473-3099(23)00359-6. Epub 2023 Jun 12.

Our Presentations


Marinelli T. Transplant Surgery and Infection Risk. Foundation Course in Infections in Immunocompromised Hosts. Melbourne. March 2023.
Marinelli T. Management of COVID-19 in Solid Organ Transplant Recipients: At the Time of Transplant and Beyond. Antimicrobials – The Annual Scientific Meeting of the Australasian Society for Antimicrobials. Brisbane. February 2023.
Marinelli T. The Donor Call. Foundation Course in Infections in Immunocompromised Hosts. Melbourne. March 2023.
Marinelli T.  BK Virus in Renal Transplant. The Transplant Society – Immunocompromised Host Special Interest Group Symposium. Adelaide. April 2023.
Marinelli T. COVID-19 in Solid Organ Transplantation. Donor and Recipient Issues. Organ and Tissue Donation Authority. Brisbane. May 2023.
Marinelli T. COVID-19 and Increased Virologic Risk Donors. Transplant Society of Australia and New Zealand Post-Graduate Course. Brisbane. June 2023. 
Marinelli T. Antifungals Use in the Immunocompromised Host. Antifungal Forum. Sydney. July 2023.
Marinelli T. Donor derived HHV-8 in liver transplant recipients. Toronto Transplant Infectious Diseases Symposium. August 2023.