Innovative research addressing microbial threats and infectious diseases
We are uniquely focussed on deciphering interlinked human, animal, plant and environmental problems in microbiology, infection and disease. Our research spans antibiotic resistance, food safety, computational biology, genomics and proteomics, microbial ecology and microbial morphology.
Key research areas
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Research Theme Leader: Dr Parisa Noorian
Clinical and Diagnostic Microbiology focuses on understanding infectious diseases in patient populations through the integration of clinical microbiology, microbial genomics, metagenomics and data science. Research within the theme spans recurrent and catheter-associated urinary tract infections, biofilm-associated infections and antimicrobial resistance. Current projects include large longitudinal clinical studies of urinary microbiomes in people with spinal cord injury, development of clinically representative mixed-species urinary catheter biofilm models, and machine learning approaches that predict infection outcomes using genomic and metagenomic data. These studies provide new insights into pathogen evolution, microbial community dynamics and antimicrobial resistance while supporting the development of improved diagnostics, preventive strategies and mRNA vaccine technologies. Together, the theme strengthens AIMI's capability in clinical genomic microbiology and translational infectious disease research.
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Research theme leader: Associate Professor Mehrad Hamidian
Associate Professor Mehrad Hamidian is a microbiologist and genomic epidemiologist whose research focuses on antimicrobial resistance (AMR) and genome evolution in Gram-negative bacterial pathogens. His research has a particular focus on Acinetobacter baumannii, a major multidrug-resistant pathogen, and increasingly includes other Gram-negative bacteria recovered from clinical, environmental and animal sources.
His research investigates how bacteria acquire, maintain and disseminate antibiotic resistance, with a particular focus on mobile genetic elements, including plasmids, insertion sequences, transposons, integrons and genomic resistance islands, as well as recombination-driven chromosomal evolution. His work combines bacterial comparative genomics and molecular microbiology to understand the emergence and spread of antimicrobial resistance.
A major focus of his research has been the genomic characterisation and epidemiology of A. baumannii, including the development of approaches and resources for tracking plasmids and other mobile genetic elements. His group developed one of the first comprehensive plasmid typing schemes for Acinetobacter and an associated open-access database and bioinformatic resource (Acinetobacter Plasmid Typing) to support surveillance and investigation of plasmid-mediated AMR.
His research also investigates emerging mechanisms of antibiotic resistance evolution, including recombination and chromosomal exchange, and how these processes contribute to the emergence of successful multidrug-resistant lineages. His work spans fundamental mechanisms of bacterial evolution through to genomic surveillance and the development of resources to support AMR research and public health.
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Research theme leader: Dr Gustavo Espinoza Vergara
Understanding the mechanisms that enable pathogens to survive and persist in the environment, and how these shape transmission, virulence and disease.
Investigating how bacteria adapt to environmental stresses can reveal the mechanisms that support pathogen persistence and transmission, providing critical knowledge to guide new interventions and inform public health.
Within the Australian Institute for Microbiology and Infection at UTS, my research focuses on interactions between bacteria and environmental protozoa. We investigate how protozoan grazing shapes bacterial physiology, virulence and community behaviour, including the production of expelled food vacuoles (EFVs)—membrane-bound structures that protect bacteria from environmental and host-associated stresses and can enhance transmission and host colonisation.
My team combines microbial ecology, molecular microbiology, functional genomics, including single-cell transcriptomics, and host-relevant models to study pathogens including Escherichia coli, Salmonella enterica Typhimurium and Vibrio cholerae. Our work has established new capabilities to resolve bacterial responses to protozoan predation at the single-cell level, supported by collaborations spanning microbiology, omics and infection biology.
A translational focus of my laboratory is harnessing protozoan biology to package beneficial bacteria within EFVs, with the aim of improving probiotic survival, intestinal colonisation and efficacy.
Current projects:Uncovering the colonisation of newly recognised “trojan horses” of bacteria (ARC DECRA DE250100444).
Evolution and mechanisms of interactions in biofilm communities (ARC DP230101760).
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Research theme leader: Distinguished Professor Steven Djordjevic
Antimicrobial resistance (AMR) is already a major public health threat globally. By 2050, estimates predict that, unless efforts are made to stop its spread, AMR will be responsible for 10 million deaths worldwide each year. (Reference: Tackling drug-resistant infections globally: Final report and recommendations. The review on antimicrobial resistance; London: HM Government and the Wellcome Trust; 2016).
We’re generating and interrogating genomic and proteomic data to tackle antimicrobial resistance, formulate a deeper understanding of pathogen evolution, and to identify and characterise novel antigens for vaccine development.
Working with a leading One Health Genomics Program in Australia – which recognises the interconnection between people, animals, plants, and their shared environment – we’re using phylogenomics and molecular biology to study mobile genetic elements that drive the evolution of antibiotic resistance and bacterial pathogenesis.
Our work sheds light on how established and emerging pathogenic bacteria (and the mobile elements they carry) evolve and circulate in clinical, livestock, agricultural, wastewater and aquatic environments. This work is foundational for the Australian Centre for Genomic Epidemiological Microbiology (AusGEM), a deeply productive collaborative partnership with the NSW Department of Primary Industries since 2013.
Working within a vaccine development program for bacterial animal pathogens (Mycoplasma hyopneumoniae), we’re also applying proteomics to study bacterial pathogenesis, and developing and refining methods to interrogate the surfaceome and N-terminome of these infectious agents.
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Improving human, agricultural and environmental health by understanding how microbial cells grow, change, and adapt to their environments.
Research theme leader: Professor Iain Duggin
Microorganisms are remarkably adaptable and can alter their shape, growth patterns and developmental programs in response to environmental change, stress and host interactions. These responses influence survival, pathogenicity and ecological function, making microbial morphology, growth and development fundamental determinants of health, disease and biotechnological performance.
AIMI's Microbial Morphology and Development research focuses on understanding the molecular mechanisms that control microbial cell division and morphological plasticity in bacteria and archaea. Using model systems including uropathogenic Escherichia coli (UPEC) and the archaeon Haloferax volcanii, we investigate how microbial cells grow, divide and respond to their environments, providing fundamental insights into infection, antimicrobial resistance, adaptation and evolution.
Our researchers combine molecular microbiology, functional genomics, advanced imaging, computational biology and synthetic biology to uncover fundamental principles of microbial cell biology and translate these discoveries into practical solutions. This work supports the development of new diagnostics, vaccines and antimicrobial strategies, while enabling innovative applications in biomedicine, biotechnology, agriculture and environmental sustainability.
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Research Theme Leader: Associate Professor Cindy Gunawan
Our interdisciplinary Biofunctional Nanomaterials Research team studies the multitargeting mechanisms of antimicrobials on bacterial pathogens, and in turn, how bacteria evolve adaptation strategies to the complex antimicrobial mechanisms in long-term exposures. The research addresses the challenges with the now widespread use of nano-antimicrobials as major alternatives in the rise of antibiotic resistance. The team discovers that bacteria are capable to develop resistance to nano-antimicrobials, presenting risks in long-term therapies. Bacteria can coordinate multiple defence strategies to survive and grow in lethal concentrations. The team works to identify the molecular basis of these defence strategies, seeking to develop technologies to overcome the genetically stable resistance phenomena.
The team also studies the co-selection potential of AMR gene pools in the environment with heavy metal contamination, which have also been linked to the widespread use of nano-antimicrobials. The knowledge is to inform strategies for risk assessments, monitoring and mitigation.
Our lab has expertise in cellular and molecular biology of bacteria, including in their biofilm form of growth, as well as in the antimicrobial activity and mechanistic studies of materials.
The team has secured Australian Research Council Discovery Project Grants (2018 – 2022, 2022 – 2026), as well as the Australian Academy of Science Thomas Davies Research Grant for Marine, Soil and Plant Biology with A/Prof Gunawan as Lead CI (UTS Chancellor’s Research Fellow 2015-2018). Gunawan has supervised to completion 7 PhDs (4 as Principal Supervisor and 3 as Co-/Joint-Supervisor) and over 30 Honours and Internship students.
Selected publications
(2013) 10.1002/smll.201300761
(2017) 10.1021/acsnano.7b01166
(2020) 10.1039/c9nr08424j
(2021) 10.1186/s12951-021-01027-8
(2021) 10.1021/acsami.9b20193
(2023) 10.1128/spectrum.02857-22
(2024) 10.1016/j.envint.2024.108512
(2025) 10.1038/s44259-025-00161-9
Selected press releases
(2013) Dr Cindy Gunawan and her nanosilver magic https://www.pcrg.unsw.edu.au/news/dr-cindy-gunawan-and-her-nanosilver-magic
(2017) Rampant use of antibacterial nanosilver is a resistance risk https://phys.org/news/2017-03-rampant-antibacterial-nanosilver-resistance.html
(2021) Nanosilver no ‘silver bullet’ in long-term treatment of infections https://www.sciencedaily.com/releases/2021/10/211012112305.htm
(2024) Researchers Link Pollution And Alzheimer’s– Channel 10 News Exclusive https://youtu.be/9w5upf0TLy4?si=-HzfvmkveuUneBfL
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Research Theme Leader: Dr Daniel Mediati
Our research aims to understand gene regulation at the cellular and evolutionary levels. We have a strong focus on mechanistic discovery, with findings that carry broad impact across Gram-negative and Gram-positive models, including clinical pathogens. By using this knowledge and associated technology in molecular and cellular microbiology, we hope to contribute to the fundaments of how cells function at the molecular level, address the growing problem of antimicrobial resistance, and leverage our mechanistic findings to develop new RNA-based therapeutic strategies for infectious diseases.
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Using advanced microscopy to generate knowledge of how bacteria behave and interact with humans in Health, Disease & Death.
Research theme leader: Associate Professor Dr Bill Söderström
Optical microscopy is an invaluable tool in modern microbiology. Within the “Imaging Microbes in Human Health, Disease & Death” theme we use a variety of microscopy approaches focusing on develop a better understanding of how bacteria behave, develop and interact with humans in various contexts.
Certain focus is placed on how Uropathogenic E. coli (UPEC) is behaving during urinary tract infections (UTI). UPEC undergoes extraordinary morphology changes during the infection cycle, and efforts are made to understand the regulation in space and time of these shape changes at a molecular level. We host a wide range of advanced imaging technologies such as Single-molecule, TIRF and Lattice Structured Illumination Microscopy (SIM), that we use to generate new fundamental knowledge that will inform the development of new therapeutics for infections otherwise hard to treat.
Work within this theme also focus on how the human microbiome can be used to study time since death during human decomposition. Working closely with academics from UTS forensics and The Australian Facility for Taphonomic Experimental Research (AFTER), we develop approaches for forensics applications by combining microbiology, microscopy and genomic sequencing. We are particularly focusing on improving approaches to determine post-mortem interval estimations of deceased individuals.
We are always looking for motivated students and interesting collaborations.
Contact us
Email: aimi@uts.edu.au
Location: Building 4, Level 7, Cnr Thomas and Harris Street, Ultimo NSW 2007
Mail: PO Box 123, Broadway NSW 2007
Australia Courier: UTS Faculty of Science Store, Building 1, Level 2, Thomas Street, Ultimo NSW 2007