We are a group of clinical scientists and medical researchers working to provide solutions for people who are critically ill with infections, based on an understanding of the biology of severe infection and its causative agents.
We are based in a university hospital research institute and have grown from a few students to become a cohesive publicly funded enterprise. We work on the transmission of antibiotic resistance in top-tier pathogens and on the biology of the diseases they cause.
Our mission is to develop sustainable positive solutions to severe bacterial infections, including extreme antibiotic resistance, with a focus on precision in medicine and bioremediation of ecosystems in humans and the environment.
Antibiotic resistance surveillance in Enterobacterales, Acinetobacter spp. and Pseudomonas aeruginosa
- Bell J.M. et al. 2020 Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Sepsis Outcome Programme (GNSOP) Annual Report 2019. Communicable Diseases Intelligence 44.
Antimicrobials use in the ICU, effects on the gut microbiome and impact on antibiotic resistance
- Venturini C. et al. 2018 Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients. Intensive Care Med Exp. 6(1):19.
- Venturini C. et al. 2021 Effects of antibiotic treatment with piperacillin/tazobactam versus ceftriaxone on the composition of the murine gut microbiota. Antimicrob Agents Chemother. 65(2):e01504-20.
- Gamage HKAH. & Venturini C. et al. 2021 Third generation cephalosporins and piperacillin/tazobactam have distinct impacts on the microbiota of critically ill patients. Sci Rep 11:7252.
- GNT1127292 2017-21 Antibiotic resistance and the ecological effects of selective decontamination of the digestive tract in Intensive Care Units.
Smart antibiotic choices
- Khalid A. et al. 2020 Characterizing the role of porin mutations in susceptibility of beta lactamase producing Klebsiella pneumoniae isolates to ceftaroline and ceftaroline-avibactam. Int J Infect Dis 93:252-257.
- Iredell J. et al. 2017 New assay for bacterial load and sepsis mortality (bliss study). Pathology 49(1):S52.
Multidrug resistance mechanisms and novel antimicrobials
Bacterial adaptation and physiology
- Petrovic Fabijan A. et al. 2021 L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli. bioRxiv 2021.06.21.449206.
- Fajardo-Lubián A. et al. 2019 Host adaptation and convergent evolution increases antibiotic resistance without loss of virulence in a major human pathogen. PLoS Pathogens 2019 15(3):e1007218.
- Tagg KA. et al. 2020 Plasmid DNA isolation and visualization: Isolation and characterization of plasmids from clinical samples. Methods Mol Biol 2075:3-20.
- Kamruzzaman M. et al. Plasmid interference for curing antibiotic resistance plasmids in vivo. PLoS One. 2017;12(2):e0172913.
Multidrug resistance regions and mobile genetic elements
- Venturini C. & Zingali T. et al. 2019 Diversity of P1 phage-like elements in multidrug resistant Escherichia coli. Sci Rep 9:18861.
- Partridge SR. and Tsafnat G. 2018 Automated annotation of mobile antibiotic resistance in Gram-negative bacteria: the Multiple Antibiotic Resistance Annotator (MARA) and database. J Antimicrob Chemother 73(4):883-890.
- Partridge SR. et al. 2018 Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev 31(4):e00088-17.
- Agyekum A. & Fajardo-Lubián A. et al. 2016 blaCTX-M-15 carried by IncF-type plasmids is the dominant ESBL gene in Escherichia coli and Klebsiella pneumoniae at a hospital in Ghana. Diag Microbiol Infect Dis 84(4):328-333.
Transfer and stability
- Kamruzzaman M. et al. 2021 Biological functions of type II toxin-antitoxin systems in bacteria. Microorganisms. 9(6):1276.
- Qi Q. et al. 2021 The higBA-type toxin-antitoxin system in IncC plasmids is a mobilizable ciprofloxacin-inducible system. mSphere 6(3):e00424-21.
- Wu A. et al. 2020 Specialised functions of two common plasmid mediated toxin-antitoxin systems, ccdAB and pemIK, in Enterobacteriaceae. PLoS One 15(6): e0230652.
- Kamrruzamman M. et al. 2019. A ParDE-family toxin antitoxin system in major resistance plasmids of Enterobacteriaceae confers antibiotic and heat tolerance. Sci Rep 9(1):9872.
Bacteriophage infection strategies
- Venturini C. & Ben Zakour NL. et al. 2020 Fine capsule variation affects bacteriophage susceptibility in Klebsiella pneumoniae ST258. FASEB J 34:10801– 10817.
- Petrovic Fabijan A. et al. 2020 Safety of bacteriophage therapy in severe Staphylococcus aureus infection. Nat Microbiol 5(3):465-472.
- Venturini C. et al. 2019 Bacteriophage therapy for severe infections. Microbiology Australia 40(1), 20-23.
OHMR Fellowships and PhD Scholarships (2021) on Phage Therapy in Humans
Pathogen Biobanking and Phage Bank
- Lin RC, Sacher JC, Ceyssens PJ, Zheng J, Khalid A, Iredell JR; Australian Phage Biobanking Network. Phage Biobank: present challenges and future perspectives. Curr Opin Biotechnol. 2021 68:221-230.
- Khalid A, Lin RCY, Iredell JR. A phage therapy guide for clinicians and basic scientists: background and highlighting applications for developing countries. Front Microbiol. 2021 11:599906.
Alternative antimicrobial therapies
Jon is an Infectious Disease Physician and Microbiologist who divides his time between Westmead Hospital in a combined Infectious Diseases and Microbiology Department and his research which is supported by the NHMRC at the University of Sydney. His major interests are in critical infection, including the study of bacterial septic shock, and in bacterial genetics and ecology.
Formal affiliations are (1) Conjoint Professor of Medicine and Microbiology, Sydney Medical School The University of Sydney/The Westmead Institute for Medical Research and the Marie Bashir Institute, (2) Senior Staff Specialist, Western Sydney and Westmead Hospital and Deputy Director Microbiology, Pathology West (NSW Pathology) and Institute of Clinical Pathology and Medical Research, (3) Director, Centre for Infectious Diseases and Microbiology at Westmead Institute for Medical Research. List of publications.
Dr Nouri Ben Zakour (PhD) is a Principal Research Scientist at the Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research. She is a recognised expert in microbial and evolutionary genomics investigating the evolution of established/emerging clinical and veterinary bacterial pathogens (staphylococci, streptococci, Escherichia coli, Klebsiella pneumoniae). She has published 45 papers in high-impact, general-interest journals including PNAS, Nature Microbiology, Nature Genetics, PLoS Pathogen, Scientific Reports and MBio (>5,000 citations, h-index 29).
Nouri is the lead bioinformatician on several bacteriophage-focused projects at CIDM and has been an early-stage contributor to kickstarting the first Australian bacteriophage therapy centre. She is also interested in information visualisation at the interface of genomics, analytics and infectious diseases and has contributed to the development of widely-used bioinformatics software (BRIG, Easyfig, SeqFindr, and Contiguity). She is actively involved in community outreach and is a certified Software Carpentry (SWC) instructor (2016-). She was ex‐officio member of the Australian Society of Microbiology Queensland branch committee (2013‐2014) and co-organised the 1st Health Hack hackathon event for medical research (Brisbane, 2015). Her twitter handle is @genomiss.
Asmaa is an internationally trained medical doctor and has a broad multidisciplinary experience, she has an extended teaching, research and clinical awareness which have augmented her skills. In addition to her experience in different teaching programmes, research and clinical laboratories she has hands-on experience in all molecular biology, tissue culture and genetic techniques. She has worked as a clinical pathologist and lecturer of Pathophysiology for 8 years before she moved to Australia. She has recently awarded her master’s degree in medicine from School of Medicine, Sydney University and joined the Centre of Infectious Disease and Microbiology, Westmead Institute for Medical Research (WIMR) as an assistant research scientist. Her master’s work has been published in one of Science journals.
Alicia is an emerging leading researcher expert in Molecular Microbiology and Antimicrobial Resistance (AMR).
Along 20 years of research experience, Dr. Fajardo-Lubián has acquired expertise in molecular biology, bacterial mutagenesis, cell culture, phage biology, safe handling of human pathogens and animal experimentation. Following undergraduate training in Parasitology (Leishmania spp.-macrophage dynamics. 2000-04, University of Extremadura, Spain), Dr. Fajardo-Lubián focused on bacteriology: during PhD and first years of post-PhD (2004-12, National Center for Biotechnology, Spain) Dr. Fajardo-Lubián analysed the molecular basis of AMR and the link with P. aeruginosa fitness and virulence. For the last 8 years, Dr. Fajardo-Lubián has investigated the evolution of outer membrane changes in a major human pathogen (K. pneumoniae) and its implication in AMR and bacterial adaptation to human host (Prof. Jon Iredell’s team, Centre for Infectious Diseases and Microbiology, The University of Sydney and The Westmead Institute for Medical Research, Australia). During this time Dr. Fajardo-Lubián has also developed expertise in phage therapy against multidrug resistant bacteria (K. pneumoniae, S. sonnei or E. coli) and phage-bacteria evolution (Westmead Bacteriophage Therapy Team and Australian Phage Network).
Dr. Fajardo-Lubián is also involved in the characterization (Whole Genome Sequencing and PCR-based methods) of AMR Gram negative bacteria as part of the AGAR National Surveillance Program (Australian Group of Antimicrobial Resistance, GNSOP program-Gram negative Sepsis Outcome Program).
During her career, Dr. Fajardo-Lubián has supervised a graduate student through completion and award of PhD (academic / research supervisor) and supervised 4 undergraduate students.
Kamal is a Research Scientist at the Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research and Senior Research Fellow (Faculty of Medicine) at the University of Sydney. He worked as a CRE Research Fellow at the University of Sydney from Sep. 2011 to February 2014.
His Mmjor research expertise is in the field of bacterial genetics, mobile genetic elements (plasmids and bacteriophages) and antibiotic resistance genetics. His research work has been published in major journals such as Nature and PNAS with >1800 citations. His current research focuses on understanding the biology of antimicrobial resistance (AMR) plasmids and designing an effective AMR plasmid curing strategy, including CRISPR-Cas-based AMR curing. He has been a Chief Investigator of NHMRC grants totalling >$1.2 million AUD.
He completed his PhD in the field of Molecular Microbiology at Kyoto University Graduate School of Medicine, Japan, in 2008 with a Monbukagakoshu scholarship (Japanese Government scholarship). He worked as an Assistant Scientist and Associate Scientist (2008-2011) at the Molecular Microbiology and Ecology research group at the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B). His research at ICDDR,B mainly focused on understanding molecular evolution and pathogenic mechanism of enteric bacterial pathogens. List of publications is available on Medline Research Gate and on Google Scholar citations.
Ali is a clinician in his final year of Ph.D. in Medicine (Microbiology) studies under the supervision of Prof Jonathan Iredell and Dr. Susan Maddocks at the Westmead Institute for Medical Research, University of Sydney.
He did his M.B.B.S from the University of Health Sciences Pakistan and then graduated from the Master of Philosophy program in Medical Microbiology from Pakistan. He also holds the prestigious Certified in Infection Control certification from USA. He has over eight years of experience working as a clinical microbiologist and infection control practitioner in different tertiary care hospitals of Pakistan and Saudi Arabia. He has published research articles in many reputed peer-reviewed journals and presented his work in national and international conferences. He is working on different strategies to address the alarming issue of antibiotic resistance in bacterial pathogens and is exploring the activity of different synergistic antibiotic combinations and bacteriophage/bacteriophage-antibiotic combinations against resistant bacteria. He is working to understand the different aspects of bacteriophage therapy to optimize the use of bacteriophages as adjunct to antibiotics for treatment of critical bacterial infections in humans. Additionally, he is also exploring avenues to establish bacteriophage therapy in developing countries where the impact of antibiotic resistance is much more pronounced.
Ameneh, BHB, MBChB, DipPaeds, MD, FRACP, is a senior lecturer in Child and Adolescent Health for The University of Sydney, based at The Children’s Hospital at Westmead where she also works as a paediatric infectious diseases specialist.
Her research focus is on novel therapeutic options for difficult to treat infections in paediatrics and optimisation of antimicrobial therapy for children with cystic fibrosis. She was the first clinician in Australia to treat a child with intravenous phage therapy in October 2019 for a highly resistant Pseudomonas aeruginosa bone infection and has been overseeing the planning and treatment of other patients using phages against Mycobacterium abscessus (including the first use of a genetically modified phage in Australia) through collaborations with Prof Iredell and the Westmead Institute for Medical Research and the Sydney Children’s Hospital Network cystic fibrosis teams.
Ameneh is the paediatric representative for the Australasian Society for Infectious Diseases Clinical Research Network with a goal to increase involvement of children in clinical research, particularly early phase studies. She is also the Phage Therapy content expert for the Sydney Children’s Hospital Network Advanced Therapeutics Steering Committee. Her other areas of research include investigating the immunological response to influenza and COVID-19 vaccination in healthcare workers, the burden of enteric fever in Western Sydney and improving molecular diagnostics of osteoarticular infections in children.
Deputy Director of Phage Australia (MRFF Frontier 2021), Stream 1 co-convenor, IP Commercialisation Working Group.
Ruby CY Lin is the Genomic Chair of the Scientific Advisory Committee of Westmead Precinct Hub (2 teaching hospitals and 3 Medical Research Institutes) and current Vice President of the Australasian Genomic Technologies Association (AGTA). She helps organisations build academic-industry hybrid teams and has secured over $6.4 million in research funding in the disciplines of genomics, cardiovascular diseases, obesity, cancer biology, tissue and pathogen biobanking, phage banking as well as phage therapy. She was a NHMRC Peter Doherty Postdoctoral Fellow (2005-8) and UNSW Global Postdoctoral Fellow (2009-14). Her research profile and publications can be referenced at ResearchGate, ORCID and Google Scholar. She officially handles @agtaGenomics and @Iredell_lab Twitter accounts and is active on LinkedIn.
During her time as the president of AGTA (2013-5), she continued to implement co-convenors for its annual meeting with a quiet room for delegates with carer duties, ECR-MCR pairing to chair sessions and 50:50 gender balanced international and local invites. AGTA proudly continues this equity diversity and inclusion guidelines in its conferences, workshops and symposiums. She is a GEDI (Gender Equality, Diversity and Inclusion) committee member of AAMRI (Association of Australian Medical Research Institutes), part of UNSW Women in Research and STEM Women (Australian Academy of Science) and advocates for girls and women in STEMM and does pro bono career coaching. She is on the Phage Futures Advisory Board, Convenor of AGTA2022 Sunshine Coast and part of organising committee for International Genetics Congress 2023 Melbourne and International Society for Viruses of Microorganisms 2024 Cairns.
Emily is the Executive Assistant to Professor Jon Iredell, Centre for Infectious Diseases and Microbiology, The University of Sydney, based at the Westmead Institute for Medical Research.
She joined the team, in 2013 as an Administrative Assistant on the NHMRC Centre of Research Excellence for Critical Infection. Since then her dynamic role has grown to include all aspects of event management for the Short Course in Critical Infection and the Molecular Microbiology Meeting as well as managing the International Visiting Scientist Program funded by the Australian Society for Microbiology. She continues to enjoy the new opportunities that come her way as she provides administrative support to Professor Jon Iredell and his research team.
Sally is a Senior Hospital Scientist at the Centre for Infectious Diseases and Microbiology/Westmead Institute for Medical Research at Westmead Hospital and an honorary Principal Research Fellow (Faculty of Medicine) at the University of Sydney.
Since completing her D. Phil at Oxford University on sporulation in Bacillus subtilis, Sally has become a leading researcher in the area of the genetics of antibiotic resistance, mobile elements and plasmids in Gram-negative bacteria, particularly Enterobacteriaceae. In addition to research articles, she has published major reviews and two book chapters in this area and co-developed an automated annotation system for antibiotic resistance genes and associated mobile genetic elements.
Sally has been a member of the Editorial Board of Antimicrobial Agents and Chemotherapy since 2009 and of the Journal of Antimicrobial Chemotherapy since 2016 and frequently reviews for these and other journals. She is a member of the National Examinations and Qualifications Board of the Australian Society for Microbiology and the committee of the Australian Society for Antimicrobials. She has also contributed to analysis of data for the Gran-negative Sepsis Outcomes Program for the Australian Group of Antimicrobial Resistance since 2017. The translational potential of Sally’s work since moving to Westmead Hospital in 2005 was recognised by admission to Royal College of Pathologists of Australasia in 2011 as a Founding Fellow of the Faculty of Science. She is currently Research Integrity Advisor for the Westmead Institute for Medical Research.
Postdoctoral Fellow, Phage Biologist, Executive Board of International Society for Viruses of Microbes.
Alex completed her PhD in phage biology at The University of Novi Sad (Serbia) in 2016 as part of the Hungary-Serbia IPA Cross-Border Cooperation Programme (European Commission HUSRB 1203/214/250). She then moved to Australia to continue her postdoctoral career under supervision of Prof. Jonathan Iredell. Since 2018, Alex’s has been working as a lead phage scientist in world first-in-human clinical trial of intravenous GMP-grade phage therapy (Petrovic-Fabijan et al, 2020 Nature Microbiology) where she studied bacteria-phage interaction and host response in critically ill patients receiving phage therapy. Her current research is mostly focused on bacterial cell and phage biology, particularly interactions between clinically important bacteria such as L-forms and therapeutic phages. Alex tackles fundamental questions aiming to generate knowledge base that will ensure success in phage therapy. Qualifications: Overseas trained Division 1 Nurse, BSc (Honours), MSc and PhD in Phage Biology.
Alex is Executive Board Member of International Society of Viruses of Microbes, professional member of ESCMID Study Group for Non-traditional Antibacterial Therapy (ESGNTA) and Australian Society for Microbiology, Bacteriophage Biology and Therapeutics Special Interest Group. Her Twitter handle is @PetrovicFabijan and she officially handles @VirusOfMicrobes Twitter account.
Scientific Officer, Centre for Infectious Diseases and Microbiology at Westmead Hospital and the Westmead Institute for Medical Research.
Belinda’s initial research in Jon Iredell’s team, involved exploring the basis of the humoral response to Bartonella henselae infection of humans, including establishment of assay systems (e.g. invasion and angiogeneisis assays) and tissue culture cell lines. This also involved the confirmation of basic virulence behaviour (attachment and invasion) by direct (imaging) and indirect methods. She has acquired experience in the development of assays relevant to the pathogenesis of disease.
Her current research is aimed at investigating the rise and spread of antimicrobial resistance in nosocomial bacterial pathogens. In 2011 and then again in 2017, she was a member of Jon Iredell’s team, who treated patients at Westmead hospital, with bacteriophage therapy. She has gained extensive experience working with specimens collected from consented patients and on projects requiring approval from the HRE Committee. Having completed the GCP training course, she is aware of and conducts her research according to the guidelines and standards, which govern the conduct of clinical research. In addition, she also has gained extensive experience with the preparation, lodgement and overseeing of licences approved by the OGTR and working with GMOs.
In her current project; NHMRC grant APP1127292; titled Ecological effects of Selective Decontamination of the Digestive Tract (eSuDDICU), she has served in a supervisory role for the laboratory work being conducted at Westmead Hospital. This role also involves the development of microbiology laboratory protocols, to process rectal, faecal and endotracheal specimens, collected from patients in the intensive care units from various Sydney and Central Coast hospitals. Belinda also has also gained extensive experience in the application of Occupational Health and Safety principles, the completion of risk assessments and undertaking risk management of safe work practices. She has also gained considerable experience with maintaining a research budget. She interacts with teams from various disciplines and Institutions; NSW Health, University of Sydney and the Westmead Institute for Medical Research.
Belinda has also been involved in the development of rapid assays using methods such as real-time PCR, commercial assays and multiplexed tandem PCR (MT-PCR) for the detection of sepsis. With a current CASA approved licence, she has experience with the packaging and dispatch of infectious and dangerous goods. Belinda has trained and supervised numerous staff and students to work safely and efficiently in a microbiology laboratory.
List of Publications:
Lee is a currently a research assistant in Professor Jon Iredell’s research group at WIMR. She is involved in research investigating the effects of antibiotic treatment and prophylaxis on the ecology of the human microbiome and also the emergence of related transmissible antibiotic resistance systems in Enterobacteriaceae.
Previously, Lee was employed by Westmead Hospital, ICPMR, in the Microbiology department where she focused on the development of rapid assays to improve turn-around-time of infection control screening. In addition, Lee evaluated new technologies and culture medias as they emerged. She also acted as intermediary between research and clinical applications with an association with the on-site research laboratory supervised by Professor Jon Iredell. Lee obtained her Masters of Science in Medicine (by Research) completed in July 2007. Title “Genetic methods for the rapid detection of medically important nosocomial bacteria.”
Carola is an expert research microbiologist whose work has primarily focused on the role of mobile genetic elements in the evolution of infectious bacteria.
Her research has a multidisciplinary approach that combines traditional microbiology, molecular methods and bioinformatics (genomics). She graduated at the University of Wollongong, where she also completed her PhD research (UOW and The Elizabeth Macarthur Agricultural Institute) on the links between antibiotic resistance, virulence and mobile DNA in pathogenic enterobacteria, which remains one of her main research interests. Post-PhD, Carola spent 4 years as a postdoctoral researcher at The University of Queensland where she investigated the links between horizontal gene transfer and pathogenicity in Streptococcus pyogenes, including the acquisition and transfer of virulence and antibiotic resistance by phage and other integrative DNA elements.
Since 2013, Dr Venturini has been part of Prof Jon Iredell’s research group at The Westmead Institute for Medical Research. Here, she has been leading large-scope research projects investigating the ecology of the gut microbiome related to antibiotic use and exploring the use of bacteriophages in combating infectious multidrug resistant bacteria of clinical relevance.
Alma is a PhD student supervised by Professor Jon Iredell and Dr Muhammad Kamruzzaman.
She completed a Bachelor of Science (Adv)(Hons I) in 2017 at the University of Sydney, with her honours thesis focusing on the specialisation of toxin-antitoxin systems in Enterobacteriaceae. Her PhD work has continued this work, as well as expanded to include conjugation systems and the development of antibiotic resistance curing plasmids.
During her undergraduate years she also completed an internship at Vanderbilt University in Nashville, Tennessee, and was part of the successful 2016 Sydney Australia iGEM team. She has a keen interest in antibiotic resistance, synthetic biology and science communication.