Current Research Projects

Major Research Projects Include:

Investigation of the abundance and diversity of the faecal resistome in clinically healthy humans and animals. Antibiotic resistance (AR), or antimicrobial resistance (AMR), is a significant global public health threat. Reservoirs of drug-resistant bacteria are ubiquitous, and the “antibiotic resistome” describes the collection of antibiotic resistance genes found in any environment. The antibiotic resistance genes found in pathogenic bacteria represent just the tip of the iceberg as a whole range of antibiotic resistance genes can be found in both pathogenic and non-pathogenic/commensal bacteria. AR in commensal bacteria is of particular concern due to the ability of some resistance genes to spread horizontally to pathogens. This research project aims to investigate the antibiotic resistome in clinically healthy humans, pigs and birds. This work will contribute towards better understanding of resistance in commensal bacteria and the potential risks of transferable resistance between different hosts.

The sequencing of the genome of a human picornavirus (human parechovirus 3) causing meningitis in young infants in Australia in 2013, 2015 and 2017. The research has focused on identifying the genomic sequence of this virus from cases in and around Geelong, Melbourne, Sydney, Adelaide, Darwin and Brisbane to provide greater understanding of the severe disease observed and the spread and epidemiology of this infection. The work is a collaborative project with Barwon Health clinicians and scientists at GCEID, Deakin University, CSIRO-AAHL, the Victorian Infectious Diseases Reference Laboratory (VIDRL) in Melbourne and with other collaborators from the APPRISE NHMRC CRE.

The screening of wild birds for the presence of coronaviruses. Coronaviruses are responsible for the emergence of epidemics/outbreaks of the Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) more recently resulting in significant human disease and mortalities. In both cases an intermediate mammal, such as bats and civets (“civet cats”) for SARS and for MERS likely dromedary camels, was/is responsible for the transfer of the virus into human hosts. Several types of coronavirus are specific to mammals and birds while some relatively closely related ones, in particular the newly discovered deltacoronaviruses, may infect both. There is limited understanding of their presence world-wide and as Australia is a regional hub for a diverse range of wild birds this project is investigating the potential presence of coronaviruses in wild birds. If such viruses are detected, they will be characterized in detail genetically. This project is a collaboration with Deakin University’s Centre for Integrative Ecology and the WHO Collaborating Centre for Reference and Research on Influenza at VIDRL in Melbourne.

The metagenomics of viruses in Australian wild birds. Australia is home to more than 800 species of birds, both endemic, introduced and migratory species. Wild birds are potential hosts of many viruses such as Murray Valley encephalitis virus, Kunjin virus, and Ross River virus. The introduction or transmission of viruses to novel hosts or habitats can have significant health and economic consequences. We currently have limited knowledge of the avian host-associated virus communities including both pathogenic and non-pathogenic viruses, yet they are potential carriers with a risk of zoonotic disease emergence. In addition, as birds can fly over large distances, they may also passively carry other viruses e.g. insect and plant viruses present in their sources of food. This research project aims to address the lack of knowledge through method development for virus community detection and characterisation using metagenomics to identify the virome of birds. This research will also help to understand the prevalence, transmission routes and associations of virus types with disease or health status. It will provide insight into the wild bird virome with relation to ecology and contribute towards better understanding of the risks from potentially zoonotic viruses in wild birds.

The comparison of methods for 16S rRNA sequencing of bacterial species. Bird and human faecal samples will be extracted using traditional microbiome methods and virome/ribosome nucleic acid extraction. The resultant sequences from sequencing of a traditional 16S amplicon will be compared to the novel virome/ribosome NGS metagenomic sequences obtained.

Other Barwon Health/Deakin Projects Include:

The scientific support for processing and analysis of samples collected in a number of national cohort studies. Including the birth cohort, Barwon Infant Study (BIS), The Environmental Determinants of Islet Autoimmunity (ENDIA) Type 1 diabetes study, the Adhesive Capsulitis Biomarker Study (AdCaB), the MANGO-SZ study, and the Melbourne Infant Study: BCG for Allergy and Infection Reduction. BIS-related research focusses on the microbiome and immunological mechanisms associated with a number of important non-communicable diseases in infancy and childhood, including food allergy, asthma, obesity, early markers of cardiovascular disease and neurodevelopmental disorders.

The investigation of the association between psychotropic medications used in the treatment of mental health disorders and skeletal integrity. Long term use of anti-depressant medications has been demonstrated to cause reduction in bone density and lead to increased incidence of fracture. Ongoing work using human in vitro models of bone remodelling are being conducted to investigate the mechanism of action of these drugs on bone cell function.