Australian centre for genomic epidemiological microbiology


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Tracking pathogens and using new tools to overcome infectious disease

University of Technology Sydney, Broadway, NSW 2007
NSW Department of Primary Industries, Menangle, NSW 2568


The latest science and technology is enabling Ausgem researchers to follow the evolution of pathogens and, for the first time, map how they infect the population. These new capabilities may soon help to prevent some disease occurring and improve the way we respond when an outbreak happens. The greatest challenge, however, is preventing the spread of antibiotic – or antimicrobial – resistance which could render much of modern medicine obsolete at great cost. Ausgem is working to understand how antibiotic resistance develops, where it resides, and how it spreads among all microorganisms.

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Fast-track identification of foodborne disease

Ausgem researchers are developing a tool to be able to quickly identify the emergence of new infections within communities and across the country.

Ausgem’s world-leading bioinformatics group has adapted existing software used to identify genomic similarities in the research environment to create a program that can process massive amounts of information contained in DNA sequence data to identify similarities in genome submissions from multiple different sources collected at different times.

If a clinician obtains the DNA analysis of a blood or tissue sample from a patient with an infectious disease – such as E. coli – the software is able to compare it with those submitted from different clinics. And, if a number of similar genomes are identified, it indicates there may be a single source of infection such as a common contaminated food source.

Identifying an infectious disease outbreak before it peaks allows governments and regulators to quickly  respond – by recalling an identified product – and therefore limiting the spread of disease.

Ausgem is working in partnership with a public health laboratory in NSW to pilot the new technology-based process.



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New Ausgem technology is enabling rapid genome comparisons of microorganisms and will soon be piloted by a NSW health service.



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Ausgem researchers have shown that antimicrobial resistance (AMR) can spread as a group of genes that inserts itself into the host’s existing DNA. This has implications for new strategies designed to combat AMR.

Hospital partnerships providing valuable insight

Ausgem research is being supported through collaboration with hospitals in NSW and internationally.

In Australia, the Royal North Shore (RNS), Concord, Orange Base and Sydney Adventist (SAN) hospitals were involved in an epidemiological survey to determine the presence of antibacterial-resistance in patient populations.

Hundreds of samples obtained from these hospitals have been sequenced and analysed to allow the characterisation of complex antibiotic resistance gene loci (CRL) – places in the genome where groups of resistance genes cluster.

As the work unfolds, it will elevate Ausgem as a world-leader in the field.

Mapping the spread of antibiotic resistance

At the start of 2017, the World Health Organization (WHO) listed the multidrug resistant Pseudomonus aeruginosa as one of the top three critical pathogens for which new antibiotics are needed.

Ausgem researchers have worked with samples from burns victims treated at RNS Hospital in Sydney who have been infected with Pseudomonus aeruginosa to better understand the way in which bacteria acquire resistance to some or all antibiotics.

Using genetic sequencing of multidrug resistant P. aeruginosa, Ausgem researchers have provided new insights on how this group of bacteria is rapidly becoming resistant to almost all known antibiotics. Their work has defied the traditional dogma about how clusters of resistance genes can move between different bacteria. Generally, genes that confer drug resistance spread through bacterial populations as mobile units called plasmids that can replicate independently.

The new discovery has revealed that antimicrobial resistance can spread as a group of genes that inserts itself into the host’s existing DNA and replicate along with it. These groups of resistance genes would therefore not be affected by the novel strategies aimed at blocking the transfer of antibiotic resistance genes through targeting plasmids.

Moreover, the gene groups that integrate into the bacterial chromosome can also include DNA segments that promote virulence, meaning that the two characteristics are dispersed together, making the pathogen untreatable.


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Without effective antibiotics, the success of major surgery and cancer chemotherapy will be undermined.



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