Our research impact

AusGEM researchers are developing molecular diagnostic tests for a range of biosecurity threats to characterise strains and assess host specificity—including Chlamydia gallinacea in poultry—and to develop diagnostics for endemic diseases and exotic disease of biosecurity concern through the development, testing, and potential use of Agriseq panels for rapid molecular diagnostics in plant industries in Australia.

A 5-year longitudinal study of pathogens present in blood stream infections of patients treated at Concord Hospital in Sydney led to the identification and characterization of an emerging variant (Sequence Type 8196) of the globally established intractable multi-drug-resistant human pathogen Escherichia coli, sublineage ST131-H30Rx (see publication #20M). The study presented evidence that the clone has evolved locally in Australia from the ST131-H30Rx sub-lineage using molecular dating approaches on a genome-scale dataset and a whistleblower, justifying the relevance of the inclusion of E. coli ST8196 in the list of high-alert pathogens in hospital-based surveillance locally and globally. Focusing on a specific emerging variant of pathogenic E. coli ST38 and including a global collection of 925 genomes reported from various hosts and environmental reservoirs, the study presented convincing data on identification of multiple putative inter-host and host-environment transmission events (for more, see publication #23C). The work emphasised the importance of adopting a One Health approach for phylogenomic studies that seek to improve understanding of antimicrobial resistance and pathogen evolution.

Pseudomonas aeruginosa is a major human pathogen on global resistance alert lists. AusGEM researchers presented evidence from genomic surveillance data to highlight that the resistance islands of P. aeruginosa, and not plasmids, are the units that mobilise complex clusters of resistance genes. You can read more about this research in publication #17C.

AusGEM researchers conducted genomic sequencing of antimicrobial resistance in Australian soil and fresh produce to address gaps in understanding microbial transmission and evolution, with the potential for identifying epidemiological risk factors and informing strategies to mitigate the spread of drug-resistant pathogens in the food chain. You can read more in publication #21A.

AusGEM researchers used metagenomics to investigate bovine respiratory disease. We also worked to address the global issue of bluetongue virus (BTV) in livestock by investigating the origins and genetic diversity of new serotypes in NSW, particularly BTV-16, to understand virus evolution, virulence markers, and risk pathways, to develop early warning systems and control strategies to mitigate trade impacts and improve animal health. You can read more in publications #22H, #22C, and #22E.

AusGEM continues to advance research in developing effective vaccines for animal diseases and to reduce the use of antibiotics in commercial herds. You can read about our progress in publications #18D and #18C.

Working with a public health laboratory in NSW, AusGEM piloted a technology-based tool to identify genomes that may be traced back to a single contaminated food source. This work will support governments and regulators to respond quickly to threats—for example, in recalling contaminated products—to limit the spread of disease.

In collaboration with researchers across the globe, AusGEM analyses genomes of hundreds of samples from sources worldwide to identify prominent sequence types of pathogens to identify non-human reservoirs of pathogens and develop a holistic understanding of transmission to humans. You can read about our progress in publications #18B, #19C, #19O, #20J, #20E, #20C, #20I, #22I, and #22F.

AusGEM collaborated with hospitals in Australia and internationally to sequence and analyse hundreds of samples to determine the presence of antibacterial resistance in patient populations. This supports characterisation of complex antibiotic resistance gene loci (CRL)—places in the genome where groups of resistance genes cluster—and better understanding of how bacteria acquire resistance to some or all antibiotics. You can read more about our research in publications #17C, #20J, #19I, #20D, and #20H.

Expanding on surveillance-based approaches, AusGEM successfully identified a novel extremely virulent clinically important pathogen (see publication #20M) and argued its inclusion in the list of high alert pathogens in hospital-based surveillance studies. Using genome scale resolutions, researchers have also identified the overseas source of a resistant strain which caused a recent hospital outbreak in Queensland. You can read more about this research in publications #20M and #23C.

AusGEM collaborated with Meat and Livestock Australia to characterise the genetic element that is circulating a new resistance gene, resulting in treatment failure of a specific bacterial illness in bovine respiratory disease affected feedlot cattle. Such treatment failures often lead to significant economic losses in the cattle industry. You can read more about this research in publications #23F, #22H, and #24B.

Using second- and third-generation genome sequencing, AusGEM works provide knowledge of diseases in water-based food sources, to determine indicators of disease resistance and susceptibility, and to support the development of advanced diagnostics and molecular epidemiological studies in disease treatment. You can read more in publications #19B, #19R, #20N, and #21B.

AusGEM worked with researchers from across the world to determine which genetic elements that enable resistance to antibiotics are present in contaminated ocean and other natural waterways; this included studying seagulls as potential carriers of resistance genes. You can read more about this research in publications #20A, #20I, #22J.

AusGEM’s researchers conducted phylogenetic and pangenome analyses to identify lineages of pathogens in wastewater, including tracking carbapenemase-producing bacteria and monitoring waste from farms, hospitals, and nursing homes. You can read more about this research in publication #22I.