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Pathogen Genomics

Tracking the spread and mutation of pathogen-based disease outbreaks.

About our Pathogen Genomics service

We are using genomics to better understand the origin of pathogen-based disease outbreaks and how infectious diseases spread.

This helps limit the spread of infectious disease in the community.

Our role in the fight against COVID-19

Our pathogen genomics service has been vital in the fight against COVID-19.

Soon after the first Australian case was confirmed, our teams provided early pathogen sequences direct from patients, grew the live virus and mapped its whole genome.

The sequences were uploaded to international databases for epidemiologists and researchers around the world. This work has been critical to:

  • detect and manage new clusters
  • minimise the spread in the community, and
  • detect new lineages.

Tracking and monitoring the spread of tuberculosis (TB) – a life-threatening respiratory infection

TB is one of the most common infectious diseases globally, infecting millions of people every year. Its treatment is prolonged - requiring at least four drugs in combination over many months.

When a person in NSW is diagnosed with TB, their pathology sample is analysed to:

  • determine the unique genetic makeup of each individual case
  • see how many other cases of TB are potentially related
  • understand whether markers of drug resistance are present.

Sequencing has helped to identify drug resistance, which helps clinicians understand which drugs will be most effective in fighting the infection, and which medications may do little to slow its progression.

NSW Health Pathology’s TB sequencing has also allowed us to forge important collaborations with international partners such as the World Health Organisation (WHO).

Australia has a low incidence of TB and NSW Health is committed to eliminating TB transmission. We participate in clinical trials of new drugs and assessment of potential anti-TB agents.

Understanding antibiotic-resistant strains of bacteria

We are working at diagnosing drug resistances using sequencing to inform targeted therapy for patients, for viral pathogens like HIV, HCV and CMV.

We are also working to better understand how bacteria, like Staphylococcus aureus (‘golden’ Staph), and other pathogens, are becoming resistant to antibiotics.

This information could lead to new ways of treating and preventing life-threatening diseases and help devise new and improved vaccines and antibiotics. This information also allows hospitals to refine infection control strategies.

NSW Health Pathology has several laboratories where we can rapidly sequence a whole bacterial or viral genome on request from clinicians.


For Clinicians

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