Q-PHIRE Genomics

Microbial genomics is a core tool in keeping Queenslanders safe from infectious diseases, including COVID-19.

Queensland Public Health and Infectious diseases REference (Q-PHIRE) Genomics is the state-wide reference centre for microbial and public health genomics. We provide cutting edge, rapid microbial genomics to support the Queensland response to health threats, including viruses and pandemics.

Q-PHIRE Genomics brings together experts and state-of-the-art equipment to deliver genomics across laboratories at Forensic and Scientific Services to respond to existing and emergent infectious diseases, and public and environmental health issues.

Rapid identification

Our NATA (National Association of Testing Authorities) accredited microbial genomics provide rapid identification and characterisation of organisms, offering superior discrimination to conventional typing methods. Our methods are utilised daily for all state and national outbreak investigations and reporting, and are well established and integrated in national public health testing.

Sequencing

We use microbial genomics for direct sequencing of clinical, water, food and environmental samples. We can reveal entire bacterial populations or fingerprints of species present; or sift through and identify a particular strain for diagnostic or investigative purposes.

Viruses are sequenced from culture or directly from clinical samples using targeted amplification or metatranscriptomics to provide further characterisation relevant to clinical management as part of outbreak investigation or public health surveillance.

Organic Chemistry and phycology applications are being explored for whole genome and metagenomics sequencing approaches to analyse food matrices and environmental samples.

Our team

Our team has extensive expertise in the generation of whole genome sequencing (WGS) data for viruses and bacteria from isolates and from clinical specimens.

We can investigate outbreaks of public health significance, including SARS-CoV-2, Salmonella and other foodborne pathogens, sexually transmitted diseases, respiratory pathogens such as Legionella, and vaccine preventable diseases.

We can characterise emerging and notifiable organisms, such as Corynebacterium diphtheriae for toxin gene functionality, antimicrobial resistance detection in cultured organisms and non-cultured or non-culturable organisms, and identify novel pathogens.

We are members of national and international genomic networks including the Australian Communicable Diseases Genomics Network (CDGN).

Facilities

The combination of numerous sequencers across multiple platforms (Illumina and Oxford Nanopore) generating both short and long read sequences and low throughput or high throughput sequencing, together with the application of extensive robotics provides the agility to adapt to any sequencing requirements. Combined, these sequencing platforms enable Q-PHIRE Genomics to produce hundreds of sequences a day in response to an outbreak, while being able to perform routine public health surveillance sequencing of hundreds of sequences per week.

Research

Current research collaborations include:

• Medical Research Future Fund (MRFF)
  • SARS-CoV-2 sequencing – a national project to increase our knowledge of the behaviour, spread and evolution of the virus​.
• Pathogen Genomics (P2HAGE)
  • National public health pathogen synchronisation and real-time genomic analysis.
• META-GP
  • Clinical metagenomic diagnostics for infectious diseases in Australia development and implementation.
• Queensland Genomics
  • Infectious diseases projects to track hospital acquired infections.

Infectious disease reporting

We provide reference confirmation and characterisation, as well as reference confirmation of sequencing performed by other pathology providers, which is required for notifiable conditions (under the Public Health Regulation 2005).

Collaboration and requests for service

The Q-PHIRE Genomics team is available to perform commercial sequencing for microbial samples and clinical specimens. Contact us for a quote.