Microbial Genomics and Bioinformatics

We envision a future where genomic data-driven approaches revolutionise our ability to control and mitigate the impact of infectious diseases worldwide

Our research focuses on microbial genomics and Bioinformatics, with key areas including patho-genomics, antimicrobial resistance (AMR), genomic epidemiology, genomic surveillance of Infectious Diseases and translating genomic research into clinical practice.

Our work delves into understanding the evolution of antimicrobial resistance (AMR), a critical global health concern, specifically focusing on mobile genetic elements and their roles in carriage and dissemination of AMR genes and driving the evolution of new resistant genotypes.

A primary focus of our clinical research is the application of computational methods for high-throughput analysis of priority pathogens, to facilitate rapid identification and characterisation of these pathogens, which is crucial for timely intervention and treatment. Specifically, we employ genomic epidemiology as a tool for elucidating the transmission dynamics of infectious diseases, aiding in the development of targeted interventions and infection prevention and control strategies. A key facet of our work in this area is to bridge the gap between genomics and routine clinical practice by developing pipelines for seamless integration of genomics into everyday healthcare. This has the potential to revolutionise healthcare delivery and improve patient outcomes.

We are commitment to translating genomic research into tangible clinical applications. Our research into transmission in healthcare facilities, along with genomic analysis workflows and visualization tools, underpin a NATA-accredited genomics surveillance program deployed with Queensland Health. This program has empowered Queensland healthcare facilities to offer microbial genomics as a clinical service, ultimately benefiting patient care.

Group leader

Dr Brian Forde

 Dr Brian Forde

Group Leader, Microbial Genomics and Bioinformatics

+61 7 3346 5474
UQ Researcher Profile

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  • Clinical implementation of routine whole-genome sequencing for hospital infection control of multi-drug resistant pathogens. Brian M Forde, Haakon Bergh, Thom Cuddihy, Krispin Hajkowicz, Trish Hurst, E Geoffrey Playford, Belinda C Henderson, Naomi Runnegar, Julia Clark, Amy V Jennison, Susan Moss, Anna Hume, Hugo Leroux, Scott A Beatson, David L Paterson, Patrick NA Harris. Clinical Infectious Diseases (2023)
  • Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection. Brian M Forde, Leah W Roberts, Minh-Duy Phan, Kate M Peters, Brittany A Fleming, Colin W Russell, Sara M Lenherr, Jeremy B Myers, Adam P Barker, Mark A Fisher, Teik-Min Chong, Wai-Fong Yin, Kok-Gan Chan, Mark A Schembri, Matthew A Mulvey, Scott A Beatson. Nature Communications (2019)
  • Using genomics to investigate an outbreak of vancomycin-resistant Enterococcus faecium ST78 at a large tertiary hospital in Queensland. Budi Permana, Patrick NA Harris, Naomi Runnegar, Margaret Lindsay, Belinda C Henderson, EG Playford, David L Paterson, Scott A Beatson, Brian M Forde. Microbiology Spectrum (2023)
  • Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unit. Paul Chapman, Brian M Forde, Leah W Roberts, Haakon Bergh, Debra Vesey, Amy V Jennison, Susan Moss, David L Paterson, Scott A Beatson, Patrick NA Harris. Journal of clinical microbiology (2020)
  • Fatal Respiratory Diphtheria Caused by ß-Lactam–Resistant Corynebacterium diphtheriae. Brian M Forde, Andrew Henderson, Elliott G Playford, David Looke, Belinda C Henderson, Catherine Watson, Jason A Steen, Hanna E Sidjabat, Gordon Laurie, Sharmini Muttaiyah, Graeme R Nimmo, Guy Lampe, Helen Smith, Amy V Jennison, Brad McCall, Heidi Carroll, Matthew A Cooper, David L Paterson, Scott A Beatson. Clinical Infectious Diseases (2021)
  • Stepwise evolution of pandrug-resistance in Klebsiella pneumoniae. Hosam M Zowawi, Brian M Forde, Mubarak Alfaresi, Abdulqadir Alzarouni, Yasser Farahat, Teik-Min Chong, Wai-Fong Yin, Kok-Gan Chan, Jian Li, Mark A Schembri, Scott A Beatson, David L Paterson. Scientific reports (2015).
  • CATHAI: cluster analysis tool for healthcare-associated infections. Thom Cuddihy, Patrick NA Harris, Budi Permana, Scott A Beatson, Brian M Forde. Bioinformatics Advances (2022)
  • HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data. Budi Permana, Patrick NA Harris, Leah W Roberts, Thom Cuddihy, David L Paterson, Scott A Beatson, Brian M Forde. Microbial Genomics (2024)
  • GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach. Budi Permana, Scott A Beatson, Brian M Forde. BMC bioinformatics (2023)

In addition to our research, we have dedicated efforts to developing bioinformatic tools to providing researchers with advanced capabilities for data analysis and interpretation. These include:

  • SnapperRocks Genome analysis pipeline for prospective genomic surveillance. SnapperRocks is a key component of the NATA-accredited genomics surveillance program deployed within Queensland Health (https://github.com/FordeGenomics/SnapperRocks)
  • Cathai: Longitudinal clustering of clinical samples alongside clinical metadata. Cathai is a key component of the NATA-accredited genomics surveillance program deployed within Queensland Health https://cathai.fordelab.com
  • GraphSNP: An interactive distance viewer for exploring genomic epidemiological data, enabling researchers to visualise pairwise SNP distances and analyse cluster and transmission patterns  https://graphsnp.fordelab.com
  • HAIviz: An interactive dashboard designed for visualising and integrating healthcare-associated genomic and epidemiological data, offering insights into outbreaks and transmission events with a focus on enhancing the infection-control responses. https://haiviz.fordelab.com

Our approach

We apply genomic and computational methods to understand the evolution and transmission of infectious diseases and develop novel strategies for disease prevention, diagnosis, and treatment.

    Research areas

    • Microbial genomics
    • Bacterial vaccines
    • Antibiotic resistance
    • Healthcare-associated infections and transmission

    Our team

    Group Leader



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