​Precision Public Health: Transforming investigations of community outbreaks using pathogen genomics

The Centre for Infectious Diseases and Microbiology – Public Health (CIDM-PH, Western Sydney LHD) in collaboration with ICPMR-NSW Health Pathology and Marie Bashir Institute of the University of Sydney has been pioneering the development and implementation of public health pathogen genomics for laboratory surveillance in NSW. They utilise the next generation sequencing technology for investigation of community outbreaks of diseases with epidemic potential. The main goal of CIDM-PH is to develop NSW capacity in public health pathogen genomics and to facilitate its translation into clinical practice. The evaluation studies in 2017-2018 highlighted the added value of high-resolution whole genome sequencing (WGS) in tracking and containment of high-profile outbreaks involving different pathogens in NSW. This helped the NSW public health epidemiologists and the NSW Food Authority to identify a point-source sooner and with higher precision than would otherwise be expected and to determine the magnitude of the outbreak. Microbial genomics can also make an important contribution to the elimination of tuberculosis in Australia as it enables faster recognition of recent transmission events and better and more targeted treatment of drug-resistant tuberculosis via genetic drug-resistance prediction. 

The CIDM-PH investigators were awarded the NSW Health Translational Research Grant 2016 'Translating pathogen genomics into improved public health outcomes: Prospective evaluation of the effectiveness of genome sequencing-guided investigation of outbreaks'. This project aimed to examine the effectiveness of WGS-based characterisation in improving patient and population health outcomes of endemic cases and community outbreaks caused by Salmonella Typhimurium, Listeria monocytogenes and Mycobacterium tuberculosis. This research improves public health outcomes and infection control practices through more targeted and cost-effective interventions and resource utilisation. The team plays an important role in training of epidemiologists and clinicians and preparing them to the era of genomic epidemiology. The application of genomics to the study of pathogenic bacteria and viruses with epidemic potential and pathogens of critical relevance to hospital epidemiology not only offers new and important insights into their transmissibility and virulence but also can offer significant improvements in public health. In recognition of the importance of this translational research and pathogen genome information for communicable disease control, NSW Health has initiated funding for the state-wide public health pathogen genomics services in 2018-2019. 

Relevant publications from this research

The following publications co-authored by CIDM-PH staff and public health professionals described specific findings and their implications for public health:

  • ​Lindsay C, Flint J, Lilly K, Hope K, Wang Q, Howard P, Sintchenko V, Durrheim D. Retrospective use of whole genome sequencing to better understand an outbreak of Salmonella enterica serovar Mbandaka in New South Wales, Australia. Western Pac Surveill Response J 2018; 9(2): 20-5. 
  • Ford L, Wang Q, Stafford R, Ressler K-A, Shadbolt, C, Hope K, Franklin N, Krsteski R, Carswell A, Carter GP, Seemann T, Howard P, Valcanis M, Castillo CFS, Bates J, Glass K, Williamson DA, Sintchenko V, Howden B, Kirk M. Seven Salmonella Typhimurium type 03-26-13-08-523 outbreaks in Australia linked to trace-back and whole genome sequencing. Foodborne Pathog Dis 2018; 15(5): 285-92. 
  • Thompson CK, Wang Q, Bag SK, Franklin N, Shadbolt CT, Howard P, Fearnley EJ, Quinn HE, Sintchenko V, Hope KG. Epidemiology and whole genome sequencing of an ongoing point-source Salmonella Agona outbreak associated with sushi consumption in western Sydney, Australia 2015. Epidemiol Infect 2017; 145(10): 2062-71.​
Current as at: Monday 31 May 2021
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