Implementing a national programme of pathogen genomics for public health: the Australian Pathogen Genomics Program (AusPathoGen)

Jessica R Webb; Patiyan Andersson; Eby Sim; Alireza Zahedi; Angela Donald; Tuyet Hoang; Anne E Watt; Jessica E Agius; Celeste M Donato; Max L Cummins; Tehzeeb Zulfiqar; Son Nghiem; Chantel Lin; Dimitrios Menouhos; Lex E X Leong; Rob Baird; Karina Kennedy; Louise Cooley; David Speers; Chuan Kok Lim; Joep de Ligt; Angeline Ferdinand; Katie Glass; Martyn D Kirk; Steven P Djordjevic; Clare Sloggett; Kristy Horan; Torsten Seemann; Vitali Sintchenko; Amy V Jennison; Benjamin P Howden; AusPathoGen Program partners

doi:10.1016/j.lanmic.2024.100969

Implementing a national programme of pathogen genomics for public health: the Australian Pathogen Genomics Program (AusPathoGen)

Lancet Microbe. 2024 Oct 7:100969. doi: 10.1016/j.lanmic.2024.100969. Online ahead of print.

Authors

Jessica R Webb¹, Patiyan Andersson², Eby Sim³, Alireza Zahedi⁴, Angela Donald⁵, Tuyet Hoang², Anne E Watt⁵, Jessica E Agius³, Celeste M Donato¹, Max L Cummins⁶, Tehzeeb Zulfiqar⁷, Son Nghiem⁷, Chantel Lin², Dimitrios Menouhos⁸, Lex E X Leong⁹, Rob Baird⁸, Karina Kennedy¹⁰, Louise Cooley¹¹, David Speers¹², Chuan Kok Lim¹³, Joep de Ligt¹⁴, Angeline Ferdinand¹⁵, Katie Glass⁷, Martyn D Kirk⁷, Steven P Djordjevic⁶, Clare Sloggett⁵, Kristy Horan⁵, Torsten Seemann², Vitali Sintchenko³, Amy V Jennison⁴, Benjamin P Howden¹⁶; AusPathoGen Program partners

Affiliations

¹ Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia.
² Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia.
³ Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia.
⁴ Public and Environmental Health, Pathology Queensland Queensland Health, Brisbane, QLD, Australia.
⁵ Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
⁶ Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, NSW, Australia.
⁷ National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia.
⁸ Territory Pathology, Royal Darwin Hospital, Darwin, NT, Australia.
⁹ SA Pathology, Adelaide, SA, Australia.
¹⁰ Department of Clinical Microbiology and Infectious Diseases, Canberra Health Services, Australian National University Medical School of Medicine and Psychology, Canberra, ACT, Australia.
¹¹ Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Tasmania, Australia; Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia.
¹² Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Perth, WA, Australia.
¹³ Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
¹⁴ Institute of Environmental Science and Research, Kenepuru, Porirua, New Zealand.
¹⁵ Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia; Centre for Health Policy, School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia.
¹⁶ Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia. Electronic address: [email protected].

PMID: 39389079
DOI: 10.1016/j.lanmic.2024.100969

Abstract

Delivering large-scale routine pathogen genomics surveillance for public health is of considerable interest, although translational research models that promote national-level implementation are not well defined. We describe the development and deployment of the Australian Pathogen Genomics Program (AusPathoGen), a comprehensive national partnership between academia, public health laboratories, and public health agencies that commenced in January, 2021. Successfully establishing and delivering a national programme requires inclusive and transparent collaboration between stakeholders, defined and clear focus on public health priorities, and support for strengthening national genomics capacity. Major enablers for delivering such a programme include technical solutions for data integration and analysis, such as the genomics surveillance platform AusTrakka, standard bioinformatic analysis methods, and national ethics and data sharing agreements that promote nationally integrated surveillance systems. Training of public health officials to interpret and act on genomic data is crucial, and evaluation and cost-effectiveness programmes will provide a benchmark and evidence for sustainable investment in genomics nationally and globally.

Publication types

Review