Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol
IntroductionPathogen genomics is rapidly becoming a cornerstone in the surveillance and response to infectious diseases. However, there is little evidence on how it shapes strategies for effective public health response and decision-making. This paper presents the evaluation protocol for the Austral...
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Frontiers Media S.A.
2025-07-01
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| author | Tehzeeb Zulfiqar Angeline S. Ferdinand Angeline S. Ferdinand Danielle M. Cribb James D. H. Ong Brad Astbury Kathryn Glass Son Nghiem Liliana Bulfone Nhung Mai Daisy Wang Susan Trevenar Patiyan Andersson Alireza Zahedi Martyn David Kirk |
| author_facet | Tehzeeb Zulfiqar Angeline S. Ferdinand Angeline S. Ferdinand Danielle M. Cribb James D. H. Ong Brad Astbury Kathryn Glass Son Nghiem Liliana Bulfone Nhung Mai Daisy Wang Susan Trevenar Patiyan Andersson Alireza Zahedi Martyn David Kirk |
| author_sort | Tehzeeb Zulfiqar |
| collection | DOAJ |
| description | IntroductionPathogen genomics is rapidly becoming a cornerstone in the surveillance and response to infectious diseases. However, there is little evidence on how it shapes strategies for effective public health response and decision-making. This paper presents the evaluation protocol for the Australian Pathogen Genomics (AusPathoGen) program, which aims to assess the utility of whole genome sequencing in informing public health responses to infectious diseases in Australia.MethodsA mixed methods approach will be adopted to systematically explore the utility of whole genome sequencing in public health action and decision-making through a series of linked projects. Methods include situation assessment surveys of Australian public health laboratories, expert elicitation, and case study analysis. The situation assessment surveys will gather data on public health laboratories’ processes, practices, and associated costs for whole genome sequencing. Expert elicitation will seek views on the prioritization of pathogens for whole genome sequencing. Case studies of specific pathogens and outbreaks will serve as the basis for both impact assessment and qualitative comparative analysis. Genomic and epidemiological data will shed light on the influence of whole genome sequencing on outbreak response.DiscussionThis comprehensive evaluation of pathogen whole genome sequencing in Australia will enhance our understanding of how this data can be applied in public health response and decision-making. The methods discussed can be adapted to different public health pathogen genomic surveillance systems globally. Undertaking evaluation of such systems is crucial for identifying areas of improvement and providing recommendations to optimize quality, efficiency and resource allocation of pathogen genomics to improve public health responses. |
| format | Article |
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| institution | Kabale University |
| issn | 2296-2565 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Public Health |
| spelling | doaj-art-d9cc14c26f4f47bb93dd2390e5e227f52025-08-20T03:33:27ZengFrontiers Media S.A.Frontiers in Public Health2296-25652025-07-011310.3389/fpubh.2025.15871121587112Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocolTehzeeb Zulfiqar0Angeline S. Ferdinand1Angeline S. Ferdinand2Danielle M. Cribb3James D. H. Ong4Brad Astbury5Kathryn Glass6Son Nghiem7Liliana Bulfone8Nhung Mai9Daisy Wang10Susan Trevenar11Patiyan Andersson12Alireza Zahedi13Martyn David Kirk14Department of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, AustraliaCentre for Pathogen Genomics, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, AustraliaDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, AustraliaCentre for Health Policy, University of Melbourne, Melbourne, VIC, AustraliaDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, AustraliaPublic and Environmental Health, Pathology Queensland, Queensland Health, Brisbane, QLD, AustraliaDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, AustraliaIntroductionPathogen genomics is rapidly becoming a cornerstone in the surveillance and response to infectious diseases. However, there is little evidence on how it shapes strategies for effective public health response and decision-making. This paper presents the evaluation protocol for the Australian Pathogen Genomics (AusPathoGen) program, which aims to assess the utility of whole genome sequencing in informing public health responses to infectious diseases in Australia.MethodsA mixed methods approach will be adopted to systematically explore the utility of whole genome sequencing in public health action and decision-making through a series of linked projects. Methods include situation assessment surveys of Australian public health laboratories, expert elicitation, and case study analysis. The situation assessment surveys will gather data on public health laboratories’ processes, practices, and associated costs for whole genome sequencing. Expert elicitation will seek views on the prioritization of pathogens for whole genome sequencing. Case studies of specific pathogens and outbreaks will serve as the basis for both impact assessment and qualitative comparative analysis. Genomic and epidemiological data will shed light on the influence of whole genome sequencing on outbreak response.DiscussionThis comprehensive evaluation of pathogen whole genome sequencing in Australia will enhance our understanding of how this data can be applied in public health response and decision-making. The methods discussed can be adapted to different public health pathogen genomic surveillance systems globally. Undertaking evaluation of such systems is crucial for identifying areas of improvement and providing recommendations to optimize quality, efficiency and resource allocation of pathogen genomics to improve public health responses.https://www.frontiersin.org/articles/10.3389/fpubh.2025.1587112/fullpathogen genomicswhole genome sequencingimplementation science researchinfectious diseaseprotocol |
| spellingShingle | Tehzeeb Zulfiqar Angeline S. Ferdinand Angeline S. Ferdinand Danielle M. Cribb James D. H. Ong Brad Astbury Kathryn Glass Son Nghiem Liliana Bulfone Nhung Mai Daisy Wang Susan Trevenar Patiyan Andersson Alireza Zahedi Martyn David Kirk Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol Frontiers in Public Health pathogen genomics whole genome sequencing implementation science research infectious disease protocol |
| title | Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol |
| title_full | Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol |
| title_fullStr | Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol |
| title_full_unstemmed | Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol |
| title_short | Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol |
| title_sort | enhancing public health infectious disease response through the australian pathogen genomics program auspathogen evaluation protocol |
| topic | pathogen genomics whole genome sequencing implementation science research infectious disease protocol |
| url | https://www.frontiersin.org/articles/10.3389/fpubh.2025.1587112/full |
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