Evidence map›Paper›PMID 40697838›Full record

ArticleFrontiers in public health2025

Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol.

Tehzeeb Zulfiqar, Angeline S Ferdinand, Danielle M Cribb, James D H Ong, Brad Astbury, Kathryn Glass, Son Nghiem, Liliana Bulfone, Nhung Mai, Daisy Wang and 4 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in public health, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Tehzeeb Zulfiqar *Department of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
Angeline S Ferdinand *Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia.
Danielle M CribbDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
James D H OngMicrobiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia.
Brad AstburyCentre for Health Policy, University of Melbourne, Melbourne, VIC, Australia.
Kathryn GlassDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
Son NghiemDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
Liliana BulfoneDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
Nhung MaiDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
Daisy WangDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
Susan TrevenarDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
Patiyan AnderssonMicrobiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia.
Alireza ZahediPublic and Environmental Health, Pathology Queensland, Queensland Health, Brisbane, QLD, Australia.
Martyn David KirkDepartment of Applied Epidemiology, National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Introduction: Pathogen 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. Methods: A 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. Discussion: This 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.

Indexed as

Communicable DiseasesGenomicsPublic HealthWhole Genome SequencingAustraliaDisease OutbreaksHumansimplementation science researchinfectious diseasepathogen genomicsprotocolwhole genome sequencing

Identifiers

PMID40697838
PMCPMC12279755

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.