Enhancing Public Health Infectious Disease Response Through the Australian Pathogen Genomics Program (AusPathoGen): Evaluation Protocol

Angeline S Ferdinand^1,2*Tehzeeb Zulfiqar³Danielle M Cribb³Ong, James¹Kathryn Glass³Son Nghiem³Liliana Bulfone³Nhung Mai³Daisy Wang³Susan Trevenar³Patiyan Andersson²Alireza Zahedi⁴Martyn David Kirk³

• ¹Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, New South Wales, Australia
• ²Centre for Pathogen Genomics, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Australia
• ³National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
• ⁴Public and Environmental Health, Pathology Queensland, Queensland Health, Brisbane, Australia

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, while qualitative data will provide insights into associated ethical and social considerations.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.