James Ong ¹ Tehzeeb Zulfiqar ² Kathryn Glass ² Martyn D. Kirk ² Brad Astbury ³ Angeline Ferdinand ^1,3*

• ¹ Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, New South Wales, Australia
• ² National Centre for Epidemiology and Population Health, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
• ³ Centre for Health Policy, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Carlton, Victoria, Australia

INTRODUCTION: Pathogen genomics, where whole genome sequencing technologies are used to produce complete genomic sequences of pathogens, is being increasingly used for infectious disease surveillance and outbreak response. Although proof-of-concept studies have highlighted the viability of using pathogen genomics in public health, few studies have investigated how end-users utilize pathogen genomics in public health. We describe a protocol for a study that aims to identify key factors that influence the use of pathogen genomics to inform public health responses against infectious diseases in Australia and New Zealand. METHODS: We will use qualitative comparative analysis (QCA), a case-oriented methodology that systematically compares and analyses multiple cases (or 'units of analysis'), to identify multiple pathways leading to the use of pathogen genomics results in public health actions. As part of the process, we will develop a rubric to identify and define the use of pathogen genomics and individual factors affecting this process. Simultaneously, we will identify cases where pathogen genomics has been used in public health across Australia and New Zealand. Data for these cases will be collected from document review of publicly available and confidential documents and semi-structured interviews with technicians and end-users and summarized in a case report. These case reports will form the basis for scoring each case on the extent of the use of pathogen genomics data and the presence or absence of specific factors such as the ease of extracting essential information from pathogen genomics reports and perceptions towards pathogen genomics. Using the scores, cases will be analyzed using QCA techniques to identify pathways leading to the use of pathogen genomics data. These pathways will be interpreted alongside the cases to provide rich explanations of the use of pathogen genomics in public health. DISCUSSION: This study will improve our understanding of the key factors that facilitate or hinder the use of pathogen genomics to inform public health authorities and end-users. These findings may inform ways to enhance the use of pathogen genomics data in public health.