Describing the outcomes and factors of using pathogen genomic results in public health.

BACKGROUND: Although many countries are incorporating pathogen genomics into their public health systems, previous studies rarely examine their implementation, use and outcomes. This study describes how pathogen genomics is implemented and used in public health to guide surveillance and outbreak responses against infectious disease. METHODS: We examined 11 case studies of pathogen genomics use in surveillance programs and outbreak responses against infectious disease across Australia and New Zealand. Information on each case study was collected via document review and key informant interviews and summarized in case reports. Case reports were then compared to identify similarities and differences in outcomes and factors. RESULTS: Although pathogen genomics served various functions in supporting public health investigations and responses against infectious disease, their impact varied. This ranged from providing information about a clinical case or public health response to informing changes in public health investigations and responses against infectious disease. Timeliness and novelty were two factors that appeared to distinguish the impact of pathogen genomics in public health among case studies. Other factors such as end users' literacy and attitudes were similar across case studies, but may help highlight the need for consistent processes to support implementation of pathogen genomics in public health. CONCLUSION: This study describes how pathogen genomics is being implemented across different pathogens and contexts in public health. These results will inform future research and implementation programs that aim to improve public health pathogen genomics programs. This may lead to enhanced use and outcomes to facilitate more tailored, timely and effective public health responses against infectious disease.