Pathogen genomics and One Health: a scoping review of current practices in zoonotic disease research

Abstract

ABSTRACTWhole-genome sequencing has revolutionised the field of infectious disease surveillance, enabling near real-time detection of pathogens and tracking how infections may spread. We performed a scoping review of studies that have applied genomic epidemiology to zoonotic disease transmission across One Health domains (human, animal, and environment). We identified 114 records published between 2005 and 2022 which reported original multi-domain genomic data of zoonotic pathogens integrated into phylogenetic models. Most studies investigated bacterial pathogens, highlighting key knowledge gaps for other zoonotic agents, particularly arboviruses. Sampling and sequencing efforts vastly varied across domains: the median number and range of pathogen genomes analysed were highest for humans (23; 1-29,586) and lowest for the environment domain (13; 1-956). Infectious disease genomics was leveraged to track zoonotic disease outbreaks and cross-domain transmission, to enhance pathogen surveillance, and to disentangle evolutionary dynamics driving lineage diversification and virulence. Our study informs effective study design for future genomic applications to multi-domain and cross-species transmission of zoonoses, with the potential to identify key infection sources and inform interventions for local and global health security.