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

Objectives

Whole-genome sequencing has revolutionized the field of infectious disease surveillance, enabling near real-time detection of pathogens and tracking how infections may spread. Our study aimed to characterize genomic applications to cross-domain zoonotic pathogen transmission at the human-animal and/or human-environment interfaces.

Methods

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 multi-domain genomic data of zoonotic pathogens integrated into phylogenetic models.

Results

Most studies investigated bacterial pathogens, highlighting key knowledge gaps for other zoonotic agents, particularly arboviruses. Sampling and sequencing efforts varied greatly across domains: the median number and range of pathogen genomes analyzed were highest for humans (23; 1–29,586) and lowest for the environment domain (13; 1–956). Genomics was used to track zoonotic disease outbreaks and cross-domain transmission, to improve pathogen surveillance, and to disentangle evolutionary dynamics driving lineage diversification and virulence.

Conclusions

Our study highlights current practices and knowledge gaps to guide future study designs and 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.