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

Whole-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. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement SC, FB, ZIT, and CJS were sponsored by the Defense Threat Reduction Agency, United States Department of the Defense (HDTRA12110028). The content of the information does not necessarily reflect the position or the policy of the federal government, and no official endorsement should be inferred. CLF was supported by a Natural Environment Research Council Independent Research Fellowship (NE/V01430/1). JR was supported by the UK Research and Innovation Global Challenges Research Fund One Health Poultry Hub (BB/S011269/1). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes