A one health approach for enhancing the integration of Salmonella enterica surveillance in Colombia

Foodborne diseases represent a link between environmental, animal, and human health interfaces from the One Health perspective. Whole genome sequencing (WGS) is becoming the gold standard in foodborne surveillance, worldwide. WGS than provides precision data from pathogens allows laboratories to resolve the genetic relations among all sources from One Health perspective, especially during outbreak investigations, getting insights into their transmission routes and pathogenicity. Salmonella spp. is the most prevalent foodborne bacteria in Colombia, in 2020, 268 foodborne outbreaks were reported to National health institute (INS) and 3079 invasive and faecal salmonellosis samples from 81% of the Colombian geographical regions. Several studies in different food sources exhibited an increase of contamination with Salmonella , a public health concern due to the steady development of antimicrobial resistance associated to specific serovars. However, integration of Salmonella spp . data including food-chain supply and clinical interfaces is very scarce in Colombia. This study carried out a national comparison of Salmonella isolates collected from food-chain supply and clinical sources. Using an epidemiological and phenotypic approach, we demonstrated the higher resolution of WGS compared with PFGE, routinely used in Salmonella surveillance in Colombia. For example, the resolution of PFGE allowed the description of two main clusters of food Salmonella Enteritidis isolates which were expanded to eight clades by using WGS. Virulence factors and antimicrobial determinant genes observed in the foodborne clades should be considered a public health concern in Colombia. WGS is a technology that provides precise and valid evidence for the establishment of dissemination routes of foodborne high-risk Salmonella clades, but it requires an integrative and continued collaboration between the stakeholders across the One Health interfaces to promote and support integrated real-time actions in public health. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was funded by the National Institute for Health Research (NIHR) (award reference 16\_136\_111) using UK aid from the UK Government to support global health research. Further funding was provided by Li Ka Shing Foundation (DMA). The project was part of the 10,000 Salmonella Genomes consortium, supported by a Global Challenges Research Fund (GCRF) data & resources grant BBS/OS/GC/000009D and the BBSRC Core Capability Grant to the Earlham Institute BB/CCG1720/1 and Core Strategic Programme Grant BBS/E/T/000PR9817. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The ethics and methodologies committee for research (CETIN/CEIN) of National Health Institute of Colombia waived ethical approval for this study and the approval registry was under the act 3 - 2017 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 Availability of sequence data. The raw sequencing data generated from this study were deposited at the EMBL European Nucleotide Archive (ENA) repository under the project accession numbers PRJEB35182 and PRJEB47910. * (Amp) : Ampicillin (C) : Chloramphenicol (Amc) : Amoxicillin-clavulanic acid (Te) : Tetracycline (Str) : Streptomycin (Cip) : Ciprofloxacin (Lvx) : Levofloxacin (Na) : Nalidixic acid (Nit) : Nitrofurantoin (Czo) : Ceftazidime (Ctx) : Cefotaxime (Cro) : Ceftriaxone (Fox) : Cefoxitin (Tzp) : Tazobactam-piperacillin (Col) : Colistin (ICA) : Instituto Colombiano Agropecuario.