{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T23:37:21Z","timestamp":1775691441020,"version":"3.50.1"},"reference-count":64,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T00:00:00Z","timestamp":1745798400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Foodborne outbreaks affecting millions of people worldwide are a significant and growing global health threat, exacerbated by the emergence of new and increasingly virulent foodborne pathogens. Traditional methods of detecting these outbreaks, including culture-based techniques, serotyping and molecular methods such as real-time PCR, are still widely used. However, these approaches often lack the precision and resolution required to definitively trace the source of an outbreak and distinguish between closely related strains of pathogens. Whole genome sequencing (WGS) has emerged as a revolutionary tool in outbreak investigations, providing high-resolution, comprehensive genetic data that allows accurate species identification and strain differentiation. WGS also facilitates the detection of virulence and antimicrobial resistance (AMR) genes, providing critical insight into the potential pathogenicity, treatment\/control options and risks of spreading foodborne pathogens. This capability enhances outbreak surveillance, source tracing and risk assessment, making WGS an increasingly integrated component of public health surveillance systems. Despite its advantages, the widespread implementation of WGS faces several pressing challenges, including high sequencing costs, the need for specialized bioinformatics expertise, limited computational infrastructure in resource-constrained settings, and the standardization of data-sharing frameworks across regulatory and public health agencies. Addressing these barriers is crucial to maximizing the impact of WGS on foodborne disease surveillance. Even so, WGS is emerging as a vital tool in food safety and public health, and its potential to become the gold standard in outbreak detection has been recognized by public health authorities in the USA, the European Union, Australia and China, for example. This review highlights the role of WGS in foodborne outbreak investigations, its implementation challenges, and its impact on public health surveillance.<\/jats:p>","DOI":"10.3389\/fcimb.2025.1593219","type":"journal-article","created":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T05:33:46Z","timestamp":1745818426000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":18,"title":["Advances in whole genome sequencing for foodborne pathogens: implications for clinical infectious disease surveillance and public health"],"prefix":"10.3389","volume":"15","author":[{"given":"Em\u00edlio","family":"Gomes","sequence":"first","affiliation":[]},{"given":"Daniela","family":"Ara\u00fajo","sequence":"additional","affiliation":[]},{"given":"Teresa","family":"Nogueira","sequence":"additional","affiliation":[]},{"given":"Ricardo","family":"Oliveira","sequence":"additional","affiliation":[]},{"given":"S\u00f3nia","family":"Silva","sequence":"additional","affiliation":[]},{"given":"Lorena V. N.","family":"Oliveira","sequence":"additional","affiliation":[]},{"given":"Nuno F.","family":"Azevedo","sequence":"additional","affiliation":[]},{"given":"Carina","family":"Almeida","sequence":"additional","affiliation":[]},{"given":"Joana","family":"Castro","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2025,4,28]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1975","DOI":"10.1128\/JCM.00081-16\/ASSET\/36ED1836-0AD4-433A-B18D-405B73EB730A\/ASSETS\/GRAPHIC\/ZJM9990949700003.JPEG","article-title":"Practical value of food pathogen traceability through building a whole-genome sequencing network and database","volume":"54","author":"Allard","year":"2016","journal-title":"J. Clin. Microbiol"},{"key":"B2","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/J.MEEGID.2019.04.026","article-title":"Whole genome sequencing uses for foodborne contamination and compliance: Discovery of an emerging contamination event in an ice cream facility using whole genome sequencing","volume":"73","author":"Allard","year":"2019","journal-title":"Infection Genet. Evol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1089\/FPD.2018.2599","article-title":"Investing in food safety for developing countries: opportunities and challenges in applying whole-genome sequencing for food safety management","volume":"16","author":"Apruzzese","year":"2019","journal-title":"Foodborne Pathog Dis."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1016\/J.FOODCONT.2021.108148","article-title":"Guidance document on the use of whole genome sequencing (WGS) for source tracking from a food industry perspective","volume":"130","author":"Baert","year":"2021","journal-title":"Food Control"},{"key":"B5","doi-asserted-by":"publisher","first-page":"448","DOI":"10.4315\/JFP-21-301","article-title":"Metagenomics approaches for improving food safety: A review","volume":"85","author":"Billington","year":"2022","journal-title":"J. Food Prot"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PONE.0258262","article-title":"An economic evaluation of the Whole Genome Sequencing source tracking program in the U.S","volume":"16","author":"Brown","year":"2021","journal-title":"PloS One"},{"key":"B7","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1089\/FPD.2019.2662\/ASSET\/IMAGES\/LARGE\/FIGURE2.JPEG","article-title":"Use of whole-genome sequencing for food safety and public health in the United States","volume":"16","author":"Brown","year":"2019","journal-title":"Foodborne Pathog Dis."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.3389\/FPUBH.2019.00317\/BIBTEX","article-title":"The transformation of reference microbiology methods and surveillance for salmonella with the use of whole genome sequencing in England and wales","volume":"7","author":"Chattaway","year":"2019","journal-title":"Front. Public Health"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1016\/J.JAFR.2020.100045","article-title":"Quantitative microbial risk assessment for Salmonella: Inclusion of whole genome sequencing and genomic epidemiological studies, and advances in the bioinformatics pipeline","volume":"2","author":"Chen","year":"2020","journal-title":"J. Agric. Food Res."},{"key":"B10","doi-asserted-by":"publisher","first-page":"724","DOI":"10.1373\/CLINCHEM.2013.209213","article-title":"Whole genome sequencing as a diagnostic test: challenges and opportunities","volume":"60","author":"Chrystoja","year":"2014","journal-title":"Clin. Chem."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2019.01107","article-title":"Integrating whole-genome sequencing data into quantitative risk assessment of foodborne antimicrobial resistance: A review of opportunities and challenges","volume":"10","author":"Collineau","year":"2019","journal-title":"Front. Microbiol"},{"key":"B12","volume-title":"Guidelines for reporting Whole Genome Sequencing-based typing data through the EFSA One Health WGS System","author":"Costa","year":"2022"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1016\/J.FOODCONT.2021.108448","article-title":"Machine learning techniques and research framework in foodborne disease surveillance system","volume":"131","author":"Du","year":"2022","journal-title":"Food Control"},{"key":"B14","doi-asserted-by":"publisher","first-page":"2422","DOI":"10.12688\/f1000research.9656.2","article-title":"Identifying ELIXIR core data resources","volume":"5","author":"Durinx","year":"2017","journal-title":"F1000Research"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.2903\/sp.efsa.2019.EN-1337","article-title":"EFSA and ECDC technical report on the collection and analysis of whole genome sequencing data from food-bornepathogens and other relevant microorganisms isolated from human, animal, food, feed and food\/feedenvironmental samples in the joint ECDC\u2013EFSA molecular typing databas","volume":"92","author":"Van Walle","year":"2019","journal-title":"EFSA supporting publication2019:EN-1337"},{"key":"B16","doi-asserted-by":"publisher","first-page":"4281","DOI":"10.1007\/S00253-020-10542-X","article-title":"Methods for detection of viable foodborne pathogens: current state-of-art and future prospects","volume":"104","author":"Foddai","year":"2020","journal-title":"Appl. Microbiol Biotechnol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/J.COFS.2016.04.004","article-title":"Significance of whole genome sequencing for surveillance, source attribution and microbial risk assessment of foodborne pathogens","volume":"8","author":"Franz","year":"2016","journal-title":"Curr. Opin. Food Sci."},{"key":"B18","doi-asserted-by":"publisher","first-page":"2877","DOI":"10.1093\/BIOINFORMATICS\/BTV271","article-title":"kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome","volume":"31","author":"Gardner","year":"2015","journal-title":"Bioinformatics"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-43751-4_1","article-title":"Role of whole genome sequencing in the public health surveillance of foodborne pathogens","author":"Gerner-Smidt","year":"2017","journal-title":"Appl. Genomics Foodborne Pathog."},{"key":"B20","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1128\/CMR.00075-13","article-title":"Whole-genome sequencing in outbreak analysis","volume":"28","author":"Gilchrist","year":"2015","journal-title":"Clin. Microbiol Rev."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2017.00777","article-title":"The importance of bacterial culture to food microbiology in the age of genomics","volume":"8","author":"Gill","year":"2017","journal-title":"Front. Microbiol"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3390\/IJERPH120910490","article-title":"Food safety in low and middle income countries","volume":"12","author":"Grace","year":"2015","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1016\/J.MICPATH.2024.107076","article-title":"Whole genome sequencing (WGS) analysis of antimicrobial resistance (AMR) milk and dairy-derived pathogens from Anand, Gujarat, India","volume":"197","author":"Hati","year":"2024","journal-title":"Microb Pathog"},{"key":"B24","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1038\/nrg2795","article-title":"Next-generation genomics: an integrative approach","volume":"11","author":"Hawkins","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1016\/J.WORLDDEV.2019.104611","article-title":"Food safety in low and middle-income countries: The evidence through an economic lens","volume":"123","author":"Hoffmann","year":"2019","journal-title":"World Dev."},{"key":"B26","doi-asserted-by":"publisher","first-page":"3565","DOI":"10.1128\/JCM.01066-15\/SUPPL_FILE\/ZJM999094590SO1.PDF","article-title":"Utility of whole-genome sequencing of Escherichia coli o157 for outbreak detection and epidemiological surveillance","volume":"53","author":"Holmes","year":"2015","journal-title":"J. Clin. Microbiol"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.28449.1","article-title":"Recommendations for the FAIRification of genomic track metadata","volume":"10","author":"Hovig","year":"2021","journal-title":"F1000Research"},{"key":"B28","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/J.TVJL.2018.12.009","article-title":"Foodborne diseases do not respect borders: Zoonotic pathogens and antimicrobial resistant bacteria in food products of animal origin illegally imported into the European Union","volume":"244","author":"Jansen","year":"2019","journal-title":"Veterinary J."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001921","article-title":"World health organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal, and viral diseases 2010: A data synthesis","volume":"12","author":"Kirk","year":"2015","journal-title":"PloS Med."},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.2903\/J.EFSA.2019.5898","article-title":"Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms","volume":"17","author":"Koutsoumanis","year":"2019","journal-title":"EFSA J."},{"key":"B31","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/B978-0-08-100596-5.22697-8","article-title":"Whole genome sequencing: the impact on foodborne outbreak investigations","author":"Kovac","year":"2021","journal-title":"Compr. Foodomics"},{"key":"B32","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1111\/1469-0691.12430","article-title":"Vaccine-preventable diseases: the role of the European Centre for Disease Prevention and Control","volume":"20","author":"Kramarz","year":"2014","journal-title":"Clin. Microbiol. Infection"},{"key":"B33","doi-asserted-by":"publisher","first-page":"22S","DOI":"10.1177\/0033354919881650","article-title":"PulseNet and the changing paradigm of laboratory-based surveillance for foodborne diseases","volume":"134","author":"Kubota","year":"2019","journal-title":"Public Health Rep."},{"key":"B34","doi-asserted-by":"publisher","first-page":"100003","DOI":"10.1016\/J.JFP.2022.10.002","article-title":"Wholegenome sequencing as the gold standard approach for control of Listeria monocytogenes in the food chain","volume":"86","author":"Lakicevic","year":"2023","journal-title":"J. Food Prot"},{"key":"B35","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1089\/FPD.2020.2908","article-title":"Application of whole-genome sequencing in the national molecular tracing network for foodborne disease surveillance in China","volume":"18","author":"Li","year":"2021","journal-title":"Foodborne Pathogens and Disease"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1016\/J.CCA.2023.117624","article-title":"Third-generation sequencing for genetic disease","volume":"551","author":"Ling","year":"2023","journal-title":"Clinica Chimica Acta"},{"key":"B37","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1016\/J.JPROT.2016.04.029","article-title":"Foodborne pathogens and their toxins","volume":"147","author":"Martinovi\u0107","year":"2016","journal-title":"J. Proteomics"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1099\/MGEN.0.001074\/CITE\/REFWORKS","article-title":"European Union Reference Laboratories support the National food, feed and veterinary Reference Laboratories with rolling out whole genome sequencing in Europe","volume":"9","author":"Michelacci","year":"2023","journal-title":"Microb Genom"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1089\/FPD.2024.0041","article-title":"Transition to Whole Genome Sequencing Surveillance: The Impact on National Outbreak Detection and Response for Listeria monocytogenes, Salmonella, Shiga Toxin\u2013Producing Escherichia coli, and Shigella Clusters in Canada 2015\u20132021","volume":"21","author":"Morton","year":"2024","journal-title":"Foodborne Pathogens and Disease"},{"key":"B40","article-title":"Biosensors: A fast-growing technology for pathogen detection in agriculture and food sector","volume-title":"Biosensing Technologies for the Detection of Pathogens - A Prospective Way for Rapid Analysis","author":"Oluwaseun","year":"2018"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.01482","article-title":"Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations","volume":"9","author":"Pightling","year":"2018","journal-title":"Front. Microbiol"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1099\/MGEN.0.000947\/CITE\/REFWORKS","article-title":"A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens","volume":"9","author":"Price","year":"2023","journal-title":"Microb Genom"},{"key":"B43","doi-asserted-by":"publisher","first-page":"327","DOI":"10.4103\/0971-5916.198677","article-title":"A review on detection methods used for foodborne pathogens","volume":"144","author":"Priyanka","year":"2016","journal-title":"Indian J. Med. Res."},{"key":"B44","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1146\/ANNUREV-FOOD-060721-013815\/CITE\/REFWORKS","article-title":"How can AI help improve food safety","volume":"14","author":"Qian","year":"2023","journal-title":"Annu. Rev. Food Sci. Technol."},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2022.1054782\/BIBTEX","article-title":"Advances, applications, and limitations of portable and rapid detection technologies for routinely encountered foodborne pathogens","volume":"13","author":"Quintela","year":"2022","journal-title":"Front. Microbiol"},{"key":"B46","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/J.IJFOODMICRO.2017.11.007","article-title":"Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment","volume":"287","author":"Rantsiou","year":"2018","journal-title":"Int. J. Food Microbiol"},{"key":"B47","first-page":"162","article-title":"Genome sequencing and bioinformatics","volume-title":"Frontiers in Molecular Genetics and Genomics","author":"Samdarshi","year":"2024"},{"key":"B48","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1007\/S10311-020-01072-Z","article-title":"Methods of detection of food-borne pathogens: a review","volume":"19","author":"Saravanan","year":"2020","journal-title":"Environ. Chem. Lett."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.3390\/BIOM14050568","article-title":"The third-generation sequencing challenge: novel insights for the omic sciences","volume":"14","author":"Scarano","year":"2024","journal-title":"Biomolecules"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1016\/J.FOODCONT.2024.110733","article-title":"An investigation of an outbreak of Salmonella Typhimurium infections linked to cantaloupe \u2013 United State","volume":"166","author":"Seelman Federman","year":"2024","journal-title":"Food Control"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1128\/MRA.00006-24","article-title":"Whole-genome sequencing of three ciprofloxacin-resistant Salmonella Reading (ST93) strains, an emerging Salmonella serovar in the poultry sector of Pakistan","volume":"13","author":"Siddique","year":"2024","journal-title":"Microbiol Resour Announc"},{"key":"B52","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1080\/0144929X.2023.2196596","article-title":"Improving big data governance in healthcare institutions: user experience research for honest broker based application to access healthcare big data","volume":"43","author":"Singh","year":"2024","journal-title":"Behav. Inf. Technol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"755","DOI":"10.4315\/JFP-21-437","article-title":"Use of whole genome sequencing by the federal interagency collaboration for genomics for food and feed safety in the United States","volume":"85","author":"Stevens","year":"2022","journal-title":"J. Food Prot"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-014-0104-4","article-title":"Stopping outbreaks with real-time genomic epidemiology","volume":"6","author":"Tang","year":"2014","journal-title":"Genome Med."},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.1002\/VMS3.1585","article-title":"Review: Impact of food safety on global trade","volume":"10","author":"Tibebu","year":"2024","journal-title":"Vet Med. Sci."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01816-18\/FORMAT\/EPUB","article-title":"Phylogenomic pipeline validation for foodborne pathogen disease surveillance","volume":"57","author":"Timme","year":"2019","journal-title":"J. Clin. Microbiol"},{"key":"B57","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1089\/FPD.2019.2637","article-title":"An overview of pulseNet USA databases","volume":"16","author":"Tolar","year":"2019","journal-title":"Foodborne Pathog Dis."},{"key":"B58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S42522-020-0010-1","article-title":"Typing methods based on whole genome sequencing data","volume":"2","author":"Uelze","year":"2020","journal-title":"One Health Outlook"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1136\/BMJGH-2019-002244","article-title":"Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap","volume":"5","author":"Vegyari","year":"2020","journal-title":"BMJ Glob Health"},{"key":"B60","doi-asserted-by":"publisher","first-page":"1337E","DOI":"10.2903\/SP.EFSA.2019.EN-1337","article-title":"EFSA and ECDC technical report on the collection and analysis of whole genome sequencing data from food-borne pathogens and other relevant microorganisms isolated from human, animal, food, feed and food\/feed environmental samples in the joint ECDC-EFSA molecular typing database","volume":"16","author":"Walle","year":"2019","journal-title":"EFSA Supporting Publications"},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanmic.2024.100969","article-title":"Implementing a national programme of pathogen genomics for public health: the Australian Pathogen Genomics Program (AusPathoGen)","volume":"6","author":"Webb","year":"2024","journal-title":"Lancet Microbe"},{"key":"B62","unstructured":"Estimating the burden of foodborne diseases\n          \n          \n          \n          2025"},{"key":"B63","volume-title":"Whole Genome Sequencing for Foodborne Disease Surveillance: Landscape Paper.","year":"2018"},{"key":"B64","doi-asserted-by":"publisher","first-page":"163","DOI":"10.21037\/TP.2020.03.06","article-title":"The third generation sequencing: the advanced approach to genetic diseases","volume":"9","author":"Xiao","year":"2020","journal-title":"Transl. Pediatr."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1593219\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T05:33:50Z","timestamp":1745818430000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1593219\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,28]]},"references-count":64,"alternative-id":["10.3389\/fcimb.2025.1593219"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2025.1593219","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,28]]},"article-number":"1593219"}}