{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T01:08:56Z","timestamp":1792631336020,"version":"4.5.0"},"reference-count":33,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T00:00:00Z","timestamp":1742342400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T00:00:00Z","timestamp":1742342400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2025,3,19]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      In the era of genomic characterization of strains for public health microbiology, whole genome sequencing (WGS)-enabled subtyping of\n                      <jats:italic>Salmonella<\/jats:italic>\n                      provides superior discrimination of strains compared to traditional methods such as serotyping. Nonetheless, serotypes are still very useful; they maintain historical continuity and facilitate clear communication. Genetic determination of serotypes from WGS data is now routine. Genetic determination of rarer serotypes can be problematic due to a lack of sequences for rare antigen types and alleles, a lack of understanding of the genetic basis for some antigens, or some inconsistencies in the White-Kauffmann-Le Minor (WKL) Scheme for\n                      <jats:italic>Salmonella<\/jats:italic>\n                      serotype designation. Here, we present a simplified interpretation of serotypes to address the shortcomings of genetic methods, which will allow the streamlined integration of serotype determination into the WGS workflow. The simplification represents a consensus perspective among major U.S. public health agencies and serves as a WGS-oriented interpretation of the WKL Scheme. We also present SeqSero2S, a bioinformatics tool for WGS-based serotype prediction using the simplified interpretation.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        The utility of\n                        <jats:italic>Salmonella<\/jats:italic>\n                        serotyping has evolved from a primary subtyping method, where the need for strain discrimination justified its complexity, to a supplemental subtyping scheme and nomenclature convention, where clarity and simplicity in communication have become important for its continued use. Compared to phenotypic methods like serotyping, whole genome sequencing (WGS)-based subtyping methods excel in recognizing natural populations, which avoids grouping together strains from different genetic backgrounds or splitting genetically related strains into different groups. This simplified interpretation of serotypes addresses a shortcoming of the original scheme by combining some serotypes that are known to be genetically related. Our simplified interpretation of the White-Kauffmann-Le Minor (WKL) Scheme facilitates a complete and smooth transition of serotyping\u2019s role, especially from the public health perspective that has been shaped by the routine use of WGS.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/aem.02600-24","type":"journal-article","created":{"date-parts":[[2025,2,24]],"date-time":"2025-02-24T09:01:09Z","timestamp":1740387669000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":13,"title":["<i>Salmonella<\/i>\n                    serotypes in the genomic era: simplified\n                    <i>Salmonella<\/i>\n                    serotype interpretation from DNA sequence data"],"prefix":"10.1128","volume":"91","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7251-2529","authenticated-orcid":true,"given":"Xiangyu","family":"Deng","sequence":"first","affiliation":[{"name":"Center for Food Safety, University of Georgia","place":["Griffin, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoting","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Food Safety, University of Georgia","place":["Griffin, USA"]},{"name":"School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3829-8688","authenticated-orcid":true,"given":"Tongzhou","family":"Xu","sequence":"additional","affiliation":[{"name":"Center for Food Safety, University of Georgia","place":["Griffin, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9783-0366","authenticated-orcid":true,"given":"Zhemin","family":"Zhou","sequence":"additional","affiliation":[{"name":"Soochow University Cancer Institute, Soochow University","place":["Suzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle M.","family":"Moore","sequence":"additional","affiliation":[{"name":"Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration","place":["Rockville, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9705-5897","authenticated-orcid":true,"given":"Ruth","family":"Timme","sequence":"additional","affiliation":[{"name":"Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration","place":["College Park, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaohua","family":"Zhao","sequence":"additional","affiliation":[{"name":"Center for Veterinary Medicine, U.S. Food and Drug Administration","place":["Laurel, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte","family":"Lane","sequence":"additional","affiliation":[{"name":"Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blake A.","family":"Dinsmore","sequence":"additional","affiliation":[{"name":"Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois\u2011Xavier","family":"Weill","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9","place":["Paris, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1199-2650","authenticated-orcid":false,"given":"Patricia I.","family":"Fields","sequence":"additional","affiliation":[{"name":"Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.mm6917a1"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.mm7326a1"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.mm7226a1"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1017\/s0022172400034677"},{"key":"e_1_3_4_6_2","unstructured":"CDC. 2013. 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