{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T02:10:30Z","timestamp":1778811030821,"version":"3.51.4"},"reference-count":24,"publisher":"SAGE Publications","issue":"6","license":[{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Foodborne Pathogens and Disease"],"published-print":{"date-parts":[[2023,6]]},"abstract":"<jats:p>\n                    Defining investigation-worthy genomic clusters among strains of\n                    <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                    Enteritidis is challenging because of their highly clonal nature. We investigated a cluster identified by core genome multilocus sequence typing (cgMLST) consisting of 265 isolates with isolation dates spanning two and a half years. This cluster experienced chaining, growing to a range of 14 alleles. The volume of isolates and broad allele range of this cluster made it difficult to ascertain whether it represented a common-source outbreak. We explored laboratory-based methods to subdivide and refine this cluster. These methods included using cgMLST with a narrower allele range, whole genome multilocus sequence typing (wgMLST) and high-quality single-nucleotide polymorphism (hqSNP) analysis. At each analysis level, epidemiologists retroactively reviewed exposures, geography, and temporality for potential commonalities. Lowering the threshold to 0 alleles using cgMLST proved an effective method to refine this analysis, resulting in this large cluster being subdivided into 34 smaller clusters. Additional analysis by wgMLST and hqSNP provided enhanced cluster resolution, with the majority of clusters being further refined. These analysis methods combined with more stringent allele thresholds and layering of epidemiologic data proved useful in helping to subdivide this large cluster into actionable subclusters.\n                  <\/jats:p>","DOI":"10.1089\/fpd.2022.0068","type":"journal-article","created":{"date-parts":[[2023,6,19]],"date-time":"2023-06-19T15:23:30Z","timestamp":1687188210000},"page":"230-236","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":13,"title":["Challenges Associated with Investigating\n                    <i>Salmonella<\/i>\n                    Enteritidis with Low Genomic Diversity in New York State: The Impact of Adjusting Analytical Methods and Correlation with Epidemiological Data"],"prefix":"10.1177","volume":"20","author":[{"given":"Deborah J.","family":"Baker","sequence":"first","affiliation":[{"name":"New York State Department of Health, Wadsworth Center, Albany, New York, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy","family":"Robbins","sequence":"additional","affiliation":[{"name":"New York State Department of Health, Bureau of Communicable Disease Control, Albany, New York, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer","family":"Newman","sequence":"additional","affiliation":[{"name":"New York State Department of Health, Bureau of Communicable Disease Control, Albany, New York, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Madhu","family":"Anand","sequence":"additional","affiliation":[{"name":"New York State Department of Health, Bureau of Communicable Disease Control, Albany, New York, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1769-0215","authenticated-orcid":false,"given":"William J.","family":"Wolfgang","sequence":"additional","affiliation":[{"name":"New York State Department of Health, Wadsworth Center, Albany, New York, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damaris V.","family":"Mendez-Vallellanes","sequence":"additional","affiliation":[{"name":"New York State Department of Health, Wadsworth Center, Albany, New York, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samantha E.","family":"Wirth","sequence":"additional","affiliation":[{"name":"New York State Department of Health, Wadsworth Center, Albany, New York, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7122-0404","authenticated-orcid":false,"given":"Lisa A.","family":"Mingle","sequence":"additional","affiliation":[{"name":"New York State Department of Health, Wadsworth Center, Albany, New York, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2023,6,15]]},"reference":[{"key":"e_1_3_6_2_1","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2019.2650"},{"key":"e_1_3_6_3_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.20"},{"key":"e_1_3_6_4_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02332-14"},{"key":"e_1_3_6_5_1","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2020.2856"},{"issue":"2","key":"e_1_3_6_6_1","first-page":"1","article-title":"Surveillance for foodborne disease outbreaks\u2014United States, 1998\u20132008","volume":"62","author":"Gould LH","year":"2013","unstructured":"Gould LH, , Walsh KA, , Vieira AR, et al. Surveillance for foodborne disease outbreaks\u2014United States, 1998\u20132008. 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Available from: https:\/\/www.wadsworth.org\/sites\/default\/files\/WebDoc\/CDRG%20NYState%202020_101920%202.pdf [Last accessed: December 30 2022]."},{"key":"e_1_3_6_24_1","unstructured":"Oregon Health Authority Binomial Probability Worksheet. 2013. Available from: https:\/\/www.oregon.gov\/oha\/ph\/diseasesconditions\/communicabledisease\/outbreaks\/gastroenteritis\/pages\/outbreak-investigation-tools.aspx#binomial [Last accessed: December 30 2022]."},{"key":"e_1_3_6_25_1","unstructured":"Centers for Disease Control and Prevention FoodNet Fast. 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