{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:50:32Z","timestamp":1789692632879,"version":"4.0.1"},"reference-count":34,"publisher":"Cambridge University Press (CUP)","license":[{"start":{"date-parts":[[2023,10,25]],"date-time":"2023-10-25T00:00:00Z","timestamp":1698192000000},"content-version":"unspecified","delay-in-days":297,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["643676"],"award-info":[{"award-number":["643676"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cambridge.org"],"crossmark-restriction":true},"short-container-title":["Epidemiol. Infect."],"published-print":{"date-parts":[[2023]]},"abstract":"<jats:title>Abstract<\/jats:title>\n\t  <jats:p>SNP addresses are a pathogen typing method based on whole-genome sequences (WGSs), assigning groups at seven different levels of genetic similarity. Public health surveillance uses it for several gastro-intestinal infections; this work trialled its use in veterinary surveillance for salmonella outbreak detection. Comparisons were made between temporal and spatio-temporal cluster detection models that either defined cases by their SNP address or by phage type, using historical data sets. Clusters of SNP incidents were effectively detected by both methods, but spatio-temporal models consistently detected these clusters earlier than the corresponding temporal models. Unlike phage type, SNP addresses appeared spatially and temporally limited, which facilitated the differentiation of novel, stable, or expanding clusters in spatio-temporal models. Furthermore, these models flagged spatio-temporal clusters containing only two to three cases at first detection, compared with a median of seven cases in phage-type models. The large number of SNP addresses will require automated methods to implement these detection models routinely. Further work is required to explore how temporal changes and different host species may impact the sensitivity and specificity of cluster detection. In conclusion, given validation with more sequencing data, SNP addresses are likely to be a valuable addition to early warning systems in veterinary surveillance.<\/jats:p>","DOI":"10.1017\/s0950268823001723","type":"journal-article","created":{"date-parts":[[2023,10,25]],"date-time":"2023-10-25T03:58:35Z","timestamp":1698206315000},"update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":4,"title":["Using SNP addresses for <i>Salmonella Typhimurium<\/i> DT104 in routine veterinary outbreak detection"],"prefix":"10.1017","volume":"151","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3917-4660","authenticated-orcid":false,"given":"J. M.","family":"Bettridge","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. 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(ISBN 1 8995 1534 8)."},{"key":"S0950268823001723_r34","doi-asserted-by":"publisher","DOI":"10.3402\/iee.v6.31782"},{"key":"S0950268823001723_r4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1008850"},{"key":"S0950268823001723_r6","doi-asserted-by":"publisher","DOI":"10.3201\/eid1106.041017"},{"key":"S0950268823001723_r3","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.70.5.2249-2255.2002"},{"key":"S0950268823001723_r15","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2019.24.4.1800346"},{"key":"S0950268823001723_r33","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12779"},{"key":"S0950268823001723_r21","doi-asserted-by":"publisher","DOI":"10.1016\/j.fm.2017.02.012"},{"key":"S0950268823001723_r9","doi-asserted-by":"publisher","DOI":"10.3201\/eid2204.150531"},{"key":"S0950268823001723_r22","unstructured":"[22] Dallman, T (2018). SnapperDB. UKHSA. 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Published by Cambridge University Press","name":"copyright","label":"Copyright","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives licence (http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0), which permits non-commercial re-use, distribution, and reproduction in any medium, provided that no alterations are made and the original article is properly cited. The written permission of Cambridge University Press must be obtained prior to any commercial use and\/or adaptation of the article.","name":"license","label":"License","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}],"article-number":"e187"}}