{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:35:06Z","timestamp":1772156106436,"version":"3.50.1"},"reference-count":52,"publisher":"The Royal Society","issue":"2019","license":[{"start":{"date-parts":[[2024,3,20]],"date-time":"2024-03-20T00:00:00Z","timestamp":1710892800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,3,20]],"date-time":"2024-03-20T00:00:00Z","timestamp":1710892800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Laboratory Directed Research and Development program of Los Alamos National Laboratory","award":["20200121ER"],"award-info":[{"award-number":["20200121ER"]}]},{"name":"Laboratory Directed Research and Development program of Los Alamos National Laboratory","award":["20210529C"],"award-info":[{"award-number":["20210529C"]}]},{"DOI":"10.13039\/100006108","name":"NIH NCATS","doi-asserted-by":"crossref","award":["KL2TR001448"],"award-info":[{"award-number":["KL2TR001448"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["royalsocietypublishing.org"],"crossmark-restriction":true},"short-container-title":["Proc. R. Soc. B."],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:p>Cholera continues to be a global health threat. Understanding how cholera spreads between locations is fundamental to the rational, evidence-based design of intervention and control efforts. Traditionally, cholera transmission models have used cholera case-count data. More recently, whole-genome sequence data have qualitatively described cholera transmission. Integrating these data streams may provide much more accurate models of cholera spread; however, no systematic analyses have been performed so far to compare traditional case-count models to the phylodynamic models from genomic data for cholera transmission. Here, we use high-fidelity case-count and whole-genome sequencing data from the 1991 to 1998 cholera epidemic in Argentina to directly compare the epidemiological model parameters estimated from these two data sources. We find that phylodynamic methods applied to cholera genomics data provide comparable estimates that are in line with established methods. Our methodology represents a critical step in building a framework for integrating case-count and genomic data sources for cholera epidemiology and other bacterial pathogens.<\/jats:p>","DOI":"10.1098\/rspb.2023.2805","type":"journal-article","created":{"date-parts":[[2024,3,19]],"date-time":"2024-03-19T20:05:55Z","timestamp":1710878755000},"update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Congruity of genomic and epidemiological data in modelling of local cholera outbreaks"],"prefix":"10.1098","volume":"291","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8539-1586","authenticated-orcid":true,"given":"Mateusz","family":"Wilinski","sequence":"first","affiliation":[{"name":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lauren","family":"Castro","sequence":"additional","affiliation":[{"name":"Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey","family":"Keithley","sequence":"additional","affiliation":[{"name":"Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, USA"},{"name":"Department of Computer Science, University of Iowa, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2534-9316","authenticated-orcid":true,"given":"Carrie","family":"Manore","sequence":"additional","affiliation":[{"name":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Josefina","family":"Campos","sequence":"additional","affiliation":[{"name":"UO Centro Nacional de Gen\u00f3mica y Bioinformtica, ANLIS \u2018Dr. Carlos G. 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CDC website. See https:\/\/www.cdc.gov\/cholera\/haiti\/index.html (accessed 4 October 2022)."},{"key":"e_1_3_7_6_2","unstructured":"Cholera situation in Yemen December 2020. See https:\/\/reliefweb.int\/report\/yemen\/cholera-situation-yemen-december-2020 (accessed 4 October 2022)."},{"key":"e_1_3_7_7_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002947"},{"key":"e_1_3_7_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg795"},{"key":"e_1_3_7_9_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1090727"},{"key":"e_1_3_7_10_2","volume-title":"Coalescent theory: an introduction","author":"Wakeley J","year":"2009","unstructured":"Wakeley J. 2009 Coalescent theory: an introduction. Greenwood Village, CO: Roberts & Co. 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