{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T03:51:47Z","timestamp":1789012307188,"version":"build-2803163510"},"reference-count":34,"publisher":"SAGE Publications","issue":"8","license":[{"start":{"date-parts":[[2021,8,1]],"date-time":"2021-08-01T00:00:00Z","timestamp":1627776000000},"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":[[2021,8]]},"abstract":"<jats:p>\n                    As an important foodborne pathogen,\n                    <jats:italic toggle=\"yes\">Salmonella enterica<\/jats:italic>\n                    serotype Enteritidis is recognized as one of the most common causes of human salmonellosis globally. Outbreak detection for this highly homogenous serotype, however, has remained challenging. Rapid advances in sequencing technologies have presented whole-genome sequencing (WGS) as a significant advancement for source tracing and molecular typing of foodborne pathogens. A retrospective analysis was conducted using\n                    <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                    Enteritidis isolates (\n                    <jats:italic toggle=\"yes\">n<\/jats:italic>\n                    \u2009=\u200965) from 11 epidemiologically confirmed outbreaks and a collection of contemporaneous sporadic isolates (\n                    <jats:italic toggle=\"yes\">n<\/jats:italic>\n                    \u2009=\u2009258) during 2007\u20132017 to evaluate the performance of WGS in delineating outbreak-associated isolates. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis revealed well-supported clades in concordance with epidemiological evidence and pairwise distances of \u22643 SNPs for all outbreaks. WGS-based framework of outbreak detection was thus proposed and applied prospectively to investigate isolates (\n                    <jats:italic toggle=\"yes\">n<\/jats:italic>\n                    \u2009=\u200966) from nine outbreaks during 2018\u20132019. We further demonstrated the superior discriminatory power and accuracy of WGS to resolve and delineate outbreaks for pragmatic food source tracing. The proposed integrated WGS framework is the first in China for\n                    <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                    Enteritidis and has the potential to serve as a paradigm for outbreak detection and source tracing of\n                    <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                    throughout the stages of food production, as well as expanded to other foodborne pathogens.\n                  <\/jats:p>","DOI":"10.1089\/fpd.2020.2856","type":"journal-article","created":{"date-parts":[[2021,1,15]],"date-time":"2021-01-15T17:13:42Z","timestamp":1610730822000},"page":"582-589","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":19,"title":["Integrated Whole-Genome Sequencing Infrastructure for Outbreak Detection and Source Tracing of\n                    <i>Salmonella enterica<\/i>\n                    Serotype Enteritidis"],"prefix":"10.1177","volume":"18","author":[{"given":"Yinhua","family":"Deng","sequence":"first","affiliation":[{"name":"Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Jiang","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick S.L.","family":"Kwan","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Yang","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."},{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiongcheng","family":"Chen","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiman","family":"Lin","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaqun","family":"Qiu","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinghui","family":"Li","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaolu","family":"Shi","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liqiang","family":"Li","sequence":"additional","affiliation":[{"name":"China National GeneBank, BGI-Shenzhen, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujun","family":"Cui","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qun","family":"Sun","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinghua","family":"Hu","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Disease Control and Prevention, Shenzhen, China."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2021,8,12]]},"reference":[{"key":"e_1_3_5_2_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007261"},{"key":"e_1_3_5_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2017.11.002"},{"key":"e_1_3_5_4_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00362"},{"key":"e_1_3_5_5_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01595-06"},{"key":"e_1_3_5_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"e_1_3_5_7_1","article-title":"Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network","volume":"2","author":"Dallman T","year":"2016","unstructured":"Dallman T, , Inns T, , Jombart T, et al. Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network. 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