{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T13:20:11Z","timestamp":1777641611159,"version":"3.51.4"},"reference-count":44,"publisher":"SAGE Publications","issue":"10","license":[{"start":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T00:00:00Z","timestamp":1737417600000},"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":[[2025,10]]},"abstract":"\n In recent years,\n Salmonella<\/jats:italic>\n infection is a major global public health concern, particularly in food safety. This study analyzed the genomes of 102\n Salmonella<\/jats:italic>\n strains isolated between 2016 and 2023 from food, foodborne disease patients, and food poisoning incidents, focusing on their molecular characteristics, antibiotic resistance genes (ARGs), and virulence genes.\n S. enterica<\/jats:italic>\n serovar Enteritidis (37.3%) and\n S. enterica<\/jats:italic>\n serovar Typhimurium (21.6%, including its monophasic variant 1,4,[5],12:i:-) were the main strains among 22 serotypes. Multilocus sequence typing revealed 23 sequence types (STs), with ST11, ST19, and ST34 as the most prevalent. All strains carried at least 24 ARGs. Detection rates for\n aac(6\u2032)-Iy<\/jats:italic>\n ,\n bla<\/jats:italic>\n TEM-1<\/jats:sub>\n , and\n sul2<\/jats:italic>\n ranged from 44.1% to 63.7%, mainly in\n S.<\/jats:italic>\n Enteritidis and\n S.<\/jats:italic>\n Typhimurium. Rates for\n qnrS1<\/jats:italic>\n ,\n sul1<\/jats:italic>\n , and\n aadA<\/jats:italic>\n were 12.8% to 16.7%, while\n mcr-1<\/jats:italic>\n appeared in one ST34\n S.<\/jats:italic>\n Typhimurium strain. All strains contained at least 98 virulence genes. The genes\n pefABCD<\/jats:italic>\n ,\n mig-5<\/jats:italic>\n , and\n spvBCD<\/jats:italic>\n were in 48.0% of strains, while\n rck<\/jats:italic>\n was found in 36.3%, mainly linked to\n S.<\/jats:italic>\n Enteritidis and\n S.<\/jats:italic>\n Typhimurium. The\n tssM<\/jats:italic>\n gene was found in 37.3% of the strains, exclusively in\n S.<\/jats:italic>\n Enteritidis. Core genome single nucleotide polymorphisms (cgSNPs) analysis grouped the strains into nine clusters, with 75.5% belonging to three major groups. Food poisoning event 1 was correlated with cluster 3, while events 2 and 3 were linked to cluster 1. Across events, SNP differences among strains were \u22646. Strains with SNP differences \u226410 were also found in other clusters. This method is promising for tracking sporadic cases and identifying potential foodborne safety incidents.\n Salmonella<\/jats:italic>\n strains in the region exhibit substantial genetic diversity, demonstrating the efficacy of cgSNPs analysis for source tracking. Ongoing surveillance is essential given the prevalence of ARGs and virulence genes. This study provides a data foundation for local\n Salmonella<\/jats:italic>\n epidemiology.\n <\/jats:p>","DOI":"10.1089\/fpd.2024.0138","type":"journal-article","created":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T10:03:06Z","timestamp":1737453786000},"page":"684-691","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["Molecular Characterization of Whole Genome Sequencing of\n Salmonella<\/i>\n spp. in Shapingba District, Chongqing, China, 2016\u20132023"],"prefix":"10.1177","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4104-2528","authenticated-orcid":false,"given":"Fei","family":"Chen","sequence":"first","affiliation":[{"name":"Chongqing Shapingba District Center for Disease Control and Prevention, Chongqing, China."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Chongqing Shapingba District Center for Disease Control and Prevention, Chongqing, China."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-3936-2148","authenticated-orcid":false,"given":"Jie","family":"Zheng","sequence":"additional","affiliation":[{"name":"College of Public Health, Southwest Medical University, Luzhou, China."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Tang","sequence":"additional","affiliation":[{"name":"Chongqing Shapingba District Center for Disease Control and Prevention, Chongqing, China."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoxia","family":"Fan","sequence":"additional","affiliation":[{"name":"Chongqing Shapingba District Center for Disease Control and Prevention, Chongqing, China."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yulan","family":"Huang","sequence":"additional","affiliation":[{"name":"Center for Disease Control and Prevention of Sichuan Province, Chengdu, China."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haihong","family":"Jia","sequence":"additional","affiliation":[{"name":"China Railway Chengdu Bureau Group Co., Ltd., Chengdu Center For Disease Control and Prevention, Chengdu, China."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaorong","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Disease Control and Prevention of Sichuan Province, Chengdu, 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