{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T15:21:22Z","timestamp":1788448882365,"version":"build-2803163510"},"reference-count":81,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T00:00:00Z","timestamp":1741046400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T00:00:00Z","timestamp":1741046400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"U.S.-ASEAN Science, Technology, Innovation, and Cooperation"},{"name":"Hong Kong Polytechnic University Start-up Fund for RAPs under the Strategic Hiring Scheme","award":["P0044917"],"award-info":[{"award-number":["P0044917"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              <jats:italic>Salmonella<\/jats:italic>\n              Enteritidis (\n              <jats:italic>S<\/jats:italic>\n              . Enteritidis) stands as a leading cause of human salmonellosis worldwide with a tendency to spread through contaminated foodstuffs and animals. In Hong Kong, a significant proportion of food products are imported, and many cases are often caused by the consumption of contaminated food, hence making the geographical surveillance of drug-resistant\n              <jats:italic>S<\/jats:italic>\n              . Enteritidis important for strong public health and food safety measures. We analyzed the whole genomes of 207\n              <jats:italic>S<\/jats:italic>\n              . Enteritidis from Hong Kong, Australia, Canada, mainland China, the United States of America, South Africa, Taiwan, and the United Kingdom to examine associated antimicrobial resistance and the transmission dynamics between continents. Phylogenetic cluster inferences and Bayesian phylogeographical analysis were performed. Overall, sequence type ST11 strains were dominant (92.8%, 192\/207). Five phylogenomic clusters A to E were identified, where most isolates from mainland China and Hong Kong were in Cluster E. Among the 22 plasmid types identified, IncX1 was dominant in the Asian isolates. Most of the virulence genes were distributed in\n              <jats:italic>Salmonella<\/jats:italic>\n              pathogenicity islands \u22121 and \u22122, with two universal virulence operons responsible for the effector delivery system and bacterial cell adhesion. The phylogeographic inference analysis showed a statistically significant link between mainland China and Hong Kong with the highest relative migration rate (relativeGeoRates mean \u00b1 standard error = 2.93 \u00b1 .07, Bayes Factor [BF] = 1285.5], with some traceable to Canada (0.61 \u00b1 0.03, BF = 6.9) and Australia (1.02 \u00b1 0.04, BF = 4.2). Our analysis suggests hypothetical transmission of\n              <jats:italic>S<\/jats:italic>\n              . Enteritidis and its associated antimicrobial resistance across borders.\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              Antimicrobial resistance and disease severity in nontyphoidal\n              <jats:italic>Salmonella<\/jats:italic>\n              have constituted a serious public health challenge worldwide. Drug-resistant\n              <jats:italic>Salmonella<\/jats:italic>\n              Enteritidis is a leading pathogen that causes human infections primarily through the consumption of contaminated food products. Previous research focuses on the whole-genome analysis of antimicrobial resistance and virulence factors in\n              <jats:italic>S<\/jats:italic>\n              . Enteritidis; however, details on how this bacterium localized, expanded, and diversified from location to location remain unknown. Our study for the first time addresses this gap by investigating the phylogeographic transmission to estimate the frequency and location of cross-border spread. By evidence-based inferred transmission, we aim to uncover novel insights into the dynamic spread of\n              <jats:italic>S<\/jats:italic>\n              . Enteritidis, revealing the route of emergence and migration. This research is crucial for enhancing our understanding of the control strategies to safeguard human health.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.02292-24","type":"journal-article","created":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T14:00:40Z","timestamp":1738936840000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":4,"title":["Bayesian phylogeographic analysis infers cross-border transmission dynamics of drug-resistant\n            <i>Salmonella<\/i>\n            Enteritidis"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5950-7883","authenticated-orcid":true,"given":"Pei Yee","family":"Woh","sequence":"first","affiliation":[{"name":"Department of Food Science and Nutrition, The Hong Kong Polytechnic University","place":["Hong Kong Special Administrative Region, China"]},{"name":"Research Institute for Future Food (RiFood), The Hong Kong Polytechnic University","place":["Hong Kong Special Administrative Region, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yehao","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Food Science and Nutrition, The Hong Kong Polytechnic University","place":["Hong Kong Special Administrative Region, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin Wing Hin","family":"Kwok","sequence":"additional","affiliation":[{"name":"Department of Food Science and Nutrition, The Hong Kong Polytechnic University","place":["Hong Kong Special Administrative Region, China"]},{"name":"Research Institute for Future Food (RiFood), The Hong Kong Polytechnic University","place":["Hong Kong Special Administrative Region, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose","family":"Quiroga","sequence":"additional","affiliation":[{"name":"Office of Global Outreach and Extended Education, Ira A. Fulton Schools of Engineering, Arizona State University","place":["Tempe, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0136153"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.4172\/2472-1212.1000109"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1080\/21645515.2018.1504717"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.4315\/0362-028x-70.3.582"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bjbas.2016.04.002"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02746-15"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.14202\/vetworld.2023.455-463"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10101240"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1186\/s41182-017-0043-z"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1327092"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meatsci.2017.01.001"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.3390\/foods10081742"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx238"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.arba-0014-2017"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.3390\/foods7100167"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2020.2856"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.187.18.6545-6555.2005"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001059"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01760-16"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000785"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.2174\/1874285801206010005"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00251-011-0523-y"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10121615"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2021.725737"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.46637-0"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00248-21"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkad092"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dki250"},{"key":"e_1_3_4_30_2","unstructured":"Hong Kong Legislative Council Secretariat. 2016. Fact sheet: regulation of imported food in Hong Kong"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01144-12"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1136\/bmjpo-2020-000898"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02618"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.3390\/foods12112245"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2022.912693"},{"key":"e_1_3_4_36_2","volume-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews S","year":"2010","unstructured":"Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom."},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_4_39_2","unstructured":"World Bank. 2023. World integrated trade solution. Available from: https:\/\/wits.worldbank.org\/default.aspx. Retrieved 1 Jul 2023."},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.899024"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.03364-22"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-022-08769-1"},{"key":"e_1_3_4_43_2","volume-title":"Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion","author":"Zwickl DJ","year":"2006","unstructured":"Zwickl DJ. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. the University of Texas at Austin."},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad235"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq228"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.96"},{"key":"e_1_3_4_49_2","unstructured":"Seemann T. 2023. MLST on Github. Available from: https:\/\/github.com\/tseemann\/mlst. Retrieved 1 Nov 2023."},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks261"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2011.03570.x"},{"key":"e_1_3_4_53_2","unstructured":"Seemann T. 2023. Abricate on Github. Available from: https:\/\/github.com\/tseemann\/abricate. Retrieved 15 Nov 2023."},{"key":"e_1_3_4_54_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1239"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab120"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006650"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syy032"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr481"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.3758\/s13423-020-01798-5"},{"key":"e_1_3_4_61_2","unstructured":"Rambaut A. 2018. FigTree v1.4.4. Available from: http:\/\/tree.bio.ed.ac.uk\/software\/figtree"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-24150-4"},{"key":"e_1_3_4_63_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.03014-22"},{"key":"e_1_3_4_64_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.84167"},{"key":"e_1_3_4_65_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2706.204486"},{"key":"e_1_3_4_66_2","doi-asserted-by":"publisher","DOI":"10.2147\/IDR.S210961"},{"key":"e_1_3_4_67_2","doi-asserted-by":"publisher","DOI":"10.4315\/0362-028X.JFP-16-255"},{"key":"e_1_3_4_68_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25319-7"},{"key":"e_1_3_4_69_2","doi-asserted-by":"publisher","DOI":"10.1086\/650733"},{"key":"e_1_3_4_70_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2019.07.031"},{"key":"e_1_3_4_71_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10123-023-00462-x"},{"key":"e_1_3_4_72_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.001255"},{"key":"e_1_3_4_73_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1503141112"},{"key":"e_1_3_4_74_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001556"},{"key":"e_1_3_4_75_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13756-019-0672-6"},{"key":"e_1_3_4_76_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijfoodmicro.2014.03.030"},{"key":"e_1_3_4_77_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2021.05.037"},{"key":"e_1_3_4_78_2","doi-asserted-by":"publisher","DOI":"10.2471\/BLT.21.286689"},{"key":"e_1_3_4_79_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12575-022-00182-y"},{"key":"e_1_3_4_80_2","unstructured":"World Organisation for Animal Health. 2016. OIE annual report on the use of antimicrobial agents in animals"},{"key":"e_1_3_4_81_2","doi-asserted-by":"publisher","DOI":"10.4102\/ojvr.v82i1.816"},{"key":"e_1_3_4_82_2","doi-asserted-by":"publisher","DOI":"10.14943\/jjvr.61.suppl.s13"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.02292-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.02292-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T14:02:17Z","timestamp":1741096937000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.02292-24"}},"subtitle":[],"editor":[{"given":"Cheryl P.","family":"Andam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,3,4]]},"references-count":81,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3,4]]}},"alternative-id":["10.1128\/spectrum.02292-24"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.02292-24","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,4]]},"assertion":[{"value":"2024-09-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-12-05","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-02-07","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e02292-24"}}