{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:58:14Z","timestamp":1787165894332,"version":"build-2736575974"},"reference-count":53,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T00:00:00Z","timestamp":1741046400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012271","name":"Shenzhen Fundamental Research and Discipline Layout Project","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012271","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012151","name":"Sanming Project of Medicine in Shenzhen","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012151","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","journalofinfection.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Infection"],"published-print":{"date-parts":[[2025,4]]},"DOI":"10.1016\/j.jinf.2025.106469","type":"journal-article","created":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T11:12:22Z","timestamp":1741345942000},"page":"106469","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":4,"title":["Genomic epidemiology and antimicrobial resistance reveal local transmission dynamics of enteric fever in Shenzhen, one of the mega cities in China"],"prefix":"10.1016","volume":"90","author":[{"given":"Yixiang","family":"Jiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1681-5469","authenticated-orcid":false,"given":"Meiying","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaolu","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinghua","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Biao","family":"Kan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"4","key":"10.1016\/j.jinf.2025.106469_bib1","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S1473-3099(18)30685-6","article-title":"The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017","volume":"19","author":"GBD 2017 Typhoid and Paratyphoid Collaborators","year":"2019","journal-title":"Lancet Infect Dis"},{"key":"10.1016\/j.jinf.2025.106469_bib2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.eclinm.2024.102883","article-title":"The global burden of enteric fever, 2017\u20132021: a systematic analysis from the global burden of disease study 2021","volume":"77","author":"Piovani","year":"2024","journal-title":"EClinicalMedicine"},{"issue":"9","key":"10.1016\/j.jinf.2025.106469_bib3","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1586\/14760584.2013.825450","article-title":"Increasing rates of Salmonella Paratyphi A and the current status of its vaccine development","volume":"12","author":"Sahastrabuddhe","year":"2013","journal-title":"Expert Rev Vaccines"},{"issue":"1","key":"10.1016\/j.jinf.2025.106469_bib4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12916-019-1443-1","article-title":"Drug-resistant enteric fever worldwide, 1990 to 2018: a systematic review and meta-analysis","volume":"18","author":"Browne","year":"2020","journal-title":"BMC Med"},{"issue":"8","key":"10.1016\/j.jinf.2025.106469_bib5","doi-asserted-by":"crossref","first-page":"e567","DOI":"10.1016\/S2666-5247(22)00093-3","article-title":"The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study","volume":"3","author":"da Silva","year":"2022","journal-title":"Lancet Microbe"},{"issue":"16","key":"10.1016\/j.jinf.2025.106469_bib6","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1056\/NEJMp1803926","article-title":"Extensively drug-resistant typhoid \u2013 are conjugate vaccines arriving just in time?","volume":"379","author":"Andrews","year":"2018","journal-title":"N Engl J Med"},{"issue":"6","key":"10.1016\/j.jinf.2025.106469_bib7","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1038\/ng.3281","article-title":"Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events","volume":"47","author":"Wong","year":"2015","journal-title":"Nat Genet"},{"issue":"12","key":"10.1016\/j.jinf.2025.106469_bib8","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofab572","article-title":"Extensively drug-resistant typhoid fever in the United States","volume":"8","author":"Hughes","year":"2021","journal-title":"Open Forum Infect Dis"},{"issue":"12","key":"10.1016\/j.jinf.2025.106469_bib9","doi-asserted-by":"crossref","first-page":"254","DOI":"10.46234\/ccdcw2022.062","article-title":"Extensively drug-resistant (XDR) Salmonella Typhi outbreak by waterborne infection - Beijing Municipality, China, January-February 2022","volume":"4","author":"Wang","year":"2022","journal-title":"China CDC Wkly"},{"issue":"3","key":"10.1016\/j.jinf.2025.106469_bib10","doi-asserted-by":"crossref","first-page":"667","DOI":"10.3390\/microorganisms11030667","article-title":"Genomic investigation of Salmonella Typhi in Hong Kong revealing the predominance of genotype 3.2.2 and the first case of an extensively drug-resistant H58 genotype","volume":"11","author":"Li","year":"2023","journal-title":"Microorganisms"},{"issue":"1","key":"10.1016\/j.jinf.2025.106469_bib11","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.03481-20","article-title":"Tracking the emergence of azithromycin resistance in multiple genotypes of Typhoidal Salmonella","volume":"12","author":"Sajib","year":"2021","journal-title":"mBio"},{"issue":"6","key":"10.1016\/j.jinf.2025.106469_bib12","doi-asserted-by":"crossref","first-page":"S499","DOI":"10.1093\/cid\/ciz705","article-title":"Spatial and temporal patterns of typhoid and paratyphoid fever outbreaks: a worldwide review, 1990-2018","volume":"69","author":"Kim","year":"2019","journal-title":"Clin Infect Dis"},{"issue":"4","key":"10.1016\/j.jinf.2025.106469_bib13","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1016\/j.jinf.2022.01.014","article-title":"British infection association guidelines for the diagnosis and management of enteric fever in England","volume":"84","author":"Nabarro","year":"2022","journal-title":"J Infect"},{"issue":"1","key":"10.1016\/j.jinf.2025.106469_bib14","doi-asserted-by":"crossref","first-page":"6502","DOI":"10.1038\/s41467-023-42353-9","article-title":"Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi","volume":"14","author":"Walker","year":"2023","journal-title":"Nat Commun"},{"key":"10.1016\/j.jinf.2025.106469_bib15","article-title":"Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016","volume":"24","author":"Davies","year":"2022","journal-title":"Lancet Reg Health West Pac"},{"issue":"5","key":"10.1016\/j.jinf.2025.106469_bib16","first-page":"743","article-title":"Epidemiological characteristics of typhoid fever and paratyphoid fever in China, 2004-2020","volume":"44","author":"Gao","year":"2023","journal-title":"Zhonghua Liu Xing Bing Xue Za Zhi"},{"issue":"5","key":"10.1016\/j.jinf.2025.106469_bib17","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J Comput Biol"},{"issue":"8","key":"10.1016\/j.jinf.2025.106469_bib18","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"issue":"23","key":"10.1016\/j.jinf.2025.106469_bib19","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.01746-19","article-title":"SeqSero2: rapid and improved Salmonella serotype determination using whole-genome sequencing data","volume":"85","author":"Zhang","year":"2019","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"10.1016\/j.jinf.2025.106469_bib20","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0147101","article-title":"The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies","volume":"11","author":"Yoshida","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.jinf.2025.106469_bib21","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms12827","article-title":"An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid","volume":"7","author":"Wong","year":"2016","journal-title":"Nat Commun"},{"issue":"1","key":"10.1016\/j.jinf.2025.106469_bib22","doi-asserted-by":"crossref","first-page":"7912","DOI":"10.1038\/s41467-022-35587-6","article-title":"Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity","volume":"13","author":"Tanmoy","year":"2022","journal-title":"Nat Commun"},{"key":"10.1016\/j.jinf.2025.106469_bib23","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.10121","article-title":"The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake","volume":"8","author":"Olawoye","year":"2020","journal-title":"PeerJ"},{"issue":"3","key":"10.1016\/j.jinf.2025.106469_bib24","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"10.1016\/j.jinf.2025.106469_bib25","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"W1","key":"10.1016\/j.jinf.2025.106469_bib26","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"10.1016\/j.jinf.2025.106469_bib27","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol"},{"key":"10.1016\/j.jinf.2025.106469_bib28","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"Drummond","year":"2007","journal-title":"BMC Evol Biol"},{"issue":"5","key":"10.1016\/j.jinf.2025.106469_bib29","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst Biol"},{"issue":"11","key":"10.1016\/j.jinf.2025.106469_bib30","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J Antimicrob Chemother"},{"issue":"7","key":"10.1016\/j.jinf.2025.106469_bib31","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"issue":"9","key":"10.1016\/j.jinf.2025.106469_bib32","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res"},{"key":"10.1016\/j.jinf.2025.106469_bib33","article-title":"Genomic investigation reveals a community typhoid outbreak caused by contaminated drinking water in China, 2016","volume":"9","author":"Hu","year":"2022","journal-title":"Front Med (Lausanne)"},{"issue":"11","key":"10.1016\/j.jinf.2025.106469_bib34","article-title":"Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013-2015","volume":"2","author":"Kuijpers","year":"2016","journal-title":"Micro Genom"},{"key":"10.1016\/j.jinf.2025.106469_bib35","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.ijid.2022.10.034","article-title":"Epidemiologic and genomic investigations of an unusual increase in Salmonella enterica serovar Paratyphi A infection among travelers returning from Myanmar in 2015","volume":"125","author":"Matono","year":"2022","journal-title":"Int J Infect Dis"},{"issue":"1","key":"10.1016\/j.jinf.2025.106469_bib36","article-title":"The genomic characterization of Salmonella Paratyphi A from an outbreak of enteric fever in Vadodara, India","volume":"9","author":"Pereira-Dias","year":"2023","journal-title":"Micro Genom"},{"issue":"7","key":"10.1016\/j.jinf.2025.106469_bib37","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0003859","article-title":"A large-scale community-based outbreak of paratyphoid fever caused by hospital-derived transmission in Southern China","volume":"9","author":"Yan","year":"2015","journal-title":"PLoS Negl Trop Dis"},{"issue":"9","key":"10.1016\/j.jinf.2025.106469_bib38","doi-asserted-by":"crossref","first-page":"689","DOI":"10.2471\/BLT.09.069310","article-title":"Trends and disease burden of enteric fever in Guangxi province, China, 1994-2004","volume":"88","author":"Dong","year":"2010","journal-title":"Bull World Health Organ"},{"issue":"33","key":"10.1016\/j.jinf.2025.106469_bib39","doi-asserted-by":"crossref","first-page":"12199","DOI":"10.1073\/pnas.1411012111","article-title":"Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever","volume":"111","author":"Zhou","year":"2014","journal-title":"Proc Natl Acad Sci USA"},{"issue":"10","key":"10.1016\/j.jinf.2025.106469_bib40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0009748","article-title":"Genetic diversity of Salmonella Paratyphi A isolated from enteric fever patients in Bangladesh from 2008 to 2018","volume":"15","author":"Rahman","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"issue":"5","key":"10.1016\/j.jinf.2025.106469_bib41","doi-asserted-by":"crossref","first-page":"833","DOI":"10.3201\/eid2305.151539","article-title":"Regional transmission of Salmonella Paratyphi A, China, 1998-2012","volume":"23","author":"Lu","year":"2017","journal-title":"Emerg Infect Dis"},{"issue":"1","key":"10.1016\/j.jinf.2025.106469_bib42","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41572-023-00480-z","article-title":"Typhoid fever","volume":"9","author":"Meiring","year":"2023","journal-title":"Nat Rev Dis Primers"},{"key":"10.1016\/j.jinf.2025.106469_bib43","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2022.945235","article-title":"Paratyphoid fever A: infection and prevention","volume":"13","author":"Xie","year":"2022","journal-title":"Front Microbiol"},{"issue":"12","key":"10.1016\/j.jinf.2025.106469_bib44","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01200-21","article-title":"Genomic epidemiology and antimicrobial resistance mechanisms of imported typhoid in Australia","volume":"65","author":"Ingle","year":"2021","journal-title":"Antimicrob Agents Chemother"},{"issue":"8","key":"10.1016\/j.jinf.2025.106469_bib45","article-title":"Phylogenomics and antimicrobial resistance of Salmonella Typhi and Paratyphi A, B and C in England, 2016-2019","volume":"7","author":"Chattaway","year":"2021","journal-title":"Micro Genom"},{"issue":"2","key":"10.1016\/j.jinf.2025.106469_bib46","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0087991","article-title":"Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica","volume":"9","author":"Leekitcharoenphon","year":"2014","journal-title":"PLoS One"},{"issue":"6","key":"10.1016\/j.jinf.2025.106469_bib47","doi-asserted-by":"crossref","first-page":"2518","DOI":"10.4269\/ajtmh.20-0258","article-title":"A systematic review on antimicrobial resistance among Salmonella Typhi worldwide","volume":"103","author":"Marchello","year":"2020","journal-title":"Am J Trop Med Hyg"},{"issue":"10","key":"10.1016\/j.jinf.2025.106469_bib48","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0006779","article-title":"A systematic review of antimicrobial resistance in Salmonella enterica serovar Typhi, the etiological agent of typhoid","volume":"12","author":"Britto","year":"2018","journal-title":"PLoS Negl Trop Dis"},{"key":"10.1016\/j.jinf.2025.106469_bib49","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/1471-2180-10-32","article-title":"Genetic diversity of Salmonella enteric serovar typhi and paratyphi in Shenzhen, China from 2002 through 2007","volume":"10","author":"Wu","year":"2010","journal-title":"BMC Microbiol"},{"key":"10.1016\/j.jinf.2025.106469_bib50","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1186\/1471-2334-14-404","article-title":"Case report: failure under azithromycin treatment in a case of bacteremia due to Salmonella enterica Paratyphi A","volume":"14","author":"Kobayashi","year":"2014","journal-title":"BMC Infect Dis"},{"issue":"3","key":"10.1016\/j.jinf.2025.106469_bib51","doi-asserted-by":"crossref","first-page":"S276","DOI":"10.1093\/cid\/ciaa1323","article-title":"Antimicrobial resistance in Typhoidal Salmonella: surveillance for enteric fever in Asia Project, 2016-2019","volume":"71","author":"Qamar","year":"2020","journal-title":"Clin Infect Dis"},{"issue":"8","key":"10.1016\/j.jinf.2025.106469_bib52","doi-asserted-by":"crossref","first-page":"e578","DOI":"10.1016\/S2666-5247(22)00114-8","article-title":"Estimating typhoid incidence from community-based serosurveys: a multicohort study","volume":"3","author":"Aiemjoy","year":"2022","journal-title":"Lancet Microbe"},{"issue":"2","key":"10.1016\/j.jinf.2025.106469_bib53","doi-asserted-by":"crossref","first-page":"S71","DOI":"10.1093\/cid\/ciaa513","article-title":"Environmental surveillance as a tool for identifying high-risk settings for typhoid transmission","volume":"71","author":"Andrews","year":"2020","journal-title":"Clin Infect Dis"}],"updated-by":[{"DOI":"10.1016\/j.jinf.2026.106809","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000}}],"container-title":["Journal of Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0163445325000635?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0163445325000635?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T02:13:13Z","timestamp":1786068793000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0163445325000635"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4]]},"references-count":53,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,4]]}},"alternative-id":["S0163445325000635"],"URL":"https:\/\/doi.org\/10.1016\/j.jinf.2025.106469","relation":{},"ISSN":["0163-4453"],"issn-type":[{"value":"0163-4453","type":"print"}],"subject":[],"published":{"date-parts":[[2025,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genomic epidemiology and antimicrobial resistance reveal local transmission dynamics of enteric fever in Shenzhen, one of the mega cities in China","name":"articletitle","label":"Article Title"},{"value":"Journal of Infection","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jinf.2025.106469","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Ltd on behalf of The British Infection Association.","name":"copyright","label":"Copyright"}],"article-number":"106469"}}