{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T13:44:35Z","timestamp":1785332675576,"version":"3.55.0"},"reference-count":49,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T00:00:00Z","timestamp":1690502400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T00:00:00Z","timestamp":1690502400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"crossref","award":["OPP1169264"],"award-info":[{"award-number":["OPP1169264"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    We performed whole-genome sequencing of 174\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Typhi and 54\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Paratyphi A isolates collected through prospective surveillance in the context of a phased typhoid conjugate vaccine introduction in Navi Mumbai, India. We investigate the temporal and geographical patterns of emergence and spread of antimicrobial resistance. We evaluated the relationship between the spatial distance between households and genetic clustering of isolates. Most isolates were non-susceptible to fluoroquinolones, with nearly 20% containing \u22653 quinolone resistance-determining region mutations. Two H58 isolates carried an IncX3 plasmid containing bla\n                    <jats:sub>SHV-12<\/jats:sub>\n                    , associated with ceftriaxone resistance, suggesting that the ceftriaxone-resistant isolates from India independently evolved on multiple occasions. Among\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi, we identified two main clades circulating (2.2 and 4.3.1 [H58]); 2.2 isolates were closely related following a single introduction around 2007, whereas H58 isolates had been introduced multiple times to the city. Increasing geographic distance between isolates was strongly associated with genetic clustering (odds ratio [OR] = 0.72 per km; 95% credible interval [CrI]: 0.66\u20130.79). This effect was seen for distances up to 5 km (OR = 0.65 per km; 95% CrI: 0.59\u20130.73) but not seen for distances beyond 5 km (OR = 1.02 per km; 95% CrI: 0.83\u20131.26). There was a non-significant reduction in odds of clustering for pairs of isolates in vaccination communities compared with non-vaccination communities or mixed pairs compared with non-vaccination communities. Our findings indicate that\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi was repeatedly introduced into Navi Mumbai and then spread locally, with strong evidence of spatial genetic clustering. In addition to vaccination, local interventions to improve water and sanitation will be critical to interrupt transmission.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Enteric fever remains a major public health concern in many low- and middle-income countries, as antimicrobial resistance (AMR) continues to emerge. Geographical patterns of typhoidal\n                      <jats:italic>Salmonella<\/jats:italic>\n                      spread, critical to monitoring AMR and planning interventions, are poorly understood. We performed whole-genome sequencing of\n                      <jats:italic>S<\/jats:italic>\n                      . Typhi and\n                      <jats:italic>S<\/jats:italic>\n                      . Paratyphi A isolates collected in Navi Mumbai, India before and after a typhoid conjugate vaccine introduction. From timed phylogenies, we found two dominant circulating lineages of\n                      <jats:italic>S<\/jats:italic>\n                      . Typhi in Navi Mumbai-lineage 2.2, which expanded following a single introduction a decade prior, and 4.3.1 (H58), which had been introduced repeatedly from other parts of India, frequently containing \u201ctriple mutations\u201d conferring high-level ciprofloxacin resistance. Using Bayesian hierarchical statistical models, we found that spatial distance between cases was strongly associated with genetic clustering at a fine scale (&lt;5 km). Together, these findings suggest that antimicrobial-resistant\n                      <jats:italic>S<\/jats:italic>\n                      . Typhi frequently flows between cities and then spreads highly locally, which may inform surveillance and prevention strategies.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.01179-23","type":"journal-article","created":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T09:00:40Z","timestamp":1690534840000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":5,"title":["Population structure and antimicrobial resistance patterns of\n                    <i>Salmonella<\/i>\n                    Typhi and Paratyphi A amid a phased municipal vaccination campaign in Navi Mumbai, India"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8593-1119","authenticated-orcid":true,"given":"Kesia Esther","family":"da Silva","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine , Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kashmira","family":"Date","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nilma","family":"Hirani","sequence":"additional","affiliation":[{"name":"Grant Government Medical College &amp; Sir J J Hospital , Mumbai, Maharashtra, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"LeBoa","sequence":"additional","affiliation":[{"name":"Division of Environmental Health Sciences, School of Public Health, University of California , Berkeley, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niniya","family":"Jayaprasad","sequence":"additional","affiliation":[{"name":"World Health Organization-Country Office for India, National Public Health Surveillance Project , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priyanka","family":"Borhade","sequence":"additional","affiliation":[{"name":"World Health Organization-Country Office for India, National Public Health Surveillance Project , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Warren","sequence":"additional","affiliation":[{"name":"Yale School of Public Health, Yale University , New Haven, Connecticut, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rahul","family":"Shimpi","sequence":"additional","affiliation":[{"name":"World Health Organization-Country Office for India, National Public Health Surveillance Project , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seth A.","family":"Hoffman","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine , Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Mikoleit","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pankaj","family":"Bhatnagar","sequence":"additional","affiliation":[{"name":"World Health Organization-Country Office for India, National Public Health Surveillance Project , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanjia","family":"Cao","sequence":"additional","affiliation":[{"name":"Department of Geography, The University of Hong Kong , Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pradeep","family":"Haldar","sequence":"additional","affiliation":[{"name":"Ministry of Health &amp; Family Welfare, Government of India , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pauline","family":"Harvey","sequence":"additional","affiliation":[{"name":"World Health Organization-Country Office for India, National Public Health Surveillance Project , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenhua","family":"Zhang","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Savita","family":"Daruwalla","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, NMMC General Hospital , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhanya","family":"Dharmapalan","sequence":"additional","affiliation":[{"name":"Dr. Yewale Multispecialty Hospital for Children , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeetendra","family":"Gavhane","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, MGM New Bombay Hospital, MGM Medical College , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shrikrishna","family":"Joshi","sequence":"additional","affiliation":[{"name":"Dr. Joshi\u2019s Central Clinical Microbiology Laboratory , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajesh","family":"Rai","sequence":"additional","affiliation":[{"name":"Department of Pediatrics &amp; Neonatology, Dr. D.Y. Patil Medical College and Hospital , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Varsha","family":"Rathod","sequence":"additional","affiliation":[{"name":"Rajmata Jijau Hospital, Airoli (NMMC) , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keertana","family":"Shetty","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Dr. D.Y. Patil Medical College and Hospital , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Divyalatha S.","family":"Warrier","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Mathadi Trust Hospital , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shalini","family":"Yadav","sequence":"additional","affiliation":[{"name":"Department of Microbiology, MGM New Bombay Hospital , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debjit","family":"Chakraborty","sequence":"additional","affiliation":[{"name":"National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research , Kolkata, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunil","family":"Bahl","sequence":"additional","affiliation":[{"name":"World Health Organization South-East Asia Regional Office , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arun","family":"Katkar","sequence":"additional","affiliation":[{"name":"World Health Organization-Country Office for India, National Public Health Surveillance Project , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abhishek","family":"Kunwar","sequence":"additional","affiliation":[{"name":"World Health Organization-Country Office for India, National Public Health Surveillance Project , New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijay","family":"Yewale","sequence":"additional","affiliation":[{"name":"Dr. Yewale Multispecialty Hospital for Children , Navi Mumbai, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanta","family":"Dutta","sequence":"additional","affiliation":[{"name":"National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research , Kolkata, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen P.","family":"Luby","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine , Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5967-251X","authenticated-orcid":true,"given":"Jason R.","family":"Andrews","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine , Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2023,7,28]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciy1094"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30685-6"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0005376"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.2471\/blt.06.039818"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07370-z"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3281"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1101\/2022.12.28.22283969"},{"key":"e_1_3_5_9_2","doi-asserted-by":"crossref","unstructured":"Carey ME Thi Nguyen TN Hoang Nhu TD Dyson ZA Duy PT Mylona E Nair S Chattaway M Baker S\n. 2022. The origins of haplotype 58 (H58) Salmonella Enterica Serovar Typhi. bioRxiv. doi:10.1101\/2022.10.03.510628","DOI":"10.1101\/2022.10.03.510628"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(22)00093-3"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1097\/MOG.0000000000000406"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMp1803926"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkz435"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1097\/MJT.0000000000000503"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00105-18"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciab897"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006779"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2018.04.022"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa597"},{"key":"e_1_3_5_20_2","unstructured":"India RG and CC of. 2011. 2011 census of India. Available from: https:\/\/www.census2011.co.in\/census\/city\/368-navi-mumbai.html. Retrieved . 12 August 2022"},{"key":"e_1_3_5_21_2","article-title":"Babraham bioinformatics - Fastqc A quality control tool for high throughput sequence data","author":"Andrews S","year":"1973","unstructured":"Andrews S . 1973. Babraham bioinformatics - Fastqc A quality control tool for high throughput sequence data. Soil","journal-title":"Soil"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw354"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0147101"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-014-0090-6"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms12827"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1411012111"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx379"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1101\/2021.11.13.21266165"},{"key":"e_1_3_5_33_2","unstructured":"Warren JL Chitwood MH Sobkowiak B Crudu V Colijn C Cohen T\n. 2021. Spatial modeling of dyadic genetic relatedness data: identifying factors associated with M. tuberculosis transmission in Moldova. doi:10.48550\/arXiv.2109.14003"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2019.00317"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz239"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vex025"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.14003"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2011.09.027"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciab745"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0010348"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1098\/rsob.110008"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0001490"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(21)01124-7"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.eclinm.2023.101925"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0005274"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa367"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2021.105093"},{"key":"e_1_3_5_49_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2021.05.003"},{"key":"e_1_3_5_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciy1111"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.01179-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.01179-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T09:00:44Z","timestamp":1690534844000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mbio.01179-23"}},"subtitle":[],"editor":[{"given":"Tom","family":"Chiller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,7,28]]},"references-count":49,"alternative-id":["10.1128\/mbio.01179-23"],"URL":"https:\/\/doi.org\/10.1128\/mbio.01179-23","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.02.23.23286256","asserted-by":"object"}]},"ISSN":["2150-7511"],"issn-type":[{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,28]]},"assertion":[{"value":"2023-05-15","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-06-22","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-07-28","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01179-23"}}