{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T05:13:12Z","timestamp":1790745192573,"version":"4.1.0"},"reference-count":26,"publisher":"National Academy of Sciences","issue":"13","license":[{"start":{"date-parts":[[2019,9,13]],"date-time":"2019-09-13T00:00:00Z","timestamp":1568332800000},"content-version":"vor","delay-in-days":184,"URL":"https:\/\/www.pnas.org\/site\/aboutpnas\/licenses.xhtml"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology , Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/MB\/THSTI\/HMC-SFC\/2011"],"award-info":[{"award-number":["BT\/MB\/THSTI\/HMC-SFC\/2011"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2019,3,26]]},"abstract":"<jats:p>\n                    The Bay of Bengal is known as the epicenter for seeding several devastating cholera outbreaks across the globe.\n                    <jats:italic>Vibrio cholerae<\/jats:italic>\n                    , the etiological agent of cholera, has extraordinary competency to acquire exogenous DNA by horizontal gene transfer (HGT) and adapt them into its genome for structuring metabolic processes, developing drug resistance, and colonizing the human intestine. Antimicrobial resistance (AMR) in\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    has become a global concern. However, little is known about the identity of the resistance traits, source of AMR genes, acquisition process, and stability of the genetic elements linked with resistance genes in\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    . Here we present details of AMR profiles of 443\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    strains isolated from the stool samples of diarrheal patients from two regions of India. We sequenced the whole genome of multidrug-resistant (MDR) and extensively drug-resistant (XDR)\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    to identify AMR genes and genomic elements that harbor the resistance traits. Our genomic findings were further confirmed by proteome analysis. We also engineered the genome of\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    to monitor the importance of the autonomously replicating plasmid and core genome in the resistance profile. Our findings provided insights into the genomes of recent cholera isolates and identified several acquired traits including plasmids, transposons, integrative conjugative elements (ICEs), pathogenicity islands (PIs), prophages, and gene cassettes that confer fitness to the pathogen. The knowledge generated from this study would help in better understanding of\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    evolution and management of cholera disease by providing clinical guidance on preferred treatment regimens.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1900141116","type":"journal-article","created":{"date-parts":[[2019,3,13]],"date-time":"2019-03-13T19:45:25Z","timestamp":1552506325000},"page":"6226-6231","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":121,"title":["Genomic plasticity associated with antimicrobial resistance in\n                    <i>Vibrio cholerae<\/i>"],"prefix":"10.1073","volume":"116","author":[{"given":"Jyoti","family":"Verma","sequence":"first","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satyabrata","family":"Bag","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bipasa","family":"Saha","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pawan","family":"Kumar","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tarini Shankar","family":"Ghosh","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mayanka","family":"Dayal","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tarosi","family":"Senapati","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seema","family":"Mehra","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prasanta","family":"Dey","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anbumani","family":"Desigamani","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhirendra","family":"Kumar","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Preety","family":"Rana","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bhoj","family":"Kumar","sequence":"additional","affiliation":[{"name":"Regional Centre for Biotechnology, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tushar K.","family":"Maiti","sequence":"additional","affiliation":[{"name":"Regional Centre for Biotechnology, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naresh C.","family":"Sharma","sequence":"additional","affiliation":[{"name":"Maharishi Valmiki Infectious Diseases Hospital, Kingsway Camp, Delhi 110009, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rupak K.","family":"Bhadra","sequence":"additional","affiliation":[{"name":"Infectious Diseases and Immunology Division, Council of Scientific &amp; Industrial Research (CSIR)\u2013Indian Institute of Chemical Biology, Kolkata 700032, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankur","family":"Mutreja","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"},{"name":"Department of Medicine, Addenbrookes Hospital, University of Cambridge, CB20QQ Cambridge, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G. Balakrish","family":"Nair","sequence":"additional","affiliation":[{"name":"Microbiome Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thandavarayan","family":"Ramamurthy","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2447-5380","authenticated-orcid":false,"given":"Bhabatosh","family":"Das","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;"},{"name":"Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2019,3,13]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1016\/S0140-6736(17)30559-7","article-title":"Cholera","volume":"390","author":"Clemens JD","year":"2017","unstructured":"JD Clemens, GB Nair, T Ahmed, F Qadri, J Holmgren, Cholera. Lancet 390, 1539\u20131549 (2017).","journal-title":"Lancet"},{"key":"e_1_3_4_2_2","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1097\/QCO.0000000000000306","article-title":"Molecular evolution and functional divergence of Vibrio cholerae","volume":"29","author":"Das B","year":"2016","unstructured":"B Das, , Molecular evolution and functional divergence of Vibrio cholerae. Curr Opin Infect Dis 29, 520\u2013527 (2016).","journal-title":"Curr Opin Infect Dis"},{"key":"e_1_3_4_3_2","doi-asserted-by":"crossref","first-page":"1824","DOI":"10.1126\/science.1120096","article-title":"Chitin induces natural competence in Vibrio cholerae","volume":"310","author":"Meibom KL","year":"2005","unstructured":"KL Meibom, M Blokesch, NA Dolganov, CY Wu, GK Schoolnik, Chitin induces natural competence in Vibrio cholerae. Science 310, 1824\u20131827 (2005).","journal-title":"Science"},{"key":"e_1_3_4_4_2","doi-asserted-by":"crossref","first-page":"2466","DOI":"10.1016\/S0140-6736(12)60436-X","article-title":"Cholera","volume":"379","author":"Harris JB","year":"2012","unstructured":"JB Harris, RC LaRocque, F Qadri, ET Ryan, SB Calderwood, Cholera. Lancet 379, 2466\u20132476 (2012).","journal-title":"Lancet"},{"key":"e_1_3_4_5_2","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1099\/jmm.0.023051-0","article-title":"Antibiotic resistance mechanisms of Vibrio cholerae","volume":"60","author":"Kitaoka M","year":"2011","unstructured":"M Kitaoka, ST Miyata, D Unterweger, S Pukatzki, Antibiotic resistance mechanisms of Vibrio cholerae. J Med Microbiol 60, 397\u2013407 (2011).","journal-title":"J Med Microbiol"},{"key":"e_1_3_4_6_2","doi-asserted-by":"crossref","first-page":"j3535","DOI":"10.1136\/bmj.j3535","article-title":"Fostering research into antimicrobial resistance in India","volume":"358","author":"Das B","year":"2017","unstructured":"B Das, S Chaudhuri, R Srivastava, GB Nair, T Ramamurthy, Fostering research into antimicrobial resistance in India. BMJ 358, j3535 (2017).","journal-title":"BMJ"},{"key":"e_1_3_4_7_2","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/S1473-3099(12)70317-1","article-title":"The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria","volume":"13","author":"Wellington EMH","year":"2013","unstructured":"EMH Wellington, , The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect Dis 13, 155\u2013165 (2013).","journal-title":"Lancet Infect Dis"},{"key":"e_1_3_4_8_2","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1038\/nrmicro3380","article-title":"Molecular mechanisms of antibiotic resistance","volume":"13","author":"Blair JM","year":"2015","unstructured":"JM Blair, MA Webber, AJ Baylay, DO Ogbolu, LJ Piddock, Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol 13, 42\u201351 (2015).","journal-title":"Nat Rev Microbiol"},{"key":"e_1_3_4_9_2","doi-asserted-by":"crossref","first-page":"14468","DOI":"10.1038\/s41598-017-14791-1","article-title":"Molecular insights into antimicrobial resistance traits of multidrug resistant enteric pathogens isolated from India","volume":"7","author":"Kumar P","year":"2017","unstructured":"P Kumar, , Molecular insights into antimicrobial resistance traits of multidrug resistant enteric pathogens isolated from India. 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Science 347, 1064\u20131066 (2015).","journal-title":"Science"},{"key":"e_1_3_4_12_2","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1016\/S0140-6736(12)60911-8","article-title":"NDM-1 polymicrobial infections including Vibrio cholerae","volume":"380","author":"Darley E","year":"2012","unstructured":"E Darley, , NDM-1 polymicrobial infections including Vibrio cholerae. Lancet 380, 1358 (2012).","journal-title":"Lancet"},{"key":"e_1_3_4_13_2","doi-asserted-by":"crossref","first-page":"43232","DOI":"10.1038\/srep43232","article-title":"In silico serine \u03b2-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species","volume":"7","author":"Brandt C","year":"2017","unstructured":"C Brandt, , In silico serine \u03b2-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species. Sci Rep 7, 43232 (2017).","journal-title":"Sci Rep"},{"key":"e_1_3_4_14_2","doi-asserted-by":"crossref","first-page":"5649","DOI":"10.1073\/pnas.1503141112","article-title":"Global trends in antimicrobial use in food animals","volume":"112","author":"Van Boeckel TP","year":"2015","unstructured":"TP Van Boeckel, , Global trends in antimicrobial use in food animals. Proc Natl Acad Sci USA 112, 5649\u20135654 (2015).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_15_2","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1093\/jac\/dks355","article-title":"Patterns of antibiotic use in the community and challenges of antibiotic surveillance in a lower-middle-income country setting: A repeated cross-sectional study in Vellore, south India","volume":"68","author":"Chandy SJ","year":"2013","unstructured":"SJ Chandy, , Patterns of antibiotic use in the community and challenges of antibiotic surveillance in a lower-middle-income country setting: A repeated cross-sectional study in Vellore, south India. J Antimicrob Chemother 68, 229\u2013236 (2013).","journal-title":"J Antimicrob Chemother"},{"key":"e_1_3_4_16_2","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1128\/br.27.1.87-115.1963","article-title":"Infective heredity of multiple drug resistance in bacteria","volume":"27","author":"Watanabe T","year":"1963","unstructured":"T Watanabe, Infective heredity of multiple drug resistance in bacteria. Bacteriol Rev 27, 87\u2013115 (1963).","journal-title":"Bacteriol Rev"},{"key":"e_1_3_4_17_2","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1126\/science.aad5901","article-title":"Genomic history of the seventh pandemic of cholera in Africa","volume":"358","author":"Weill FX","year":"2017","unstructured":"FX Weill, , Genomic history of the seventh pandemic of cholera in Africa. Science 358, 785\u2013789 (2017).","journal-title":"Science"},{"key":"e_1_3_4_18_2","first-page":"665","article-title":"Clinical and physiological observations during an epidemic outbreak of non-vibrio cholera-like disease in Calcutta","volume":"33","author":"Carpenter CC","year":"1965","unstructured":"CC Carpenter, , Clinical and physiological observations during an epidemic outbreak of non-vibrio cholera-like disease in Calcutta. Bull World Health Organ 33, 665\u2013671 (1965).","journal-title":"Bull World Health Organ"},{"key":"e_1_3_4_19_2","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1136\/bmj.4.5730.281","article-title":"Comparative trial of tetracycline, chloramphenicol, and trimethoprim-sulphamethoxazole in eradication of Vibrio cholerae El Tor","volume":"4","author":"Gharagozloo RA","year":"1970","unstructured":"RA Gharagozloo, K Naficy, M Mouin, MH Nassirzadeh, R Yalda, Comparative trial of tetracycline, chloramphenicol, and trimethoprim-sulphamethoxazole in eradication of Vibrio cholerae El Tor. BMJ 4, 281\u2013282 (1970).","journal-title":"BMJ"},{"key":"e_1_3_4_20_2","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1126\/science.aao2136","article-title":"Integrated view of Vibrio cholerae in the Americas","volume":"358","author":"Domman D","year":"2017","unstructured":"D Domman, , Integrated view of Vibrio cholerae in the Americas. Science 358, 789\u2013793 (2017).","journal-title":"Science"},{"key":"e_1_3_4_21_2","first-page":"138","article-title":"Genomic plasticity of Vibrio cholerae","volume":"20","author":"Escudero JA","year":"2017","unstructured":"JA Escudero, D Mazel, Genomic plasticity of Vibrio cholerae. Int Microbiol 20, 138\u2013148 (2017).","journal-title":"Int Microbiol"},{"key":"e_1_3_4_22_2","unstructured":"; Global Antibiotic Resistance Partnership-India National Working Group (GARP) (2011). Situation analysis: Antibiotic use and resistance in India (Public Health Foundation of India Gurugram India). Available at https:\/\/www.cddep.org\/wp-content\/uploads\/2017\/06\/india-report-web_8.pdf. Accessed August 15 2018."},{"key":"e_1_3_4_23_2","unstructured":"B Das Vibrio cholerae strain IDH046 whole genome shotgun sequencing project. NCBI Nucleotide database. Available at https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/SISO00000000.1\/. Deposited February 19 2019. (2019)."},{"key":"e_1_3_4_24_2","unstructured":"B Das Vibrio cholerae strain IDH06781 whole genome shotgun sequencing project. NCBI Nucleotide database. Available at https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/SISP00000000.1\/. Deposited February 19 2019. (2019)."},{"key":"e_1_3_4_25_2","unstructured":"B Das Vibrio cholerae strain IDH08148 whole genome shotgun sequencing project. NCBI Nucleotide database. Available at https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/SISQ00000000.1\/. Deposited February 19 2019. (2019)."},{"key":"e_1_3_4_26_2","unstructured":"B Das Vibrio cholerae strain VCE232 whole genome shotgun sequencing project. NCBI Nucleotide database. Available at https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/SISR00000000.1\/. Deposited February 19 2019. (2019)."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.pnas.org\/syndication\/doi\/10.1073\/pnas.1900141116","content-type":"unspecified","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1900141116","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T15:05:34Z","timestamp":1654614334000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1900141116"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,13]]},"references-count":26,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2019,3,26]]}},"alternative-id":["10.1073\/pnas.1900141116"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1900141116","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,13]]},"assertion":[{"value":"2019-03-13","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}