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In 2012, diarrheal outbreaks affected three districts of Nepal with confirmed cases of mortality. This study was designed to understand the drug response patterns, source, and transmission of<jats:italic>Vibrio cholerae<\/jats:italic>associated with 2012 cholera outbreaks in Nepal.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p><jats:italic>V. cholerae<\/jats:italic>(n\u2009=\u200928) isolated from 2012 diarrhea outbreaks {n\u2009=\u200922; Kathmandu (n\u2009=\u200912), Doti (n\u2009=\u20099), Bajhang (n\u2009=\u20091)}, and surface water (n\u2009=\u20096; Kathmandu) were tested for antimicrobial response. Virulence properties and DNA fingerprinting of the strains were determined by multi-locus genetic screening employing polymerase chain reaction, DNA sequencing, and pulsed-field gel electrophoresis (PFGE).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>All<jats:italic>V. cholerae<\/jats:italic>strains isolated from patients and surface water were confirmed to be toxigenic, belonging to serogroup O1, Ogawa serotype, biotype El Tor, and possessed classical biotype cholera toxin (CTX). Double-mismatch amplification mutation assay (DMAMA)-PCR revealed the<jats:italic>V. cholerae<\/jats:italic>strains to possess the B-7 allele of<jats:italic>ctx<\/jats:italic>subunit B. DNA sequencing of<jats:italic>tcpA<\/jats:italic>revealed a point mutation at amino acid position 64 (N\u2009\u2192\u2009S) while the<jats:italic>ctxAB<\/jats:italic>promoter revealed four copies of the tandem heptamer repeat sequence 5<jats:italic>'<\/jats:italic>-TTTTGAT-3<jats:italic>'<\/jats:italic>.<jats:italic>V. cholerae<\/jats:italic>possessed all the ORFs of the Vibrio seventh pandemic island (VSP)-I but lacked the ORFs 498\u2013511 of VSP-II. All strains were multidrug resistant with resistance to trimethoprim-sulfamethoxazole (SXT), nalidixic acid (NA), and streptomycin (S); all carried the SXT genetic element. DNA sequencing and deduced amino acid sequence of<jats:italic>gyrA<\/jats:italic>and<jats:italic>parC<\/jats:italic>of the NA<jats:sup>R<\/jats:sup>strains (n\u2009=\u20094) revealed point mutations at amino acid positions 83 (S\u2009\u2192\u2009I), and 85 (S\u2009\u2192\u2009L), respectively. Similar PFGE (<jats:italic>Not<\/jats:italic>I) pattern revealed the Nepalese<jats:italic>V. cholerae<\/jats:italic>to be clonal, and related closely with<jats:italic>V. cholerae<\/jats:italic>associated with cholera in Bangladesh and Haiti.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>In 2012, diarrhea outbreaks in three districts of Nepal were due to transmission of multidrug resistant<jats:italic>V. cholerae<\/jats:italic>El Tor possessing cholera toxin (<jats:italic>ctx<\/jats:italic>) B-7 allele, which is clonal and related closely with<jats:italic>V. cholerae<\/jats:italic>associated with cholera in Bangladesh and Haiti.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2334-14-392","type":"journal-article","created":{"date-parts":[[2014,7,15]],"date-time":"2014-07-15T07:01:22Z","timestamp":1405407682000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Cholera outbreaks (2012) in three districts of Nepal reveal clonal transmission of multi-drug resistant Vibrio choleraeO1"],"prefix":"10.1186","volume":"14","author":[{"given":"Sameer M","family":"Dixit","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatema-Tuz","family":"Johura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sulochana","family":"Manandhar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdus","family":"Sadique","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajesh M","family":"Rajbhandari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahnewaj B","family":"Mannan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahamud-ur","family":"Rashid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saiful","family":"Islam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dibesh","family":"Karmacharya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haruo","family":"Watanabe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R Bradley","family":"Sack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Cravioto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Munirul","family":"Alam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,7,15]]},"reference":[{"key":"3695_CR1","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1128\/CMR.8.1.48","volume":"8","author":"JB Kaper","year":"1995","unstructured":"Kaper JB, Morris JG, Levine MM: Cholera. 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