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Therefore, to study whether environmental nonO1-nonO139 isolates, which are native to the aquatic ecosystem, act as precursors for pathogenic O1 strains, their virulence potential and evolutionary relatedness was checked.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p><jats:italic>V. cholerae<\/jats:italic>was isolated from clinical cases of cholera and from water and plankton samples collected from freshwater bodies and cholera-affected areas. PCR analysis for the<jats:italic>ctxA, ctxB, tcpA, toxT<\/jats:italic>and<jats:italic>toxR<\/jats:italic>genes and AFLP with six primer combinations was performed on 52 isolates (13 clinical, 34 environmental and 5 reference strains).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>All clinical and 3 environmental isolates belonged to serogroup O1 and remaining 31 environmental<jats:italic>V. cholerae<\/jats:italic>were nonO1-nonO139. Serogroup O1 isolates were<jats:italic>ctxA, tcpA<\/jats:italic>(ElTor),<jats:italic>ctxB<\/jats:italic>(Classical),<jats:italic>toxR<\/jats:italic>and<jats:italic>toxT<\/jats:italic>positive. NonO1-nonO139 isolates possessed<jats:italic>toxR<\/jats:italic>, but lacked<jats:italic>ctxA<\/jats:italic>and<jats:italic>ctxB<\/jats:italic>; only one isolate was positive for<jats:italic>toxT<\/jats:italic>and<jats:italic>tcpA<\/jats:italic>. Using AFLP, 2.08% of the<jats:italic>V. cholerae<\/jats:italic>genome was interrogated. Dendrogram analysis showed one large heterogeneous clade (n = 41), with two compact and distinct subclades (1a and 1b), and six small mono-phyletic groups. Although<jats:italic>V. cholerae<\/jats:italic>O1 isolates formed a distinct compact subclade, they were not clonal. A clinical O1 strain clustered with the nonO1-nonO139 isolates; one strain exhibited 70% similarity to the Classical control strain, and all O1 strains possessed an ElTor variant-specific fragment identified with primer ECMT. Few nonO1-nonO139 isolates from widely separated geographical locations intermingled together. Three environmental O1 isolates exhibited similar profiles to clinical O1 isolates.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>In a unique study from freshwater environs of a cholera-endemic area in India over a narrow time frame, environmental<jats:italic>V. cholerae<\/jats:italic>population was found to be highly heterogeneous, diverse and devoid of major virulence genes. O1 and nonO1-nonO139 isolates showed distinct lineages. Clinical isolates were not clonal but were closely related, indicating accumulation of genetic differences over a short time span. Though, environment plays an important role in the spread of cholera, the possibility of an origin of pathogenic O1 strains from environmental nonO1-nonO139 strains seems to be remote in our region.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2334-11-249","type":"journal-article","created":{"date-parts":[[2011,9,22]],"date-time":"2011-09-22T06:24:09Z","timestamp":1316672649000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Amplified fragment length polymorphism of clinical and environmental Vibrio cholerae from a freshwater environment in a cholera-endemic area, India"],"prefix":"10.1186","volume":"11","author":[{"given":"Arti","family":"Mishra","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neelam","family":"Taneja","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ram K","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rahul","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naresh C","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meera","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,9,22]]},"reference":[{"key":"1611_CR1","first-page":"117","volume":"85","author":"WHO","year":"2010","unstructured":"WHO: Cholera vaccines: WHO position paper. 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