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Development of simple and rapid PCR‐fingerprinting methods for Vibrio cholerae on the basis of genetic diversity of the superintegron
Author(s) -
Chowdhury N.,
Asakura M.,
Neogi S.B.,
Hinenoya A.,
Haldar S.,
Ramamurthy T.,
Sarkar B.L.,
Faruque S.M.,
Yamasaki S.
Publication year - 2010
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/j.1365-2672.2009.04658.x
Subject(s) - vibrio cholerae , biology , amplified fragment length polymorphism , el tor , dna profiling , pulsed field gel electrophoresis , typing , genetics , restriction enzyme , restriction fragment length polymorphism , genetic diversity , polymerase chain reaction , microbiology and biotechnology , dna , gene , genotype , bacteria , population , demography , sociology
Aims: To develop simple and rapid PCR‐fingerprinting methods for Vibrio cholerae O1 (El Tor and classical biotypes) and O139 serogroup strains which cause major cholera epidemics, on the basis of the diversity of superintegron (SI) carried by these strains. Methods and Results: PCR‐restriction fragment length polymorphism (PCR‐RFLP) assay was developed targeting region between integrase gene in the SI and its nearby ORF, followed by Bgl I digestion. Besides, a V. cholerae repeat‐amplified fragment length polymorphism (VCR‐AFLP) assay was also developed. In the PCR‐RFLP, 94 El Tor, 29 classical and 54 O139 strains produced nine, three and six different DNA fingerprints, respectively. On the other hand, VCR‐AFLP distinguished these El Tor, classical and O139 strains into five, nine and two DNA fingerprints, respectively. Combining both assays the El Tor, classical and O139 strains could be differentiated into 11, 10 and seven different types, respectively. In a comparative study, pulsed‐field gel electrophoresis (PFGE) showed similar differentiation for El Tor (11 types), but lower discrimination for O139 (two types) and classical strains (five types). Conclusions: The PCR assays based on SI diversity can be used as a useful typing tool for epidemiological studies of V. cholerae . Significance and Impact of Study: This newly developed method is more discriminatory, simple, rapid and cost‐effective in comparison with PFGE, and thus can be widely applicable.