title: Development of simple and rapid PCR-fingerprinting methods for Vibrio cholerae on the basis of genetic diversity of the superintegron.
abstract: OBJECTIVE
  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.
  
  
  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 BglI 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.
  
  
  CONCLUSIONS
  This newly developed method is more discriminatory, simple, rapid and cost-effective in comparison with PFGE, and thus can be widely applicable.
authors.affiliation: Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan.
authors.forename: N
authors.initials: N
authors.lastname: Chowdhury
authors.forename: M
authors.initials: M
authors.lastname: Asakura
authors.forename: S B
authors.initials: SB
authors.lastname: Neogi
authors.forename: A
authors.initials: A
authors.lastname: Hinenoya
authors.forename: S
authors.initials: S
authors.lastname: Haldar
authors.forename: T
authors.initials: T
authors.lastname: Ramamurthy
authors.forename: B L
authors.initials: BL
authors.lastname: Sarkar
authors.forename: S M
authors.initials: SM
authors.lastname: Faruque
authors.forename: S
authors.initials: S
authors.lastname: Yamasaki
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis; D015373:Bacterial Typing Techniques / Q000379:methods*; D016172:DNA Fingerprinting / Q000379:methods; D004269:DNA, Bacterial / Q000032:analysis; D016521:Electrophoresis, Gel, Pulsed-Field; D014644:Genetic Variation; D032023:Integrons; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA; D014734:Vibrio cholerae / Q000145:classification* / Q000235:genetics
chemical_list: D004269:DNA, Bacterial