title: Comparative PCR-based fingerprinting of Vibrio cholerae isolated in Malaysia.
abstract: Vibrio cholerae, the causative agent of cholera, is endemic in many parts of the world, especially in countries poor in resources. Molecular subtyping of V. cholerae is useful to trace the regional spread of a clone or multidrug-resistant strains during outbreaks of cholera. Current available PCR-based fingerprinting methods such as Random Amplified Polymorphic DNA (RAPD)-PCR, Enterobacterial Repetitive Intergenic Consensus Sequence (ERIC)-PCR, and Repetitive Extragenic Palindromic (REP)-PCR were used to subtype V. cholerae. However, there are problems for inter-laboratory comparison as these PCR methods have their own limitations especially when different PCR methods have been used for molecular typing. In this study, a Vibrio cholerae Repeats-PCR (VCR-PCR) approach which targets the genetic polymorphism of the integron island of Vibrios was used and compared with other PCR-based fingerprinting methods in subtyping. Forty-three V. cholerae of different serogroups from various sources were tested. The PCR-fingerprinting approaches were evaluated on typeability, reproducibility, stability and discriminatory power. Overall, Malaysian non-O1/non-O139 V. cholerae were more diverse than O1 strains. Four non-O1/non-O139 strains were closely related with O1 strains. The O139 strain in this study shared similarity with strains of both O1 and non-O1/non-O139 serogroups. ERIC-PCR was the most discriminative approach (D value = 0.996). VCR-PCR was useful in discriminating non-O1/non-O139 strains. RAPD-PCR and REP-PCR were less suitable for efficient subtyping purposes as they were not reproducible and lacked stability. The combination of the ERIC-PCR and VCR-PCR may overcome the inadequacy of any one approach and hence provide more informative data.
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Cindy
authors.initials: C
authors.lastname: Shuan Ju Teh
authors.forename: Kwai Lin
authors.initials: KL
authors.lastname: Thong
authors.forename: Ro
authors.initials: R
authors.lastname: Osawa
authors.forename: Kek
authors.initials: K
authors.lastname: Heng Chua
mesh_terms: D002771:Cholera / Q000453:epidemiology* / Q000382:microbiology; D016000:Cluster Analysis; D016172:DNA Fingerprinting / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics; D004196:Disease Outbreaks; D005243:Feces / Q000382:microbiology; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008296:Malaysia / Q000453:epidemiology; D058889:Molecular Typing / Q000379:methods*; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results; D017747:Seafood / Q000382:microbiology; D012680:Sensitivity and Specificity; D014734:Vibrio cholerae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D014871:Water Microbiology
chemical_list: D004269:DNA, Bacterial