Application of DNA-based methods in typing Vibrio cholerae strains

Future Microbiology

Volumn 3, Issue 1, 2008, Pages 87-96

  Singh, Drug V ^a   Mohapatra, Harapriya ^a  

^a INSTITUTE OF LIFE SCIENCES   (India)

Author keywords

AFLP; ERIC PCR; Microarray; MLST; PFGE; Ribotyping; Vibrio cholerae

Indexed keywords

ANTIINFECTIVE AGENT; BACTERIAL DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BIODIVERSITY; CHOLERA; COMPARATIVE GENOMIC HYBRIDIZATION; CONSENSUS SEQUENCE; DNA DNA HYBRIDIZATION; DNA MICROARRAY; DNA SEQUENCE; GENE AMPLIFICATION; GENOMIC INSTABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; INTERMETHOD COMPARISON; MULTILOCUS SEQUENCE TYPING; NONHUMAN; OPEN READING FRAME; PATHOGENESIS; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; RIBOTYPING; STRAIN DIFFERENCE; STRAIN IDENTIFICATION; TOXICOGENETICS; VIBRIO CHOLERAE; ANIMAL; BACTERIUM IDENTIFICATION; CLASSIFICATION; DRUG EFFECT; GENETICS; HUMAN; METHODOLOGY; MICROBIOLOGY;

VIBRIO CHOLERAE;

ANIMALS; BACTERIAL TYPING TECHNIQUES; CHOLERA; DNA, BACTERIAL; GENOTYPE; HUMANS; VIBRIO CHOLERAE;

EID: 39049148087     PISSN: 17460913     EISSN: None     Source Type: Journal    
DOI: 10.2217/17460913.3.1.87     Document Type: Review

References (51)

1. Colwell RR, Kaper J, Joseph SW: Vibrio cholerae, Vibrio parahaemolyticus, and other vibrios: occurrence and distribution in Chesapeake Bay. Science 198, 394-396 (1977).
2. Islam MS, Drasar BS, Sack RB: The aquatic flora and fauna as reservoir of Vibrio cholerae. a review. J. Diarrhoeal Dis. Res. 12, 87-96 (1994).
3. Kaper JB, Morris JG Jr, Levine MM: Cholera. Clin. Microbiol. Rev. 8, 48-86 (1995).
4. Faruque SM, Albert MJ, Mekalanos JJ: Epidemiology, genetics, and ecology of toxigenic Vibrio cholerae. Microbdol Mol. Biol. Rev. 62, 1301-1314 (1998).
5. Sack DA, Sack RB, Nair GB, Siddique AK: Cholera. Lancet 363, 223-233 (2004).
6. Faruque SM, Chowdhury N, Kamruzzaman M et al.: Genetic diversity and virulence potential of environmental V. cholerae population in a cholera-endemic area. Proc. Natl. Acad. Sci. USA 15, 2123-2128 (2004).
7. Scrascia M, Maimone F, Mohamud KA et al.: Clonal relationship among Vibrio cholerae O1 E1 Tor strain causing the largest cholera epidemic in Kenya in late 1990s. J. Clin. Microbiol. 44, 3401-3404 (2006)
8. Faruque SM, Tam VC, Chowdhury N et ai.: Genomic analysis of the Mozambique strains of Vibrio cholerae O1 reveal the origin of E1 Tor strains carrying classical CTX prophage. Proc. Natl Acad. Sci. USA 104, 5151-5156 (2007).
9. Ramamurthy T, Garg S, Sharma R et al.: Emergence of novel strain of V. cholerae with epidemic potential in southern and eastern India. Lancet 341, 703-704 (1993).
10. Faruque SM, Sack DA, Sack BR, Colwell RR, Takeda Y, Nair GB: Emergence and evolution of V. cholerae O139 Proc. Natl Acad. Sd. USA 100, 304-309 (2003). ae.
11. Mantri CK, Mohapatra SS, Ramamurthy T, Ghosh R, Colwell RR, Singh DV: Septaplex PCR assay for rapid detection of Vibrio cholerae including detection of virulence and intSXT genes. FEMS Microbiol. Lett. 265, 208-214 (2006).
12. Karaolis DKR, Lan R, Reeves PR: The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae. J. Bacteriol. 177, 3191-3198 (1995).
13. Bag PK, Maiti S, Sharma C et al.: Rapid spread of new clone of Vibrio cholerae O1 biotype E1 Tor in cholera endemic areas in India. Epidemiol. Infect. 121, 245-251 (1998).
14. Cooper KL, Lucy CK, Bird M et al.: Development and validation of a Pulsenet standardized pulse field gel electrophoresis protocol for sub-typing of Vibrio cholerae. Foodborne Pathog. Dis. 3, 51-58 (2006).
15. Safa A, Bhuiyan NA, Alam M, Sack DA, Nair GB: Genomic relatedness of the new Matlab variants of Vibrio cholerae O1 to the classical and E1 Tor biotypes as determined by pulse field gel electrophoresis. J. Clin. Microbiol. 43, 1401-1404 (2005).
16. Yamasaki S, Nair GB, Bhattacharya SK, Yamamoto S, Kurazono H, Takeda Y: Cryptic appearance of a new clone of Vibrio cholerae serogroup O1 biotype E1 Tor in Calcutta, India. Microbiol. Immunol. 41, 1-6 (1997).
17. Chatterjee S, Ghosh K, Raychoudhuri A et al.: Phenotypic and genotypic traits and epidemiological implication of Vibrio cholerae O1 and O139 strains in India during 2003. J. Med. Microbiol. 56, 824-832 (2007).
18. Chakraborty S, Garg P, Ramamurthy T et al.: Comparison of antibiogram, virulence genes, ribotypes and DNA fingerprints of V. cholerae of matching serogroups isolated from hospitalized diarrhoea cases and from the environment during 1997-98 in Calcutta, India. J. Med. Microbiol. 50, 879-888 (2001).
19. Popovic T, Bopp C, Olsvik Ø. Wachsmuth K: Epidemiologic application of a standardized ribotype scheme for V. cholerae O1. J. Clin. Microbiol. 31, 2474-2482 (1993).
20. Sharma, C, Nair GB, Mukhopadhyay AK, Bhattacharya SK, Ghosh RK, Ghosh A: Molecular characterization of V. cholerae O1 biotype E1 Tor strains isolated between 1992 and 1995 in Calcutta, India: evidence for the emergence of a new clone of the E1 Tor biotype. J. Infect. Dis. 175, 1134-1141 (1997).
21. Faruque SM, Islam MJ, Ahmad QS, Biswas K: An improved technique for isolation of environmental Vibrio cholerae with epidemic potential: monitoring the emergence of a multiple-antibiotic-resistant epidemic strain in Bangladesh. J. Infect. Dis. 193, 1029-1036 (2006).
22. Dutta B, Ghosh R, Sharma NC et al.: Spread of cholera with newer clones of Vibrio cholerae O1 E1 Tor serotype Inaba in India. J. Clin. Microbiol. 44, 3391-3393 (2006).
23. Mohapatra SS, Ramachandran D, Mantri CK, Singh DV: Characterization of genetic background of Vibrio cholerae O1 biotype E1 Tor serotype Inaba strains isolated in Trivandrum, southern India. J. Med. Microbiol. 56, 260-265 (2007).
24. Faruque SM, Ahmed KM, Abdul Alim AR, Qadri F, Siddique AK, Albert MJ: Emergence of a new clone of toxigenic V. cholerae O1 biotype E1 Tor displacing V. cholerae O139 Bengal in Bangladesh. J. Clin. Microbiol. 35, 624-630 (1997).
25. Faruque SM, Siddique AK, Saha MN et al.: Molecular characterization of a new ribotype of V. cholerae O139 Bengal associated with an outbreak of cholera in Bangladesh. J. Clin. Microbiol. 37, 1313-1318 (1999).
26. Vos P, Hogers R, Bleeker M et al.: AFLP: a new concept for DNA fingerprinting. Nucleic Acids Res. 21, 4407-4414 (1995).
27. Coelho A, Andrade JRC, Vicente ACP, Salles CA: New variant of Vibrio cholerae O1 from clinical isolates in Amazonia. J. Clin. Microbiol. 33, 114-118 (1995).
28. Lan R, Reeves PR: Pandemic spread of cholera: genetic diversity and relationship within the seventh pandemic clones of Vibrio cholerae determined by amplified fragment length polymorphism. J. Clin. Microbiol. 40, 172-181 (2002).
29. Jiang SC, Matte M, Matte G, Huq A, Colwell RR: Genetic diversity of clinical and environmental isolates of V. cholerae determined by amplified fragment length polymorphism (AFLP). Appl. Environ. Microbiol. 66, 148-153 (2000).
30. Thompson FL, Thompson CC, Vicente ACP et al.: Genomic diversity of clinical and environmental Vibrio cholerae strains isolated in Brazil between 1991 and 2001 as revealed by fluorescent amplified fragment length polymorphism analysis. J. Clin. Microbiol. 41, 1946-1950 (2003).
31. Rivera ING, Chowdhury MAR, Huq A, Jacobs D, Martins MT, Colwell RR: Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from V. cholerae O1, O139, and non-O1 strains. Appl. Environ. Microbiol. 61, 2898-2904 (1995).
32. Singh DV, Matte MH, Matte GR et al.: Molecular analysis of V. cholerae O1, O139, non-O1, and non-O139 strains: clonal relationships between clinical and environmental isolates. Appl. Environ. Microbiol. 67, 910-921 (2001).
33. Bhanumathi R, Sabeena F, Isac SR, Radhakutty G, Singh DV: Characterization of a toxigenic Vibrio cholerae O139 strains belonging to a new ribotype and isolated from a diarrheal patient. J. Clin. Microbiol. 40, 4779-4781 (2002).
34. Zo Y, Rivera ING, Russek-Cohen E et al.: Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera endemic areas in Bangladesh. Proc. Natl. Acad. Sci. USA 99, 12409-12414 (2002).
35. Son R, Rusul G, Samuel L et al.: Characterization of Vibrio cholerae O139 Bengal isolated from water in Malaysia. J. Appl. Microbiol. 85, 1075-1077 (1998).
36. Mukhopadhyay AK, Chakraborty S, Takeda Y et al.: Characterization of VPI pathogenicity island and CTXφ prophage in environmental strains of Vibrio cholerae. J. Bacteriol. 183, 4737-4746 (2001).
37. Byun R, Elbourne LDH, Lan R, Reeves PR: Evolutionary relationships of pathogenic clones of Vibrio cholerae by sequence analysis of housekeeping genes. Infect. Immun. 67, 1116-1124 (1999).
38. Farfan M, Minana-Galbis D, Fuste MC, Loreo JG: Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis. J. Bacteriol. 184, 1304-1313 (2002).
39. Danin-Poleg Y, Cohen LA, Ganecz H et al.: Vibrio cholerae strain typing and phylogeny study based on sample sequence repeats. J. Clin. Microbiol. 45, 736-746 (2007).
40. Koletishvili M, Stine OC, Chen Y et al.: Multilocus sequence typing has better discriminatory ability for typing Vibrio cholerae than does pulse field gel electrophoresis and provides measure of phylogenetic relatedness. J. Clin. Microbiol. 41, 2191-2196 (2003).
41. Dziejman M, Balon, E, Boyd D, Fraser CM, Heidelberg JF, Mekalanos JJ: Comparative genomic analysis of Vibrio cholerae genes that correlate with cholera endemic and pandemic disease. Proc. Natl. Acad. Sci. USA 99, 1556-1561 (2002).
42. Thompson FL, Iida T, Swings J: Biodiversity of vibrios. Microbiol. Mol. Biol. Rev. 68, 403-431 (2004).
43. Pang B, Yan M, Cui Z et al.: Genetic diversity of toxigenic and nontoxigenic Vibrio cholerae serogroups O1 and O139 revealed by array-based comparative genomic hybridization. J. Bacteriol. 189, 4837-4849 (2007).
44. Vora GJ, Meador CE, Bird MM et al.: Microarray based detection of genetic heterogeneity, antimicrobial resistance and its viable but nonculturable state in human pathogenic Vibrio spp. Proc. Natl. Acad. Sci. USA 102, 19109-19114 (2005).
45. Keymer DP, Miller MC. Schoolink GK et al.: Genomic and phenotypic diversity of coastal Vibrio cholerae strains is linked to environmental factors. Appl. Environ. Microbiol. 73, 3705-3714 (2007).
46. Davis BM, Kimsey HH, Chang W, Waldor MK: The V. cholerae O139 Calcutta bacteriophage CTXphi is infectious and encodes a novel repressor. J. Bacteriol. 181, 6779-6787 (1999).
47. Nair GB, Faruque SM, Bhuiyan NA, Kamaruzzaman M, Siddique AK, Sack DA: New variants of Vibrio cholerae O1 biotype El Tor with attributes of the classical biotype from hospitalized patients with acute diarrhea in Bangladesh. J. Clin Microbiol. 40, 3296-3299 (2002).
48. Lee JH, Han KH, Choi SY et al.: Multilocus sequence typing (MIST) analysis of Vibrio cholerae O1 El Tor isolates from Mozambique that harbor the classical CTX prophage. J. Med. Microbiol. 55, 165-170 (2006).
49. Nair GB, Qadri F, Holmgren J et al.: Cholera due to altered El Tor strains of Vibrio cholerae O1 in Bangladesh. J. Clin. Microbiol. 44, 4211-4213 (2006).
50. Marchlewicz BA, Finkelstein RA: Immunological differences among cholera/ coli family of enterotoxins. Dign. Microbiol. Infect. Dis. 1, 128-138 (1983).
51. Clements JD, Sack DA, Harris JR et al.: Field trial of oral cholera vaccines in Bangladesh: results from a three year follow up. Lancet 335, 270-273 (1990).