Identification of environmental mycobacteria isolated from Agra, north India by conventional & molecular approaches

Indian Journal of Medical Research

Volumn 129, Issue 4, 2009, Pages 424-431

  Parashar, Deepti ^a   Das, Ram ^a   Chauhan, D S ^a   Sharma, V D ^a   Lavania, Mallika ^a   Yadav, V S ^a   Chauhan, S V S ^a   Katoch, Vishwa Mohan ^a,b,c  

^a DR B R AMBEDKAR UNIVERSITY   (India)

^b GOVERNMENT OF INDIA   (India)

^c INDIAN COUNCIL OF MEDICAL RESEARCH   (India)

Author keywords

Environmental mycobacteria; Gene amplification restriction analysis

Indexed keywords

RNA 16S; RNA 23S; PRIMER DNA; RIBOSOME RNA;

ARTICLE; BACTERIAL GROWTH; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CHEMICAL ANALYSIS; CONTROLLED STUDY; ENVIRONMENT; INDIA; MICROBIAL MORPHOLOGY; MICROBIAL POPULATION DYNAMICS; MICROSPORUM GYPSEUM; MYCOBACTERIUM; MYCOBACTERIUM AVIUM; MYCOBACTERIUM CHELONEI; MYCOBACTERIUM FORTUITUM; MYCOBACTERIUM KANSASII; MYCOBACTERIUM MANITOBENSE; MYCOBACTERIUM MARINUM; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TERRAE; NONHUMAN; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RESTRICTION MAPPING; RNA SEQUENCE; RNA STRUCTURE; SEASONAL VARIATION; SOIL ANALYSIS; SPECIES IDENTIFICATION; WATER SAMPLING; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; CLASSIFICATION; DNA SEQUENCE; GENETICS; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENCE;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; BASE SEQUENCE; DNA PRIMERS; ENVIRONMENTAL MICROBIOLOGY; INDIA; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM; RNA, RIBOSOMAL; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 70149105369     PISSN: 09715916     EISSN: 09715916     Source Type: Journal    
DOI: None     Document Type: Article

References (40)

1. Falkinham JO 3rd. Epidemiology of infection by nontuberculous mycobacteria. Clin Microbiol Rev 1996; 9: 177-215.
2. Kazda JF. The principles of the ecology of mycobacteria. In: Ratledge C, Stanford J, editors. The biology of mycobacteria, Vol. II. London, United Kingdom: Academic Press; 1983. p. 323-41.
3. Le Dantec C, Duguet JP, Montiel A, Dumoutier N, Dubrou S, Vincent V. Occurrence of mycobacteria in water treatment lines and in water distribution systems. Appl Environ Microbiol 2002; 68: 5318-25.
4. Katoch VM, Mohan Kumar T. Atypical mycobacterial infections. In: Sharma SK, editor. Tuberculosis, 1st ed. New Delhi: Jaypee Brothers Medical Publishers (P) Ltd.; 2001. p. 439-51.
5. Katoch VM. Infections due to non-tuberculous mycobacteria (NTM). Indian J Med Res 2004; 120: 290-304.
6. Wolinsky E. Nontuberculous mycobacteria and associated diseases. Am Rev Respir Dis 1979; 119: 107-59.
7. Kaur H, Chitkara NL. A study of mycobacteria including acid fast bacilli (culture and biochemical characteristic). Indian J Tuberc 1964; 12: 16-8.
8. Chakrabarti A, Sharma M, Dubey ML. Isolation rates of different mycobacterial species from Chandigarh (North India). Indian J Med Res 1990; 91: 111-4.
9. Singh S, Rattan A, Kumar S. Severe cutaneous Mycobacterium chelonei infection following a yellow jacket sting. Tuber Lung Dis 1992; 73: 305-6.
10. Sachdeva R, Gadre DV, Talwar V. Characterisation & drug susceptibility patterns of extrapulmonary mycobacterial isolates. Indian J Med Res 2002; 115: 102-7.
11. Katoch K, Katoch VM, Dutta AK, Sharma VD, Ramu G. Chest infection due to M. fortuitum in a case of lepromatous leprosy - a case report. Indian J Lepr 1985; 57: 399-403.
12. Sharma M, Gupta V, Ray P. Present status of mycobacterial species in Chandigarh. Bull PGI 1997; 31: 50-3.
13. Stanford JL, Paul RC, Penketh A, Thurlow S, Carswell JW, Barker DJP, et al. A preliminary study of the effect of contact with environmental mycobacteria on the pattern of sensitivity to a range of new tuberculins amongst Ugandan adults. J Hyg (London) 1976; 76: 205-14.
14. Stanford JL, Shield MJ, Rook GA. How environmental mycobacteria may predetermine the protective efficacy of BCG. Tubercle 1981; 62: 55-62.
15. Stanford JL, Rook GAW. Environmental mycobacteria and immunization with BCG. In: Easmon CSF, Jeljaszewicz J, editors. Medical microbiology, Vol. II. London: Academic Press; 1983. p. 55-62.
16. Brandt L, Feino Cunha J, Weinreicholsen A, Chilima B, Hirsch P, Appelberg R, et al. Failure of the Mycobacterium bovis BCG vaccine: some species of environmental mycobacteria block multiplication of BCG and induction of protective immunity to tuberculosis. Infect Immun 2002; 70: 672-8.
17. Kamala T, Paramasivan CN, Herbert D, Venkatesan P, Prabhakar R. Isolation and identification of environmental mycobacteria in the Mycobacterium bovis BCG trial area of South India. Appl Environ Microbiol 1994; 60: 2180-3.
18. Gupte MD. South India immunoprophylaxis trial against leprosy: relevance of findings in the context of leprosy trends. Int J Lepr Other Mycobact Dis 2001; 69 (2 Suppl): S10-3.
19. Sharma P, Mukherjee R, Talwar GP, Sarathchandra KG, Walia R, Parida SC, et al. Immunoprophylactic effects of the anti-leprosy Mw vaccine in household contacts of leprosy patients: clinical field trials with a follow up of 8-10 years. Lepr Rev 2005; 76: 127-43.
20. Primm TP, Lucero CA, Falkinham J 3rd. Health impacts of environmental mycobacteria. Clin Microbiol Rev 2004; 17: 98-106.
21. Parashar D, Chauhan DS, Sharma VD, Chauhan A, Chauhan SV, Katoch VM. Optimization of procedures for isolation of mycobacteria from soil and water samples obtained in northern India. Appl Environ Microbiol 2004; 70: 3751-3.
22. Steed KA, Falkinham JO 3rd. Effect of growth in biofilms on chlorine susceptibility of Mycobacterium avium and Mycobacterium intracellulare. Appl Environ Microbiol 2006; 72: 4007-11.
23. Tortoli E, Bartoloni A, Bottger EC, Emler S, Garzelli C, Magliano E. Burden of unidentifiable mycobacteria in a reference laboratory. J Clin Microbiol 2001; 39: 4058-65.
24. Lappayawichit P, Rienthong S, Rienthong D, Chuchottaworn C, Chaiprasert A, Panbangrid W, et al. Differentiation of Mycobacterium species by restriction enzyme analysis of amplified 16S-23S ribosomal DNA spacer sequences. Tuber Lung Dis 1996; 77: 257-63.
25. Park H, Jang H, Kim C, Chung B, Chang CL, Park SK, et al. Detection and identification of mycobacteria by amplification of the internal transcribed spacer regions with genus- and species-specific PCR primers. J Clin Microbiol 2000; 38: 4080-5.
26. Roth A, Reischl U, Streubel A, Naumann L, Kroppenstedt RM, Habicht M, et al. Novel diagnostic algorithm for identification of mycobacteria using genus-specific amplification of the 16S-23S rRNA gene spacer and restriction endonucleases. J Clin Microbiol 2000; 38: 1094-104.
27. van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting recommendations for a standardized methodology. J Clin Microbiol 1993; 31: 406-9.
28. Khan IU, Selvaraju SB, Yadav JS. Method for rapid identification and differentiation of the species of the Mycobacterium chelonae complex based on 16S-23S rRNA gene internal transcribed spacer PCR-restriction analysis. Clin Microbiol 2005; 43: 4466-72.
29. Selvaraju SB, Khan IU, Yadav JS. A new method for species identification and differentiation of Mycobacterium chelonae complex based on amplified hsp65 restriction analysis (AHSPRA). Mol Cell Probes 2005; 19: 93-9.
30. Vestal AL. In: Procedure for isolation and identification of mycobacteria. 1997 US Department of Health, Education and Welfare, Atlanta, Georgia. Publication No. CDC 77-8230.
31. Katoch VM, Parashar D, Chauhan DS, Singh D, Sharma VD, Ghosh S. Rapid identification of mycobacteria by gene amplification restriction analysis technique targeting 16S-23S ribosomal RNA internal transcribed spacer and flanking region. Indian J Med Res 2007; 125: 155-62.
32. Edwards U, Rogall T, Blocker H, Emde M, Bottger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17: 7843-53.
33. Devallois A, Goh KS, Rastogi N. Rapid identification of mycobacteria to species level by PCR-restriction fragment length polymorphism analysis of the hsp65 gene and proposition of an algorithm to differentiate 34 mycobacterial species. J Clin Micorbiol 1997; 35: 2969-73.
34. Telenti A, Marchesi F, Balz M, Bally F, Bottger EC, Bodmer T. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 1993; 31: 175-8.
35. Kim BJ, Lee KH, Park BN, Kim SJ, Bai GH, Kim SJ, et al. Differentiation of mycobacterial species by PCR- restriction analysis of DNA (342 base pairs) of the RNA polymerase gene (rpo B). J Clin Microbiol 2001; 39: 2102-9.
36. Takewaki S, Okuzumi K, Manabe I, Tanimura M, Miyamura K, Nakahara K, et al. Nucleotide sequence comparison of the mycobacterial dnaJ gene and PCR restriction fragment length polymorphism analysis for identification of mycobacterial species. Int J Syst Bacteriol 1994; 44: 159-66.
37. Soini H, Viljanen MK. Diversity of the 32- kilodalton protein gene may form a basis for species determination of potentially pathogenic mycobacterial species. J Clin Microbiol 1997; 35: 769-73.
38. Vaneechoutte M, De Beanhouwer H, Claeys G, Verschraegen G, De Rouck A, Paepe N, et al. Identification of mycobacterium species by using amplified ribosomal DNA restriction analysis. J Clin Microbiol 1993; 31: 2061-5.
39. Dobner P, Feldmann K, Rifai M, Loscher T, Rinder H. Rapid identification of mycobacterial species by PCR amplification of hypervariable 16S rRNA gene promoter region. J Clin Microbiol 1996; 34: 866-9.
40. Zelazny AM, Calhoun LB, Li L, Shear YR, Fischer SH. Identification of mycobacterium species by Sec A 1 sequences. J Clin Microbiol 2005; 43: 1051-8.