Genomic diversity in Mycobacterium avium: Single nucleotide polymorphisms between the S and C strains of M. avium subsp. paratuberculosis and with M. a. avium

Molecular and Cellular Probes

Volumn 21, Issue 1, 2007, Pages 66-75

  Marsh, I B ^a   Whittington, R J ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Genome comparison; in silico; Johne's disease; Mycobacterium avium subsp. avium; Mycobacterium avium subsp. paratuberculosis; Single nucleotide polymorphism (SNP)

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING) B; HEAT SHOCK PROTEIN 65; HEAT SHOCK PROTEIN 70; POLYKETIDE SYNTHASE; RNA POLYMERASE BETA SUBUNIT; SUPEROXIDE DISMUTASE;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; CATTLE; CONTROLLED STUDY; DNAA GENE; DNAN GENE; GENE; GENE FREQUENCY; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; GYRB GENE; HSP65 GENE; INHA GENE; MYCOBACTERIUM AVIUM; MYCOBACTERIUM PARATUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PKS8 GENE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RECF GENE; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; SODA GENE;

ANIMALS; BASE SEQUENCE; CATTLE; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM AVIUM; MYCOBACTERIUM PARATUBERCULOSIS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SHEEP;

BOS TAURUS; MYCOBACTERIUM AVIUM; MYCOBACTERIUM AVIUM SUBSP. AVIUM; MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS; OVIS ARIES;

EID: 33845186091     PISSN: 08908508     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mcp.2006.08.002     Document Type: Article

References (58)

1. Collins D.M., Gabric D.M., and de Lisle G.W. Identification of two groups of Mycobacterium paratuberculosis strains by restriction endonuclease analysis and DNA hybridization. J Clin Microbiol 28 (1990) 1591-1596
2. Marsh I.B., Bannantine J.P., Paustian M.L., Tizard M.L., Kapur V., and Whittington R.J. Genomic comparison of Mycobacterium avium subsp. paratuberculosis sheep and cattle strains by microarray hybridization,. J Bacteriol 188 (2006) 2290-2293
3. Marsh I.B., and Whittington R.J. Deletion of an mmpL gene and multiple associated genes from the genome of the S strain of Mycobacterium avium subsp. paratuberculosis identified by representational difference analysis and in silico analysis,. Mol Cell Probes 19 (2005) 371-384
4. Dohmann K., Strommenger B., Stevenson K., de Juan L., Stratmann J., Kapur V., Bull T.J., and Gerlach G.F. Characterization of genetic differences between Mycobacterium avium subsp. paratuberculosis type I and type II isolates. J Clin Microbiol 41 (2003) 5215-5223
5. Behr M.A., Schroeder B.G., Brinkman J.N., Slayden R.A., and Barry III C.E. A point mutation in the mma3 gene is responsible for impaired methoxymycolic acid production in Mycobacterium bovis BCG strains obtained after 1927. J Bacteriol 182 (2000) 3394-3399
6. Collins D.M., Kawakami R.P., de Lisle G.W., Pascopella L., Bloom B.R., and Jacobs Jr. W.R. Mutation of the principal sigma factor causes loss of virulence in a strain of the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA 92 (1995) 8036-8040
7. Alland D., Whittam T.S., Murray M.B., Cave M.D., Hazbon M.H., Dix K., Kokoris M., Duesterhoeft A., Eisen J.A., Fraser C.M., and Fleischmann R.D. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J Bacteriol 185 (2003) 3392-3399
8. Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J., DeBoy R., Dodson R., Gwinn M., Haft D., Hickey E., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M., Salzberg S.L., Delcher A., Utterback T., Weidman J., Khouri H., Gill J., Mikula A., Bishai W., Jacobs Jr. W.R., Venter J.C., and Fraser C.M. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 184 (2002) 5479-5490
9. Gutacker M.M., Smoot J.C., Migliaccio C.A., Ricklefs S.M., Hua S., Cousins D.V., Graviss E.A., Shashkina E., Kreiswirth B.N., and Musser J.M. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics 162 (2002) 1533-1543
10. Hughes A.L., Friedman R., and Murray M. Genome wide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis. Emerg Infect Dis 8 (2002) 1342-1346
11. Stevenson K., Hughes V.M., de Juan L., Inglis N.F., Wright F., and Sharp J.M. Molecular characterization of pigmented and nonpigmented isolates of Mycobacterium avium subsp. paratuberculosis. J Clin Microbiol 40 (2002) 1798-1804
12. Whittington R., Marsh I., Choy E., and Cousins D. Polymorphisms in IS1311, an insertion sequence common to Mycobacterium avium and M. avium subsp. paratuberculosis, can be used to distinguish between and within these species. Mol Cell Probes 12 (1998) 349-358
13. Marsh I., Whittington R., and Cousins D. PCR-restriction endonuclease analysis for identification and strain typing of Mycobacterium avium subsp. paratuberculosis and Mycobacterium avium subsp. avium based on polymorphisms in IS1311. Mol Cell Probes 13 (1999) 115-126
14. Whittington R.J., Marsh I.B., and Whitlock R.H. Typing of IS1311 polymorphisms confirms that bison (Bison bison) with paratuberculosis in Montana are infected with a strain of Mycobacterium avium subsp. paratuberculosis distinct from that occurring in cattle and other domesticated livestock,. Mol Cell Probes 15 (2001) 139-145
15. Sevilla I., Singh S.V., Garrido J.M., Aduriz G., Rodriguez S., Geijo M.V., Whittington R.J., Saunders V., Whitlock R.H., and Juste R.A. Molecular typing of Mycobacterium avium subspecies paratuberculosis strains from different hosts and regions. Rev Sci Tech 24 (2005) 1061-1066
16. Turenne C.Y., Semret M., Cousins D.V., Collins D.M., and Behr M.A. Sequencing of hsp65 distinguishes among subsets of the Mycobacterium avium complex. J Clin Microbiol 44 (2006) 433-440
17. Whittington R.J., Marsh I., McAllister S., Turner M.J., Marshall D.J., and Fraser C.A. Evaluation of modified BACTEC 12B radiometric medium and solid media for culture of Mycobacterium avium subsp. paratuberculosis from sheep. J Clin Microbiol 37 (1999) 1077-1083
18. Choy E., Whittington R.J., Marsh I., Marshall J., and Campbell M.T. A method for purification and characterisation of Mycobacterium avium subsp. paratuberculosis from the intestinal mucosa of sheep with Johne's disease,. Vet Microbiol 64 (1998) 51-60
19. Kim B.J., Lee S.H., Lyu M.A., Kim S.J., Bai G.H., Chae G.T., Kim E.C., Cha C.Y., and Kook Y.H. Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol 37 (1999) 1714-1720
20. el-Zaatari F.A., Naser S.A., Engstrand L., Burch P.E., Hachem C.Y., Whipple D.L., and Graham D.Y. Nucleotide sequence analysis and seroreactivities of the 65 K heat shock protein from Mycobacterium paratuberculosis. Clin Diagn Lab Immunol 2 (1995) 657-664
21. Koets A.P., Rutten V.P., de Boer M., Bakker D., Valentin-Weigand P., and van Eden W. Differential changes in heat shock protein-, lipoarabinomannan-, and purified protein derivative-specific immunoglobulin G1 and G2 isotype responses during bovine Mycobacterium avium subsp. paratuberculosis infection. Infect Immun 69 (2001) 1492-1498
22. Cobb A.J., and Frothingham R. The GroES antigens of Mycobacterium avium and Mycobacterium paratuberculosis. Vet Microbiol 67 (1999) 31-35
23. Liu X., Feng Z., Harris N.B., Cirillo J.D., Bercovier H., and Barletta R.G. Identification of a secreted superoxide dismutase in Mycobacterium avium ssp. paratuberculosis. FEMS Microbiol Lett 202 (2001) 233-238
24. Zhang Y., Heym B., Allen B., Young D., and Cole S. The catalase-peroxidase gene and isoniazid resistance of Mycobacterium tuberculosis. Nature 358 (1992) 591-593
25. Dheenadhayalan V., Shin K.S., Chang C.F., Chang C.D., Wang S.J., McDonough S., McDonough P., Stehman S., Shin S., Torres A., and Chang Y.F. Cloning and characterization of the genes coding for antigen 85A, 85B and 85C of Mycobacterium avium subsp. paratuberculosis. DNA Seq 13 (2002) 287-294
26. Haile Y., Caugant D.A., Bjune G., and Wiker H.G. Mycobacterium tuberculosis mammalian cell entry operon (mce) homologs in Mycobacterium other than tuberculosis (MOTT). FEMS Immunol Med Microbiol 33 (2002) 125-132
27. Bannantine J.P., and Stabel J.R. Identification of two Mycobacterium avium subspecies paratuberculosis gene products differentially recognised by sera from rabbits immunised with live mycobacteria but not heat-killed mycobacteria. J Med Microbiol 50 (2001) 795-804
28. Poupart P., Coene M., Van Heuverswyn H., and Cocito C. Preparation of a specific RNA probe for detection of Mycobacterium paratuberculosis and diagnosis of Johne's disease. J Clin Microbiol 31 (1993) 1601-1605
29. Gupta S., Pandit S.B., Srinivasan N., and Chatterji D. Proteomics analysis of carbon-starved Mycobacterium smegmatis: induction of Dps-like protein. Protein Eng 15 (2002) 503-512
30. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 (1997) 3389-3402
31. Bull T.J., Hermon-Taylor J., Pavlik I., El-Zaatari F., and Tizard M. Characterization of IS900 loci in Mycobacterium avium subsp. paratuberculosis and development of multiplex PCR typing,. Microbiology 146 (2000) 2185-2197
32. Telenti A., Marchesi F., Balz M., Bally F., Bottger E.C., and Bodmer T. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 31 (1993) 175-178
33. Rozen S, Skaletsky HJ. (Primer3). 1996, 1997, 1998.
34. Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48 (1970) 443-453
35. Lim D.V. Microbiology (1989), West Publing Company, United States of America
36. Whittington R.J., Hope A.F., Marshall D.J., Taragel C.A., and Marsh I. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis: IS900 restriction fragment length polymorphism and IS1311 polymorphism analyses of isolates from animals and a human in Australia. J Clin Microbiol 38 (2000) 3240-3248
37. Bannantine J.P., Baechler E., Zhang Q., Li L., and Kapur V. Genome scale comparison of Mycobacterium avium subsp. paratuberculosis with Mycobacterium avium subsp. avium reveals potential diagnostic sequences. J Clin Microbiol 40 (2002) 1303-1310
38. Li L., Bannantine J.P., Zhang Q., Amonsin A., May B.J., Alt D., Banerji N., Kanjilal S., and Kapur V. The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc Natl Acad Sci USA 102 (2005) 12344-12349
39. Paustian M.L., Kapur V., and Bannantine J.P. Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates. J Bacteriol 187 (2005) 2406-2415
40. Semret M., Alexander D.C., Turenne C.Y., de Haas P., Overduin P., van Soolingen D., Cousins D., and Behr M.A. Genomic polymorphisms for Mycobacterium avium subsp. paratuberculosis diagnostics,. J Clin Microbiol 43 (2005) 3704-3712
41. Semret M., Zhai G., Mostowy S., Cleto C., Alexander D., Cangelosi G., Cousins D., Collins D.M., van Soolingen D., and Behr M.A. Extensive genomic polymorphism within Mycobacterium avium. J Bacteriol 186 (2004) 6332-6334
42. Pavlik I., Horvathova A., Dvorska L., Bartl J., Svastova P., du Maine R., and Rychlik I. Standardisation of restriction fragment length polymorphism analysis for Mycobacterium avium subspecies paratuberculosis. J Microbiol Methods 38 (1999) 155-167
43. Amonsin A., Li L.L., Zhang Q., Bannantine J.P., Motiwala A.S., Sreevatsan S., and Kapur V. Multilocus short sequence repeat sequencing approach for differentiating among Mycobacterium avium subsp. paratuberculosis strains. J Clin Microbiol 42 (2004) 1694-1702
44. Motiwala A.S., Amonsin A., Strother M., Manning E.J., Kapur V., and Sreevatsan S. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolates recovered from wild animal species. J Clin Microbiol 42 (2004) 1703-1712
45. Tanaka A., Hoshinoo K., Hoshino T., and Tagawa Y. Differentiation between bovine and ovine strains of Histophilus somni based on the sequences of 16S rDNA and rpoB gene. J Vet Med Sci 67 (2005) 255-262
46. Eriks I.S., Munck K.T., Besser T.E., Cantor G.H., and Kapur V. Rapid differentiation of Mycobacterium avium and M. paratuberculosis by PCR and restriction enzyme analysis. J Clin Microbiol 34 (1996) 734-737
47. Motiwala A.S., Strother M., Amonsin A., Byrum B., Naser S.A., Stabel J.R., Shulaw W.P., Bannantine J.P., Kapur V., and Sreevatsan S. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis: evidence for limited strain diversity, strain sharing, and identification of unique targets for diagnosis. J Clin Microbiol 41 (2003) 2015-2026
48. Fabre M., Koeck J.L., Le Fleche P., Simon F., Herve V., Vergnaud G., and Pourcel C. High genetic diversity revealed by variable-number tandem repeat genotyping and analysis of hsp65 gene polymorphism in a large collection of "Mycobacterium canettii" strains indicates that the M. tuberculosis complex is a recently emerged clone of "M. canettii". J Clin Microbiol 42 (2004) 3248-3255
49. Goh K.S., Legrand E., Sola C., and Rastogi N. Rapid differentiation of "Mycobacterium canettii" from other Mycobacterium tuberculosis complex organisms by PCR-restriction analysis of the hsp65 gene. J Clin Microbiol 39 (2001) 3705-3708
50. Huard R.C., de Oliveira Lazzarini L.C., Butler W.R., van Soolingen D., and Ho J.L. PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J Clin Microbiol 41 (2003) 1637-1650
51. Sola C., Rastogi N., Gutierrez M.C., Vincent V., Brosch R., and Parsons L. Is Mycobacterium africanum subtype II (Uganda I and Uganda II) a genetically well-defined subspecies of the Mycobacterium tuberculosis complex?. J Clin Microbiol 41 (2003) 1345-1346
52. Misawa N., Allos B.M., and Blaser M.J. Differentiation of Campylobacter jejuni serotype O19 strains from non-O19 strains by PCR. J Clin Microbiol 36 (1998) 3567-3573
53. Kasai H., Ezaki T., and Harayama S. Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 38 (2001) 301-308
54. Hazbon M.H., and Alland D. Hairpin primers for simplified single-nucleotide polymorphism analysis of Mycobacterium tuberculosis and other organisms. J Clin Microbiol 42 (2004) 1236-1242
55. Sreevatsan S., Pan X., Stockbauer K.E., Connell N.D., Kreiswirth B.N., Whittam T.S., and Musser J.M. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci USA 94 (1997) 9869-9874
56. Kapur V., Whittam T.S., and Musser J.M. Is Mycobacterium tuberculosis 15,000 years old?. J Infect Dis 170 (1994) 1348-1349
57. Filliol I., Motiwala A.S., Cavatore M., Qi W., Hazbon M.H., Bobadilla del Valle M., Fyfe J., Garcia-Garcia L., Rastogi N., Sola C., Zozio T., Guerrero M.I., Leon C.I., Crabtree J., Angiuoli S., Eisenach K.D., Durmaz R., Joloba M.L., Rendon A., Sifuentes-Osornio J., Ponce de Leon A., Cave M.D., Fleischmann R., Whittam T.S., and Alland D. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol 188 (2006) 759-772
58. Semret M., Turenne C.Y., de Haas P., Collins D.M., and Behr M.A. Differentiating host-associated variants of Mycobacterium avium by PCR for detection of large sequence polymorphisms. J Clin Microbiol 44 (2006) 881-887