Mycobacterium avium subsp. paratuberculosis and M. avium subsp. avium are independently evolved pathogenic clones of a much broader group of M. avium organisms

Journal of Bacteriology

Volumn 190, Issue 7, 2008, Pages 2479-2487

  Turenne, Christine Y ^a   Collins, Desmond M ^b   Alexander, David C ^a   Behr, Marcel A ^a,c  

^a MCGILL UNIVERSITY HEALTH CENTRE   (Canada)

^b AGRESEARCH   (New Zealand)

^c MONTREAL GENERAL HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; GENE LOCUS; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; MOLECULAR CLONING; MULTILOCUS SEQUENCE TYPING; MYCOBACTERIUM AVIUM; NONHUMAN; PARATUBERCULOSIS; PHYLOGENY; PRIORITY JOURNAL;

BACTERIAL PROTEINS; DNA, BACTERIAL; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM AVIUM; MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SUPEROXIDE DISMUTASE;

MYCOBACTERIUM AVIUM; MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS;

EID: 41549146303     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01691-07     Document Type: Article

References (41)

1. Achtman, M., G. Morelli, P. Zhu, T. Wirth, I. Diehl, B. Kusecek, A. J. Vogler, D. M. Wagner, C. J. Allender, W. R. Easterday, V. Chenal-Francisque, P. Worsham, N. R. Thomson, J. Parkhill, L. E. Lindler, E. Carniel, and P. Keim. 2004. Microevolution and history of the plague bacillus, Yersinia pestis. Proc. Natl. Acad. Sci. USA 101:17837-17842.
2. Angenent, L. T., S. T. Kelley, A. St. Amand, N. R. Pace, and M. T. Hernandez. 2005. Molecular identification of potential pathogens in water and air of a hospital therapy pool. Proc. Natl. Acad. Sci. USA 102:4860-4865.
3. Bartos, M., P. Hlozek, P. Svastova, L. Dvorska, T. Bull, L. Matlova, I. Parmova, I. Kuhn, J. Stubbs, M. Moravkova, J. Kintr, V. Beran, I. Melicharek, M. Ocepek, and I. Pavlik. 2006. Identification of members of Mycobacterium avium species by Accu-Probes, serotyping, and single IS900, IS901, IS1245 and IS901-flanking region PCR with internal standards. J. Microbiol. Methods 64:333-345.
4. Collins, D. M., D. M. Gabric, and G. W. de Lisle. 1990. Identification of two groups of Mycobacterium paratuberculosis strains by restriction endonuclease analysis and DNA hybridization. J. Clin. Microbiol. 28:1591-1596.
5. de Lisle, G. W., D. M. Collins, and H. F. Huchzermeyer. 1992. Characterization of ovine strains of Mycobacterium paratuberculosis by restriction endonuclease analysis and DNA hybridization. Onderstepoort. J. Vet. Res. 59:163-165.
6. de Lisle, G. W., B. J. Wards, B. M. Buddle, and D. M. Collins. 2005. The efficacy of live tuberculosis vaccines after presensitization with Mycobacterium avium. Tuberculosis 85:73-79.
7. Diavatopoulos, D. A., C. A. Cummings, L. M. Schouls, M. M. Brinig, D. A. Relman, and F. R. Mooi. 2005. Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica. PLoS Pathog. 1:e45.
8. Falkinham, J. O., III, C. D. Norton, and M. W. LeChevallier. 2001. Factors influencing numbers of Mycobacterium avium, Mycobacterium intracellulare, and other mycobacteria in drinking water distribution systems. Appl. Environ. Microbiol. 67:1225-1231.
9. Gutacker, M. M., J. C. Smoot, C. A. Migliaccio, S. M. Ricklefs, S. Hua, D. V. Cousins, E. A. Graviss, E. Shashkina, B. N. Kreiswirth, and J. M. Musser. 2002. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics 162:1533-1543.
10. Huson, D. H., and T. H. Kloepper. 2005. Computing recombination networks from binary sequences. Bioinformatics 21(Suppl. 2):ii159-ii165.
11. Jolley, K. A., E. J. Feil, M. S. Chan, and M. C. Maiden. 2001. Sequence type analysis and recombinational tests (START). Bioinformatics 17:1230-1231.
12. Kidgell, C., U. Reichard, J. Wain, B. Linz, M. Torpdahl, G. Dougan, and M. Achtman. 2002. Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old. Infect. Genet. Evol. 2:39-45.
13. Kirschner, R. A., Jr., B. C. Parker, and J. O. Falkinham III. 1992. Epidemiology of infection by nontuberculous mycobacteria. Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum in acid, brown-water swamps of the southeastern United States and their association with environmental variables. Am. Rev. Respir. Dis. 145:271-275.
14. Krzywinska, E., J. Krzywinski, and J. S. Schorey. 2004. Naturally occurring horizontal gene transfer and homologous recombination in Mycobacterium. Microbiology 150:1707-1712.
15. Kunze, Z. M., F. Portaels, and J. J. Mcfadden. 1992. Biologically distinct subtypes of Mycobacterium avium differ in possession of insertion sequence IS901. J. Clin. Microbiol. 30:2366-2372.
16. Li, L., J. P. Bannantine, Q. Zhang, A. Amonsin, B. J. May, D. Alt, N. Banerji, S. Kanjilal, and V. Kapur. 2005. The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc. Natl. Acad. Sci. USA 102:12344-12349.
17. Maiden, M. C., J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell, R. Urwin, Q. Zhang, J. Zhou, K. Zurth, D. A. Caugant, I. M. Feavers, M. Achtman, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:3140-3145.
18. Marsh, I. B., and R. J. Whittington. 2007. Genomic diversity in Mycobacterium avium: single nucleotide polymorphisms between the S and C strains of M. avium subsp. paratuberculosis and with M. a. avium. Mol. Cell. Probes 21:66-75.
19. Martin, D. P., C. Williamson, and D. Posada. 2005. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260-262.
20. Matlova, L., L. Dvorska, W. Y. Ayele, M. Bartos, T. Amemori, and I. Pavlik. 2005. Distribution of Mycobacterium avium complex isolates in tissue samples of pigs fed peat naturally contaminated with mycobacteria as a supplement. J. Clin. Microbiol. 43:1261-1268.
21. Matlova, L., L. Dvorska, K. Palecek, L. Maurenc, M. Bartos, and I. Pavlik. 2004. Impact of sawdust and wood shavings in bedding on pig tuberculous lesions in lymph nodes, and IS1245 RFLP analysis of Mycobacterium avium subsp. hominissuis of serotypes 6 and 8 isolated from pigs and environment. Vet. Microbiol. 102:227-236.
22. Mijs, W., P. de Haas, R. Rossau, L. T. Van der, L. Rigouts, F. Portaels, and D. van Soolingen. 2002. Molecular evidence to support a proposal to reserve the designation Mycobacterium avium subsp. avium for bird-type isolates and 'M. avium subsp. hominissuis' for the human/porcine type of M. avium. Int. J. Syst. Evol. Microbiol. 52:1505-1518.
23. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
24. Padidam, M., S. Sawyer, and C. M. Fauquet. 1999. Possible emergence of new geminiviruses by frequent recombination. Virology 265:218-225.
25. Pavlik, I., A. Horvathova, L. Dvorska, J. Bartl, P. Svastova, R. du Maine, and I. Rychlik. 1999. Standardisation of restriction fragment length polymorphism analysis for Mycobacterium avium subspecies paratuberculosis. J. Microbiol. Methods 38:155-167.
26. Rocha, E. P., J. M. Smith, L. D. Hurst, M. T. Holden, J. E. Cooper, N. H. Smith, and E. J. Feil. 2006. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J. Theor. Biol. 239:226-235.
27. Rozas, J., J. C. Sanchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
28. Semret, M., D. C. Alexander, C. Y. Turenne, P. de Haas, P. Overduin, D. van Soolingen, D. Cousins, and M. A. Behr. 2005. Genomic polymorphisms for Mycobacterium avium subsp. paratuberculosis diagnostics. J. Clin. Microbiol. 43:3704-3712.
29. Semret, M., C. Y. Turenne, P. de Haas, D. M. Collins, and M. A. Behr. 2006. Differentiating host-associated variants of Mycobacterium avium by PCR for detection of large sequence polymorphisms. J. Clin. Microbiol. 44:881-887.
30. Semret, M., G. Zhai, S. Mostowy, C. Cleto, D. Alexander, G. Cangelosi, D. Cousins, D. M. Collins, D. van Soolingen, and M. A. Behr. 2004. Extensive genomic polymorphism within Mycobacterium avium. J. Bacteriol. 186:6332-6334.
31. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
32. Thorel, M. F., M. Krichevsky, and V. V. Levy-Frebault. 1990. Numerical taxonomy of mycobactin-dependent mycobacteria, emended description of Mycobacterium avium, and description of Mycobacterium avium subsp. avium subsp. nov., Mycobacterium avium subsp. paratuberculosis subsp. nov., and Mycobacterium avium subsp. silvaticum subsp. nov. Int. J. Syst. Bacteriol. 40:254-260.
33. Turenne, C. Y., M. Semret, D. V. Cousins, D. M. Collins, and M. A. Behr. 2006. Sequencing of hsp65 distinguishes among subsets of the Mycobacterium avium complex. J. Clin. Microbiol. 44:433-440.
34. Turenne, C. Y., R. Wallace, Jr., and M. A. Behr. 2007. Mycobacterium avium in the postgenomic era. Clin. Microbiol. Rev. 20:205-229.
35. Vaerewijck, M. J., G. Huys, J. C. Palomino, J. Swings, and F. Portaels. 2005. Mycobacteria in drinking water distribution systems: ecology and significance for human health. FEMS Microbiol. Rev. 29:911-934.
36. van Soolingen, D., P. E. de Haas, P. W. Hermans, and J. D. van Embden. 1994. DNA fingerprinting of Mycobacterium tuberculosis. Methods Enzymol. 235:196-205.
37. Wasem, C. F., C. M. McCarthy, and L. W. Murray. 1991. Multilocus enzyme electrophoresis analysis of the Mycobacterium avium complex and other mycobacteria. J. Clin. Microbiol. 29:264-271.
38. Whittington, R. J., A. F. Hope, D. J. Marshall, C. A. Taragel, and I. Marsh. 2000. 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. 38:3240-3248.
39. Wu, C. W., J. Glasner, M. Collins, S. Naser, and A. M. Talaat. 2006. Whole-genome plasticity among Mycobacterium avium subspecies: insights from comparative genomic hybridizations. J. Bacteriol. 188:711-723.
40. Yakrus, M. A., M. W. Reeves, and S. B. Hunter. 1992. Characterization of isolates of Mycobacterium avium serotypes 4 and 8 from patients with AIDS by multilocus enzyme electrophoresis. J. Clin. Microbiol. 30:1474-1478.
41. Yip, M. J., J. L. Porter, J. A. Fyfe, C. J. Lavender, F. Portaels, M. Rhodes, H. Kator, A. Colorni, G. A. Jenkin, and T. Stinear. 2007. Evolution of Mycobacterium ulcerans and other mycolactone-producing mycobacteria from a common Mycobacterium marinum progenitor. J. Bacteriol. 189:2021-2029.