1887

Abstract

A polymorphic region was discovered in the genetically uncharacterized opportunistic pathogen . The region contains a novel 17 kb insertion sequence (IS) named ISMab1. ISMab1 contains two complete ORFs and one partial ORF located in segments with over 80% nucleotide identity to IS and IS and to previously unreported IS-like elements from . The marked similarity within this family of elements is supportive of horizontal transfer between environmental mycobacterial species. In clinical isolates, ISMab1 was either present as a single copy or absent. The polymorphic region containing ISMab1 was identified by genomic subtraction between a parental strain and phenotypic variant. The variant has a 142 kb genomic deletion and this is flanked in the parental strain by complex arrays of inverted and direct repeats. Clinical isolates of were probed for the deletion and flanking sequences and two were found to be missing more than 20 kb. No regional deletions were found in the type strain, ATCC 19977. Although is a rapidly growing species, comparative sequence analysis of 23 kb from the polymorphic region showed that most local ORFs have greater amino acid identity to proteins encoded by genes from the slowly growing mycobacteria, and , than to the rapid-grower . Several ORFs also have strong similarity to genes with a potential role in β-oxidation.

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2002-10-01
2024-03-29
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References

  1. Ainsa J. A, Blokpoel M. C, Otal I, Young D. B, De Smet K. A., Martin C. 1998; Molecular cloning and characterization of Tap, a putative multidrug efflux pump present in Mycobacterium fortuitum and Mycobacterium tuberculosis . J Bacteriol 180:5836–5843
    [Google Scholar]
  2. Alland D, Steyn A. J, Weisbrod T, Aldrich K., Jacobs W. R. Jr 2000; Characterization of the Mycobacterium tuberculosis ini BAC promoter, a promoter that responds to cell wall biosynthesis inhibition. J Bacteriol 182:1802–1811
    [Google Scholar]
  3. Altschul S. F, Madden T. L, Schaffer A. A, Zhang J, Zhang Z, Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
    [Google Scholar]
  4. Belisle J. T, McNeil M. R, Chatterjee D, Inamine J. M., Brennan P. J. 1993a; Expression of the core lipopeptide of the glycopeptidolipid surface antigens in rough mutants of Mycobacterium avium . J Biol Chem 268:10510–10516
    [Google Scholar]
  5. Belisle J. T, Klaczkiewicz K, Brennan P. J, Jacobs W. R., Inamine J. M. 1993b; Rough morphological variants of Mycobacterium avium . J Biol Chem 268:10517–10523
    [Google Scholar]
  6. Brown B. A, Springer B, Steingrube V. A. 10 other authors 1999; Mycobacterium wolinskyi sp. nov. and Mycobacterium goodii sp. nov., two new rapidly growing species related to Mycobacterium smegmatis and associated with human wound infections: a cooperative study from the International Working Group on Mycobacterial Taxonomy. Int J Syst Bacteriol 49:1493–1511
    [Google Scholar]
  7. Byrd T. F., Lyons C. R. 1999; Preliminary characterization of a Mycobacterium abscessus mutant in human and murine models of infection. Infect Immun 67:4700–4707
    [Google Scholar]
  8. Chadha R, Grover M, Sharma A, Lakshmy A, Deb M, Kumar A., Mehta G. 1998; An outbreak of post-surgical wound infections due to Mycobacterium abscessus . Pediatr Surg Int 13:406–410
    [Google Scholar]
  9. Chandler M. S. 1998; Insertion sequences and transposons. In Bacterial Genomes, Physical Structure and Analysis pp 30–37 Edited by de Bruijn F. J., Lupski J. R., Weinstock G. M. New York: International Thomson Publishing;
    [Google Scholar]
  10. Cole S. T, Brosch R, Parkhill J. 39 other authors 1998; Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544
    [Google Scholar]
  11. Cole S. T, Eiglmeier K, Parkhill J. 41 other authors 2001; Massive gene decay in the leprosy bacillus. Nature 409:1007–1011
    [Google Scholar]
  12. Domenech P, Jimenez M. S, Menendez M. C, Bull T. J, Samper S, Manrique A., Garcia M. J. 1997; Mycobacterium mageritense sp. nov. Int J Syst Bacteriol 47:535–540
    [Google Scholar]
  13. Dussurget O, Timm J, Gomez M, Gold B, Yu S, Sabol S. Z, Holmes R. K, Jacobs W. R. Jr, Smith I. 1999; Transcriptional control of the iron-responsive fxbA gene by the mycobacterial regulator IdeR. J Bacteriol 181:3402–3408
    [Google Scholar]
  14. Eckstein T. M, Inamine J. M, Lambert M. L., Belisle J. T. 2000; A genetic mechanism for deletion of the ser 2 gene cluster and formation of rough morphological variants of Mycobacterium avium . J Bacteriol 182:6177–6182
    [Google Scholar]
  15. Emmerth M, Goebel W, Miller S. I., Hueck C. J. 1999; Genomic subtraction identifies Salmonella typhimurium prophages, F-related plasmid sequences, and a novel fimbrial operon, stf , which are absent in Salmonella typhi . J Bacteriol 181:5652–5661
    [Google Scholar]
  16. Falkinham J. O.III. 1996; Epidemiology of infection by nontuberculous mycobacteria. Clin Microbiol Rev 9:177–215
    [Google Scholar]
  17. Fujii S, Akiyama M, Aoki K. 10 other authors 1999; DNA replication errors produced by the replicative apparatus of Escherichia coli . J Mol Biol 18:835–850
    [Google Scholar]
  18. Galil K, Miller L. A, Yakrus M. A, Wallace R. J. Jr, Mosley D. G, England B, Huitt G, McNeil M. M., Perkins B. A. 1999; Abscesses due to Mycobacterium abscessus linked to injection of unapproved alternative medication. Emerg Infect Dis 5:681–687
    [Google Scholar]
  19. Glickman B. W., Ripley L. S. 1984; Structural intermediates of deletion mutagenesis: a role for palindromic DNA. Proc Natl Acad Sci USA 81:512–516
    [Google Scholar]
  20. Goodchild J, Michniewicz J, Seto-Young D., Narang S. 1985; A novel deletion found during cloning of a synthetic palindromic DNA. Gene 33:367–371
    [Google Scholar]
  21. Gordon S. V, Heym B, Parkhill J, Barrell B., Cole S. T. 1999; New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv. Microbiology 145:881–892
    [Google Scholar]
  22. Griffith D. E, Girard W. M., Wallace R. J. Jr 1993; Clinical features of pulmonary disease caused by rapidly growing mycobacteria. Am Rev Respir Dis 147:1271–1278
    [Google Scholar]
  23. Guillemin I, Cambau E., Jarlier V. 1995; Sequences of conserved region in the A subunit of DNA gyrase from nine species of the genus Mycobacterium : phylogenetic analysis and implication for intrinsic susceptibility to quinolones. Antimicrob Agents Chemother 39:2145–2149
    [Google Scholar]
  24. Henderson S. T., Petes T. D. 1993; Instability of a plasmid-borne inverted repeat in Saccharomyces cerevisiae . Genetics 133:57–62
    [Google Scholar]
  25. Ho T. B, Robertson B. D, Taylor G. M, Shaw R. J., Young D. B. 2000; Comparison of Mycobacterium tuberculosis genomes reveals frequent deletions in a 20 kb variable region in clinical isolates. Yeast 17:272–282
    [Google Scholar]
  26. Howard S. T., Byrd T. F. 2000; The rapidly-growing mycobacteria: saprophytes and parasites. Microbes Infect 11:1845–1853
    [Google Scholar]
  27. Kim B. J, Lee S. H, Lyu M. A, Kim S. J, Bai G. H, Chae G. T, Kim E. C, Cha C. Y., Kook Y. H. 1999; Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene ( rpoB ). J Clin Microbiol 37:1714–1720
    [Google Scholar]
  28. Kusunoki S., Ezaki T. 1992; Proposal of Mycobacterium peregrinum sp. nov., nom. rev., and elevation of Mycobacterium chelonae subsp. abscessus (Kubica et al.) to species status: Mycobacterium abscessus comb. nov. Int J Syst Bacteriol 42:240–245
    [Google Scholar]
  29. Lee J. H., Holmes R. K. 2000; Characterization of specific nucleotide substitutions in DtxR-specific operators of Corynebacterium diphtheriae that dramatically affect DtxR binding, operator function, and promoter strength. J Bacteriol 182:432–438
    [Google Scholar]
  30. López-Marı́n L. M, Gautier N, Lanéelle M. A, Silve G., Daffé M. 1994; Structures of the glycopeptidolipid antigens of Mycobacterium abscessus and Mycobacterium chelonae and possible chemical basis of the serological cross-reactions in the Mycobacterium fortuitum complex. Microbiology 140:1109–1118
    [Google Scholar]
  31. Mahairas G. G, Sabo P. J, Hickey M. J, Singh D. C., Stover C. K. 1996; Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis . J Bacteriol 178:1274–1282
    [Google Scholar]
  32. McAdam R. A, Hermans P. W, van Soolingen D, Zainuddin Z. F, Catty D, van Embden J. D., Dale J. W. 1990; Characterization of a Mycobacterium tuberculosis insertion sequence belonging to the IS 3 family. Mol Microbiol 4:1607–1613
    [Google Scholar]
  33. Morrow B. J, Graham J. E., Curtiss R.III. 1999; Genomic subtractive hybridization and selective capture of transcribed sequences identify a novel Salmonella typhimurium fimbrial operon and putative transcriptional regulator that are absent from the Salmonella typhi genome. Infect Immun 67:5106–5116
    [Google Scholar]
  34. Nasar F, Jankowski C., Nag D. K. 2000; Long palindromic sequences induce double-strand breaks during meiosis in yeast. Mol Cell Biol 20:3449–3458
    [Google Scholar]
  35. Nierman W. C, Feldblyum T. V, Laub M. T. 34 other authors 2001; Complete genome sequence of Caulobacter crescentus . Proc Natl Acad Sci USA 98:4136–4141
    [Google Scholar]
  36. Pascopella L, Collins F. M, Martin J. M, Lee M. H, Hatfull G. F, Stover C. K, Bloom B. R., Jacobs W. R. 1994; Use of in vivo complementation in Mycobacterium tuberculosis to identify a genomic fragment associated with virulence. Infect Immun 62:1313–1319
    [Google Scholar]
  37. Pitulle C, Dorsch M, Kazda J, Wolters J., Stackebrandt E. 1992; Phylogeny of rapidly growing members of the genus Mycobacterium . Int J Syst Bacteriol 42:337–343
    [Google Scholar]
  38. Prammananan T, Sander P, Brown B. A, Frischkorn K, Onyi G. O, Zhang Y, Bottger E. C., Wallace R. J. Jr 1998; A single 16S ribosomal RNA substitution is responsible for resistance to amikacin and other 2-deoxystreptamine aminoglycosides in Mycobacterium abscessus and Mycobacterium chelonae . J Infect Dis 177:1573–1581
    [Google Scholar]
  39. Recht J, Martinez A, Torello S., Kolter R. 2000; Genetic analysis of sliding motility in Mycobacterium smegmatis . J Bacteriol 182:4348–4351
    [Google Scholar]
  40. Reckseidler S. L, DeShazer D, Sokol P. A., Woods D. E. 2001; Detection of bacterial virulence genes by subtractive hybridization: identification of capsular polysaccharide of Burkholderia pseudomallei as a major virulence determinant. Infect Immun 69:34–44
    [Google Scholar]
  41. Redenbach M, Kieser H. M, Denapaite D, Eichner A, Cullum J, Kinashi H., Hopwood D. A. 1996; A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Mol Microbiol 21:77–96
    [Google Scholar]
  42. Ringuet H, Akoua-Koffi C, Honore S, Varnerot A, Vincent V, Berche P, Gaillard J. L., Pierre-Audigier C. 1999; hsp65 sequencing for identification of rapidly growing mycobacteria. J Clin Microbiol 37:852–857
    [Google Scholar]
  43. Sambrook J, Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  44. Sawada K, Kokeguchi S, Hongyo H, Sawada S, Miyamoto M, Maeda H, Nishimura F, Takashiba S., Murayama Y. 1999; Identification by subtractive hybridization of a novel insertion sequence specific for virulent strains of Porphyromonas gingivalis . Infect Immun 67:5621–5625
    [Google Scholar]
  45. Schmidt K. D, Schmidt-Rose T, Romling U., Tummler B. 1999; Differential genome analysis of bacteria by genomic subtractive hybridization and pulsed field gel electrophoresis. Electrophoresis 19:509–514
    [Google Scholar]
  46. Shinnick T. M., Good R. C. 1994; Mycobacterial taxonomy. Eur J Clin Microbiol Infect Dis 13:884–901
    [Google Scholar]
  47. Shojaei H, Goodfellow M, Magee J. G, Freeman R, Gould F. K., Brignall C. G. 1997; Mycobacterium novocastrense sp. nov., a rapidly growing photochromogenic mycobacterium. Int J Syst Bacteriol 47:1205–1207
    [Google Scholar]
  48. Stover C. K, Pham X. Q, Erwin A. L. 23 other authors 2000; Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959–964
    [Google Scholar]
  49. Straus D., Ausubel F. M. 1990; Genomic subtraction for cloning DNA corresponding to deletion mutations. Proc Natl Acad Sci USA 87:1889–1893
    [Google Scholar]
  50. Tatusova T. A., Madden T. L. 1999; Blast 2 sequences – a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247–250
    [Google Scholar]
  51. Thierry D, Cave M. D, Eisenach K. D, Crawford J. T, Bates J. H, Gicquel B., Guesdon J. L. 1990; IS 6110 , an IS-like element of Mycobacterium tuberculosis complex. Nucleic Acids Res 18:188
    [Google Scholar]
  52. Timsit Y. 1999; DNA structure and polymerase fidelity. J Mol Biol 293:835–853
    [Google Scholar]
  53. Vera-Cabrera L, Howard S. T, Laszlo A., Johnson W. M. 1997; Analysis of genetic polymorphism in the phospholipase region of Mycobacterium tuberculosis . J Clin Microbiol 35:1190–1195
    [Google Scholar]
  54. Villaneuva A, Calderon R. V, Vargas B. A, Ruiz F, Aguero S, Zhang Y, Brown B. A., Wallace R. J. Jr 1997; Report of an outbreak of postinjection abscesses due to Mycobacterium abscessus , including management with surgery and clarithromycin therapy and comparison of strains by random amplified polymorphic DNA polymerase chain reaction. Clin Infect Dis 24:1147–1153
    [Google Scholar]
  55. Wallace R. J. Jr, Zhang Y, Brown B. A, Fraser V, Mazurek G. H., Maloney S. 1993; DNA large restriction fragment patterns of sporadic and epidemic nosocomial strains of Mycobacterium chelonae and Mycobacterium abscessus . J Clin Microbiol 31:2697–2701
    [Google Scholar]
  56. Wright P. W., Wallace R. J. Jr 1995; Syndromes, diagnosis, and treatment of rapidly growing mycobacteria. In Tuberculosis: Clinical Management and New Challenges pp 373–389 Edited by Rossman M. R. R. New York: McGraw-Hill;
    [Google Scholar]
  57. Zeng X., Saxild H. H. 1999; Identification and characterization of a DeoR-specific operator sequence essential for induction of dra-nupC-pdp operon expression in Bacillus subtilis . J Bacteriol 181:1719–1727
    [Google Scholar]
  58. Zhang Y, Rajagopalan M, Brown B. A., Wallace R. J. Jr 1997; Randomly amplified polymorphic DNA PCR for comparison of Mycobacterium abscessus strains from nosocomial outbreaks. J Clin Microbiol 35:3132–3139
    [Google Scholar]
  59. Zhang Y. L, Ong C. T., Leung K. Y. 2000; Molecular analysis of genetic differences between virulent and avirulent strains of Aeromonas hydrophila isolated from diseased fish. Microbiology 146:999–1009
    [Google Scholar]
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