1887

Abstract

Nearly half of US clinical isolates of the emerging pathogen were reported to exhibit smeared DNA during PFGE. This DNA degradation (Dnd) phenotype results from DNA phosphorothioation, a sulfur modification found in other bacteria and conferred by genes located on mobile elements. Putative genes are located on a 19.6 kbp genomic island (GI) in the type strain ATCC 19977. We confirmed that ATCC 19977 is Dnd-positive by PFGE and we developed a PCR assay to predict Dnd phenotype. Dnd-positive strains generated an amplicon from whereas Dnd-negative strains generated a bridge amplicon that spanned the GI insertion site, indicating they lacked the entire ‘Dnd-GI’. Comparative analyses of sequences from the bridge amplicon with ATCC 19977 revealed the Dnd-GI is flanked by 22 bp repeats in and inserted downstream of a gene and between inverted repeats. Regions flanking the Dnd-GI were highly conserved within the complex. Bioinformatics studies suggest the Dnd-GI inserted independently into a strain of and that other species of mycobacteria also have genes, supporting reports that the Dnd phenotype is common among actinomycetes. Within the complex, Dnd-positive clinical isolates were primarily , and tandem repeat typing indicated these isolates were highly related, confirming previous PFGE studies and revealing a widespread family of strains with significance in human disease.

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2013-11-01
2019-10-14
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References

  1. Altschul S. F., Madden T. L., Schäffer 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. [CrossRef][PubMed]
    [Google Scholar]
  2. Bastian S., Veziris N., Roux A. L., Brossier F., Gaillard J. L., Jarlier V., Cambau E.. ( 2011;). Assessment of clarithromycin susceptibility in strains belonging to the Mycobacterium abscessus group by erm(41) and rrl sequencing. . Antimicrob Agents Chemother 55:, 775–781. [CrossRef][PubMed]
    [Google Scholar]
  3. Becq J., Gutierrez M. C., Rosas-Magallanes V., Rauzier J., Gicquel B., Neyrolles O., Deschavanne P.. ( 2007;). Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli. . Mol Biol Evol 24:, 1861–1871. [CrossRef][PubMed]
    [Google Scholar]
  4. Brown-Elliott B. A., Nash K. A., Wallace R. J. Jr. ( 2012;). Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. . Clin Microbiol Rev 25:, 545–582. [CrossRef][PubMed]
    [Google Scholar]
  5. Cáp M., Váchová L., Palková Z.. ( 2012;). Reactive oxygen species in the signaling and adaptation of multicellular microbial communities. . Oxid Med Cell Longev 2012:, 976753. [CrossRef][PubMed]
    [Google Scholar]
  6. Chen S., Wang L., Deng Z.. ( 2010;). Twenty years hunting for sulfur in DNA. . Protein Cell 1:, 14–21. [CrossRef][PubMed]
    [Google Scholar]
  7. Cole S. T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S. V., Eiglmeier K., Gas S. et al. ( 1998;). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. . Nature 393:, 537–544. [CrossRef][PubMed]
    [Google Scholar]
  8. Corkill J. E., Graham R., Hart C. A., Stubbs S.. ( 2000;). Pulsed-field gel electrophoresis of degradation-sensitive DNAs from Clostridium difficile PCR ribotype 1 strains. . J Clin Microbiol 38:, 2791–2792.[PubMed]
    [Google Scholar]
  9. Das T., Manefield M.. ( 2012;). Pyocyanin promotes extracellular DNA release in Pseudomonas aeruginosa. . PLoS ONE 7:, e46718. [CrossRef][PubMed]
    [Google Scholar]
  10. Dyson P., Evans M.. ( 1998;). Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101. . Nucleic Acids Res 26:, 1248–1253. [CrossRef][PubMed]
    [Google Scholar]
  11. Esteban J., Martín-de-Hijas N. Z., Kinnari T. J., Ayala G., Fernández-Roblas R., Gadea I.. ( 2008;). Biofilm development by potentially pathogenic non-pigmented rapidly growing mycobacteria. . BMC Microbiol 8:, 184. [CrossRef][PubMed]
    [Google Scholar]
  12. Fraser V. J., Jones M., Murray P. R., Medoff G., Zhang Y., Wallace R. J. Jr. ( 1992;). Contamination of flexible fiberoptic bronchoscopes with Mycobacterium chelonae linked to an automated bronchoscope disinfection machine. . Am Rev Respir Dis 145:, 853–855. [CrossRef][PubMed]
    [Google Scholar]
  13. Furuya E. Y., Paez A., Srinivasan A., Cooksey R., Augenbraun M., Baron M., Brudney K., Della-Latta P., Estivariz C. et al. ( 2008;). Outbreak of Mycobacterium abscessus wound infections among “lipotourists” from the United States who underwent abdominoplasty in the Dominican Republic. . Clin Infect Dis 46:, 1181–1188. [CrossRef][PubMed]
    [Google Scholar]
  14. Greendyke R., Byrd T. F.. ( 2008;). Differential antibiotic susceptibility of Mycobacterium abscessus variants in biofilms and macrophages compared to that of planktonic bacteria. . Antimicrob Agents Chemother 52:, 2019–2026. [CrossRef][PubMed]
    [Google Scholar]
  15. Hacker J., Blum-Oehler G., Mühldorfer I., Tschäpe H.. ( 1997;). Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. . Mol Microbiol 23:, 1089–1097. [CrossRef][PubMed]
    [Google Scholar]
  16. Harris K. A., Kenna D. T., Blauwendraat C., Hartley J. C., Turton J. F., Aurora P., Dixon G. L.. ( 2012;). Molecular fingerprinting of Mycobacterium abscessus strains in a cohort of pediatric cystic fibrosis patients. . J Clin Microbiol 50:, 1758–1761. [CrossRef][PubMed]
    [Google Scholar]
  17. He X., Ou H. Y., Yu Q., Zhou X., Wu J., Liang J., Zhang W., Rajakumar K., Deng Z.. ( 2007;). Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria. . Mol Microbiol 65:, 1034–1048. [CrossRef][PubMed]
    [Google Scholar]
  18. Heydari H., Wee W. Y., Lokanathan N., Hari R., Mohamed Yusoff A., Beh C. Y., Yazdi A. H., Wong G. J., Ngeow Y. F., Choo S. W.. ( 2013;). MabsBase: a Mycobacterium abscessus genome and annotation database. . PLoS ONE 8:, e62443. [CrossRef][PubMed]
    [Google Scholar]
  19. Howard S. T., Rhoades E., Recht J., Pang X., Alsup A., Kolter R., Lyons C. R., Byrd T. F.. ( 2006;). Spontaneous reversion of Mycobacterium abscessus from a smooth to a rough morphotype is associated with reduced expression of glycopeptidolipid and reacquisition of an invasive phenotype. . Microbiology 152:, 1581–1590. [CrossRef][PubMed]
    [Google Scholar]
  20. Jönsson B. E., Gilljam M., Lindblad A., Ridell M., Wold A. E., Welinder-Olsson C.. ( 2007;). Molecular epidemiology of Mycobacterium abscessus, with focus on cystic fibrosis. . J Clin Microbiol 45:, 1497–1504. [CrossRef][PubMed]
    [Google Scholar]
  21. Kim H. Y., Kim B. J., Kook Y., Yun Y. J., Shin J. H., Kim B. J., Kook Y. H.. ( 2010;). Mycobacterium massiliense is differentiated from Mycobacterium abscessus and Mycobacterium bolletii by erythromycin ribosome methyltransferase gene (erm) and clarithromycin susceptibility patterns. . Microbiol Immunol 54:, 347–353. [CrossRef][PubMed]
    [Google Scholar]
  22. Koh W. J., Jeon K., Lee N. Y., Kim B. J., Kook Y. H., Lee S. H., Park Y. K., Kim C. K., Shin S. J. et al. ( 2011;). Clinical significance of differentiation of Mycobacterium massiliense from Mycobacterium abscessus. . Am J Respir Crit Care Med 183:, 405–410. [CrossRef][PubMed]
    [Google Scholar]
  23. 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. [CrossRef][PubMed]
    [Google Scholar]
  24. Langille M. G., Hsiao W. W., Brinkman F. S.. ( 2010;). Detecting genomic islands using bioinformatics approaches. . Nat Rev Microbiol 8:, 373–382. [CrossRef][PubMed]
    [Google Scholar]
  25. Leao S. C., Tortoli E., Viana-Niero C., Ueki S. Y., Lima K. V., Lopes M. L., Yubero J., Menendez M. C., Garcia M. J.. ( 2009;). Characterization of mycobacteria from a major Brazilian outbreak suggests that revision of the taxonomic status of members of the Mycobacterium chelonae–M. abscessus group is needed. . J Clin Microbiol 47:, 2691–2698. [CrossRef][PubMed]
    [Google Scholar]
  26. Leao S. C., Tortoli E., Euzéby J. P., Garcia M. J.. ( 2011;). Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov., and emended description of Mycobacterium abscessus. . Int J Syst Evol Microbiol 61:, 2311–2313. [CrossRef][PubMed]
    [Google Scholar]
  27. Lesnik E. A., Sampath R., Levene H. B., Henderson T. J., McNeil J. A., Ecker D. J.. ( 2001;). Prediction of rho-independent transcriptional terminators in Escherichia coli. . Nucleic Acids Res 29:, 3583–3594. [CrossRef][PubMed]
    [Google Scholar]
  28. Lew J. M., Kapopoulou A., Jones L. M., Cole S. T.. ( 2011;). TubercuList – 10 years after. . Tuberculosis (Edinb) 91:, 1–7. [CrossRef][PubMed]
    [Google Scholar]
  29. Liu H. L., Zhu J.. ( 2010;). Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus. . J Zhejiang Univ Sci B 11:, 708–718. [CrossRef][PubMed]
    [Google Scholar]
  30. Macheras E., Roux A. L., Ripoll F., Sivadon-Tardy V., Gutierrez C., Gaillard J. L., Heym B.. ( 2009;). Inaccuracy of single-target sequencing for discriminating species of the Mycobacterium abscessus group. . J Clin Microbiol 47:, 2596–2600. [CrossRef][PubMed]
    [Google Scholar]
  31. Macheras E., Roux A. L., Bastian S., Leão S. C., Palaci M., Sivadon-Tardy V., Gutierrez C., Richter E., Rüsch-Gerdes S. et al. ( 2011;). Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains. . J Clin Microbiol 49:, 491–499. [CrossRef][PubMed]
    [Google Scholar]
  32. Matsumoto C. K., Chimara E., Bombarda S., Duarte R. S., Leão S. C.. ( 2011;). Diversity of pulsed-field gel electrophoresis patterns of Mycobacterium abscessus type 2 clinical isolates. . J Clin Microbiol 49:, 62–68. [CrossRef][PubMed]
    [Google Scholar]
  33. Medjahed H., Gaillard J. L., Reyrat J. M.. ( 2010;). Mycobacterium abscessus: a new player in the mycobacterial field. . Trends Microbiol 18:, 117–123. [CrossRef][PubMed]
    [Google Scholar]
  34. Miotto P., Forti F., Ambrosi A., Pellin D., Veiga D. F., Balazsi G., Gennaro M. L., Di Serio C., Ghisotti D., Cirillo D. M.. ( 2012;). Genome-wide discovery of small RNAs in Mycobacterium tuberculosis. . PLoS ONE 7:, e51950. [CrossRef][PubMed]
    [Google Scholar]
  35. Mitra A., Angamuthu K., Nagaraja V.. ( 2008;). Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium. . Tuberculosis (Edinb) 88:, 566–575. [CrossRef][PubMed]
    [Google Scholar]
  36. Nash K. A., Brown-Elliott B. A., Wallace R. J. Jr. ( 2009;). A novel gene, erm(41), confers inducible macrolide resistance to clinical isolates of Mycobacterium abscessus but is absent from Mycobacterium chelonae. . Antimicrob Agents Chemother 53:, 1367–1376. [CrossRef][PubMed]
    [Google Scholar]
  37. Olivier K. N., Weber D. J., Wallace R. J. Jr, Faiz A. R., Lee J. H., Zhang Y., Brown-Elliot B. A., Handler A., Wilson R. W. et al. ( 2003;). Nontuberculous mycobacteria. I: multicenter prevalence study in cystic fibrosis. . Am J Respir Crit Care Med 167:, 828–834. [CrossRef][PubMed]
    [Google Scholar]
  38. Ou H. Y., Chen L. L., Lonnen J., Chaudhuri R. R., Thani A. B., Smith R., Garton N. J., Hinton J., Pallen M. et al. ( 2006;). A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. . Nucleic Acids Res 34:, e3. [CrossRef][PubMed]
    [Google Scholar]
  39. Ou H. Y., He X., Shao Y., Tai C., Rajakumar K., Deng Z.. ( 2009;). dndDB: a database focused on phosphorothioation of the DNA backbone. . PLoS ONE 4:, e5132. [CrossRef][PubMed]
    [Google Scholar]
  40. Raiol T., Ribeiro G. M., Maranhão A. Q., Bocca A. L., Silva-Pereira I., Junqueira-Kipnis A. P., Brigido M. M., Kipnis A.. ( 2012;). Complete genome sequence of Mycobacterium massiliense. . J Bacteriol 194:, 5455. [CrossRef][PubMed]
    [Google Scholar]
  41. Ray T., Weaden J., Dyson P.. ( 1992;). Tris-dependent site-specific cleavage of Streptomyces lividans DNA. . FEMS Microbiol Lett 75:, 247–252. [CrossRef][PubMed]
    [Google Scholar]
  42. Ray T., Mills A., Dyson P.. ( 1995;). Tris-dependent oxidative DNA strand scission during electrophoresis. . Electrophoresis 16:, 888–894. [CrossRef][PubMed]
    [Google Scholar]
  43. Reiter W. D., Palm P., Yeats S.. ( 1989;). Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. . Nucleic Acids Res 17:, 1907–1914. [CrossRef][PubMed]
    [Google Scholar]
  44. Ripoll F., Deshayes C., Pasek S., Laval F., Beretti J. L., Biet F., Risler J. L., Daffé M., Etienne G. et al. ( 2007;). Genomics of glycopeptidolipid biosynthesis in Mycobacterium abscessus and M. chelonae. . BMC Genomics 8:, 114. [CrossRef][PubMed]
    [Google Scholar]
  45. Ripoll F., Pasek S., Schenowitz C., Dossat C., Barbe V., Rottman M., Macheras E., Heym B., Herrmann J. L. et al. ( 2009;). Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus. . PLoS ONE 4:, e5660. [CrossRef][PubMed]
    [Google Scholar]
  46. Rosas-Magallanes V., Deschavanne P., Quintana-Murci L., Brosch R., Gicquel B., Neyrolles O.. ( 2006;). Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis. . Mol Biol Evol 23:, 1129–1135. [CrossRef][PubMed]
    [Google Scholar]
  47. Sermet-Gaudelus I., Le Bourgeois M., Pierre-Audigier C., Offredo C., Guillemot D., Halley S., Akoua-Koffi C., Vincent V., Sivadon-Tardy V. et al. ( 2003;). Mycobacterium abscessus and children with cystic fibrosis. . Emerg Infect Dis 9:, 1587–1591. [CrossRef][PubMed]
    [Google Scholar]
  48. Shallom S. J., Gardina P. J., Myers T. G., Sebastian Y., Conville P., Calhoun L. B., Tettelin H., Olivier K. N., Uzel G. et al. ( 2013;). New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identification of Mycobacterium massiliense with inducible clarithromycin resistance. . J Clin Microbiol 51:, 2943–2949. [CrossRef][PubMed]
    [Google Scholar]
  49. Talaat A. M., Lyons R., Howard S. T., Johnston S. A.. ( 2004;). The temporal expression profile of Mycobacterium tuberculosis infection in mice. . Proc Natl Acad Sci U S A 101:, 4602–4607. [CrossRef][PubMed]
    [Google Scholar]
  50. Telenti A., Marchesi F., Balz M., Bally F., Böttger E. C., Bodmer T.. ( 1993;). Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. . J Clin Microbiol 31:, 175–178.[PubMed]
    [Google Scholar]
  51. Vaerewijck M. J., Huys G., Palomino J. C., Swings J., Portaels F.. ( 2005;). Mycobacteria in drinking water distribution systems: ecology and significance for human health. . FEMS Microbiol Rev 29:, 911–934. [CrossRef][PubMed]
    [Google Scholar]
  52. Villanueva A., Calderon R. V., Vargas B. A., Ruiz F., Aguero S., Zhang Y., Brown B. A., Wallace R. J. Jr. ( 1997;). Report on 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. [CrossRef][PubMed]
    [Google Scholar]
  53. 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.[PubMed]
    [Google Scholar]
  54. Wang L., Chen S., Xu T., Taghizadeh K., Wishnok J. S., Zhou X., You D., Deng Z., Dedon P. C.. ( 2007;). Phosphorothioation of DNA in bacteria by dnd genes. . Nat Chem Biol 3:, 709–710. [CrossRef][PubMed]
    [Google Scholar]
  55. Wang L., Chen S., Vergin K. L., Giovannoni S. J., Chan S. W., DeMott M. S., Taghizadeh K., Cordero O. X., Cutler M. et al. ( 2011;). DNA phosphorothioation is widespread and quantized in bacterial genomes. . Proc Natl Acad Sci U S A 108:, 2963–2968. [CrossRef][PubMed]
    [Google Scholar]
  56. Williams K. P.. ( 2002;). Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. . Nucleic Acids Res 30:, 866–875. [CrossRef][PubMed]
    [Google Scholar]
  57. Wong Y. L., Ong C. S., Ngeow Y. F.. ( 2012;). Molecular typing of Mycobacterium abscessus based on tandem-repeat polymorphism. . J Clin Microbiol 50:, 3084–3088. [CrossRef][PubMed]
    [Google Scholar]
  58. Xie X., Liang J., Pu T., Xu F., Yao F., Yang Y., Zhao Y. L., You D., Zhou X. et al. ( 2012;). Phosphorothioate DNA as an antioxidant in bacteria. . Nucleic Acids Res 40:, 9115–9124. [CrossRef][PubMed]
    [Google Scholar]
  59. Xu T., Liang J., Chen S., Wang L., He X., You D., Wang Z., Li A., Xu Z. et al. ( 2009;). DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus. . BMC Microbiol 9:, 41. [CrossRef][PubMed]
    [Google Scholar]
  60. Xu T., Yao F., Zhou X., Deng Z., You D.. ( 2010;). A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella. . Nucleic Acids Res 38:, 7133–7141. [CrossRef][PubMed]
    [Google Scholar]
  61. Yao F., Xu T., Zhou X., Deng Z., You D.. ( 2009;). Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1. . FEBS Lett 583:, 729–733. [CrossRef][PubMed]
    [Google Scholar]
  62. You D., Wang L., Yao F., Zhou X., Deng Z.. ( 2007;). A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron–sulfur cluster protein in Streptomyces lividans. . Biochemistry 46:, 6126–6133. [CrossRef][PubMed]
    [Google Scholar]
  63. Zelazny A. M., Root J. M., Shea Y. R., Colombo R. E., Shamputa I. C., Stock F., Conlan S., McNulty S., Brown-Elliott B. A. et al. ( 2009;). Cohort study of molecular identification and typing of Mycobacterium abscessus, Mycobacterium massiliense, and Mycobacterium bolletii. . J Clin Microbiol 47:, 1985–1995. [CrossRef][PubMed]
    [Google Scholar]
  64. Zhang Y., Yakrus M. A., Graviss E. A., Williams-Bouyer N., Turenne C., Kabani A., Wallace R. J. Jr. ( 2004;). Pulsed-field gel electrophoresis study of Mycobacterium abscessus isolates previously affected by DNA degradation. . J Clin Microbiol 42:, 5582–5587. [CrossRef][PubMed]
    [Google Scholar]
  65. Zhou X., Deng Z., Firmin J. L., Hopwood D. A., Kieser T.. ( 1988;). Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron. . Nucleic Acids Res 16:, 4341–4352. [CrossRef][PubMed]
    [Google Scholar]
  66. Zhou X., He X., Li A., Lei F., Kieser T., Deng Z.. ( 2004;). Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66. . Appl Environ Microbiol 70:, 7110–7118. [CrossRef][PubMed]
    [Google Scholar]
  67. Zhou X., He X., Liang J., Li A., Xu T., Kieser T., Helmann J. D., Deng Z.. ( 2005;). A novel DNA modification by sulphur. . Mol Microbiol 57:, 1428–1438. [CrossRef][PubMed]
    [Google Scholar]
  68. Zhu L., Kreth J.. ( 2012;). The role of hydrogen peroxide in environmental adaptation of oral microbial communities. . Oxid Med Cell Longev 2012:, 717843. [CrossRef][PubMed]
    [Google Scholar]
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