Separation of Mycobacterium abscessus into subspecies or genotype level by direct application of peptide nucleic acid multi-probe- real-time PCR method into sputa samples

BMC Infectious Diseases

Volumn 15, Issue 1, 2015, Pages

  Kim, Kijeong ^b   Hong, Seok Hyun ^a   Kim, Byoung Jun ^a   Kim, Bo Ram ^a   Lee, So Young ^a   Kim, Ga Na ^a   Shim, Tae Sun ^c   Kook, Yoon Hoh ^a   Kim, Bum Joon ^a  

^a Seoul National University College of Medicine   (South Korea)

^b Chung Ang University College of Medicine   (South Korea)

^c University of Ulsan College of Medicine   (South Korea)

Author keywords

Genotype; hsp65; Mycobacterium abscessus; Mycobacterium massiliense; Peptide nucleic acid (PNA); Real time PCR

Indexed keywords

PEPTIDE NUCLEIC ACID; BACTERIAL DNA; BACTERIAL PROTEIN; CHAPERONIN 60; HEAT-SHOCK PROTEIN 65, MYCOBACTERIUM;

ARTICLE; BACTERIAL GENE; BACTERIUM CULTURE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; DNA EXTRACTION; GENE TARGETING; GENOTYPE; HSP65 GENE; INTERMETHOD COMPARISON; MYCOBACTERIOSIS; MYCOBACTERIUM ABSCESSUS; NONHUMAN; PEPTIDE NUCLEIC ACID MULTIPROBE REAL TIME POLYMERASE CHAIN REACTION; REAL TIME POLYMERASE CHAIN REACTION; RESTRICTION MAPPING; RPOB GENE; SENSITIVITY ANALYSIS; SPECIES IDENTIFICATION; SPUTUM ANALYSIS; ATYPICAL MYCOBACTERIUM; CLASSIFICATION; EVALUATION STUDY; GENETICS; HUMAN; MICROBIOLOGY; MYCOBACTERIUM INFECTIONS; PREDICTIVE VALUE; PROCEDURES; SPUTUM; TUBERCULOSIS, PULMONARY;

BACTERIAL PROTEINS; CHAPERONIN 60; DNA, BACTERIAL; GENOTYPE; HUMANS; MYCOBACTERIUM INFECTIONS; NONTUBERCULOUS MYCOBACTERIA; PEPTIDE NUCLEIC ACIDS; PREDICTIVE VALUE OF TESTS; REAL-TIME POLYMERASE CHAIN REACTION; SPUTUM; TUBERCULOSIS, PULMONARY;

EID: 84938804124     PISSN: None     EISSN: 14712334     Source Type: Journal    
DOI: 10.1186/s12879-015-1076-8     Document Type: Article

References (36)

1. Harris KA, Kenna DT, Blauwendraat C, Hartley JC, Turton JF, Aurora P, et al. Molecular fingerprinting of Mycobacterium abscessus strains in a cohort of pediatric cystic fibrosis patients. J Clin Microbiol. 2012;50(5):1758-61.
2. Maurer FP, Ruegger V, Ritter C, Bloemberg GV, Bottger EC. Acquisition of clarithromycin resistance mutations in the 23S rRNA gene of Mycobacterium abscessus in the presence of inducible erm(41). J Antimicrob Chemoth. 2012;67(11):2606-11.
3. Choi WS, Kim MJ, Park DW, Son SW, Yoon YK, Song T, et al. Clarithromycin and amikacin vs. clarithromycin and moxifloxacin for the treatment of post-acupuncture cutaneous infections due to Mycobacterium abscessus: a prospective observational study. Clin Microbiol Infect. 2011;17(7):1084-90.
4. Nash KA, Brown-Elliott BA, Wallace RJ. A novel gene, erm(41), confers inducible macrolide resistance to clinical isolates of Mycobacterium abscessus but is absent from Mycobacterium chelonae. Antimicrob Agents Chemother. 2009;53(4):1367-76.
5. Kim HY, Kook Y, Yun YJ, Park CG, Lee NY, Shim TS, et al. Proportions of Mycobacterium massiliense and Mycobacterium bolletii strains among Korean Mycobacterium chelonae-Mycobacterium abscessus group isolates. J Clin Microbiol. 2008;46(10):3384-90.
6. Leao SC, Tortoli E, Viana-Niero C, Ueki SYM, Lima KVB, Lopes ML, et al. 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. 2009;47(9):2691-8.
7. Macheras E, Roux AL, Bastian S, Leao SC, Palaci M, Sivadon-Tardy V, et al. Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (Sensu Lato) strains. J Clin Microbiol. 2011;49(2):491-9.
8. Leao SC, Tortoli E, Euzeby JP, Garcia MJ. 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. 2011;61:2311-3.
9. Kim BJ, Yi SY, Shim TS, Do SY, Yu HK, Park YG, et al. Discovery of a Novel hsp65 Genotype within Mycobacterium massiliense associated with the rough colony morphology. Plos One. 2012;7(6):e38420.
10. Kim BJ, Kim BR, Hong SH, Seok SH, Kook YH, Kim BJ. Complete Genome Sequence of Mycobacterium massiliense Clinical Strain Asan 50594, Belonging to the Type II Genotype. Genome Announc. 2013;1(4) pii: e00429-13. doi: 10.1128/genomeA.00429-13 .
11. Kim BJ, Kim BR, Lee SY, Kook YH, Kim BJ. Rough colony morphology of Mycobacterium massiliense Type II genotype is due to the deletion of glycopeptidolipid locus within its genome. BMC Genomics. 2013;14:890.
12. Jeon SM, Lim NR, Kwon SJ, Shim TS, Park MS, Kim BJ, et al. Analysis of species and intra-species associations between the Mycobacterium abscessus complex strains using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). J Microbiol Methods. 2014;104:19-25.
13. Leao SC, Viana-Niero C, Matsumoto CK, Lima KV, Lopes ML, Palaci M, et al. Epidemic of surgical-site infections by a single clone of rapidly growing mycobacteria in Brazil. Future Microbiol. 2010;5(6):971-80.
14. Aitken ML, Limaye A, Pottinger P, Whimbey E, Goss CH, Tonelli MR, et al. Respiratory outbreak of Mycobacterium abscessus subspecies massiliense in a lung transplant and cystic fibrosis center. Am J Respir Crit Care Med. 2012;185(2):231-2.
15. Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, et al. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet. 2013;381(9877):1551-60.
16. Bastian S, Veziris N, Roux AL, Brossier F, Gaillard JL, Jarlier V, et al. Assessment of Clarithromycin Susceptibility in Strains Belonging to the Mycobacterium abscessus Group by erm(41) and rrl Sequencing. Antimicrob Agents Chemother. 2011;55(2):775-81.
17. Shallom SJ, Gardina PJ, Myers TG, Sebastian Y, Conville P, Calhoun LB, et al. New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identifying Mycobacterium massiliense isolates with inducible clarithromycin resistance. J Clin Microbiol. 2013;51(9):2943-9.
18. Porcheddu A, Giacomelli G. Peptide nucleic acids (PNAs), a chemical overview. Curr Med Chem. 2005;12(22):2561-99.
19. Choi YJ, Kim HS, Lee SH, Park JS, Nam HS, Kim HJ, et al. Evaluation of peptide nucleic acid array for the detection of hepatitis B virus mutations associated with antiviral resistance. Archives of virology. 2011;156(9):1517-24.
20. Kim JW, Choi YJ, Kim HJ, Park JS, Nam HS, Hwangbo Y, et al. Comparison of PNA probe-based real-time PCR and Cobas TaqMan MTB for detection of MTBC. Biochip J. 2013;7(2):85-8.
21. Choi YJ, Kim HJ, Shin HB, Nam HS, Lee SH, Park JS, et al. Evaluation of peptide nucleic acid probe-based real-time PCR for detection of Mycobacterium tuberculosis complex and nontuberculous mycobacteria in respiratory specimens. Ann Lab Med. 2012;32(4):257-63.
22. Kim K, Kim BJ, Shim TS, Hong SH, Kook YH, Kim BJ. Development of a Peptide nucleic acid-based multiprobe real-time PCR method targeting the hsp65 gene for differentiation among Mycobacterium abscessus strains. J Clin Microbiol. 2015;53(4):1403-5.
23. Kim K, Lee H, Lee MK, Lee SA, Shim TS, Lim SY, et al. Development and application of multiprobe real-time PCR method targeting the hsp65 gene for differentiation of Mycobacterium species from isolates and sputum specimens. J Clin Microbiol. 2010;48(9):3073-80.
24. Kent PK,G. Public Health Mycobacteriology. A Guide for the Level III Laboratory. Atlanta, GA: Centers for Disease Control and Prevention; 1985.
25. Taylor Z, Nolan CM, Blumberg HM, American Thoracic S, Centers for Disease C, Prevention, Infectious Diseases Society of A. Controlling tuberculosis in the United States. Recommendations from the American Thoracic Society, CDC, and the Infectious Diseases Society of America. MMWR Recomm Rep. 2005;54(RR-12):1-81.
26. Kim BJ, Lee SH, Lyu MA, Kim SJ, Bai GH, Chae GT, et al. Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol. 1999;37(6):1714-20.
27. Schaaf CP, Wiszniewska J, Beaudet AL. Copy number and SNP arrays in clinical diagnostics. Annu Rev Genom Hum G. 2011;12:25-51.
28. Tang JF, Zhou L, Liu XY, Zhang CM, Zhao YY, Wang YF. Novel multiplex real-time PCR system using the SNP technology for the simultaneous diagnosis of Chlamydia trachomatis, Ureaplasma parvum and Ureaplasma urealyticum and genetic typing of serovars of C. trachomatis and U. parvum in NGU. Mol Cell Probe. 2011;25(1):55-9.
29. Eeles RA, Kote-Jarai Z, Giles GG, Olama AA, Guy M, Jugurnauth SK, et al. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet. 2008;40(3):316-21.
30. Goel G, Kumar A, Puniya AK, Chen W, Singh K. Molecular beacon: a multitask probe. J Appl Microbiol. 2005;99(3):435-42.
31. Zhang N, Appella DH. Colorimetric detection of anthrax DNA with a Peptide nucleic acid sandwich-hybridization assay. J Am Chem Soc. 2007;129(27):8424-5.
32. Grossmann TN, Roglin L, Seitz O. Target-catalyzed transfer reactions for the amplified detection of RNA. Angew Chem Int Ed Engl. 2008;47(37):7119-22.
33. Petersen K, Vogel U, Rockenbauer E, Nielsen KV, Kolvraa S, Bolund L, et al. Short PNA molecular beacons for real-time PCR allelic discrimination of single nucleotide polymorphisms. Mol Cell Probes. 2004;18(2):117-22.
34. Nielsen P. Peptide Nucleic Acids-Protocol and Applications. Norfolk: Horizon Bioscience; 2004.
35. Funes-Huacca ME, Opel K, Thompson R, McCord BR. A comparison of the effects of PCR inhibition in quantitative PCR and forensic STR analysis. Electrophoresis. 2011;32(9):1084-9.
36. Opel KL, Chung D, McCord BR. A study of PCR inhibition mechanisms using real time PCR. J Forensic Sci. 2010;55(1):25-33.