Utility of rpoB gene sequencing for identification of nontuberculous mycobacteria in the Netherlands

Journal of Clinical Microbiology

Volumn 52, Issue 7, 2014, Pages 2544-2551

  De Zwaan, Rina ^a   Van Ingen, Jakko ^b   Van Soolingen, Dick ^a,b  

^a NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; RNA POLYMERASE BETA SUBUNIT; BACTERIAL DNA; DNA DIRECTED RNA POLYMERASE; RIBOSOME DNA;

ANALYTICAL EQUIPMENT; ARTICLE; ATYPICAL MYCOBACTERIUM; BACTERIAL GENE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CORRELATIONAL STUDY; GENE SEQUENCE; GENETIC PROCEDURES; GENETIC SCREENING; GENETIC VARIABILITY; HYBRIDIZATION; INTERMETHOD COMPARISON; MYCOBACTERIUM GORDONAE; MYCOBACTERIUM INTERJECTUM; MYCOBACTERIUM KANSASII; NETHERLANDS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROSPECTIVE STUDY; REVERSE LINE BLOT ASSAY; RNA SEQUENCE; RPOB GENE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; SPECIES IDENTIFICATION; UNINDEXED SEQUENCE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; EVALUATION STUDY; GENETICS; HUMAN; MICROBIOLOGY; MOLECULAR GENETICS; MYCOBACTERIUM INFECTIONS, NONTUBERCULOUS; PHYLOGENY;

CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; DNA-DIRECTED RNA POLYMERASES; HUMANS; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM INFECTIONS, NONTUBERCULOUS; NETHERLANDS; NONTUBERCULOUS MYCOBACTERIA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84903755992     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00233-14     Document Type: Article

References (26)

1. van Ingen J, van der Laan T, Dekhuijzen R, Boeree M, van Soolingen D. 2010. In vitro drug susceptibility of 2275 clinical non-tuberculous Mycobacterium isolates of 49 species in The Netherlands. Int. J. Antimicrob. Agents 35:169-173. http://dx.doi.org/10.1016/j.ijantimicag.2009.09.023.
2. Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, Gordin F, Holland SM, Horsburgh R, Huitt G, Iademarco MF, Iseman M, Olivier K, Ruoss S, von Reyn CF, Wallace RJ, Jr, Winthrop K. 2007. An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am. J. Respir. Crit. Care Med. 175:367-416. http://dx.doi.org/10.1164/rccm. 200604-571ST.
3. van Ingen J, Bendien SA, de Lange WC, Hoefsloot W, Dekhuijzen PN, Boeree MJ, van Soolingen D. 2009. Clinical relevance of non-tuberculous mycobacteria isolated in the Nijmegen-Arnhem region, The Netherlands. Thorax 64:502-506. http://dx.doi.org/10.1136/thx.2008.110957.
4. van Ingen J. 2013. Diagnosis of nontuberculous mycobacterial infections. Sem. Respir. Crit. Care Med. 34:103-109. http://dx.doi.org/10.1055/s-0033- 1333569.
5. Springer B, Bottger EC, Kirschner P, Wallace RJ, Jr. 1995. Phylogeny of the Mycobacterium chelonae-like organism based on partial sequencing of the 16SrRNAgene and proposal of Mycobacterium mucogenicum sp. nov. Int. J. Syst. Bacteriol. 45:262-267. http://dx.doi.org/10.1099/00207713-45-2-262.
6. Tortoli E. 2012. Phylogeny of the genus Mycobacterium: many doubts, few certainties. Infect. Genet. Evol. 12:827-831. http://dx.doi.org/10.1016/j. meegid.2011.05.025.
7. Turenne CY, Tschetter L, Wolfe J, Kabani A. 2001. Necessity of qualitycontrolled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J. Clin. Microbiol. 39:3637-3648. http://dx.doi.org/10. 1128/JCM.39.10.3638-3648.2001. (Pubitemid 32954514)
8. Ben Salah I, Adekambi T, Raoult D, Drancourt M. 2008. rpoB sequencebased identification of Mycobacterium avium complex species. Microbiology 154:3715-3723. http://dx.doi.org/10.1099/mic.0.2008/020164-0.
9. Adékambi T, Colson P, Drancourt M. 2003. rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J. Clin. Microbiol. 41:5699-5708. http://dx.doi.org/10.1128/JCM.41.12.5699-5708.2003.
10. Reischl U, Feldmann K, Naumann L, Gaugler BJ, Ninet B, Hirschel B, Emler S. 1998. 16S rRNA sequence diversity in Mycobacterium celatum strains caused by presence of two different copies of 16S rRNA gene. J. Clin. Microbiol. 36:1761-1764. (Pubitemid 28226068)
11. Tortoli E. 2010. Standard operating procedure for optimal identification of mycobacteria using 16S rRNA gene sequences. Stand. Genomic Sci. 3:145-152. http://dx.doi.org/10.4056/sigs.932152.
12. Tortoli E, Gitti Z, Klenk HP, Lauria S, Mannino R, Mantegani P, Mariottini A, Neonakis I. 2013. Survey of 150 strains belonging to the Mycobacterium terrae complex and description of Mycobacterium engbaekii sp. nov., Mycobacterium heraklionense sp. nov. and Mycobacterium longobardum sp. nov. Int. J. Syst. Evol. Microbiol. 63:401-411. http://dx.doi.org/10.1099/ijs.0. 038737-0.
13. Hartwig NG, Warris A, van de Vosse E, van der Zanden AG, Schulin-Casonato T, van Ingen J, van Hest R. 2011. "Mycobacterium tilburgii" infection in two immunocompromised children: importance of molecular tools in culture-negative mycobacterial disease diagnosis. J. Clin. Microbiol. 49:4409-4411. http://dx.doi.org/10.1128/JCM.05460-11.
14. Shojaei H, Daley C, Gitti Z, Hashemi A, Heidarieh P, Moore ER, Naser AD, Russo C, van Ingen J, Tortoli E. 2013. Mycobacterium iranicum sp. nov., a rapidly growing scotochromogenic species isolated from clinical specimens on three different continents. Int. J. Syst. Evol. Microbiol. 63: 1383-1389. http://dx.doi.org/10.1099/ijs.0.043562-0.
15. Higgins J, Camp P, Farrell D, Bravo D, Pate M, Robbe-Austerman S. 2011. Identification of Mycobacterium spp. of veterinary importance using rpoB gene sequencing. BMC Vet. Res. 7:77. http://dx.doi.org/10.1186/1746-6148-7-77.
16. Simmon KE, Kommedal O, Saebo O, Karlsen B, Petti CA. 2010. Simultaneous sequence analysis of the 16S rRNA and rpoB genes by use of RipSeq software to identify Mycobacterium species. J. Clin. Microbiol. 48:3231-3235. http://dx.doi.org/10.1128/JCM.00362-10.
17. Tortoli E, Pecorari M, Fabio G, Messino M, Fabio A. 2010. Commercial DNA probes for mycobacteria incorrectly identify a number of less frequently encountered species. J. Clin. Microbiol. 48:307-310. http://dx.doi.org/10.1128/ JCM.01536-09.
18. van Ingen J, de Zwaan R, Enaimi M, Dekhuijzen PN, Boeree MJ, van Soolingen D. 2010. Re-analysis of 178 previously unidentifiable Mycobacterium isolates in the Netherlands in 1999-2007. Clin. Microbiol. Infect. 16:1470-1474. http://dx.doi.org/10.1111/j.1469-0691.2010.03123.x.
19. van Ingen J, Tortoli E, Selvarangan R, Coyle MB, Crump JA, Morrissey AB, Dekhuijzen PN, Boeree MJ, van Soolingen D. 2011. Mycobacterium sherrisii sp. nov., a slow-growing non-chromogenic species. Int. J. Syst. Evol. Microbiol. 61:1293-1298. http://dx.doi.org/10.1099/ijs.0.024752-0.
20. Tortoli E, Bottger EC, Fabio A, Falsen E, Gitti Z, Grottola A, Klenk HP, Mannino R, Mariottini A, Messino M, Pecorari M, Rumpianesi F. 2011. Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex. Int. J. Syst. Evol. Microbiol. 61: 1606-1611. http://dx.doi.org/10.1099/ijs.0.025601-0.
21. Picardeau M, Prod'Hom G, Raskine L, LePennec MP, Vincent V. 1997. Genotypic characterization of five subspecies of Mycobacterium kansasii. J. Clin. Microbiol. 35:25-32.
22. Itoh S, Kazumi Y, Abe C, Takahashi M. 2003. Heterogeneity of RNA polymerase gene (rpoB) sequences of Mycobacterium gordonae clinical isolates identified with a DNA probe kit and by conventional methods. J. Clin. Microbiol. 41:1656-1663. http://dx.doi.org/10.1128/JCM.41.4.1656-1663.2003.
23. Tortoli E, Rindi L, Garcia MJ, Chiaradonna P, Dei R, Garzelli C, Kroppenstedt RM, Lari N, Mattei R, Mariottini A, Mazzarelli G, Murcia MI, Nanetti A, Piccoli P, Scarparo C. 2004. Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov. Int. J. Syst. Evol. Microbiol. 54:1277-1285. http://dx.doi.org/10.1099/ijs.0.02777-0. (Pubitemid 39139851)
24. Leao SC, Tortoli E, Euzeby JP, Garcia MJ. 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. http://dx.doi.org/10.1099/ijs.0.023770-0.
25. Kim HY, Kim BJ, Kook Y, Yun YJ, Shin JH, Kook YH. 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. http://dx.doi.org/10.1111/j.1348-0421.2010.00221.x.
26. Macheras E, Roux AL, Bastian S, Leao SC, Palaci M, Sivadon-Tardy V, Gutierrez C, Richter E, Rusch-Gerdes S, Pfyffer G, Bodmer T, Cambau E, Gaillard JL, Heym B. 2011. Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains. J. Clin. Microbiol. 49:491-499. http://dx.doi.org/10.1128/JCM.01274-10.