Identification of pathogenic Nocardia species by reverse line blot hybridization targeting the 16S rRNA and 16S-23S rRNA gene spacer regions

Journal of Clinical Microbiology

Volumn 48, Issue 2, 2010, Pages 503-511

  Xiao, Meng ^a,b   Kong, Fanrong ^b   Sorrell, Tania C ^b   Cao, Yongyan ^c   Lee, Ok Cha ^b   Liu, Ying ^d   Sintchenko, Vitali ^b   Chen, Sharon C A ^b  

^a PEKING UNIVERSITY   (China)

^b UNIVERSITY OF SYDNEY   (Australia)

^c First Hospital of Wuhan   (China)

^d CAPITAL MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; RNA 23S;

ARTICLE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CONTROLLED STUDY; GENE PROBE; GENE SEQUENCE; HYBRIDIZATION; NOCARDIA; NOCARDIA ASTEROIDES; NOCARDIA BRASILIENSIS; NOCARDIA FARCINICA; NONHUMAN; NONTARGET ORGANISM; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVERSE LINE BLOT HYBRIDIZATION; SENSITIVITY AND SPECIFICITY;

BACTERIOLOGICAL TECHNIQUES; DNA, BACTERIAL; DNA, RIBOSOMAL; DNA, RIBOSOMAL SPACER; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; NOCARDIA; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY;

NOCARDIA; NOCARDIA ASTEROIDES; NOCARDIA BRASILIENSIS; NOCARDIA CYRIACIGEORGICA; NOCARDIA FARCINICA; NOCARDIA PAUCIVORANS; NOCARDIA THAILANDICA;

EID: 75649115721     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.01761-09     Document Type: Article

References (34)

1. Alfaresi, M., and A. Elkosh. 2006. Rapid identification of clinically relevant Nocardia species using real-time PCR with SYBR green and melting-curve analysis. J. Med. Microbiol. 55:1711-1715.
2. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Becker, K., D. Harmsen, A. Mellmann, C. Meier, P. Schumann, G. Peters, and C. von Eiff. 2004. Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species. J. Clin. Microbiol. 42:4988-4995.
4. Brown, J. M., K. N. Pham, M. M. McNeil, and B. A. Lasker. 2004. Rapid identification of Nocardia farcinica clinical isolates by a PCR assay targeting a 314-base-pair species-specific DNA fragment. J. Clin. Microbiol. 42:3655-3660.
5. Brown-Elliott, B. A., J. M. Brown, P. S. Conville, and R. J. Wallace, Jr. 2006. Clinical and laboratory features of the Nocardia spp. based on current molecular taxonomy. Clin. Microbiol. Rev. 19:259-282.
6. Clarridge, J. E., III. 2004. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin. Microbiol. Rev. 17:840-1862.
7. Cloud, J. L., P. S. Conville, A. Croft, D. Harmsen, F. G. Witebsky, and K. C. Carroll. 2004. Evaluation of partial 16S ribosomal DNA sequencing for identification of Nocardia species by using the MicroSeq 500 system with an expanded database. J. Clin. Microbiol. 42:578-584.
8. Conville, P. S., J. M. Brown, A. G. Steigerwalt, B. A. Brown-Elliott, and F. G. Witebsky. 2008. Nocardia wallacei sp. nov. and Nocardia blacklockiae sp. nov., human pathogens and members of the "Nocardia transvalensis complex." J. Clin. Microbiol. 46:1178-1184.
9. Conville, P. S., and F. G. Witebsky. 2004. Current issues pertaining to the Nocardia species. Clin. Microbiol. Newsl. 26:57-62.
10. Conville, P. S., and F. G. Witebsky. 2005. Multiple copies of the 16S rRNA gene in Nocardia nova isolates and implications for sequence-based identification procedures. J. Clin. Microbiol. 43:2881-2885.
11. Conville, P. S., and F. G. Witebsky. 2007. Analysis of multiple differing copies of the 16S rRNA gene in five clinical isolates and three type strains of Nocardia species and implications for species assignment. J. Clin. Microbiol. 45:1146-1151.
12. Conville, P. S., A. M. Zelazny, and F. G. Witebsky. 2006. Analysis of secA1 gene sequences for identification of Nocardia species. J. Clin. Microbiol. 44:2760-2766.
13. Conville, P. S., and F. G. Witebsky. 2007. Nocardia, Rhodococcus, Gordonia, Actinomadura, Streptomyces, and other aerobic actinomycetes, p. 515-542. In P. R. Murray, E. J. Baron, J. H. Jorgensen, M. L. Landry, and M. A. Pfaller (ed.), Manual of clinical microbiology, 9th ed. ASM Press, Washington, DC.
14. Gold, B. 2003. Origin and utility of the reverse dot-blot. Expert Rev. Mol. Diagn. 3:143-152.
15. Gurtler, V., R. Smith, B. C. Mayall, G. Potter-Reinemann, E. Stackebrandt, and R. M. Kroppenstedt. 2001. Nocardia veterana sp. nov., isolated from human bronchial lavage. Int. J. Syst. Evol. Microbiol. 51:933-936.
16. Hasegawa, T., T. Gonoi, J. Ito, T. Kogure, K. Yazawa, and Y. Mikami. 2007. Identification of Nocardia farcinica by a PCR primer amplifying a specific DNA band for the bacterium. Nippon Ishinkin Gakkai Zasshi 48:173-175. (In Japanese.)
17. Isik, K., and M. Goodfellow. 2002. Differentiation of Nocardia species by PCR-randomly amplified polymorphic DNA fingerprinting. Syst. Appl. Microbiol. 25:60-67.
18. Janda, J. M., and S. L. Abbott. 2007. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J. Clin. Microbiol. 45:2761-2764.
19. Kong, F., S. C. Chen, X. Chen, V. Sintchenko, C. Halliday, L. Cai, Z. Tong, O. C. Lee, and T. C. Sorrell. 2009. Assignment of reference 5′-end 16S rDNA sequences and species-specific sequence polymorphisms improves species identification of Nocardia. Open Microbiol. J. 3:97-105.
20. Kong, F., and G. L. Gilbert. 2006. Multiplex PCR-based reverse line blot hybridization assay (mPCR/RLB) - a practical epidemiological and diagnostic tool. Nat. Protoc. 1:2668-2680.
21. McNeil, M. M., and J. M. Brown. 1994. The medically important aerobic actinomycetes: epidemiology and microbiology. Clin. Microbiol. Rev. 7:357-417.
22. Minero, M. V., M. Marin, E. Cercenado, P. M. Rabadan, E. Bouza, and P. Munoz. 2009. Nocardiosis at the turn of the century. Medicine 88:250-261.
23. Patel, J. B., R. J. Wallace, Jr., B. A. Brown-Elliott, T. Taylor, C. Imperatrice, D. G. Leonard, R. W. Wilson, L. Mann, K. C. Jost, and I. Nachamkin. 2004. Sequence-based identification of aerobic actinomycetes. J. Clin. Microbiol. 42:2530-2540.
24. Rodriguez-Nava, V., A. Couble, G. Devulder, J. P. Flandrois, P. Boiron, and F. Laurent. 2006. Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species. J. Clin. Microbiol. 44:536-546.
25. Roth, A., S. Andrees, R. M. Kroppenstedt, D. Harmsen, and H. Mauch. 2003. Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons. J. Clin. Microbiol. 41:851-856.
26. Saubolle, M. A., and D. Sussland. 2003. Nocardiosis: review of clinical and laboratory experience. J. Clin. Microbiol. 41:4497-4501.
27. Schlaberg, R., R. C. Huard, and P. Della-Latta. 2008. Nocardia cyriacigeorgica, an emerging pathogen in the United States. J. Clin. Microbiol. 46:265-273.
28. Steingrube, V. A., B. A. Brown, J. L. Gibson, R. W. Wilson, J. Brown, Z. Blacklock, K. Jost, S. Locke, R. F. Ulrich, and R. J. Wallace, Jr. 1995. DNA amplification and restriction endonuclease analysis for differentiation of 12 species and taxa of Nocardia, including recognition of four new taxa within the Nocardia asteroides complex. J. Clin. Microbiol. 33:3096-3101.
29. Su, S. C., M. Vaneechoutte, L. Dijkshoorn, Y. F. Wei, Y. L. Chen, and T. C. Chang. 2009. Identification of non-fermenting Gram-negative bacteria of clinical importance by an oligonucleotide array. J. Med. Microbiol. 58:596-605.
30. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
31. Wallace, R. J., Jr., M. Tsukamura, B. A. Brown, J. Brown, V. A. Steingrube, Y. S. Zhang, and D. R. Nash. 1990. Cefotaxime-resistant Nocardia asteroides strains are isolates of the controversial species Nocardia farcinica. J. Clin. Microbiol. 28:2726-2732.
32. Wang, Y., F. Kong, Y. Yang, and G. L. Gilbert. 2008. A multiplex PCR-based reverse line blot hybridization (mPCR/RLB) assay for detection of bacterial respiratory pathogens in children with pneumonia. Pediatr. Pulmonol. 43:150-159.
33. Xiong, L., F. Kong, Y. Yang, J. Cheng, and G. L. Gilbert. 2006. Use of PCR and reverse line blot hybridization macroarray based on 16S-23S rRNA gene internal transcribed spacer sequences for rapid identification of 34 Mycobacterium species. J. Clin. Microbiol. 44:3544-3550.
34. Zeng, X., F. Kong, C. Halliday, S. Chen, A. Lau, G. Playford, and T. C. Sorrell. 2007. Reverse line blot hybridization assay for identification of medically important fungi from culture and clinical specimens. J. Clin. Microbiol. 45:2872-2880.