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

Journal of Clinical Microbiology

Volumn 45, Issue 4, 2007, Pages 1146-1151

  Conville, Patricia S ^a   Witebsky, Frank G ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; RNA 16S;

ARTICLE; DNA DNA HYBRIDIZATION; GENE AMPLIFICATION; GENE SEQUENCE; MOLECULAR CLONING; NOCARDIA; NOCARDIA CONCAVA; NOCARDIA IGNORATA; NOCARDIA YAMANASHIENSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; STRAIN IDENTIFICATION;

BASE SEQUENCE; DNA, BACTERIAL; DNA, RIBOSOMAL; GENE DOSAGE; HUMANS; MOLECULAR SEQUENCE DATA; NOCARDIA; NOCARDIA INFECTIONS; NUCLEIC ACID HYBRIDIZATION; POINT MUTATION; POLYMORPHISM, GENETIC; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

NOCARDIA; NOCARDIA CONCAVA; NOCARDIA IGNORATA; NOCARDIA YAMANASHIENSIS;

EID: 34247217536     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.02482-06     Document Type: Article

References (21)

1. Brenner, D. J., F. W. Hickman-Brenner, J. V. Lee, A. G. Steigerwalt, G. R. Fanning, D. G. Mollis, J. J. Farmer III, R. E. Weaver, S. W. Joseph, and R. Seidler. 1983. Vibrio fumissii (formerly aerogenic biogroup of Vibrio fluvialis), a new species isolated from human feces and the environment. J. Clin. Microbiol. 18:816-824.
2. Brenner, D. J., A. C. McWhorter, J. K. Leete Knutson, and A. G. Steigerwalt. 1982. Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J. Clin. Microbiol. 15:1133-1140.
3. Cilia, V., B. Lafay, and R. Christen. 1996. Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol. Biol. Evol. 13:451-461.
4. 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.
5. Conville, P. S., J. M. Brown, A. G. Steigerwalt, J. W. Lee, V. L. Anderson, J. T. Fishbain, S. M. Holland, and F. G. Witebsky. 2004. Nocardia kruczakaie sp. nov., a pathogen in immunocompromised patients and a member of the "N nova complex." J. Clin. Microbiol. 42:5139-5145.
6. Conville, P. S., J. M. Brown, A. G. Steigerwalt, J. W. Lee, D. E. Byrer, V. L. Anderson, S. E. Dorman, S. M. Holland, B. Cahill, K. C. Carroll, and F. G. Witebsky. 2003. Nocardia veterana as a pathogen in North American patients. J. Clin. Microbiol. 41:2560-2568.
7. Conville, P. S., S. H. Fischer, C. P. Cartwright, and F. G. Witebsky. 2000. Identification of Nocardia species by restriction endonuclease analysis of an amplified portion of the 16S rRNA gene. J. Clin. Microbiol. 38:158-164.
8. 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.
9. 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.
10. Ishikawa, J., A. Yamashita, Y. Mikami, Y. Hoshino, H. Kurita, K. Hotta, T. Shiba, and M. Hattori. 2004. The complete genomic sequence of Nocardia farcinica IFM 10152. Proc. Natl. Acad. Sci. USA 101:14925-14930.
11. Kageyama, A., K. Yazawa, K. Nishimura, and Y. Mikami. 2004. Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens. Int. J. Syst. Evol. Microbiol. 54:563-569.
12. Kageyama, A., K. Yazawa, H. Taniguchi, H. Chibana, K. Nishimura, R. M. Kroppenstedt, and Y. Mikami. 2005. Nocardia concava sp. nov., isolated from Japanese patients. Int. J. Syst. Evol. Microbiol. 55:2081-2083.
13. Loeffelholz, M. J., and D. R. Scholl. 1989. Method for improved extraction of DNA from Nocardia asteroides. J. Clin. Microbiol. 27:1880-1881.
14. Ninet, B., M. Monod, S. Emler, J. Pawlowski, C. Metral, P. Rohner, R. Auckenthaler, and B. Hirschel. 1996. Two different 16S rRNA genes in a mycobacterial strain. J. Clin. Microbiol. 34:2531-2536.
15. Patel, J. B., R. J. Wallace, Jr., B. A. Brown-Elliott, T. Taylor, C. Imperatrice, D. G. B. 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.
16. Reischl, U., K. Feldmann, L. Naumann, B. J. M. Gaugler, B. Ninet, B. Hirschel, and S. Emler. 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.
17. Rodríguez-Nava, V., A. Couble, Z. U. Khan, M. Pérouse de Montclos, L. Brasme, C. Villuendas, C. Molinard, P. Boiron, and F. Laurent. 2005. Nocardia ignorata, a new agent of human nocardiosis isolated from respiratory specimens in Europe and soil samples from Kuwait. J. Clin. Microbiol. 43:6167-6170.
18. Steingrube, V. A., R. W. Wilson, B. A. Brown, K. C. Jost, Jr., Z. Blacklock, J. L. Gibson, and R. J. Wallace, Jr. 1997. Rapid identification of clinically significant species and taxa of aerobic actinomycetes, including Actinomadura, Gordona, Nocardia, Rhodococcus, Streptomyces, and Tsukamurella isolates, by DNA amplification and restriction endonuclease analysis. J. Clin. Microbiol. 35:817-822.
19. Telenti, A., F. Marchesi, M. Balz, F. Bally, E. C. Böttger, and T. Bodmer. 1993. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J. Clin. Microbiol. 31:175-178.
20. Wang, Y., Z. Zhang, and N. Ramanan. 1997. The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J. Bacteriol. 179:3270-3276.
21. Yassin, A. F., F. A. Rainey, and U. Steiner. 2001. Nocardia ignorata sp. nov. Int. J. Syst. Evol. Microbiol. 51:2127-2131.