Analysis of the 16S-23S rRNA gene internal transcribed spacer region in Klebsiella species

Journal of Clinical Microbiology

Volumn 46, Issue 11, 2008, Pages 3555-3563

  Wang, Min ^a,b   Cao, Boyang ^a,b   Yu, Qunfang ^a,b   Liu, Lei ^a,b   Gao, Qili ^b   Wang, Lei ^a,b,c   Feng, Lu ^a,b,c  

^a NANKAI UNIVERSITY   (China)

^b TEDA   (China)

^c Tianjin Biochip Corporation   (China)

Author keywords

[No Author keywords available]

Indexed keywords

INTERNAL TRANSCRIBED SPACER; RNA 16S; RNA 23S; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; DNA POLYMORPHISM; KLEBSIELLA; KLEBSIELLA OXYTOCA; KLEBSIELLA PNEUMONIAE; KLEBSIELLA RHINOSCLEROMATIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA ANALYSIS; UNINDEXED SEQUENCE;

CONSERVED SEQUENCE; DNA, BACTERIAL; DNA, RIBOSOMAL SPACER; GENES, BACTERIAL; HUMANS; KLEBSIELLA; KLEBSIELLA INFECTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ENTEROBACTERIACEAE; KLEBSIELLA; KLEBSIELLA OXYTOCA; KLEBSIELLA PNEUMONIAE SUBSP. OZAENAE; KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE; KLEBSIELLA PNEUMONIAE SUBSP. RHINOSCLEROMATIS; RAOULTELLA ORNITHINOLYTICA; RAOULTELLA PLANTICOLA; RAOULTELLA TERRIGENA;

EID: 55849109971     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.00927-08     Document Type: Article

References (42)

1. Antón, A. I., A. J. Martinez-Murcia, and F. Rodriguez-Valera. 1998. Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. J. Mol. Evol. 47:62-72.
2. Barry, T., G. Colleran, M. Glennon, L. K. Dunican, and F. Gannon. 1991. The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl. 1:51-56.
3. Biedenbach, D. J., G. J. Moet, and R. N. Jones. 2004. Occurrence and antimicrobial resistance pattern comparisons among bloodstream infection isolates from the SENTRY Antimicrobial Surveillance Program (1997-2002). Diagn. Microbiol. Infect. Dis. 50:59-69.
4. Boye, K., and D. S. Hansen. 2003. Sequencing of 16S rDNA of Klebsiella: taxonomic relations within the genus and to other Enterobacteriaceae. Int. J. Med. Microbiol. 292:495-503.
5. Boyer, S. L., V. R. Flechtner, and J. R. Johansen. 2001. Is the 16S-23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in cyanobacteria. Mol. Biol. Evol. 18:1057-1069.
6. Brisse, S., D. Milatovic, A. C. Fluit, J. Verhoef, and F. J. Schmitz. 2000. Epidemiology of quinolone resistance of Klebsiella pneumoniae and Klebsiella oxytoca in Europe. Eur. J. Clin. Microbiol. Infect. Dis. 19:64-68.
7. Carter, J. S., F. J. Bowden, I. Bastian, G. M. Myers, K. S. Sriprakash, and D. J. Kemp. 1999. Phylogenetic evidence for reclassification of Calymmatobacterium granulomatis as Klebsiella granulomatis comb. nov. Int. J. Syst. Bacteriol. 49:1695-1700.
8. Cordery, R. J., C. H. Roberts, S. J. Cooper, G. Bellinghan, and N. Shetty. 2008. Evaluation of risk factors for the acquisition of bloodstream infections with extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella species in the intensive care unit; antibiotic management and clinical outcome. J. Hosp. Infect. 68:108-115.
9. Drancourt, M., C. Bollet, A. Carta, and P. Rousselier. 2001. Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int. J. Syst. Evol. Microbiol. 51:925-932.
10. García San Miguel, L., J. Cobo, A. Valverde, T. M. Coque, S. Diz, F. Grill, and R. Canton. 2007. Clinical variables associated with the isolation of Klebsiella pneumoniae expressing different extended-spectrum beta-lactamases. Clin. Microbiol. Infect. 13:532-538.
11. Gonçalves, E. R., and Y. B. Rosato. 2002. Phylogenetic analysis of Xanthomonas species based upon 16S-23S rDNA intergenic spacer sequences. Int. J. Syst. Evol. Microbiol. 52:355-361.
12. Gürtler, V. 1999. The role of recombination and mutation in 16S-23S rDNA spacer rearrangements. Gene 238:241-252.
13. Gürtler, V., Y. Rao, S. R. Pearson, S. M. Bates, and B. C. Mayall. 1999. DNA sequence heterogeneity in the three copies of the long 16S-23S rDNA spacer of Enterococcus faecalis isolates. Microbiology 145:1785-1796.
14. Gürtler, V., and V. A. Stanisich. 1996. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142:3-16.
15. Gutell, R. R., N. Larsen, and C. R. Woese. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58:10-26.
16. Hansen, D. S., H. M. Aucken, T. Abiola, and R. Podschun. 2004. Recommended test panel for differentiation of Klebsiella species on the basis of a trilateral interlaboratory evaluation of 18 biochemical tests. J. Clin. Microbiol. 42:3665-3669.
17. Jeng, R. S., A. M. Svircev, A. L. Myers, L. Beliaeva, D. M. Hunter, and M. Hubbes. 2001. The use of 16S and 16S-23S rDNA to easily detect and differentiate common Gram-negative orchard epiphytes. J. Microbiol. Methods 44:69-77.
18. Jonas, D., B. Spitzmuller, F. D. Daschner, J. Verhoef, and S. Brisse. 2004. Discrimination of Klebsiella pneumoniae and Klebsiella oxytoca phylogenetic groups and other Klebsiella species by use of amplified fragment length polymorphism. Res. Microbiol. 155:17-23.
19. Kurupati, P., C. Chow, G. Kumarasinghe, and C. L. Poh. 2004. Rapid detection of Klebsiella pneumoniae from blood culture bottles by real-time PCR. J. Clin. Microbiol. 42:1337-1340.
20. Lee, S. Y., S. Kotapati, J. L. Kuti, C. H. Nightingale, and D. P. Nicolau. 2006. Impact of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella species on clinical outcomes and hospital costs: a matched cohort study. Infect. Control Hosp. Epidemiol. 27:1226-1232.
21. Liu, Y., B. J. Mee, and L. Mulgrave. 1997. Identification of clinical isolates of indole-positive Klebsiella spp., including Klebsiella planticola, and a genetic and molecular analysis of their beta-lactamases. J. Clin. Microbiol. 35:2365-2369.
22. Liu, Y., C. Liu, W. Zheng, X. Zhang, J. Yu, Q. Gao, Y. Hou, and X. Huang. 2008. PCR detection of Klebsiella pneumoniae in infant formula based on 16S-23S internal transcribed spacer. Int. J. Food Microbiol. 125:230-235.
23. Livermore, D. M., and N. Woodford. 2006. The beta-lactamase threat in Enterobacteriaceae, Pseudomonas and Acinetobacter. Trends Microbiol. 14: 413-420.
24. Lopes, A. C., J. F. Rodrigues, M. B. Clementino, C. A. Miranda, A. P. Nascimento, and M. A. de Morais Júnior. 2007. Application of PCR ribotyping and tDNA-PCR for Klebsiella pneumoniae identification. Mem. Inst. Oswaldo Cruz 102:827-832.
25. Maggi, R. G., B. Chomel, B. C. Hegarty, J. Henn, and E. B. Breitschwerdt. 2006. A Bartonella vinsonii berkhoffii typing scheme based upon 16S-23S ITS and Pap31 sequences from dog, coyote, gray fox, and human isolates. Mol. Cell. Probes 20:128-134.
26. Monnet, D., and J. Freney. 1994. Method for differentiating Klebsiella planticola and Klebsiella terrigena from other Klebsiella species. J. Clin. Microbiol. 32:1121-1122.
27. Mora, D., G. Ricci, S. Guglielmetti, D. Daffonchio, and M. G. Fortina. 2003. 16S-23S rRNA intergenic spacer region sequence variation in Streptococcus thermophilus and related dairy streptococci and development of a multiplex ITS-SSCP analysis for their identification. Microbiology 149:807-813.
28. Nakagawa, T., T. Uemori, K. Asada, I. Kato, and R. Harasawa. 1992. Acholeplasma laidlawii has tRNA genes in the 16S-23S spacer of the rRNA operon. J. Bacteriol. 174:8163-8165.
29. Nakanishi, S., T. Kuwahara, H. Nakayama, M. Tanaka, and Y. Ohnishi. 2005. Rapid species identification and partial strain differentiation of Clostridium butyricum by PCR using 16S-23S rDNA intergenic spacer regions. Microbiol. Immunol. 49:613-621.
30. Orskov, I. 1984. Genus V. Klebsiella, p. 461-465. In N. R. Krieg and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, 1st ed. Williams & Wilkins, Baltimore, MD.
31. Palasubramaniam, S., S. Muniandy, and P. Navaratnam. 2008. Rapid detection of ESBL-producing Klebsiella pneumoniae in blood cultures by fluorescent in-situ hybridization. J. Microbiol. Methods 72:107-109.
32. Palys, T., L. K. Nakamura, and F. M. Cohan. 1997. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47:1145-1156.
33. Pérez Luz, S., F. Rodriguez-Valera, R. Lan, and P. R. Reeves. 1998. Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies. J. Bacteriol. 180:2144-2151.
34. Peterson, L. R. 2008. Antibiotic policy and prescribing strategies for therapy of extended-spectrum beta-lactamase-producing Enterobacteriaceae: the role of piperacillin-tazobactam. Clin. Microbiol. Infect. 14(Suppl. 1):181-184.
35. Podschun, R., S. Pietsch, C. Holler, and U. Ullmann. 2001. Incidence of Klebsiella species in surface waters and their expression of virulence factors. Appl. Environ. Microbiol. 67:3325-3327.
36. Podschun, R., and U. Ullmann. 1998. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin. Microbiol. Rev. 11:589-603.
37. Regassa, L. B., K. M. Stewart, A. C. Murphy, F. E. French, T. Lin, and R. F. Whitcomb. 2004. Differentiation of group VIII Spiroplasma strains with sequences of the 16S-23S rDNA intergenic spacer region. Can. J. Microbiol. 50:1061-1067.
38. Roth, A., M. Fischer, M. E. Hamid, S. Michalke, W. Ludwig, and H. Mauch. 1998. Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J. Clin. Microbiol. 36:139-147.
39. Sahly, H., R. Podschun, and U. Ullmann. 2000. Klebsiella infections in the immunocompromised host. Adv. Exp. Med. Biol. 479:237-249.
40. Sakazaki, R., K. Tamura, Y. Kosako, and E. Yoshizaki. 1989. Klebsiella ornithinolytica sp. nov., formerly known as ornithine-positive Klebsiella oxytoca. Curr. Microbiol. 18:201-206.
41. Stamm, L. V., H. L. Bergen, and R. L. Walker. 2002. Molecular typing of papillomatous digital dermatitis-associated Treponema isolates based on analysis of 16S-23S ribosomal DNA intergenic spacer regions. J. Clin. Microbiol. 40:3463-3469.
42. Westbrook, G. L., C. M. O'Hara, S. B. Roman, and J. M. Miller. 2000. Incidence and identification of Klebsiella planticola in clinical isolates with emphasis on newborns. J. Clin. Microbiol. 38:1495-1497.