Use of tuf as a target for sequence-based identification of Gram-positive cocci of the genus Enterococcus, Streptococcus, coagulase-negative Staphylococcus, and Lactococcus

Annals of Clinical Microbiology and Antimicrobials

Volumn 11, Issue , 2012, Pages

  Li, Xuerui ^a   Xing, Juan ^a   Li, Baoyu ^a   Wang, Pu ^b   Liu, Jixing ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b WISTAR INSTITUTE   (United States)

Author keywords

Enterococcus; Lactococcus; species identification; Staphylococcus; Streptococcus; tuf

Indexed keywords

ELONGATION FACTOR; RNA 16S;

ARTICLE; BACTERIAL GENE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; COAGULASE NEGATIVE STAPHYLOCOCCUS; ENTEROCOCCUS; ENTEROCOCCUS AVIUM; ENTEROCOCCUS FAECALIS; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC CODE; LACTOCOCCUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; SEQUENCE ANALYSIS; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS CARNOSUS; STAPHYLOCOCCUS EPIDERMIDIS; STAPHYLOCOCCUS HAEMOLYTICUS; STAPHYLOCOCCUS HYICUS; STAPHYLOCOCCUS LUGDUNENSIS; STAPHYLOCOCCUS SAPROPHYTICUS; STAPHYLOCOCCUS WARNERI; STREPTOCOCCUS; STREPTOCOCCUS AGALACTIAE; STREPTOCOCCUS ANGINOSUS; STREPTOCOCCUS BOVIS; STREPTOCOCCUS CONSTELLATUS; STREPTOCOCCUS DYSGALACTIAE; STREPTOCOCCUS EQUINUS; STREPTOCOCCUS GALLOLYTICUS; STREPTOCOCCUS GORDONII; STREPTOCOCCUS INTERMEDIUS; STREPTOCOCCUS MITIS; STREPTOCOCCUS MUTANS; STREPTOCOCCUS ORALIS; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS PYOGENES; STREPTOCOCCUS SALIVARIUS; STREPTOCOCCUS SUIS; STREPTOCOCCUS THERMOPHILUS; STREPTOCOCCUS UBERIS; TUF GENE;

BACTERIAL PROTEINS; COAGULASE; DNA PRIMERS; DNA, BACTERIAL; ENTEROCOCCUS; PEPTIDE ELONGATION FACTOR TU; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; STAPHYLOCOCCUS; STREPTOCOCCUS; SUPEROXIDE DISMUTASE;

EID: 84869871100     PISSN: None     EISSN: 14760711     Source Type: Journal    
DOI: 10.1186/1476-0711-11-31     Document Type: Article

References (37)

1. Calvo JJ, et al. Osteomyelitis caused by Staphylococcus schleiferi and evidence for misidentification of this Staphylococcus species by an automated identification system. J Clin Microbiol 2000, 38:3887-3889. 87502, 11015429.
2. Flynn CE, Ruoff KL. Identification of Streptococcus milleri group isolates to the species level with a commercially available rapid test. J. Clin. Microbiol 1995, 33:2704-2706. 228559, 8567909.
3. Ieven MJ, et al. Rapid and economical method for species identification of clinically significant coagulase-negative staphylococci. J Clin Microbiol 1995, 33:1060-1063. 228104, 7615705.
4. Moore DF, et al. Comparison of 16S rRNA sequencing with conventional and commercial phenotypic techniques for identification of enterococci from the marine environment. J. Appl. Microbiol 2006, 100:1272-1281. 10.1111/j.1365-2672.2006.02879.x, 16696674.
5. Teng LJ, et al. GroESL sequence determination, phylogenetic analysis, and species differentiation for viridans group streptococci. J. Clin. Microbiol 2002, 40:3172-3178. 10.1128/JCM.40.9.3172-3178.2002, 130726, 12202549.
6. Urbach EB, et al. The ldh phylogeny for environmental isolates of Lactococcus lactis is consistent with rRNA genotypes but not with phenotypes. Appl. Environ. Microbiol 1997, 63:694-702. 168359, 9023947.
7. Fihman V, et al. Lactococcus garvieae endocarditis: identification by 16S rRNA and sodA sequence analysis. J Infect 2006, 52(1):e3-e6. 10.1016/j.jinf.2005.04.021, 15936823.
8. Ghebremedhin B, Layer F, König W, König B. Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences. J Clin Microbiol 2008, 46(3):1019-1025. 10.1128/JCM.02058-07, 2268370, 18174295.
9. Glazunova OO, Raoult D, Roux V. Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus. Int J Syst Evol Microbiol 2010, 60(Pt 9):2140-2148.
10. Rahkila R, et al. Identification of enterococci from broiler products and a broiler processing plant and description of Enterococcus viikkiensis sp. nov. Appl Environ Microbiol 2011, 77(4):1196-1203. 10.1128/AEM.02412-10, 3067211, 21183650.
11. Drancourt MV, et al. rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J. Clin. Microbiol 2004, 42:497-504. 10.1128/JCM.42.2.497-504.2004, 344509, 14766807.
12. Hung WC, et al. Use of groESL as a target for identification of Abiotrophia, Granulicatella, and Gemella species. J Clin Microbiol 2010, 48:3532-3538. 10.1128/JCM.00787-10, 2953133, 20686088.
13. Sakamoto M, Ohkuma M. Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods. J Med Microbiol 2010, 59(Pt 11):1293-1302.
14. Wang T, et al. Improved identification of Gordonia, Rhodococcus and Tsukamurella species by 5′-end 16S rRNA gene sequencing. Pathology 2011, 43(1):58-63. 10.1097/PAT.0b013e328340e431, 21240067.
15. Woo PC, et al. Usefulness of the MicroSeq 500 16S ribosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. J. Clin. Microbiol 2003, 41:1996-2001. 10.1128/JCM.41.5.1996-2001.2003, 154750, 12734240.
16. Drancourt M, Raoult D. rpoB gene sequence-based identification of Staphylococcus species. J Clin Microbiol 2002, 40(4):1333-1338. 10.1128/JCM.40.4.1333-1338.2002, 140360, 11923353.
17. Ke D, et al. Development of a PCR assay for rapid detection of enterococci. J Clin Microbiol 1999, 37(11):3497-3503. 85677, 10523541.
18. Martineau F, et al. Development of a PCR assay for identification of staphylococci at genus and species levels. J Clin Microbiol 2001, 39(7):2541-2547. 10.1128/JCM.39.7.2541-2547.2001, 88182, 11427566.
19. Picard FJ, et al. Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 2004, 42(8):3686-3695. 10.1128/JCM.42.8.3686-3695.2004, 497632, 15297518.
20. Tamura K, et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
21. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985, 39:783-791.
22. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 1980, 16:111-120. 10.1007/BF01731581, 7463489.
23. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 1987, 4:406-425.
24. Cui-Fang S, et al. Identification of the Pathogen for Antheraea pernyi Empty-gut Disease by Using 16S rRNA Gene Sequence. Science of Sericulture 2011, 37(5):0931-0936.
25. Achtman M, Wagner M. Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 2008, 6(6):431-440.
26. Carpaij N, et al. Comparison of the identification of coagulase-negative staphylococci by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and tuf sequencing. Eur. J. Clin. Microbiol. Infect. Dis 2011, 30:1169-1172. 10.1007/s10096-011-1204-3, 3172412, 21359622.
27. Loonen AJ, et al. Comparative study using phenotypic, genotypic, and proteomics methods for identification of coagulase-negative staphylococci. JClin Microbiol 2012, 50(4):1437-1439.
28. Becker K, et al. Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species. J Clin Microbiol 2004, 42:4988-4995. 10.1128/JCM.42.11.4988-4995.2004, 525259, 15528685.
29. Bialkowska-Hobrzanska H, et al. Typing of coagulase-negative staphylococci by Southern hybridization of chromosomal DNA fingerprints using a ribosomal RNA probe. Eur. J Microbiol Infect. Dis 1990, 9:588-594.
30. Buyser D, et al. Evaluation of ribosomal RNA gene probe for the identification of species and sub-species within the genus Staphylococcus. J Gen Microbiol 1992, 138:889-899. 10.1099/00221287-138-5-889, 1353785.
31. Sakamoto M, Kitahara M, Benno Y. Parabacteroides johnsonii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2007, 57:293-296. 10.1099/ijs.0.64588-0, 17267966.
32. Kim BJ, et al. Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol 1999, 37:1714-1720. 84932, 10325313.
33. Mignard S, Flandrois JP. Identification of Mycobacterium using the EF-Tu encoding (tuf) gene and the tmRNA encoding (ssrA) gene. J Med Microbiol 2007, 56(Pt 8):1033-1041.
34. Roth A, et al. Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spaces sequences. J Clin Microbiol 1998, 36:139-147. 124824, 9431937.
35. Poyart C, Quesnes G, Trieu-Cuot P. Sequencing the gene encoding manganese-dependent superoxide dismutase for rapid species identification of enterococci. J Clin Microbiol 2000, 38(1):415-418. 88737, 10618129.
36. Poyart C, et al. Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target. J Clin Microbiol 2001, 39:4296-4301. 10.1128/JCM.39.12.4296-4301.2001, 88539, 11724835.
37. Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. Chichester, UK: Wiley, Stackebrandt E, Goodfellow M.