| Extended Bibliography: |
Show bibliography
| Ref #: |
43856 |
| Author(s): |
Naimi,A.;Beck,G.;Branlant,C. |
| Journal: |
Microbiology |
| Title: |
Primary and secondary structures of rRNA spacer regions in enterococci |
| Volume: |
143 ( Pt 3) |
| Page(s): |
823-34 |
| Year: |
1997 |
| Keyword(s): |
GENBANK/X87177
GENBANK/X87178
GENBANK/X87179
GENBANK/X87180
GENBANK/X87181
GENBANK/X87182
GENBANK/X87183
GENBANK/X87184
GENBANK/X87185
GENBANK/X87186
GENBANK/X87187
GENBANK/X87188
GENBANK/X87189
GENBANK/X87190
GENBANK/X87191
Base Sequence
Enterococcus/*genetics
Molecular Sequence Data
Nucleic Acid Conformation
RNA, Bacterial/chemistry/*genetics
RNA, Ribosomal/chemistry/*genetics
RNA, Transfer/genetics
Sequence Alignment
|
| Remarks: |
The 16S-23S and 23S-5S rRNA spacer DNA regions (spacer regions 1 and 2, respectively) from Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, Enterococcus durans and Enterococcus mundtii were amplified by PCR. Their nucleotide sequences were established and a secondary structure model showing the interaction between the two spacer regions was built. Whereas lactococci and Streptococcus sensu stricto are characterized by a single type of spacer region 1, the enterococci show a high degree of variability in this region; thus the spacer regions 1 with and without tRNA(Ala) were characterized. However, as shown for lactococci and Streptococcus sensu stricto, the tRNA(Ala) gene does not encode the 3'-terminal CCA trinucleotide. A putative antitermination signal is found downstream from the tRNA(Ala) gene. Based on comparison with Lactococcus lactis and Streptococcus thermophilus, a double-stranded processing stem is proposed. In E, hirae, one of the three different types of spacer region 1 contains no tRNA(Ala), but displays a 107 nt insertion that forms a long stem-loop structure. A similar insertion (115 nt in length) was found in E. faecium and base compensatory mutations preserve the ability to form the long stem-loop structure. Such insertions may correspond to mobile intervening sequences, as found in the 23S rRNA coding sequences of some Gram-negative bacteria. The spacer regions 1 and 2 from the three subgroups of streptococci were compared, and except for the tRNA(Ala) gene and the double-stranded processing sites, little similarity was found, which opens large possibilities for future development of DNA-based typing methods. |
| URL: |
9084166 |
|
| Ref #: |
95521 |
| Author(s): |
Monstein,H.J.;Quednau,M.;Samuelsson,A.;Ahrne,S.;Isaksson,B.;Jonasson,J. |
| Journal: |
Microbiology |
| Title: |
Division of the genus Enterococcus into species groups using PCR-based molecular typing methods |
| Volume: |
144 ( Pt 5) |
| Page(s): |
1171-9 |
| Year: |
1998 |
| Keyword(s): |
GENBANK/Y12905
GENBANK/Y12906
GENBANK/Y12907
GENBANK/Y12908
GENBANK/Y12909
GENBANK/Y12910
GENBANK/Y12911
GENBANK/Y12912
GENBANK/Y12913
GENBANK/Y12914
GENBANK/Y12915
GENBANK/Y12916
GENBANK/Y12917
GENBANK/Y12918
GENBANK/Y12919
GENBANK/Y12920
GENBANK/Y12921
GENBANK/Y12922
GENBANK/Y12923
GENBANK/Y12924
*Bacterial Typing Techniques
Base Sequence
Blotting, Southern
DNA, Bacterial/analysis/genetics
DNA, Ribosomal/analysis/genetics
Electrophoresis, Agar Gel
Enterococcus/*classification/genetics/isolation & purification
Epidemiology, Molecular
Gram-Positive Bacterial Infections/*microbiology
Humans
Molecular Sequence Data
Polymerase Chain Reaction/*methods
RNA, Ribosomal, 16S/genetics
Random Amplified Polymorphic DNA Technique
Sequence Alignment
Sequence Analysis, DNA
Species Specificity
|
| Remarks: |
Broad-range 16S rDNA PCR (BR-PCR) applied to DNA from 32 clinical enterococcal isolates and 12 other enterococci from a clinical reference collection followed by species-specific hybridization analysis identified 25 strains of Enterococcus faecalis and 19 Enterococcus species. Randomly amplified polymorphic DNA (RAPD) analysis using UPGMA clustering on the same material revealed four different clusters at a similarity level of 49%. Based on partial 16S rDNA sequence analysis of variable regions V4 and V9, it was possible to divide the 19 type strains specifying the genus Enterococcus into 12 different 16S rDNA species groups. The type strain distribution then served as a template for the analysis of the other 44 strains which were assigned to four different species groups (a-d) based on their 16S rDNA motifs. There was good agreement with the RAPD clusters. Species group a was an individual species line containing 25 strains that were identified as E. faecalis. Group b also represented an individual species line of 12 strains identified as E. faecium. The remaining seven strains that formed species groups c and d could not be fully identified to species by this analysis. It was concluded that BR-PCR of 16S rDNA followed by partial sequence analysis of the PCR products is a reliable technique for the identification and classification of enterococci. Further division of unresolved species groups should be achievable if regions other than V4 and V9 of 16S rDNA are also analysed. |
| URL: |
9611791 |
|
| Ref #: |
82554 |
| Author(s): |
Chen,C.C.;Teng,L.J.;Chang,T.C. |
| Journal: |
J Clin Microbiol |
| Title: |
Identification of clinically relevant viridans group streptococci by sequence analysis of the 16S-23S ribosomal DNA spacer region |
| Volume: |
42 |
| Page(s): |
2651-7 |
| Year: |
2004 |
| Keyword(s): |
DNA, Ribosomal Spacer/*chemistry
Humans
Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/*genetics
RNA, Ribosomal, 23S/*genetics
Sequence Analysis, DNA
Viridans Streptococci/classification/genetics/*isolation & purification
|
| Remarks: |
The feasibility of sequence analysis of the 16S-23S ribosomal DNA (rDNA) intergenic spacer (ITS) for the identification of clinically relevant viridans group streptococci (VS) was evaluated. The ITS regions of 29 reference strains (11 species) of VS were amplified by PCR and sequenced. These 11 species were Streptococcus anginosus, S. constellatus, S. gordonii, S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguinis, S. salivarius, S. sanguinis, and S. uberis. The ITS lengths (246 to 391 bp) and sequences were highly conserved among strains within a species. The intraspecies similarity scores for the ITS sequences ranged from 0.98 to 1.0, except for the score for S. gordonii strains. The interspecies similarity scores for the ITS sequences varied from 0.31 to 0.93. Phylogenetic analysis of the ITS regions revealed that evolution of the regions of some species of VS is not parallel to that of the 16S rRNA genes. One hundred six clinical isolates of VS were identified by the Rapid ID 32 STREP system (bioMerieux Vitek, Marcy l'Etoile, France) and by ITS sequencing, and the level of disagreement between the two methods was 18% (19 isolates). Most isolates producing discrepant results could be unambiguously assigned to a specific species by their ITS sequences. The accuracy of using ITS sequencing for identification of VS was verified by 16S rDNA sequencing for all strains except strains of S. oralis and S. mitis, which were difficult to differentiate by their 16S rDNA sequences. In conclusion, identification of species of VS by ITS sequencing is reliable and could be used as an alternative accurate method for identification of VS. |
| URL: |
15184447 |
|
| Ref #: |
13717 |
| Author(s): |
Monstein,H.J.;Quednau,M.;Samuelsson,A.;Ahrne,S.;Isaksson,B.;Jonasson,J. |
| Journal: |
Microbiology |
| Title: |
Division of the genus Enterococcus into species groups using PCR-based molecular typing methods |
| Volume: |
144 ( Pt 5) |
| Page(s): |
1171-9 |
| Year: |
1998 |
| Keyword(s): |
GENBANK/Y12905
GENBANK/Y12906
GENBANK/Y12907
GENBANK/Y12908
GENBANK/Y12909
GENBANK/Y12910
GENBANK/Y12911
GENBANK/Y12912
GENBANK/Y12913
GENBANK/Y12914
GENBANK/Y12915
GENBANK/Y12916
GENBANK/Y12917
GENBANK/Y12918
GENBANK/Y12919
GENBANK/Y12920
GENBANK/Y12921
GENBANK/Y12922
GENBANK/Y12923
GENBANK/Y12924
*Bacterial Typing Techniques
Base Sequence
Blotting, Southern
DNA, Bacterial/analysis/genetics
DNA, Ribosomal/analysis/genetics
Electrophoresis, Agar Gel
Enterococcus/*classification/genetics/isolation & purification
Epidemiology, Molecular
Gram-Positive Bacterial Infections/*microbiology
Human
Molecular Sequence Data
Polymerase Chain Reaction/*methods
RNA, Ribosomal, 16S/genetics
Random Amplified Polymorphic DNA Technique
Sequence Alignment
Sequence Analysis, DNA
Species Specificity
Support, Non-U.S. Gov't
|
| Remarks: |
Broad-range 16S rDNA PCR (BR-PCR) applied to DNA from 32 clinical enterococcal isolates and 12 other enterococci from a clinical reference collection followed by species-specific hybridization analysis identified 25 strains of Enterococcus faecalis and 19 Enterococcus species. Randomly amplified polymorphic DNA (RAPD) analysis using UPGMA clustering on the same material revealed four different clusters at a similarity level of 49%. Based on partial 16S rDNA sequence analysis of variable regions V4 and V9, it was possible to divide the 19 type strains specifying the genus Enterococcus into 12 different 16S rDNA species groups. The type strain distribution then served as a template for the analysis of the other 44 strains which were assigned to four different species groups (a-d) based on their 16S rDNA motifs. There was good agreement with the RAPD clusters. Species group a was an individual species line containing 25 strains that were identified as E. faecalis. Group b also represented an individual species line of 12 strains identified as E. faecium. The remaining seven strains that formed species groups c and d could not be fully identified to species by this analysis. It was concluded that BR-PCR of 16S rDNA followed by partial sequence analysis of the PCR products is a reliable technique for the identification and classification of enterococci. Further division of unresolved species groups should be achievable if regions other than V4 and V9 of 16S rDNA are also analysed. |
| URL: |
98274725 |
|
| Ref #: |
1300 |
| Author(s): |
Skerman,V.B.D.;McGowan,V.;Sneath,P.H.A.(ed) |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Approved Lists of Bacterial Names. |
| Volume: |
30 |
| Page(s): |
225-420 |
| Year: |
1980 |
|
| Ref #: |
2392 |
| Author(s): |
Ottogalli,G.;Galli,A.;Dellaglio,F. |
| Journal: |
J. Dairy Res. |
| Title: |
Taxonomic relationships between Streptococcus thermophilus and some other streptococci. |
| Volume: |
46 |
| Page(s): |
127-131 |
| Year: |
1979 |
|
| Ref #: |
2681 |
| Author(s): |
Schleifer,K.H.;Kilpper-Bälz,R. |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Transfer of Streptococcus faecalis and Streptococcus faecium to the genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov. |
| Volume: |
34 |
| Page(s): |
31-34 |
| Year: |
1984 |
|
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