Extended Bibliography: |
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Ref #: |
19216 |
Author(s): |
Greisen,K.;Loeffelholz,M.;Purohit,A.;Leong,D. |
Journal: |
J Clin Microbiol |
Title: |
PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid |
Volume: |
32 |
Page(s): |
335-51 |
Year: |
1994 |
Keyword(s): |
GENBANK/U02893
GENBANK/U02894
GENBANK/U02895
GENBANK/U02896
GENBANK/U02897
GENBANK/U02898
GENBANK/U02899
GENBANK/U02900
GENBANK/U02901
GENBANK/U02902
GENBANK/U02903
GENBANK/U02904
GENBANK/U02905
GENBANK/U02906
GENBANK/U02907
GENBANK/U02908
GENBANK/U02909
GENBANK/U02910
GENBANK/U02911
GENBANK/U02912
GENBANK/U02913
GENBANK/U02914
GENBANK/U02915
GENBANK/U02916
GENBANK/U02917
GENBANK/U02918
GENBANK/U02919
GENBANK/U02920
GENBANK/U02921
GENBANK/U02922
Bacteremia/diagnosis/microbiology
Bacteria/*genetics/isolation & purification/pathogenicity
Bacterial Infections/diagnosis/microbiology
Base Sequence
Cerebrospinal Fluid/microbiology
DNA Primers/genetics
DNA Probes/genetics
Genes, Bacterial
Gram-Negative Bacteria/genetics
Gram-Positive Bacteria/genetics
Humans
Meningitis, Bacterial/diagnosis/microbiology
Molecular Sequence Data
Nucleic Acid Hybridization
*Polymerase Chain Reaction/statistics & numerical data
RNA, Bacterial/*genetics
RNA, Ribosomal, 16S/*genetics
Sensitivity and Specificity
Sequence Homology, Nucleic Acid
Species Specificity
|
Remarks: |
A set of broad-range PCR primers for the 16S rRNA gene in bacteria were tested, along with three series of oligonucleotide probes to detect the PCR product. The first series of probes is broad in range and consists of a universal bacterial probe, a gram-positive probe, a Bacteroides-Flavobacterium probe, and two probes for other gram-negative species. The second series was designed to detect PCR products from seven major bacterial species or groups frequently causing meningitis: Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, S. agalactiae, Escherichia coli and other enteric bacteria, Listeria monocytogenes, and Staphylococcus aureus. The third series was designed for the detection of DNA from species or genera commonly considered potential contaminants of clinical samples, including cerebrospinal fluid (CSF): Bacillus, Corynebacterium, Propionibacterium, and coagulase-negative Staphylococcus spp. The primers amplified DNA from all 124 different species of bacteria tested. Southern hybridization testing of the broad-range probes with washes containing 3 M tetramethylammonium chloride indicated that this set of probes correctly identified all but two of the 102 bacterial species tested, the exceptions being Deinococcus radiopugnans and Gardnerella vaginalis. The gram-negative and gram-positive probes hybridized to isolates of two newly characterized bacteria, Alloiococcus otitis and Rochalimaea henselii, as predicted by Gram stain characteristics. The CSF pathogen and contaminant probe sequences were compared with available sequence information and with sequencing data for 32 different species. Testing of the CSF pathogen and contaminant probes against DNA from over 60 different strains indicated that, with the exception of the coagulase-negative Staphylococcus probes, these probes provided the correct identification of bacterial species known to be found in CSF. |
URL: |
7512093 |
|
Ref #: |
83651 |
Author(s): |
Mora,D.;Ricci,G.;Guglielmetti,S.;Daffonchio,D.;Fortina,M.G. |
Journal: |
Microbiology |
Title: |
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 |
Volume: |
149 |
Page(s): |
807-13 |
Year: |
2003 |
Keyword(s): |
Bacterial Typing Techniques
DNA, Ribosomal Spacer/*genetics
Dairy Products/*microbiology
Dairying
Heat
*Polymorphism, Single-Stranded Conformational
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 23S/genetics
Species Specificity
Streptococcus/*classification/genetics
*Variation (Genetics)
|
Remarks: |
The 16S-23S rRNA internal transcribed spacer (ITS) region of several Streptococcus thermophilus strains and some related dairy streptococci, S. macedonicus, S. salivarius and S. bovis, was analysed by sequence analysis. All the Streptococcus species were easily discriminated on the basis of sequence variations principally located upstream and downstream of the region encompassing the double-stranded processing sites and the tRNA(Ala) gene. Comparison between tRNA(Ala) gene sequences highlighted a high level of sequence conservation among the Streptococcus species investigated despite their belonging to separated phylogenetic clusters, i.e. the S. salivarius and S. bovis rRNA groups. A low but significant degree of variability was detected among the S. thermophilus strains, allowing the identification of four different ITS sequences. Similarity analysis of the ITS sequences showed that the Streptococcus species were clustered in two main branches, one containing S. macedonicus and S. bovis strains, and one containing S. thermophilus and S. salivarius strains. With the aim of developing a rapid tool for the identification of the dairy streptococci species a multiplex ITS-SSCP analysis of two discrete regions within the ITS locus was carried out. |
URL: |
12634348 |
|
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 #: |
13687 |
Author(s): |
Greisen,K.;Loeffelholz,M.;Purohit,A.;Leong,D. |
Journal: |
J Clin Microbiol |
Title: |
PCR primers and probes for the 16S rRNA gene of most species of pathogenic |
Volume: |
32 |
Page(s): |
335-351 |
Year: |
1994 |
Keyword(s): |
0 (DNA Primers)
0 (DNA Probes)
0 (RNA, Bacterial)
0 (RNA, Ribosomal, 16S)
Bacteremia/diagnosis/microbiology
Bacteria/*genetics/isolation & purification/pathogenicity
Bacterial Infections/diagnosis/microbiology
Base Sequence
Cerebrospinal Fluid/microbiology
DNA Primers/genetics
DNA Probes/genetics
Genes, Bacterial
Gram-Negative Bacteria/genetics
Gram-Positive Bacteria/genetics
Human
Meningitis, Bacterial/diagnosis/microbiology
Molecular Sequence Data
Nucleic Acid Hybridization
*Polymerase Chain Reaction/statistics & numerical data
RNA, Bacterial/*genetics
RNA, Ribosomal, 16S/*genetics
Sensitivity and Specificity
Sequence Homology, Nucleic Acid
Species Specificity
|
Remarks: |
A set of broad-range PCR primers for the 16S rRNA gene in bacteria were |
URL: |
94201356 |
|
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 #: |
3345 |
Author(s): |
Kilpper-Bälz,R.;Wenzig,P.;Schleifer,K.H. |
Journal: |
Int. J. Syst. Bacteriol. |
Title: |
Molecular relationships and classification of some viridans streptococci as Streptococcus oralis and emended description of Streptococcus oralis (Bridge and Sneath 1982). |
Volume: |
35 |
Page(s): |
482-488 |
Year: |
1985 |
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