| Extended Bibliography: |
Show bibliography
| 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 #: |
83019 |
| Author(s): |
Kawata,K.;Minakami,T.;Mori,Y.;Katsumi,M.;Kataoka,Y.;Ezawa,A.;Kikuchi,N.;Takahashi,T. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
rDNA sequence analyses of Streptococcus dysgalactiae subsp. equisimilis isolates from pigs |
| Volume: |
53 |
| Page(s): |
1941-6 |
| Year: |
2003 |
| Keyword(s): |
Animals
Base Sequence
DNA Primers
DNA, Bacterial/genetics
DNA, Ribosomal/*genetics
*Phylogeny
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 23S/genetics
Sequence Alignment
Sequence Homology, Nucleic Acid
Streptococcus/*classification/*genetics/isolation & purification
Swine/*microbiology
|
| Remarks: |
The nucleotide sequences of 16S and 23S rRNA genes (rDNA) were determined for 11 isolates of Streptococcus dysgalactiae subsp. equisimilis from slaughtered pigs with endocarditis, arthritis or lymphadenitis and strain ATCC 35666, designated as a strain of subspecies equisimilis. The sequences of each of the genes were compared phylogenetically with the corresponding sequences of S. dysgalactiae subsp. dysgalactiae ATCC 43078(T) and ATCC 27957, which were also determined in this study. Based on the 16S rDNA analysis, the isolates of S. dysgalactiae subsp. equisimilis were divided into two distinct groups, designated groups 1 and 2. S. dysgalactiae subsp. equisimilis ATCC 35666 was closely related to the group 2 strains. The S. dysgalactiae subsp. dysgalactiae strains seemed to be associated with the group 1 strains, which was not consistent with the conventional subspecific classification of S. dysgalactiae. In contrast, the 23S rDNA analysis distinguished S. dysgalactiae subsp. dysgalactiae strains from subsp. equisimilis strains. This inconsistency between phylogenies based on 16S and 23S rDNA indicates that 23S rDNA is a more rigid marker for determining the phylogenetic relationships and taxonomic position of these organisms than is 16S rDNA. |
| URL: |
14657127 |
|
| 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 #: |
84110 |
| Author(s): |
Bekal,S.;Gaudreau,C.;Laurence,R.A.;Simoneau,E.;Raynal,L. |
| Journal: |
J Clin Microbiol |
| Title: |
Streptococcus pseudoporcinus sp. nov., a novel species isolated from the genitourinary tract of women |
| Volume: |
44 |
| Page(s): |
2584-6 |
| Year: |
2006 |
| Keyword(s): |
GENBANK/DQ303183
GENBANK/DQ303184
GENBANK/DQ303185
GENBANK/DQ303186
GENBANK/DQ303187
GENBANK/DQ303188
GENBANK/DQ303189
GENBANK/DQ303190
GENBANK/DQ303191
GENBANK/DQ303192
GENBANK/DQ303193
GENBANK/DQ303194
GENBANK/DQ303195
GENBANK/DQ303196
GENBANK/DQ303197
GENBANK/DQ303198
GENBANK/DQ303199
GENBANK/DQ303200
GENBANK/DQ303201
GENBANK/DQ303202
GENBANK/DQ303203
GENBANK/DQ303204
GENBANK/DQ303205
GENBANK/DQ303206
GENBANK/DQ303207
GENBANK/DQ303208
GENBANK/DQ303209
GENBANK/DQ340843
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Female
Female Urogenital Diseases/*microbiology
Genes, rRNA
Humans
Molecular Sequence Data
Phylogeny
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Streptococcal Infections/*microbiology
Streptococcus/*classification/genetics/*isolation & purification
Urogenital System/*microbiology
|
| Remarks: |
Streptococcus strains from animal and human sources identified biochemically as Streptococcus porcinus were investigated by 16S rRNA gene sequencing. The nine human strains isolated between 1997 and 2005 formed a single cluster with more than 2.1% dissimilarity with S. porcinus strains from animal sources. A novel species, Streptococcus pseudoporcinus sp. nov., is proposed. |
| URL: |
16825387 |
|
| 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 #: |
6924 |
| Author(s): |
DeutschesInstitutfürNormungDIN.NormenausschußMedizin(NAMed) |
| Title: |
DIN 58959-7. Qualitätsmanagement in der medizinischen Mikrobiologie. Teil 7: Allgemeine Anforderungen an das Mitführen von Kontrollstämmen. Beiblatt 2: ATCC- und DSM-Nummern häufig verwendeter Kontrollstämme. |
| Year: |
1997 |
|
|
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