| 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 #: |
95509 |
| Author(s): |
Majewski,J.;Zawadzki,P.;Pickerill,P.;Cohan,F.M.;Dowson,C.G. |
| Journal: |
J Bacteriol |
| Title: |
Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation |
| Volume: |
182 |
| Page(s): |
1016-23 |
| Year: |
2000 |
| Keyword(s): |
GENBANK/AF194507
GENBANK/AF194508
GENBANK/AF194509
GENBANK/AF194510
GENBANK/AF194511
GENBANK/AF194512
GENBANK/AF194513
GENBANK/AF194514
GENBANK/AF194515
GENBANK/AF194516
GENBANK/AF194517
GENBANK/AF194518
GENBANK/AF194519
GENBANK/AF194520
GENBANK/AF194521
GENBANK/AF194522
GENBANK/AF194523
GENBANK/AF194524
GENBANK/AF194525
GENBANK/AF194526
GENBANK/AF194527
GENBANK/AF194528
Base Pair Mismatch/*genetics
DNA Repair/*genetics
DNA, Bacterial/genetics
DNA-Directed RNA Polymerases/genetics
Molecular Sequence Data
Phylogeny
Recombination, Genetic
Sequence Analysis, DNA
Streptococcus/genetics
Streptococcus pneumoniae/*genetics/growth & development
*Transformation, Bacterial
|
| Remarks: |
Interspecies genetic exchange is an important evolutionary mechanism in bacteria. It allows rapid acquisition of novel functions by transmission of adaptive genes between related species. However, the frequency of homologous recombination between bacterial species decreases sharply with the extent of DNA sequence divergence between the donor and the recipient. In Bacillus and Escherichia, this sexual isolation has been shown to be an exponential function of sequence divergence. Here we demonstrate that sexual isolation in transformation between Streptococcus pneumoniae recipient strains and donor DNA from related strains and species follows the described exponential relationship. We show that the Hex mismatch repair system poses a significant barrier to recombination over the entire range of sequence divergence (0.6 to 27%) investigated. Although mismatch repair becomes partially saturated, it is responsible for 34% of the observed sexual isolation. This is greater than the role of mismatch repair in Bacillus but less than that in Escherichia. The remaining non-Hex-mediated barrier to recombination can be provided by a variety of mechanisms. We discuss the possible additional mechanisms of sexual isolation, in view of earlier findings from Bacillus, Escherichia, and Streptococcus. |
| URL: |
10648528 |
|
| Ref #: |
95488 |
| Author(s): |
Whiley,R.A.;Fraser,H.Y.;Douglas,C.W.;Hardie,J.M.;Williams,A.M.;Collins,M.D. |
| Journal: |
FEMS Microbiol Lett |
| Title: |
Streptococcus parasanguis sp. nov., an atypical viridans Streptococcus from human clinical specimens |
| Volume: |
56 |
| Page(s): |
115-21 |
| Year: |
1990 |
| Keyword(s): |
Base Sequence
DNA, Bacterial/genetics
Humans
Molecular Sequence Data
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Sequence Homology, Nucleic Acid
Serotyping
Streptococcus/*classification/genetics
|
| Remarks: |
Molecular taxonomic studies were performed on ten strains of an unusual 'viridans streptococcus' that were originally isolated from human throats, blood and urine. On the basis of DNA-DNA hybridization studies the strains formed a single homology group distinct from all recognized species of oral and viridans streptococci. 16S ribosomal RNA reverse transcriptase sequence studies confirmed the genealogical distinctiveness of the human strains. The results of the present study clearly demonstrate that the human strains represent a new species of the viridans group for which the name Streptococcus parasanguis sp. nov. is proposed. The type strain is ATCC 15912. |
| URL: |
1692001 |
|
| Ref #: |
95478 |
| Author(s): |
Pan,Y.P.;Li,Y.;Caufield,P.W. |
| Journal: |
Oral Microbiol Immunol |
| Title: |
Phenotypic and genotypic diversity of Streptococcus sanguis in infants |
| Volume: |
16 |
| Page(s): |
235-42 |
| Year: |
2001 |
| Keyword(s): |
Bacterial Typing Techniques
Chromosome Mapping
Chromosomes, Bacterial/genetics
Cohort Studies
Culture Media
DNA Fingerprinting
DNA, Bacterial/analysis
DNA, Intergenic/genetics
Genotype
Humans
Infant
Infant, Newborn
Longitudinal Studies
Mouth/*microbiology
Phenotype
Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 23S/genetics
Sequence Analysis, DNA
Statistics
Streptococcus sanguis/classification/*genetics
Variation (Genetics)
|
| Remarks: |
Streptococcus sanguis comprises a heterogeneous group of oral streptococci indigenous to the oral cavity of humans. A total of 289 isolates from an infant population (n=37) were tentatively identified as S. sanguis on the basis of the distinctive colony morphology as shown on MM10-sucrose non-selective medium. These isolates were divided into four biovars of S. sanguis as determined by an extended panel of biochemical attributes. Chromosomal DNA was extracted from each isolate, and an AP-PCR fingerprint profile was obtained to allow study of the diversity within and among the infants. In this study, all four biovars of S. sanguis were detected in the infants. A wide genotypic diversity of S. sanguis was observed among these isolates; on average, each infant harbored 2.7 unique amplitypes as shown by the AP-PCR fingerprints. To explore the phylogenic relationship among these S. sanguis isolates, 20 strains representing the four biovars were selected at random for sequencing of their 16S rDNA and 16S-23S rDNA intergenic spacer chromosomal loci. Two major sequence patterns were identified within the 16S rDNA sequences. A phylogenic analysis showed that members from each of the four biovars of S. sanguis bore close relationship with the type-strain ATCC 10556 sequence, and that all of the isolates representing the four biovars could be clustered into two main phylotypes. The biovars were distributed throughout the phylotypes, indicating no correlation between the genetic and phenotypic groupings. |
| URL: |
11442849 |
|
| Ref #: |
17178 |
| Author(s): |
Kawata,K.;Anzai,T.;Senna,K.;Kikuchi,N.;Ezawa,A.;Takahashi,T. |
| Journal: |
FEMS Microbiol Lett |
| Title: |
Simple and rapid PCR method for identification of streptococcal species relevant to animal infections based on 23S rDNA sequence |
| Volume: |
237 |
| Page(s): |
57-64 |
| Year: |
2004 |
| Keyword(s): |
GENBANK/AB168118
GENBANK/AB168119
GENBANK/AB168120
GENBANK/AB168121
GENBANK/AB168122
GENBANK/AB168123
GENBANK/AB168124
GENBANK/AB168125
GENBANK/AB168126
GENBANK/AB168127
GENBANK/AB168128
Animals
DNA, Bacterial/*analysis/chemistry
DNA, Ribosomal/*analysis/chemistry
Electrophoresis, Agar Gel
Genes, rRNA
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction/*methods
RNA, Bacterial/genetics
RNA, Ribosomal, 23S/genetics
Sequence Analysis, DNA
Streptococcal Infections/microbiology/*veterinary
Streptococcus/*classification/genetics/*isolation & purification
|
| Remarks: |
A PCR identification system targeting 23S rDNA sequences for the identification of eight streptococcal species relevant to animal infections (Streptococcus agalactiae, S. bovis, S. canis, S. dysgalactiae, S. equi, S. porcinus, S. suis and S. uberis) was developed. This system consists of two PCR reactions, A and B, in which seven and eight primers, respectively, are used simultaneously, and was designed so that each amplification product indicates a species by its size. A total of 111 cultures, including the type strain of eight species, could be successfully identified and differentiated as individual species, except for the cross reactivity between S. bovis and S. equinus. The developed PCR system can complete the identification procedure for eight streptococcal species through two tube reactions per isolate, and, therefore, might provide a rapid, simple and accurate diagnostic tool for veterinary laboratories. |
| URL: |
15268938 |
|
| 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 #: |
82526 |
| Author(s): |
Hoshino,T.;Fujiwara,T.;Kilian,M. |
| Journal: |
J Clin Microbiol |
| Title: |
Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients |
| Volume: |
43 |
| Page(s): |
6073-85 |
| Year: |
2005 |
| Keyword(s): |
GENBANK/AB199330
GENBANK/AB199331
GENBANK/AB199332
GENBANK/AB199333
GENBANK/AB199334
GENBANK/AB199335
GENBANK/AB199336
GENBANK/AB199337
GENBANK/AB199338
GENBANK/AB199339
GENBANK/AB199340
GENBANK/AB199341
GENBANK/AB199342
GENBANK/AB199343
GENBANK/AB199344
GENBANK/AB199345
GENBANK/AB199346
GENBANK/AB199347
GENBANK/AB199348
GENBANK/AB199349
GENBANK/AB199350
GENBANK/AB199351
GENBANK/AB199352
GENBANK/AB199353
GENBANK/AB199354
GENBANK/AB199355
GENBANK/AB199356
GENBANK/AB199357
GENBANK/AB199358
GENBANK/AB199359
GENBANK/AB199360
GENBANK/AB199361
GENBANK/AB199362
GENBANK/AB199363
GENBANK/AB199364
GENBANK/AB199365
GENBANK/AB199366
GENBANK/AB199367
GENBANK/AB199368
GENBANK/AB199369
GENBANK/AB199370
GENBANK/AB199371
GENBANK/AB199372
GENBANK/AB199373
GENBANK/AB199374
GENBANK/AB199375
GENBANK/AB199376
GENBANK/AB199377
GENBANK/AB199378
GENBANK/AB199379
GENBANK/AB199380
GENBANK/AB199381
GENBANK/AB199382
GENBANK/AB199383
GENBANK/AB199384
GENBANK/AB199385
GENBANK/AB199386
GENBANK/AB199387
GENBANK/AB199388
GENBANK/AB199389
GENBANK/AB199390
GENBANK/AB199391
GENBANK/AB199392
GENBANK/AB199393
GENBANK/AB199394
GENBANK/AB199395
GENBANK/AB199396
GENBANK/AB199397
GENBANK/AB199398
GENBANK/AB199399
GENBANK/AB199400
GENBANK/AB199401
GENBANK/AB199402
GENBANK/AB199403
GENBANK/AB199404
GENBANK/AB199405
GENBANK/AB199406
GENBANK/AB199407
GENBANK/AB199408
GENBANK/AB199409
GENBANK/AB199410
GENBANK/AB199411
GENBANK/AB199412
GENBANK/AB199413
GENBANK/AB199414
GENBANK/AB199415
GENBANK/AB199416
GENBANK/AB199417
GENBANK/AB199418
GENBANK/AB199419
GENBANK/AB199420
GENBANK/AB199421
GENBANK/AB199422
GENBANK/AB199423
GENBANK/AB199424
GENBANK/AB199425
GENBANK/AB199426
GENBANK/AB199427
GENBANK/AB199428
GENBANK/AB199429
GENBANK/AB199430
GENBANK/AB199431
GENBANK/AB199432
GENBANK/AB199433
GENBANK/AB199434
GENBANK/AB199435
GENBANK/AB199436
GENBANK/AB199437
GENBANK/AB199438
GENBANK/AB199439
GENBANK/AB199440
GENBANK/AB199441
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GENBANK/AB199443
GENBANK/AB199444
GENBANK/AB199445
GENBANK/AB199446
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GENBANK/AB199460
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GENBANK/AB199471
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GENBANK/AB199475
GENBANK/AB199476
GENBANK/AB199477
GENBANK/AB199478
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GENBANK/AB199480
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GENBANK/AB199499
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GENBANK/AB199502
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GENBANK/AB199510
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GENBANK/AB200153
GENBANK/AB200154
GENBANK/AB200155
GENBANK/AB200156
GENBANK/AB200157
GENBANK/AB200158
GENBANK/AB200159
GENBANK/AB200160
GENBANK/AB200161
GENBANK/AB200162
GENBANK/AB200163
GENBANK/AB200164
GENBANK/AB200165
GENBANK/AB200166
GENBANK/AB200167
GENBANK/AB218984
GENBANK/AB218985
Bacteremia/*microbiology
Bacterial Proteins/genetics
*Bacterial Typing Techniques
*Hemolysis
Humans
Molecular Sequence Data
Phenotype
*Phylogeny
Polymerase Chain Reaction/methods
Reagent Kits, Diagnostic
Sequence Analysis, DNA
Species Specificity
Streptococcal Infections/microbiology
Streptococcus/*classification/genetics/isolation &
purification/*physiology
|
| Remarks: |
The aim of this study was to evaluate molecular and phenotypic methods for the identification of nonhemolytic streptococci. A collection of 148 strains consisting of 115 clinical isolates from cases of infective endocarditis, septicemia, and meningitis and 33 reference strains, including type strains of all relevant Streptococcus species, were examined. Identification was performed by phylogenetic analysis of nucleotide sequences of four housekeeping genes, ddl, gdh, rpoB, and sodA; by PCR analysis of the glucosyltransferase (gtf) gene; and by conventional phenotypic characterization and identification using two commercial kits, Rapid ID 32 STREP and STREPTOGRAM and the associated databases. A phylogenetic tree based on concatenated sequences of the four housekeeping genes allowed unequivocal differentiation of recognized species and was used as the reference. Analysis of single gene sequences revealed deviation clustering in eight strains (5.4%) due to homologous recombination with other species. This was particularly evident in S. sanguinis and in members of the anginosus group of streptococci. The rate of correct identification of the strains by both commercial identification kits was below 50% but varied significantly between species. The most significant problems were observed with S. mitis and S. oralis and 11 Streptococcus species described since 1991. Our data indicate that identification based on multilocus sequence analysis is optimal. As a more practical alternative we recommend identification based on sodA sequences with reference to a comprehensive set of sequences that is available for downloading from our server. An analysis of the species distribution of 107 nonhemolytic streptococci from bacteremic patients showed a predominance of S. oralis and S. anginosus with various underlying infections. |
| URL: |
16333101 |
|
| 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 |
|
|
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