| Extended Bibliography: |
Show bibliography
| Ref #: |
95525 |
| Author(s): |
Godfrey,V.;Logan,J.M.;Nicholson,G.;Maggs,A.F. |
| Journal: |
Br J Biomed Sci |
| Title: |
Problems in identifying blood culture isolates |
| Volume: |
55 |
| Page(s): |
12-3 |
| Year: |
1998 |
| Keyword(s): |
GENBANK/AJ001236
GENBANK/AJ001237
GENBANK/AJ001238
GENBANK/AJ001239
GENBANK/AJ001240
GENBANK/AJ001241
GENBANK/AJ001242
GENBANK/AJ001243
GENBANK/AJ001244
GENBANK/AJ001245
Adolescent
*Bacterial Typing Techniques
Blood/*microbiology
Female
Gram-Negative Bacteria/*classification
Humans
Phylogeny
RNA, Bacterial/genetics
Sequence Analysis, RNA
|
| URL: |
9684412 |
|
| Ref #: |
95492 |
| Author(s): |
Fukushima,M.;Kakinuma,K.;Kawaguchi,R. |
| Journal: |
J Clin Microbiol |
| Title: |
Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence |
| Volume: |
40 |
| Page(s): |
2779-85 |
| Year: |
2002 |
| Keyword(s): |
DNA Gyrase/*genetics
DNA, Bacterial/analysis
DNA, Ribosomal/analysis
Escherichia coli/classification/*genetics
Humans
Molecular Sequence Data
*Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/genetics
Salmonella/classification/*genetics
Shigella/classification/*genetics
|
| Remarks: |
Phylogenetic analysis of about 200 strains of Salmonella, Shigella, and Escherichia coli was carried out using the nucleotide sequence of the gene for DNA gyrase B (gyrB), which was determined by directly sequencing PCR fragments. The results establish a new phylogenetic tree for the classification of Salmonella, Shigella, and Escherichia coli in which Salmonella forms a cluster separate from but closely related to Shigella and E. coli. In comparison with 16S rRNA analysis, the gyrB sequences indicated a greater evolutionary divergence for the bacteria. Thus, in screening for the presence of bacteria, the gyrB gene might be a useful tool for differentiating between closely related species of bacteria such as Shigella spp. and E. coli. At present, 16S rRNA sequence analysis is an accurate and rapid method for identifying most unknown bacteria to the genus level because the highly conserved 16S rRNA region is easy to amplify; however, analysis of the more variable gyrB sequence region can identify unknown bacteria to the species level. In summary, we have shown that gyrB sequence analysis is a useful alternative to 16S rRNA analysis for constructing the phylogenetic relationships of bacteria, in particular for the classification of closely related bacterial species. |
| URL: |
12149329 |
|
| Ref #: |
43062 |
| Author(s): |
Hoffmann,H.;Roggenkamp,A. |
| Journal: |
Appl Environ Microbiol |
| Title: |
Population genetics of the nomenspecies Enterobacter cloacae |
| Volume: |
69 |
| Page(s): |
5306-18 |
| Year: |
2003 |
| Keyword(s): |
Anti-Bacterial Agents/pharmacology
Base Sequence
Chaperonin 60/genetics
DNA Primers
DNA, Bacterial/genetics
Enterobacter cloacae/*classification/drug effects/*genetics/isolation &
purification
Humans
Microbial Sensitivity Tests
Multigene Family
Nucleic Acid Hybridization
*Phylogeny
Polymerase Chain Reaction/methods
*Polymorphism, Restriction Fragment Length
|
| Remarks: |
The genetic heterogeneity of the nomenspecies Enterobacter cloacae is well known. Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter dissolvens, Enterobacter hormaechei, Enterobacter kobei, and Enterobacter nimipressuralis are closely related to it and are subsumed in the so-called E. cloacae complex. DNA-DNA hybridization studies performed previously identified at least five DNA-relatedness groups of this complex. In order to analyze the genetic structure and the phylogenetic relationships between the clusters of the nomenspecies E. cloacae, 206 strains collected from 22 hospitals, a veterinarian, and an agricultural center in 11 countries plus all 13 type strains of the genus and reference strain CDC 1347-71(R) were examined with a combination of sequence and PCR-restriction fragment length polymorphism (PCR-RFLP) analyses of the three housekeeping genes hsp60, rpoB, and hemB as well as ampC, the gene of a class C beta-lactamase. Based on the neighbor-joining tree of the hsp60 sequences, 12 genetic clusters (I to XII) and an unstable sequence crowd (xiii) were identified. The robustness of the genetic clusters was confirmed by analyses of rpoB and hemB sequences and ampC PCR-RFLPs. Sequence crowd xiii split into two groups after rpoB analysis. Only three strains formed a cluster with the type strain of E. cloacae, indicating that the minority of isolates identified as E. cloacae truly belong to the species; 13% of strains grouped with other type strains of the genus, suggesting that the phenotypes of these species seem to be more heterogeneous than so far believed. Three clusters represented 70% of strains, but none of them included a type or reference strain. The genetic clustering presented in this study might serve as a framework for future studies dealing with taxonomic, evolutionary, epidemiological, or pathogenetic characteristics of bacteria belonging to the E. cloacae complex. |
| URL: |
12957918 |
|
| Ref #: |
95479 |
| Author(s): |
Mitterer,G.;Huber,M.;Leidinger,E.;Kirisits,C.;Lubitz,W.;Mueller,M.W.;Schmidt,W.M. |
| Journal: |
J Clin Microbiol |
| Title: |
Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences |
| Volume: |
42 |
| Page(s): |
1048-57 |
| Year: |
2004 |
| Keyword(s): |
Abortion, Veterinary/microbiology
Animals
Bacteria/*genetics/*isolation & purification
Base Sequence
DNA Primers
DNA, Bacterial/genetics/isolation & purification
DNA, Ribosomal/*genetics/isolation & purification
Female
Horses
*Oligonucleotide Array Sequence Analysis
Polymerase Chain Reaction/*methods
Pregnancy
Pregnancy Complications, Infectious/microbiology/veterinary
RNA, Bacterial/genetics/isolation & purification
RNA, Ribosomal, 23S/*genetics/isolation & purification
|
| Remarks: |
The rapid identification of the bacteria in clinical samples is important for patient management and antimicrobial therapy. We describe a DNA microarray-based PCR approach for the quick detection and identification of bacteria from cervical swab specimens from mares. This on-chip PCR method combines the amplification of a variable region of bacterial 23S ribosomal DNA and the simultaneous sequence-specific detection on a solid phase. The solid phase contains bacterial species-specific primers covalently bound to a glass support. During the solid-phase amplification reaction the polymerase elongates perfectly matched primers and incorporates biotin-labeled nucleotides. The reaction products are visualized by streptavidin-cyanine 5 staining, followed by fluorescence scanning. This procedure successfully identified from pure cultures 22 bacteria that are common causes of abortion and sterility in mares. Using the on-chip PCR method, we also tested 21 cervical swab specimens from mares for the presence of pathogenic bacteria and compared the results with those of conventional bacteriological culture methods. Our method correctly identified the bacteria in 12 cervical swab samples, 8 of which contained more than one bacterial species. Due to the higher sensitivity of the on-chip PCR, this method identified bacteria in five cervical swab samples which were not detected by the conventional identification procedure. Our results show that this method will have great potential to be incorporated into the routine microbiology laboratory. |
| URL: |
15004052 |
|
| Ref #: |
48709 |
| Author(s): |
Dauga,C. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies |
| Volume: |
52 |
| Page(s): |
531-47 |
| Year: |
2002 |
| Keyword(s): |
GENBANK/AJ300528
GENBANK/AJ300529
GENBANK/AJ300530
GENBANK/AJ300531
GENBANK/AJ300532
GENBANK/AJ300533
GENBANK/AJ300534
GENBANK/AJ300535
GENBANK/AJ300536
GENBANK/AJ300537
GENBANK/AJ300538
GENBANK/AJ300539
GENBANK/AJ300540
GENBANK/AJ300541
GENBANK/AJ300542
GENBANK/AJ300543
GENBANK/AJ300544
GENBANK/AJ300545
GENBANK/AJ300546
GENBANK/AJ300547
GENBANK/AJ300548
GENBANK/AJ300549
GENBANK/AJ300550
GENBANK/AJ300551
GENBANK/AJ300552
GENBANK/AJ300553
GENBANK/AJ300554
DNA Gyrase/*genetics
Enterobacteriaceae/*classification/genetics
Evolution, Molecular
Genes, rRNA
Molecular Sequence Data
Phenotype
RNA, Bacterial/chemistry
RNA, Ribosomal, 16S/chemistry
|
| Remarks: |
Phylogenetic trees showing the evolutionary relatedness of Enterobacteriaceae based upon gyrB and 16S rRNA genes were compared. Congruence among trees of these molecules indicates that the genomes of these species are not completely mosaic and that molecular systematic studies can be carried out. Phylogenetic trees based on gyrB sequences appeared to be more reliable at determining relationships among Serratia species than trees based on 16S rRNA gene sequences. gyrB sequences from Serratia species formed a monophyletic group validated by significant bootstrap values. Serratia fonticola had the most deeply branching gyrB sequence in the Serratia monophyletic group, which was consistent with its atypical phenotypic characteristics. Klebsiella and Enterobacter genera seemed to be polyphyletic, but the branching patterns of gyrB and 16S rRNA gene trees were not congruent. Enterobacter aerogenes was grouped with Klebsiella pneumoniae on the gyrB phylogenetic tree, which supports that this species could be transferred to the Klebsiella genus. Unfortunately, 16S rRNA and gyrB phylogenetic trees gave conflicting evolutionary relationships for Citrobacter freundii because of its unusual gyrB evolutionary process. gyrB lateral gene transfer was suspected for Hafnia alvei. Saturation of gyrB genes was observed by the pairwise comparison of Proteus spp., Providencia alcalifaciens and Morganella morganii sequences. Depending on their level of variability, 16S rRNA gene sequences were useful for describing phylogenetic relationships between distantly related Enterobacteriaceae, whereas gyrB sequence comparison was useful for inferring intra- and some intergeneric relationships. |
| URL: |
11931166 |
|
| Ref #: |
12648 |
| Author(s): |
Godfrey,V.;Logan,J.M.;Nicholson,G.;Maggs,A.F. |
| Journal: |
Br J Biomed Sci |
| Title: |
Problems in identifying blood culture isolates |
| Volume: |
55 |
| Page(s): |
12-3 |
| Year: |
1998 |
| Keyword(s): |
GENBANK/AJ001236
GENBANK/AJ001237
GENBANK/AJ001238
GENBANK/AJ001239
GENBANK/AJ001240
GENBANK/AJ001241
GENBANK/AJ001242
GENBANK/AJ001243
GENBANK/AJ001244
GENBANK/AJ001245
Adolescent
*Bacterial Typing Techniques
Blood/*microbiology
Case Report
Female
Gram-Negative Bacteria/*classification
Human
Phylogeny
RNA, Bacterial/genetics
Sequence Analysis, RNA
Support, Non-U.S. Gov't
|
| URL: |
98349037 |
|
| 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 #: |
3825 |
| Author(s): |
Izard,D.;Gavini,F.;Leclerc,H. |
| Journal: |
Zbl. Bakt. Hyg., I. Abt. Orig. C |
| Title: |
Polynucleotide sequence relatedness and genome size among Enterobacter intermedius sp. nov. and the species Enterobacter cloacae and Klebsiella pneumoniae. |
| Volume: |
1 |
| Page(s): |
57 |
| 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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