| 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 #: |
45324 |
| Author(s): |
Sproer,C.;Mendrock,U.;Swiderski,J.;Lang,E.;Stackebrandt,E. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
The phylogenetic position of Serratia, Buttiauxella and some other genera of the family Enterobacteriaceae |
| Volume: |
49 Pt 4 |
| Page(s): |
1433-8 |
| Year: |
1999 |
| Keyword(s): |
GENBANK/AJ233400
GENBANK/AJ233401
GENBANK/AJ233402
GENBANK/AJ233403
GENBANK/AJ233404
GENBANK/AJ233405
GENBANK/AJ233406
GENBANK/AJ233407
GENBANK/AJ233408
GENBANK/AJ233409
GENBANK/AJ233410
GENBANK/AJ233411
GENBANK/AJ233412
GENBANK/AJ233413
GENBANK/AJ233414
GENBANK/AJ233415
GENBANK/AJ233416
GENBANK/AJ233417
GENBANK/AJ233418
GENBANK/AJ233419
GENBANK/AJ233420
GENBANK/AJ233421
GENBANK/AJ233422
GENBANK/AJ233423
GENBANK/AJ233424
GENBANK/AJ233425
GENBANK/AJ233426
GENBANK/AJ233427
GENBANK/AJ233428
GENBANK/AJ233429
etc.
DNA, Ribosomal/genetics
Enterobacteriaceae/classification/*genetics
Molecular Sequence Data
*Phylogeny
Polymerase Chain Reaction/methods
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Serratia/classification/*genetics
|
| Remarks: |
The phylogenetic relationships of the type strains of 38 species from 15 genera of the family Enterobacteriaceae were investigated by comparative 16S rDNA analysis. Several sequences of strains from the genera Citrobacter, Erwinia, Pantoea, Proteus, Rahnella and Serratia, analysed in this study, have been analysed previously. However, as the sequences of this study differ slightly from the published ones, they were included in the analysis. Of the 23 enterobacterial genera included in an overview dendrogram of relatedness, members of the genera Xenorhabdus, Photorhabdus, Proteus and Plesiomonas were used as a root. The other genera formed two groups which could be separated, although not exclusively, by signature nucleotides at positions 590-649 and 600-638. Group A contains species of Brenneria, Buttiauxella, Citrobacter, Escherichia, Erwinia, Klebsiella, Pantoea, Pectobacterium and Salmonella. All seven type strains of Buttiauxella share 16S rDNA similarities greater than 99%. Group B embraces two phylogenetically separate Serratia clusters, a lineage containing Yersinia species, Rahnella aquatica, Ewingella americana, and also the highly related pair Hafnia alvei and Obesumbacterium proteus. |
| URL: |
10555323 |
|
| 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 #: |
95472 |
| Author(s): |
Rojas,A.M.;de Los Rios,J.E.;Fischer-Le Saux,M.;Jimenez,P.;Reche,P.;Bonneau,S.;Sutra,L.;Mathieu-Daude,F.;McClelland,M. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots |
| Volume: |
54 |
| Page(s): |
2217-22 |
| Year: |
2004 |
| Keyword(s): |
GENBANK/AF130885
GENBANK/AF130909
GENBANK/AF130910
GENBANK/AF130953
GENBANK/AF130962
GENBANK/AF130963
GENBANK/AF130964
GENBANK/AF130965
GENBANK/AF130966
GENBANK/AF130968
Bacterial Typing Techniques
DNA, Bacterial/chemistry/isolation +ACY-amp+ADs- purification
DNA, Ribosomal/chemistry/isolation +ACY-amp+ADs- purification
Erwinia/+ACo-classification/cytology/+ACo-isolation +ACY-amp+ADs- purification/metabolism
Genes, rRNA
Gentian Violet
Molecular Sequence Data
Nucleic Acid Hybridization
Olea/+ACo-microbiology
Phenazines
Phylogeny
Plant Diseases/+ACo-microbiology
Pseudomonas/+ACo-isolation +ACY-amp+ADs- purification
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
|
| Remarks: |
Gram-negative bacteria were isolated from knots induced by Pseudomonas savastanoi in olive trees (Olea europaea L.). A total of nine endophytic bacterial strains were isolated, each from inside a different tree knot. Biochemical characterization indicated that all the strains belong to the family Enterobacteriaceae. Phylogenetic analyses of the 16S rRNA genes of these novel isolates revealed that they formed a homogeneous cluster within Erwinia species. DNA signatures of these isolates were identical to those described for the genus Erwinia. The strains formed a homogeneous group as shown by DNA-DNA hybridization analysis and numerical analysis of phenotypic data, clearly differentiated from all species of Erwinia with validly published names. The data provide strong evidence of the differentiation of these strains from the most closely related species. Therefore, these isolates represent a novel species, for which the name Erwinia toletana sp. nov. is proposed. The isolates are available at CFBP, CECT and ATCC. The G content is 520.5 mol+ACU-. The type strain is CFBP 6631(T) (+AD0-A37(T)+AD0-ATCC 700880(T)+AD0-CECT 5263(T)). |
| URL: |
15545461 |
|
| Ref #: |
43181 |
| Author(s): |
Delmas,J.;Breysse,F.;Devulder,G.;Flandrois,J.P.;Chomarat,M. |
| Journal: |
Diagn Microbiol Infect Dis |
| Title: |
Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene |
| Volume: |
55 |
| Page(s): |
263-8 |
| Year: |
2006 |
| Keyword(s): |
Bacterial Typing Techniques/*methods
DNA Gyrase/*genetics
Enterobacteriaceae/enzymology/genetics/*isolation & purification
Genotype
Humans
Sequence Analysis, DNA/methods
|
| Remarks: |
Real-time polymerase chain reaction and sequencing were used to characterize a 506-bp-long DNA fragment internal to the gyrB gene (gyrBint). The sequences obtained from 32 Enterobacteriaceae-type strains and those available in the Genbank nucleotide sequence database (n = 24) were used as a database to identify 240 clinical enterobacteria isolates. Sequence analysis of the gyrBint fragment of 240 strains showed that gyrBint constitutes a discriminative target sequence to differentiate between Enterobacteriaceae species. Comparison of these identifications with those obtained by phenotypic methods (Vitek 1 system and/or Rapid ID 32E; bioMerieux, Marcy l'Etoile, France) revealed discrepancies essentially with genera Citrobacter and Enterobacter. Most of the strains identified as Enterobacter cloacae by phenotypic methods were identified as Enterobacter hormaechei strains by gyrBint sequencing. The direct sequencing of gyrBint would be useful as a complementary tool in the identification of clinical Enterobacteriaceae isolates. |
| URL: |
16626902 |
|
| Ref #: |
12300 |
| Author(s): |
Sproer,C.;Mendrock,U.;Swiderski,J.;Lang,E.;Stackebrandt,E. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
The phylogenetic position of Serratia, Buttiauxella and some other genera of the family Enterobacteriaceae |
| Volume: |
49 Pt 4 |
| Page(s): |
1433-8 |
| Year: |
1999 |
| Keyword(s): |
GENBANK/AJ233400
GENBANK/AJ233401
GENBANK/AJ233402
GENBANK/AJ233403
GENBANK/AJ233404
GENBANK/AJ233405
GENBANK/AJ233406
GENBANK/AJ233407
GENBANK/AJ233408
GENBANK/AJ233409
GENBANK/AJ233410
GENBANK/AJ233411
GENBANK/AJ233412
GENBANK/AJ233413
GENBANK/AJ233414
GENBANK/AJ233415
GENBANK/AJ233416
GENBANK/AJ233417
GENBANK/AJ233418
GENBANK/AJ233419
GENBANK/AJ233420
GENBANK/AJ233421
GENBANK/AJ233422
GENBANK/AJ233423
GENBANK/AJ233424
GENBANK/AJ233425
GENBANK/AJ233426
GENBANK/AJ233427
GENBANK/AJ233428
GENBANK/AJ233429
etc.
DNA, Ribosomal/genetics
Enterobacteriaceae/classification/*genetics
Molecular Sequence Data
*Phylogeny
Polymerase Chain Reaction/methods
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Serratia/classification/*genetics
|
| Remarks: |
The phylogenetic relationships of the type strains of 38 species from 15 genera of the family Enterobacteriaceae were investigated by comparative 16S rDNA analysis. Several sequences of strains from the genera Citrobacter, Erwinia, Pantoea, Proteus, Rahnella and Serratia, analysed in this study, have been analysed previously. However, as the sequences of this study differ slightly from the published ones, they were included in the analysis. Of the 23 enterobacterial genera included in an overview dendrogram of relatedness, members of the genera Xenorhabdus, Photorhabdus, Proteus and Plesiomonas were used as a root. The other genera formed two groups which could be separated, although not exclusively, by signature nucleotides at positions 590-649 and 600-638. Group A contains species of Brenneria, Buttiauxella, Citrobacter, Escherichia, Erwinia, Klebsiella, Pantoea, Pectobacterium and Salmonella. All seven type strains of Buttiauxella share 16S rDNA similarities greater than 99%. Group B embraces two phylogenetically separate Serratia clusters, a lineage containing Yersinia species, Rahnella aquatica, Ewingella americana, and also the highly related pair Hafnia alvei and Obesumbacterium proteus. |
| URL: |
20023023 |
|
| 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 #: |
2942 |
| Author(s): |
Ewing,W.H.;Five,M.A. |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Enterobacter agglomerans (Beijerinck) comb. nov. (the herbicola-lathyri bacteria). |
| Volume: |
22 |
| Page(s): |
4-11 |
| Year: |
1972 |
|
| Ref #: |
3841 |
| Author(s): |
Beji,A.;Mergaert,J.;Gavini,F.;Izard,D.;Kersters,K.;Leclerc,H.;DeLey,J. |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Subjective synonymy of Erwinia herbicola, Erwinia milletiae and Enterobacter agglomerans and redefinition of the taxon by genotypic and phenotypic data. |
| Volume: |
38 |
| Page(s): |
77-88 |
| Year: |
1988 |
|
| Ref #: |
4035 |
| Author(s): |
Gavini,F.;Mergaert,J.;Beji,A.;Mielcarek,C.;Izard,D.;Kersters,K.;DeLey,J. |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Transfer of Enterobacter agglomerans (Beijerinck 1888) Ewing and Fife 1972 to Pantoea gen. nov. as Pantoea agglomerans comb. nov. and description of Pantoea dispersa sp. nov. |
| Volume: |
39 |
| Page(s): |
337-345 |
| Year: |
1989 |
|
|
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