| Extended Bibliography: |
Show bibliography
| Ref #: |
95540 |
| Author(s): |
Gensberg,K.;Jin,Y.F.;Piddock,L.J. |
| Journal: |
FEMS Microbiol Lett |
| Title: |
A novel gyrB mutation in a fluoroquinolone-resistant clinical isolate of Salmonella typhimurium |
| Volume: |
132 |
| Page(s): |
57-60 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/U30842
Anti-Infective Agents/*pharmacology
Base Sequence
Ciprofloxacin/pharmacology
DNA Gyrase
DNA Topoisomerases, Type II/*genetics
DNA, Bacterial/chemistry
Drug Resistance, Microbial/genetics
*Fluoroquinolones
Humans
Microbial Sensitivity Tests
Molecular Sequence Data
*Mutation
Nalidixic Acid/pharmacology
Quinolones/pharmacology
Salmonella typhimurium/drug effects/*genetics
|
| Remarks: |
In order to study the role of gyrB in antibiotic resistance in post-ciprofloxacin therapy fluoroquinolone-resistant clinical isolates of Salmonella typhimurium, plasmid pBP548, which contains the Escherichia coli gyrB gene, was used in complementation studies. In a heterodiploid strain, the wild-type (quinolone sensitive) allele is dominant over the resistant allele therefore, eleven clinical isolates were complemented with gyrB encoded on pBP548. Only one transformant, L18pBP548, exhibited increased susceptibility to the quinolones nalidixic acid, ciprofloxacin and sparfloxacin. The amino acid sequence of the gyrase B protein from a wild-type and the pre-therapy S. typhimurium (deduced from the nucleotide sequence) was identical to that of E. coli from codons 436 to 470; however, a point mutation was identified in codon 463 of gyrB of the quinolone-resistant post-therapy isolate L18, giving rise to an amino acid substitution of serine to tyrosine. |
| URL: |
7590165 |
|
| Ref #: |
95539 |
| Author(s): |
Cilia,V.;Lafay,B.;Christen,R. |
| Journal: |
Mol Biol Evol |
| Title: |
Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level |
| Volume: |
13 |
| Page(s): |
451-61 |
| Year: |
1996 |
| Keyword(s): |
GENBANK/X80675
GENBANK/X80676
GENBANK/X80677
GENBANK/X80678
GENBANK/X80679
GENBANK/X80680
GENBANK/X80681
GENBANK/X80682
GENBANK/X80683
GENBANK/X80684
GENBANK/X80721
GENBANK/X80722
GENBANK/X80723
GENBANK/X80724
GENBANK/X80725
GENBANK/X80726
GENBANK/X80727
GENBANK/X80728
GENBANK/X80729
GENBANK/X80730
GENBANK/X80731
GENBANK/X80732
GENBANK/X80733
GENBANK/X80734
Bacteria/classification/*genetics
Base Sequence
DNA, Bacterial/chemistry
Escherichia coli/classification/genetics
Molecular Sequence Data
Operon
*Phylogeny
Polymerase Chain Reaction
RNA, Bacterial/chemistry/genetics
RNA, Ribosomal, 16S/chemistry/*genetics
Salmonella/classification/genetics
Sequence Homology, Nucleic Acid
Shigella/classification/genetics
|
| Remarks: |
We have analyzed what phylogenetic signal can be derived by small subunit rRNA comparison for bacteria of different but closely related genera (enterobacteria) and for different species or strains within a single genus (Escherichia or Salmonella), and finally how similar are the ribosomal operons within a single organism (Escherichia coli). These sequences have been analyzed by neighbor-joining, maximum likelihood, and parsimony. The robustness of each topology was assessed by bootstrap. Sequences were obtained for the seven rrn operons of E. coli strain PK3. These data demonstrated differences located in three highly variable domains. Their nature and localization suggest that since the divergence of E. coli and Salmonella typhimurium, most point mutations that occurred within each gene have been propagated among the gene family by conversions involving short domains, and that homogenization by conversions may not have affected the entire sequence of each gene. We show that the differences that exist between the different operons are ignored when sequences are obtained either after cloning of a single operon or directly from polymerase chain reaction (PCR) products. Direct sequencing of PCR products produces a mean sequence in which mutations present in the most variable domains become hidden. Cloning a single operon results in a sequence that differs from that of the other operons and of the mean sequence by several point mutations. For identification of unknown bacteria at the species level or below, a mean sequence or the sequence of a single nonidentified operon should therefore be avoided. Taking into account the seven operons and therefore mutations that accumulate in the most variable domains would perhaps increase tree resolution. However, if gene conversions that homogenize the rRNA multigene family are rare events, some nodes in phylogenetic trees will reflect these recombination events and these trees may therefore be gene trees rather than organismal trees. |
| URL: |
8742634 |
|
| 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 #: |
12690 |
| Author(s): |
Cilia,V.;Lafay,B.;Christen,R. |
| Journal: |
Mol Biol Evol |
| Title: |
Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level |
| Volume: |
13 |
| Page(s): |
451-61 |
| Year: |
1996 |
| Keyword(s): |
GENBANK/X80675
GENBANK/X80676
GENBANK/X80677
GENBANK/X80678
GENBANK/X80679
GENBANK/X80680
GENBANK/X80681
GENBANK/X80682
GENBANK/X80683
GENBANK/X80684
GENBANK/X80721
GENBANK/X80722
GENBANK/X80723
GENBANK/X80724
GENBANK/X80725
GENBANK/X80726
GENBANK/X80727
GENBANK/X80728
GENBANK/X80729
GENBANK/X80730
GENBANK/X80731
GENBANK/X80732
GENBANK/X80733
GENBANK/X80734
Bacteria/classification/*genetics
Base Sequence
Comparative Study
DNA, Bacterial/chemistry
Escherichia coli/classification/genetics
Molecular Sequence Data
Operon
*Phylogeny
Polymerase Chain Reaction
RNA, Bacterial/chemistry/genetics
RNA, Ribosomal, 16S/chemistry/*genetics
Salmonella/classification/genetics
Sequence Homology, Nucleic Acid
Shigella/classification/genetics
Support, Non-U.S. Gov't
|
| Remarks: |
We have analyzed what phylogenetic signal can be derived by small subunit rRNA comparison for bacteria of different but closely related genera (enterobacteria) and for different species or strains within a single genus (Escherichia or Salmonella), and finally how similar are the ribosomal operons within a single organism (Escherichia coli). These sequences have been analyzed by neighbor-joining, maximum likelihood, and parsimony. The robustness of each topology was assessed by bootstrap. Sequences were obtained for the seven rrn operons of E. coli strain PK3. These data demonstrated differences located in three highly variable domains. Their nature and localization suggest that since the divergence of E. coli and Salmonella typhimurium, most point mutations that occurred within each gene have been propagated among the gene family by conversions involving short domains, and that homogenization by conversions may not have affected the entire sequence of each gene. We show that the differences that exist between the different operons are ignored when sequences are obtained either after cloning of a single operon or directly from polymerase chain reaction (PCR) products. Direct sequencing of PCR products produces a mean sequence in which mutations present in the most variable domains become hidden. Cloning a single operon results in a sequence that differs from that of the other operons and of the mean sequence by several point mutations. For identification of unknown bacteria at the species level or below, a mean sequence or the sequence of a single nonidentified operon should therefore be avoided. Taking into account the seven operons and therefore mutations that accumulate in the most variable domains would perhaps increase tree resolution. However, if gene conversions that homogenize the rRNA multigene family are rare events, some nodes in phylogenetic trees will reflect these recombination events and these trees may therefore be gene trees rather than organismal trees. |
| URL: |
96351315 |
|
| 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 #: |
4006 |
| Journal: |
Int. Bull. Bacteriol. Nomencl. Taxon. |
| Volume: |
13 |
| Page(s): |
36 |
| Year: |
1963 |
|
| Ref #: |
4007 |
| Journal: |
Int. Bull. Bacteriol. Nomencl. Taxon. |
| Volume: |
9 |
| Page(s): |
108-109 |
| Year: |
1959 |
|
| 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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