scholarly journals Rapid Detection of the Chlamydiaceae and Other Families in the Order Chlamydiales: Three PCR Tests

1999 ◽  
Vol 37 (3) ◽  
pp. 575-580 ◽  
Author(s):  
Karin D. E. Everett ◽  
Linda J. Hornung ◽  
Arthur A. Andersen
Keyword(s):  
Sequence Data ◽  
Epidemiologic Study ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Direct Sequence ◽  
Identification Methods ◽  
The Third ◽  
23S Rrna Gene ◽  
Direct Sequence Analysis

Few identification methods will rapidly or specifically detect all bacteria in the order Chlamydiales, familyChlamydiaceae. In this study, three PCR tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. Two tests exclusively recognized theChlamydiaceae: a multiplex test targeting theompA gene and the rRNA intergenic spacer and a TaqMan test targeting the 23S ribosomal DNA. The multiplex test was able to detect as few as 200 inclusion-forming units (IFU), while the TaqMan test could detect 2 IFU. The amplicons produced in these tests ranged from 132 to 320 bp in length. The third test, targeting the 23S rRNA gene, produced a 600-bp amplicon from strains belonging to several families in the order Chlamydiales. Direct sequence analysis of this amplicon has facilitated the identification of new chlamydial strains. These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation.

scholarly journals Amplification and Direct Sequence Analysis of the 23S rRNA Gene from Thermophilic Bacteria

BioTechniques ◽  
2001 ◽  
Vol 30 (2) ◽  
pp. 414-420 ◽  
Author(s):  
Ashraf Ibrahim ◽  
Jacob Hofman-Bang ◽  
Birgitte K. Ahring
Keyword(s):  
Sequence Analysis ◽  
Thermophilic Bacteria ◽  
23S Rrna ◽  
Rrna Gene ◽  
Direct Sequence ◽  
23S Rrna Gene ◽  
Direct Sequence Analysis

scholarly journals Presence of a novel 16S–23S rRNA gene intergenic spacer insert in Bradyrhizobium canariense strains

2007 ◽  
Vol 269 (2) ◽  
pp. 207-212 ◽  
Author(s):  
Vera Safronova ◽  
Elena Chizhevskaya ◽  
Simonetta Bullitta ◽  
Evgeny Andronov ◽  
Andrei Belimov ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
23S Rrna Gene

scholarly journals Intrinsic Macrolide Resistance in Mycobacterium smegmatis Is Conferred by a Novel erm Gene, erm(38)

2003 ◽  
Vol 47 (10) ◽  
pp. 3053-3060 ◽  
Author(s):  
Kevin A. Nash
Keyword(s):  
Mycobacterium Smegmatis ◽  
Sequence Data ◽  
Macrolide Resistance ◽  
23S Rrna ◽  
Cross Resistance ◽  
Rrna Gene ◽  
Mycobacterium Fortuitum ◽  
Knockout Mutant ◽  
23S Rrna Gene ◽  
High Level

ABSTRACT High-level, acquired macrolide resistance in mycobacteria is conferred by mutation within the 23S rRNA gene. However, several mycobacteria are naturally resistant to macrolides, including the Mycobacterium smegmatis group and Mycobacterium tuberculosis complex. Thus, the aim of this study was to characterize this resistance. Intrinsic macrolide resistance in M. smegmatis was inducible and showed cross-resistance to lincosamides but not to streptogramin B (i.e., ML resistance). A similar phenotype was found with Mycobacterium microti and macrolide-resistant Mycobacterium fortuitum. A search of the DNA sequence data for M. smegmatis strain mc2155 identified a novel erm gene, erm(38), and expression analysis showed that erm(38) RNA levels increased >10-fold after a 2-h incubation with macrolide. Inducible ML resistance was not expressed by an erm(38) knockout mutant, and complementation of this mutant with intact erm(38) in trans resulted in high-level ML resistance (e.g., clarithromycin MIC of >512 μg/ml). Thus, the results indicate that erm(38) confers the intrinsic ML resistance of M. smegmatis. Southern blot analysis with an erm(38)-specific probe indicated that a similar gene may be present in macrolide-resistant M. fortuitum. This finding, with the presence of the erm(37) gene (Rv1988) in the M. tuberculosis complex, suggests that such genes are widespread in mycobacteria with intrinsic macrolide resistance.

scholarly journals 16S–23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

2016 ◽  
Vol 7 ◽  
Author(s):  
Sima Tokajian ◽  
Nahla Issa ◽  
Tamara Salloum ◽  
Joe Ibrahim ◽  
Maya Farah
Keyword(s):  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Intergenic Spacer Region ◽  
23S Rrna Gene

scholarly journals Geographic Distribution and Genetic Diversity of Ceanothus-Infective FrankiaStrains

1999 ◽  
Vol 65 (4) ◽  
pp. 1378-1383 ◽  
Author(s):  
Nancy J. Ritchie ◽  
David D. Myrold
Keyword(s):  
Root Nodules ◽  
Intergenic Spacer ◽  
Taxonomic Diversity ◽  
Molecular Techniques ◽  
23S Rrna ◽  
Rrna Gene ◽  
Sample Collection ◽  
Pcr Product ◽  
Pcr Rflp ◽  
23S Rrna Gene

ABSTRACT Little is known about Ceanothus-infectiveFrankia strains because no Frankia strains that can reinfect the host plants have been isolated fromCeonothus spp. Therefore, we studied the diversity of theCeonothus-infective Frankia strains by using molecular techniques. Frankia strains inhabiting root nodules of nine Ceanothus species were characterized. The Ceanothus species used represent the taxonomic diversity and geographic range of the genus; therefore, the breadth of the diversity of Frankia strains that infectCeanothus spp. was studied. DNA was amplified directly from nodular material by using the PCR. The amplified region included the 3′ end of the 16S rRNA gene, the intergenic spacer, and a large portion of the 23S rRNA gene. A series of restriction enzyme digestions of the PCR product allowed us to identify PCR-restriction fragment length polymorphism (RFLP) groups among theCeanothus-infective Frankia strains tested. Twelve different enzymes were used, which resulted in four different PCR-RFLP groups. The groups did not follow the taxonomic lines of the Ceanothus host species. Instead, theFrankia strains present were related to the sample collection locales.

scholarly journals Genotyping of Mycoplasma pneumoniaeClinical Isolates Reveals Eight P1 Subtypes within Two Genomic Groups

2000 ◽  
Vol 38 (3) ◽  
pp. 965-970 ◽  
Author(s):  
J. Wendelien Dorigo-Zetsma ◽  
Jacob Dankert ◽  
Sebastian A. J. Zaat
Keyword(s):  
Sequence Data ◽  
Rflp Analysis ◽  
Clinical Isolates ◽  
23S Rrna ◽  
Rrna Gene ◽  
Intergenic Spacer Region ◽  
Long Pcr ◽  
23S Rrna Gene

Three methods for genotyping of Mycoplasma pneumoniaeclinical isolates were applied to 2 reference strains and 21 clinical isolates. By a modified restriction fragment length polymorphism (RFLP) analysis of PCR products of the M. pneumoniae cytadhesin P1 gene, 5 subtypes were discriminated among 13 P1 type 1 strains and 3 subtypes were discriminated among 8 P1 type 2 strains. Sequence analysis of the 16S-23S rRNA gene spacer region and part of the 23S rRNA gene revealed one nucleotide difference in the intergenic spacer region in 3 of the 21 isolates. In the 23S rRNA gene sequence of the 8 P1 type 2 strains an extra adenosine was present, but it was absent from the 13 P1 type 1 strains. On the basis of M. pneumoniae genome sequence data, primers were designed to amplify large interrepeat fragments by long PCR, and these fragments were subsequently analyzed by RFLP analysis. Only two types, long PCR types 1 and 2, could be discriminated among the M. pneumoniaeisolates. All P1 type 1 strains were assigned to long PCR type 1, and all P1 type 2 strains were assigned to long PCR type 2. These data obtained by three independent typing methods thus confirm the existence of two distinct M. pneumoniae genomic groups but expand the possibility of strain typing on the basis of variations within their P1 genes.

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