scholarly journals The 23S rRNA gene PCR-RFLP used for characterization of porcine intestinal spirochete isolates

2006 ◽  
Vol 7 (3) ◽  
pp. 277
Author(s):  
Tae Jung Kim ◽  
Jae Il Lee
Keyword(s):  
23S Rrna ◽  
Rrna Gene ◽  
Pcr Rflp ◽  
23S Rrna Gene

scholarly journals Molecular characterization of a ceftriaxone-resistant Neisseria gonorrhoeae strain found in Switzerland: a case report

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Konrad Egli ◽  
Anna Roditscheff ◽  
Ursula Flückiger ◽  
Martin Risch ◽  
Lorenz Risch ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
23S Rrna ◽  
Rrna Gene ◽  
Limited Information ◽  
Specific Pcr ◽  
Appropriate Treatment ◽  
23S Rrna Gene ◽  
Allele Type ◽  
Ciprofloxacin Resistance

Abstract Background The resistance of Neisseria gonorrhoeae to ceftriaxone is unusual in Switzerland. The underlying genotype responsible for resistance is suspected to be novel. Generally, resistance in Neisseria gonorrhoeae (Ng) involves a comprehensive set of genes with many different mutations leading to resistance to different β-lactams and fluoroquinolones. Case presentation A patient had a positive result from specific PCR for Ng. We routinely culture all clinical specimens with a positive NG-PCR. In this particular case, we isolated a strain with resistance to ceftriaxone in Switzerland. A total of seven different genes (penA, ponA, porinB, mtr, gyrA, parC, 23S rRNA gene) in this strain were partially sequenced for comparison with phenotypic susceptibility testing. Interestingly, two different mutations in the porinB gene were observed, and data on this gene are limited. Information on the identified allele type of the penA gene is very limited as well. Three different mutations of parC and gyrA that correlate with ciprofloxacin resistance were found. The combination of ceftriaxone and ciprofloxacin resistance makes an appropriate treatment difficult to obtain due to multidrug resistance. Conclusion The combined results for all genes show the appearance of new mutations in central Europe either due to worldwide spread or the emergence of new genetic combinations of mutations.

scholarly journals Genotypic Characterization of Clarithromycin-Resistant and -Susceptible Helicobacter pylori Strains from the Same Patient Demonstrates Existence of Two Unrelated Isolates

1998 ◽  
Vol 36 (9) ◽  
pp. 2730-2731 ◽  
Author(s):  
Ge Wang ◽  
Qin Jiang ◽  
Diane E. Taylor
Keyword(s):  
Helicobacter Pylori ◽  
Gel Electrophoresis ◽  
Genomic Dna ◽  
Pulsed Field Gel Electrophoresis ◽  
23S Rrna ◽  
Rrna Gene ◽  
Clarithromycin Resistance ◽  
23S Rrna Gene ◽  
Mode Of Development

Clarithromycin-susceptible and clarithromycin-resistantHelicobacter pylori isolates from the same patient were investigated for the mode of development and mechanism of clarithromycin resistance. The clarithromycin-resistant strain UA1182 harbors homozygous A-to-G mutations at position 2143 in both copies of the 23S rRNA gene and has a phenotype of resistance to clarithromycin and clindamycin but no significant resistance to streptogramin B. Pulsed-field gel electrophoresis patterns of NruI- andNotI-digested genomic DNA from the Clas and Clar isolates demonstrated that they are genetically distinct, suggesting that the development of clarithromycin resistance is not from the mutation of the existing Clas strain but from a completely new strain.

Co-infection with two different strains of Bordetella pertussis in an infant

2008 ◽  
Vol 57 (3) ◽  
pp. 388-391 ◽  
Author(s):  
Pamela K. Cassiday ◽  
Melissa Tobin-D'Angelo ◽  
J. Renee Watson ◽  
Kai-Hui Wu ◽  
Mahin M. Park ◽  
...  
Keyword(s):  
Bordetella Pertussis ◽  
Gene Sequence ◽  
Profile Analysis ◽  
23S Rrna ◽  
Rrna Gene ◽  
Pcr Rflp ◽  
23S Rrna Gene ◽  
History Of ◽  
Simultaneous Infection ◽  
Different Strains

We report co-infection with two phenotypically and genotypically distinct strains of Bordetella pertussis in an infant male hospitalized with a 2-week history of cough, paroxysms and vomiting. Colonies from the two B. pertussis phenotypes were isolated and evaluated by PFGE profile analysis, gene sequence typing and PCR-RFLP of a portion of the 23S rRNA gene. These results demonstrated simultaneous infection with two different strains of B. pertussis.

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 Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia

2005 ◽  
Vol 55 (4) ◽  
pp. 1439-1452 ◽  
Author(s):  
Endalkachew Wolde-meskel ◽  
Zewdu Terefework ◽  
Åsa Frostegård ◽  
Kristina Lindström
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Genes ◽  
Partial Sequence ◽  
23S Rrna ◽  
Southern Ethiopia ◽  
Rrna Gene ◽  
Pcr Rflp ◽  
23S Rrna Gene

The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR–RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500–1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR–RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100 % similar to those of previously described species and 34 were novel sequences with 94–99 % similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.

scholarly journals Rapid Identification of Listeria Species by Using Restriction Fragment Length Polymorphism of PCR-Amplified 23S rRNA Gene Fragments

2003 ◽  
Vol 69 (11) ◽  
pp. 6386-6392 ◽  
Author(s):  
Delphine Paillard ◽  
Véronique Dubois ◽  
Robert Duran ◽  
Fany Nathier ◽  
Catherine Guittet ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
23S Rrna ◽  
Rrna Gene ◽  
Pcr Rflp ◽  
23S Rrna Gene ◽  
Restriction Fragment Length

ABSTRACT A molecular method based on restriction fragment length polymorphism (RFLP) of PCR-amplified fragments of the 23S rRNA gene was designed to rapidly identify Listeria strains to the species level. Two fragments (S1, 460 bp, and S2, 890 bp) were amplified from boiled DNA. S2 was cut with the restriction enzymes XmnI or CfoI and, if needed, S1 was digested by either AluI or ClaI. This method was first optimized with six reference strains and then applied to 182 isolates collected from effluents of treatment plants. All isolates were also identified by the API Listeria kit, hemolysis, and phosphatidylinositol-specific phospholipase C production (PI-PLC) on ALOA medium. The PCR-RFLP method unambiguously identified 160 environmental strains, including 131 in concordance with the API system, and revealed that 22 isolates were mixed cultures of Listeria monocytogenes and Listeria innocua. Discrepant results were resolved by a multiplex PCR on the iap gene, which confirmed the PCR-RFLP data for 49 of the 51 discordances, including the 22 mixed cultures. Sequencing of the 16S rRNA gene for 12 selected strains and reconstruction of a phylogenetic tree validated the molecular methods, except for two unclassifiable strains. The 158 single identifiable isolates were 92 L. monocytogenes (including seven nonhemolytic and PI-PLC-negative strains), 61 L. innocua, 4 Listeria seeligeri, and 1 Listeria welshimeri strain. The PCR-RFLP method proposed here provides rapid, easy-to-use, inexpensive, and reliable identification of the six Listeria species. Moreover, it can detect mixtures of Listeria species and thus is particularly adapted to environmental and food microbiology.

scholarly journals Analysis of methods commonly used for glycopeptide and oxazolidinone susceptibility testing in Enterococcus faecium isolates

2010 ◽  
Vol 59 (6) ◽  
pp. 672-678 ◽  
Author(s):  
Giammarco Raponi ◽  
Maria Cristina Ghezzi ◽  
Giovanni Gherardi ◽  
Giulia Lorino ◽  
Giordano Dicuonzo
Keyword(s):  
Enterococcus Faecium ◽  
Susceptibility Testing ◽  
23S Rrna ◽  
Rrna Gene ◽  
Disc Diffusion ◽  
Pcr Rflp ◽  
23S Rrna Gene ◽  
Vitek 2 ◽  
Resistance Rates ◽  
The Phoenix

The susceptibility to teicoplanin, vancomycin and linezolid of 30 clinical isolates of Enterococcus faecium was tested by Vitek 2, Phoenix, Etest, broth microdilution and disc diffusion tests. The vanA and vanB resistance genes and the 23S rRNA gene G2576T mutation were detected by PCR and PCR-RFLP, respectively. Resistance rates to teicoplanin ranged from 3 % for Vitek 2 to 57.6 % for the Phoenix test, and those to vancomycin ranged from 56.7 % for Vitek 2 to 86.7 % for the Phoenix test. Only two out of 25 strains carrying the vanA gene were univocally recognized as the VanA phenotype. The only strain with the G2576T mutation did not carry the vanA gene and showed resistance to linezolid by the disc diffusion, Vitek 2 and broth dilution methods (MIC >8 μg ml−1), but was susceptible when tested with the Phoenix test and Etest (MIC ≤4 μg ml−1). Therefore, the resistance to glycopeptides and linezolid was not univocally detected by the susceptibility testing methods used in this study.

scholarly journals PCR-RFLP detection of point mutations A2143G and A2142G in 23S rRNA gene conferring resistance to clarithromycin in Helicobacter pylori strains.

2014 ◽  
Vol 61 (2) ◽  
Author(s):  
Karolina Klesiewicz ◽  
Paweł Nowak ◽  
Elżbieta Karczewska ◽  
Iwona Skiba ◽  
Izabela Wojtas-Bonior ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Point Mutations ◽  
Rflp Analysis ◽  
23S Rrna ◽  
Rrna Gene ◽  
Efficient Management ◽  
Clarithromycin Resistance ◽  
Pcr Rflp ◽  
23S Rrna Gene ◽  
H Pylori

The occurrence of clarithromycin resistance among Helicobacter pylori strains is a major cause of the treatment failure. Resistance to this drug is conferred by point mutations in 23S rRNA gene and the most prevalent mutations are A2143G and A2142G. The aim of the study was to evaluate the occurrence of A2143G and A2142G mutations in a group of H. pylori strains resistant to clarithromycin. The study included 21 clarithromycin-resistant H. pylori strains collected between 2006 and 2009 in southern Poland. Resistance to clarithromycin was quantitatively tested with the E-test to determine the minimal inhibitory concentration (MIC value). The point mutations of H. pylori isolates were detected by PCR followed by RFLP analysis. The MIC values for clarithromycin for the analyzed strains ranged from 1.5 mg/L to 64 mg/L. Nine H. pylori strains exhibited A2143G mutation and A2142G mutation was found in 9 isolates as well. The results of RFLP analysis of 3 clarithromycin-resistant strains were negative for both mutations. The average MIC values for A2143G and A2142G mutants were 6 and 30 mg/L, respectively. Frequencies of A2143G and A2142G mutations were the same in all isolates tested. Strains with A2143G mutation exhibited lower MIC values than A2142G mutants. Application of PCR-RFLP method for detection of clarithromycin resistance allows for better and more efficient management of H. pylori infections.

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