ABSTRACT
Objective To establish a real time PCR assay with a novel fluorescence quencher for identification of mutation of clarithromycin -resistance gene of Helicobacter pylori.Methods Two mutations of 23S rDNA gene in Helicobacter pylori,No.2142 and 2143,were chosen as targets for detection,and then the primers and the probe with a novel fluorescence quencher were designed.The genome DNA of Helicobacter pylori was extracted,and then detected by real time PCR reported here.Meanwhile,the specificity,reproducibility and sensitivity of the assay were evaluated.Finally,the real time PCR described here,the real time PCR based on TaqMan,and a sequencing assay were applied to detect 55 Helicobacter pylori strains isolated from clinical specimens,respectively.The results from three assays were compared with each other in order to further evaluate the applicability of this assay in clinic.Results It indicated that the mutation points related to clarithromycin -resistance,A2142G and A2143G,were identified by real time PCR with a novel fluorescence quencher rapidly and accurately.Moreover the coefficient of variation was less than 5%.The limit of detection was 100 copies/reaction.While this assay was applied directly to detect 55 Helicobacter pylori strains,the results were in accordance with those obtained from a TaqMan real time PCR and a sequencing assay,respectively.Conclusion The real time PCR described here was a simple,reliable and accurate approach and substituted for the TaqMan real time PCR for identification of two mutation points of clarithromycin -resistance,A2142G and A2143G in Helicobacter pylori.Thus,a novel tool for diagnosis of gene mutation was provided and the results might be regarded as a substantial evidence for clinical individual therapy.
ABSTRACT
<p><b>OBJECTIVE</b>To develop a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Acinetobacter pittii typing.</p><p><b>METHODS</b>Polymorphic VNTRs were searched by Tandem Repeats Finder. The distribution and polymorphism of each VNTR locus were analyzed in all the A. pittii genomes deposited in the NCBI genome database by BLAST and were evaluated with a collection of 20 well-characterized clinical A. pittii strains and one reference strain. The MLVA assay was compared with pulsed-field gel electrophoresis (PFGE) for discriminating A. pittii isolates.</p><p><b>RESULTS</b>Ten VNTR loci were identified upon bioinformatic screening of A. pittii genomes, but only five of them showed full amplifiability and good polymorphism. Therefore, an MLVA assay composed of five VNTR loci was developed. The typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. Compared with PFGE, the new optimized MLVA typing scheme provided the same and even greater discrimination.</p><p><b>CONCLUSION</b>Compared with PFGE, MLVA typing is a faster and more standardized alternative for studying the genetic relatedness of A. pittii isolates in disease surveillance and outbreak investigation.</p>
Subject(s)
Acinetobacter , Classification , Genetics , DNA Fingerprinting , Methods , Electrophoresis, Gel, Pulsed-Field , Minisatellite Repeats , Polymerase Chain ReactionABSTRACT
Objective To develop a rapid, sensitive and specific assay method, based on multiplex real time PCR for identifying Vibrio cholerae and distinguishing Vibrio cholerae O139 serotype from Vibrio cholerae. Methods Cholera toxin A subunit gene (ctxA) and glycosyltransferase gene (LPSgt) were chosen as targets according to Vibrio cholerae and Vibrio cholerae O139 serotype,and then the primers and TaqMan-MGB probe were designed. The 5'end of probes was labeled with FAM and VIC fluoresceins respectively while the 3' end of probes was labeled with MGB. The PCR reaction was optimized systematically. Then the specificity, sensitivity and reproducibility of multiplex real time PCR were estimated. Finally, multiplex real time PCR was applied to detect the clinical specimens. Results Vibrio cholerae was identified by multiplex real time PCR accurately and quickly,which could distinguish Vibrio cholerae O139 serotype from Vibrio cholerae. Vibrio cholerae was identified positive for primer pairs and probes from ctxA gene, and Vibrio cholerae O139 serotype tested was positive for LPSgt gene. Meanwhile, none of other bacteria was identified. Sensitivity of the test was 2 × 102 cfu/ml. When this assay was applied directly to identify 45 clinical specimens, results showed that 10 were positive to Vibrio cholerae, in which 4 clinical specimens were positive to Vibrio cholerae O139 serotype. All the results were the same to the one that had been obtained from the conventional assays. Conclusion Our rsults showed that the multiplex real time PCR was a reliable,accurate and feasible method for identifying Vibrio cholerae that carrying toxin gene and distinguishing Vibrio cholerae O139 serotype from Vibrio cholerae. This method could be applied to the cholera surveillance, prevention and control system for identifying and distinguishing Vibrio cholerae in the labs.
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<p><b>OBJECTIVE</b>To develop a loop-mediated isothermal amplification (LAMP) method for rapidly diagnosing of Escherichia coli (EHEC) O157:H7 in pathogen detection department or small-scale laboratories.</p><p><b>METHODS</b>Primers for LAMP test were designed by targeting the antigen coding rfbE of EHEC O157:H7, the Shiga-like toxin stx2 and the fliC encoding gene of H7 flagella antigen, respectively. The reaction condition and reaction system of LAMP were optimized. 2 EHEC O157:H7 type strains, 17 local strains and 33 other enterobacteria were analyzed to evaluate the LAMP's specificity and sensitivity. The results of the LAMP reaction were also compared with routine PCR method.</p><p><b>RESULTS</b>The amplification products of O157 which had the corresponding target genes turned green by visual inspection and had ladder-like pattern on the gel, but products of other enterobacteria remained orange by visual examination and had no band on the gel. The detection results of LAMP were the same as of routine PCR method. The reaction time of the LAMP method was only 1.5 hours and the detection limit of LAMP assay was 26 CFU/reaction. In addition, the LAMP results could be determined only by visual inspection.</p><p><b>CONCLUSION</b>LAMP assay is rapid, specific, and sensitive for the detection of EHEC O157:H7. This method might not only reduce the dependence of complicated equipments but also be a potential method for wider use in pathogen detection department, small-scale laboratory, emergency motor vehicle or field survey.</p>
Subject(s)
Environmental Monitoring , Methods , Escherichia coli O157 , Genetics , Nucleic Acid Amplification Techniques , Methods , Sensitivity and SpecificityABSTRACT
Objective To identify the presence of candidate pathogenicity island 89K DNA sequence of Streptococcus suis serotype 2 (SS2) strains isolated from patient in Zhejiang province. Methods Genes and DNA fragments were amplified by PCR, using specific primers, and three amplified fragments of the89K sequence were directly sequenced. The results were analyzed using software related to bioinformaties and epidemiology. Results 8 strains of SS2 all contained 89K sequence, cps2J and mrp virulent genes, and species-specific 16S rDNA. 3 amplified fragments of 89K candidate pathogenicity island of SS2 ZJ0501 were above 99% similar to SS2 strain identified from outbreaks in Jiangsu in 1998, and the gene fragment of coding DNA recombinant protein in the 89K sequence was highly homological with that of S. dysgalactiae and S. agalactiae. Conclusion In recent years SS2 strains isolaed from patients with clinical symptoms in Zhejiang province had been detected to have contained candidate pathogenicy 89K DNA fragment.
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Human bocavirus, which was firstly discovered in 2005, is a new human parvovirus associated with lower respiratory tract infection in children. In this study, a human bocavirus, named WLL-1 isolate, was identified in Wenlin County, Zhejiang Province. The genome of bocavirus WLL-1 has been sequenced and analyzed. Phylogenetic analyses showed that WLL-1 shares 99% homology with other bocaviruses recently reported, but also has some special variations.