Sensitive detection of Helicobacter pylori by using polymerase chain reaction.

A polymerase chain reaction (PCR) for the specific detection of Helicobacter pylori was developed with a single primer pair derived from the nucleotide sequence of the urease A gene of H. pylori. We achieved specific amplification of a 411-bp DNA fragment in H. pylori. After 35 cycles of amplification, the product could be detected by agarose gel electrophoresis and contained conserved single HinfI and AluI restriction sites. This fragment was amplified in all 50 strains of H. pylori tested, but it was not detected in other bacterial species, showing the PCR assay to be 100% specific. PCR DNA amplification was able to detect as few as 10 H. pylori cells. PCR detected H. pylori in 15 of 23 clinical human gastric biopsy samples, whereas culturing and microscopy detected H. pylori in only 7 of the samples found to be positive by PCR. Additional primer pairs based on the urease genes enabled the detection of H. pylori in paraffin-embedded human gastric biopsy samples. The detection of H. pylori by PCR will enable both retrospective and prospective analyses of clinical samples, elucidating the role of this organism in gastroduodenal disease.     

Detection of Helicobacter pylori by using the polymerase chain reaction.

A 1.9-kb cloned fragment of chromosomal DNA randomly selected from a Helicobacter pylori cloned library was evaluated as a potential probe. The probe detected 19 of 19 H. pylori strains and yielded a specificity of 98.7% when tested against 306 other bacterial strains representing 32 different species. False-positive results with non-H. pylori strains were due to the presence of contaminating vector sequences. A polymerase chain reaction (PCR) assay was developed by using 20-base oligonucleotide primers homologous to a portion of the 1.9-kb fragment. The PCR assay amplified a 203-nucleotide-pair product which was analyzed by agarose gel electrophoresis and Southern hybridization by using a third 20-base 32P-labeled oligonucleotide complementary to a region of DNA between the primers. The PCR assay was 100% sensitive, detecting all 35 H. pylori strains tested, and did not amplify sequences in several closely related species. The assay was sensitive for as little as one copy of the cloned plasmid DNA or 100 H. pylori bacterial cells. To evaluate the PCR assay for clinical samples, gastric biopsy and aspirate specimens were tested by PCR, and the results were compared with those of microbiologic culture and histologic examination. In fresh biopsy specimens, H. pylori sequences were detected by PCR in 13 of 14 (93%) positive tissues and 0 of 19 negative tissues. In gastric aspirate specimens, 11 of 13 (85%) positive tissues were positive by PCR. H. pylori DNA was detected in 1 of 14 aspirate specimens negative by culture, histology, and PCR of the accompanying biopsy tissue. PCR is a rapid, accurate, and sensitive method for the detection of H. pylori.     

Development of epidemiological method for the Helicobacter pylori by polymerase chain reaction.

The polymerase chain reaction was used to develop a method for the detection of Helicobacter pylori, a causative agent of gastritis, as well as for the elucidation of its mode of transmission. A genomic library of Helicobacter pylori DNA in Escherichia coli JM109 was constructed by cloning Hind III-digested DNA fragments into plasmid vector pUC18. The nucleotide sequences from seven recombinant clones were determined and five sets of oligonucleotide primers were synthesized on the basis of the sequences from five clones (B4, B9, B10, C15 and I22). The PCR amplifications with these primers were performed using DNA samples from five strains of Helicobacter pylori, two Campylobacter spp. and eleven species of enteric bacteria. Amplifications of the target DNA fragments in all of 5 strains of Helicobacter pylori were observed from the PCR with primers derived from clone B4, B9, C15 and I22. When the specificity was checked with the DNA samples from 13 other bacteria as template DNA for the PCR, specific amplification that produced the correct size of the target DNA of Helicobacter pylori was shown only in the PCR with primers derived from clone B9 and C15. The detection limit in the PCR amplification, determined by the heat-lysis method, was 500 cells of Helicobacter pylori.     

Single-tube real-time nested polymerase chain reaction for detecting human papillomavirus DNA.

A single-tube real-time nested polymerase chain reaction (PCR) was developed to detect human Papillomavirus (HPV) DNA in a closed tube system. The oligonucleotide primers MY09/MY11 and GP5+/GP6+ were included in contiguous reactions, thus eliminating the need to transfer first round PCR product into a second tube. The sensitivity and specificity of the optimized single-tube nested PCR were comparable with that achieved by two separate reactions on a conventional thermal block system using serial dilutions derived from plasmids containing DNA of 20 HPV types. A minimum of 10 copies of HPV types 11 and 16 DNA could be detected by both systems. In clinical samples, HPV types 1A, 2, 3, 5, 6-8, 10, 11, 14, 16, 17, 18, 20, 31, 33, 35, 39, 45, 49, 50, 52-54, 57, 62, 66, 70, CP8304 and LVX82/MM7 could be detected by both PCR methods. A total of 145 samples collected from patients were tested for the presence of HPV DNA with the two PCR systems; 124 (86.1%) of 144 samples gave concordant results in both assays. The HPV DNA positive PCR amplicons were typed and concordant results were obtained in 47 of 67 positive samples tested in both amplicons. In samples containing multiple HPV types at least one type was common to both amplicons.     

Detection and identification of Helicobacter pylori by the polymerase chain reaction.

A polymerase chain reaction for the specific detection of Helicobacter pylori was developed using a primer pair derived from the nucleotide sequence of the urease A gene of H pylori. Specific amplification of a 411 base pair DNA fragment from all strains of H pylori tested was achieved. Ten organisms were detected using the PCR and the technique permitted direct detection of H pylori in clinical biopsy samples. PCR will be useful for both prospective and retrospective investigation of the aetiology and epidemiology of H pylori associated disease.     

Direct polymerase chain reaction test for detection of Helicobacter pylori in humans and animals.

We designed a polymerase chain reaction (PCR) for amplifying the Helicobacter pylori gene encoding 16S rRNA. Primers for the specific detection of H. pylori were designed for areas of the 16S rRNA gene in which there is the least sequence homology between H. pylori and its closest relatives. The specificity of detection was confirmed by ensuring that the primers did not amplify DNA extracts from the campylobacters H. cinaedi, H. mustelae, and Wolinella succinogenes, which are the closest relatives of H. pylori, as determined by 16S rRNA sequencing. Serial dilution experiments revealed the detection of as little as 0.1 pg of DNA by PCR and 0.01 pg by nested PCR. H. pylori DNA was detected successfully in clinical paraffin-embedded and fresh gastric biopsy specimens from patients positive for the bacterium and also in fecal suspensions seeded with the organism. The DNA from the nonculturable coccoid form of H. pylori was also identified by the primers. Universal primers designed for highly conserved areas on the 16S rRNA gene enabled large amplification products to be produced for direct sequencing analysis. Gastric bacteria resembling H. pylori have been isolated from animals. DNA of these animal gastric bacteria amplified with H. pylori-specific primers yielded PCR products identical to those from human isolates of H. pylori, as confirmed by the use of a 20-base radiolabelled probe complementary to an internal sequence flanked by the H. pylori-specific primers. The results of PCR amplification and partial 16S rRNA gene sequence analysis strongly support the contention that the gastric organisms previously recovered from a pig, a baboon, and rhesus monkeys are H. pylori.     

Rapid detection of Helicobacter pylori in gastric biopsy material by polymerase chain reaction.

By using primers based on the sequence of a species-specific antigen of Helicobacter pylori (P. O'Toole, S.M. Logan, M. Kostrzynska. T. Wadstr?m, and T.J. Trust, J. Bacteriol. 173:505-513, 1991), a protocol was established for detection of this microorganism in gastric biopsy samples by the polymerase chain reaction (PCR). A single primer pair was used to specifically amplify a 298-bp sequence in a rapid two-step PCR. The primers exhibited the same specificity in PCR as that which we reported for the species-specific gene probe on which they were based. The sensitivity of the method was 20 copies of the target sequence, or 70 bacterial cells, under the lysis conditions used for patient-derived material. When amplification was performed for a saturating number of cycles, visual examination of ethidium bromide-stained gels successfully detected all samples subsequently judged to be positive by Southern hybridization of the gel with a probe specific for the PCR product. The bacterium could be detected in gastric biopsy samples from patients with various gastric diseases, including samples from which the bacterium could not be cultured. Only 9 of 19 patients who tested positive by PCR of gastric biopsy material were positive when a saliva sample was analyzed. Protocols for sample handling which minimized the risk of contamination while maximizing the sensitivity of the reaction were established. The results support a role for PCR in the rapid identification of H. pylori in clinical samples.     

Novel polymerase chain reaction method for detecting cutaneous human papillomavirus DNA

There is no simple test to identify the human papillomavirus (HPV) genotypes that cause cutaneous warts. A new polymerase chain reaction (PCR) method, called SK-PCR, was developed for this purpose. This PCR amplifies 210-238 base pairs of L1 DNA of 17 HPV types (HPV-1a, -2a, -3, -4, -7, -10, -27, -28, -29, -40, -57, -60, -63, -65, -77, -91, and -94), which are thought to cause various cutaneous warts, including common, flat, butcher's, punctate, and pigmented warts. The method is novel because the location of these primers is completely different from that of any previous PCR method for HPV. The target sequences are specific to alpha-, gamma-, and mu-papillomaviruses (PVs), but not to beta-PVs. Furthermore, direct sequencing and restriction fragment length polymorphism (RFLP) were used to determine the HPV genotypes. Fifty of samples of plantar warts were examined, and HPV-27 was identified in 22 warts, HPV-57 in 15 warts, and HPV-2a in 9 warts. These PVs, which are alpha species 4, were the most common. HPV-4 and -65 (gamma-PVs) and HPV-1a and -63 (mu-PVs) were detected in one case each. A single HPV type was identified in all of these warts. This method appears to be useful for genotyping the HPVs causing skin warts, and for distinguishing between HPV-induced warts and warty lesions unrelated to HPV infection.     

Detection of murine cytomegalovirus (MCMV) DNA in skin using the polymerase chain reaction (PCR)

We used the polymerase chain reaction (PCR) and primers for the immediate early gene of murine cytomegalovirus (MCMV) to detect MCMV DNA in skin harvested from mice during acute infection. MCMV DNA was also detected in DNA extracted from spleen and salivary gland of MCMV-infected mice, but not in the skin, salivary gland, or spleen of uninfected, seronegative mice. Detection of MCMV DNA in skin provides direct evidence that skin can serve as a vehicle for transmission of MCMV. This observation is relevant to humans, such as burn patients, who receive skin allografts that may be infected with cytomegalovirus.     

Quantitation of Helicobacter pylori in dental plaque samples by competitive polymerase chain reaction

AIM: To establish a competitive PCR (cPCR) assay for quantitation of H pylori organisms in dental plaque samples. METHODS: The cPCR co-amplified target H pylori DNA and a known amount of internal standard template in the same tube with the same primers directed to 0.86 kb DNA of H pylori. The internal standard was a synthesised DNA bearing the same primer recognition sites at two ends and a non-homologous core sequence as the target DNA fragment. Quantitation was based on determination of the relative, not absolute, amounts of the differently sized and [32P]-dCTP labelled products derived from H pylori DNA and the competitive internal standard after gel electrophoresis separation. RESULTS: A significant correlation between known amounts of H pylori added to dental plaque samples and the results of the cPCR was found, and a standard line was developed which allowed quantitation of H pylori in the plaque samples. cPCR was performed on supragingival plaque samples from 10 adult patients with H pylori infection in the stomach, and from five adults and six children without H pylori infection in the stomach. The ranges of H pylori numbers were 1-213 (median 25), 6-76 (10), and 4-94 (14) cells/mg of dental plaque in the three groups, respectively. CONCLUSIONS: cPCR is useful for quantitation of H pylori in supragingival dental plaque samples; however, the number of the organisms in dental plaque samples seems very low.     

Comparison of fluorometric detection methods for quantitative polymerase chain reaction (PCR)

In this study, we compared the sensitivity of two different detection methods for quantitative polymerase chain reaction (PCR). Various amounts of a 75 mer single-stranded deoxyribonucleic acid (DNA) fragment, which can be used as a DNA label for the immuno-PCR (iPCR) assays, were amplified by PCR. The amount of amplified DNA fragments was determined by the fluorescence (FL) of SYBR Green dye that specifically interacts with double-stranded DNA fragments. In the first selected detection method, real-time PCR, FL measurements were carried out at each thermal cycle, as the DNA was being amplified by PCR. This was achieved using the Applied Biosystems (ABI) Prism 7000 Sequence Detection System and its standard protocol. In the second detection method, referred to as end-point detection, after the PCR amplification was completed, off-line FL measurements were subsequently carried out using a conventional plate reader. In order to achieve the lowest limit of detection (LOD) from the off-line measurement, we have optimized a wide variety of parameters. Our data have indicated the LOD of real-time PCR method was approximately three orders of magnitude lower than the end-point measurement method, with a linear range spanning six orders of magnitude; 10 fmol to 10 zmol of PCR template. The lower LOD of the real-time PCR method could be partly due to the ability to maximize the number of thermal cycles that could be carried out in PCR, without increasing the non-specific amplification of any contaminating DNA. The results of this study can be applied to the development of ultra-sensitive iPCR assays for various disease markers.     

Detection of HPV 16/18 DNA in cervical adenocarcinoma using polymerase chain reaction (PCR) methodology.

Twenty-two tissue samples of primary adenocarcinoma (adenoCA) of the uterine cervix were evaluated for the presence of HPV 16/18 DNA using the polymerase chain reaction (PCR). PCR was used to specifically amplify the E6-E7 gene region of HPV 16/18 DNA. The amplification products were analyzed using gel electrophoresis and Southern dot blotting with 32p labeled type-specific oligonucleotide probes. HPV 18 DNA was identified in 13/22 (59%) and HPV 16 DNA was identified in 5/22 (23%) of the tumors. There were no tumors with mixed infections. In three patients, two different specimens were evaluated, and there was concordance of HPV typing. The presence of squamous carcinoma in situ, koilocytosis and younger patient age were associated with an increased incidence of HPV 16/18 DNA detection. HPV 16/18 DNA was not detected in six metastatic adenoCA to cervix (four endometrial, two ovarian). We conclude that HPV 16/18 DNA is present in a significant proportion of primary adenoCA of the cervix, and we have identified some clinicopathologic associations. The detection of HPV DNA may be useful in distinguishing primary from metastatic adenoCA of the cervix.     

Structural analysis of abnormal hemoglobin by the polymerase chain reaction (PCR) of genomic DNA

Determination of the primary structure of abnormal Hbs on the basis of DNA sequencing of the globin gene obtained from a carrier of abnormal Hb was performed. DNA obtained from the leukocytes of the peripheral blood was amplified by the polymerase chain reaction (PCR) using the proper amplification primer set. Amplified DNA was digested with two different restriction endonucleases and cloned to vector M 13 mp 18 or mp 19, which had been digested with the same enzymes. DNA sequencing was done by the dideoxy chain termination method using T 7 DNA polymerase, and the abnormal Hbs whose primary structure was determined were as follows: Hb Fukuoka [beta 2 His(CAC/T)----Tyr(TAT)], Hb Machida [beta 6 Glu(GAG)----Gln (CAG)], Hb Hope [beta 136 Gly(GGT)----Asp(GAT)], Hb Hiroshima [beta 146 His(CAC)----Asp(GAC)] and Hb Kodaira [beta 146 His(CAC)----Gln(CAA)]. This method for determining the primary structure of abnormal Hbs might be more effective than the ordinary method, which involves amino acid analysis and amino acid sequencing of the abnormal peptide obtained from abnormal Hb.     

Evaluation of CLO test and polymerase chain reaction for biopsy-dependent diagnosis of Helicobacter pylori infection

Helicobacter pylori is now recognized as possibly playing an etiologic role on the development of chronic gastritis, peptic ulcers and adenocarcinoma of the distal stomach. CLO test and polymerase chain reaction (PCR) assay are rapid, biopsy-dependent diagnostic tests for H. pylori identification. In this study, we assessed four diagnostic methods (CLO test, PCR assay, culture and histological examination) for H. pylori detection in biopsy specimens from 78 patients with gastroduodenal diseases and investigating the efficiency of CLO test and PCR assay for the diagnosis of H. pylori infection. H. pylori was identified in 75.6%, 75.6%, 64.1%, 69.2% of patients by CLO test, PCR assay, culture and histological examination, respectively. Compared with the detection of H. pylori by culture and/or histological examination, the sensitivity and specificity of the CLO test were 98.2% and 81.8%, respectively, whereas the sensitivity and specificity of PCR assay were 96.4% and 77.3%, respectively. According to the H. pylori infection state as determined from the results of three concordant tests, the sensitivities of culture, CLO test, histological examination, and PCR assay were 90.9%, 96.4%, 98.2% and 100%, respectively. Whereas, the specificity was 100%, 95%, 95% and 90% for culture, CLO test, histological examination, and PCR assay, respectively. We found that both CLO test and PCR assay were highly sensitive and specific for H. pylori identification; however, PCR assay was more sensitive than other methods for detecting the specimens after patients received treatment. The results of this study suggest that CLO test is a rapid and sensitive method of screening for H. pylori infection and that PCR assay could provide an accurate indication of the state of infection both during treatment for eradication of H. pylori and at follow-up.     

Utility of the polymerase chain reaction (PCR) for prenatal diagnosis of genetic disease.

Gene amplification by the polymerase chain reaction (PCR) has been applied to prenatal diagnosis for alpha and beta thalassemias (1 and 5 cases respectively), Hemoglobin (Hb) Lepore/beta thalassemia (1 case) and cystic fibrosis (14 cases). Chorionic villus samples were obtained in the tenth week of pregnancy and DNA analysed in parallel with conventional gene mapping. Direct diagnosis of the common Mediterranean beta-thalassemia mutations (IVS-1-110 and codon 39), Hb Lepore, and the delta F508 mutation causing cystic fibrosis was achieved by hybridization of amplified material with pairs of allele-specific oligonucleotide (ASO) probes or by restriction enzyme digestion of PCR products. Results were confirmed by DNA mapping. Definitive diagnosis or exclusion of an affected fetus was possible in 17 of 21 cases thus examined. PCR reduces the time required for prenatal diagnosis. DNA contamination is a potential source of error.     

Rapid fingerprinting of Helicobacter pylori by polymerase chain reaction and restriction fragment length polymorphism analysis.

A simple and reliable technique was developed for differentiating Helicobacter pylori strains by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-amplified DNAs. Oligonucleotide primer pairs developed to the urease, 48-kDa stress protein (htrA), and 26-kDa antigen-encoding genes were used to amplify fragments of the appropriate size from crude boiled cell preparations. The PCR-amplified products were digested with Sau3A, HaeIII, MspI, AluI, MluI, HinfI, and XbaI restriction endonucleases. Restriction fragment length polymorphisms were particularly evident within the urease and htrA genes and were easily detected by Sau3A, HaeIII, MspI, and AluI restriction endonuclease analysis. Double digestion of these separately amplified products or restriction analysis of multiple PCR-amplified fragments was found to discriminate 17 of 17 (100%) H. pylori strains which had unique genomic DNA fingerprints. Results of an investigation of multiple isolate sets obtained from patients before and after therapy was consistent with the hypothesis that treatment failures were due to the persistence of the same strain but did not discount the possibility that the patients were reinfected with a strain shared by family members or close contacts. The results indicate that the PCR-restriction endonuclease analysis method can be applied directly to biopsy samples, has the potential to fingerprint H. pylori isolates rapidly, and may permit detailed epidemiological investigations on the transmission of this important pathogen.     

Application of polymerase chain reaction (PCR) to HLA-C locus typing

Polymerase chain reaction/oligonucleotide typing was used to identify HLA-Cw*0601 (Cw6) in patients with psoriasis and psoriatic arthritis. The assignment of HLA-Cw*0601 was established by the concordant presence of codons for alanine (position 73), lysine (position 80) and tryptophan (position 97). The frequencies of all three codons were increased in the patient groups.     

特异性引物聚合酶链反应乙型肝炎病毒基因分型法的建立及应用

目的应用型特异性引物聚合酶链反应法（PCR）进行乙型肝炎病毒基因分型并分析该法的可靠性。方法应用型特异性引物PCR和INNO-LiPA分别对深圳、长春、北京152份HBV DNA阳性慢性乙型肝炎患者的血清标本进行了基因型分型，对该两种分型法不一致的血清标本再进行S区基因测序分型，以确定该两法的可靠性。结果型特异性引物PCR和INNO-LiPA的总符合率为86．8％（132／152），不一致率为13．2％（20／152）。型特异性引物PCR检测到81份（53．3％）B型；58份（38．2％）C型；13份（8．5％）B＋C型混合感染，未检出其他基因型或混合感染的基因型。INNO-LiPA检测到74份（48．7％）B型；61份（40．1％）C型；5份（3．3％）B＋C型混合感染；另检出3份（2．0％）A＋B型混合感染；1份（0．7％）B＋E型混合感染；1份（0．7％）C型与D型，1份（0．7％）D型感染，3份（2．0％）B／C／D型及3份未能分型。20份两法分型不一致的标本中，6份无剩余血清，对其余14份进行了S区基因测序分型，结果型特异性引物PCR与S区基因测序分型法的符合率为71．4％（10／14），而INNO-LiPA与S区测序法的符合率仅为7．1％（1／14），前者明显高于后者（P〈0．05）。结论型特异性引物PCR和INNO-LiPA均可鉴定HBV基因型，但前者较为简便和可靠，且费用较低，可用于临床标本的检测和流行病学调查。