Detection of Campylobacter species by using polymerase chain reaction and nonradioactive DNA probes. II. PCR direct sequencing of the Campylobacter DNA]

We have developed a sensitive DNA hybridization assay for the detection and identification of Campylobacter species which are recognized as important pathogens of acute diarrheal disease in humans. This technique utilizes DNA probes complementary to nucleotide sequences present in 16S ribosomal RNA (rRNA) of C. jejuni, C. coli, C. laridis, C. fetus, C. fetus subsp. fetus, C. fetus subsp. venerealis and C. hyointestinalis, and polymerase chain reaction. The partial sequence of DNAs encoding the Campylobacter rRNA was first analyzed by direct solid phase sequencing in order to select suitable DNA probes. Amplified target DNA of 240 base pairs could be resolved on ethidium bromide-stained gels, and hybridized with DNA probes conjugated to alkaline phosphatase. In identification experiments, one of the 10 probes tested here gave a positive hybridization reaction with C. jejuni, C. coli and C. hyointestinalis but not with other Campylobacter species. The other was specifically reactive with C. fetus, C. fetus subsp. fetus and C. fetus subsp. venerealis. When applied to stool specimens, a good correlation was found between the results obtained by the present assay and by biochemical tests. These findings suggest that the nonradioactive probe assay can be used as the practical criterion for differentiating Campylobacter species.     

DNA analysis by polymerase chain reaction]

Polymerase chain reaction (PCR) is a technique to amplify only a specific segment of DNA without using a plasmid or a phage vector. It is a powerful tool for genetic analysis of various diseases including inherited and viral diseases, and is now being applied to clinical diagnosis. Here, presented are several methods using PCR mainly for diagnosis of hemoglobinopathy which we have been engaged in. Some other diseases are also included.     

聚合酶链反应标记轮状病毒地高辛素探针的初步应用

目的为探讨聚合酶链反应（ＰＣＲ）技术标记的地高辛素（ＤＩＧ）探针的特异性和敏感性。方法用聚合酶链反应技术制备地高辛素标记的人类轮状病毒（ＨＲＶ）ｃＤＮＡ探针，经ｃＤＮＡ－ＲＮＡ斑点杂交。结果该探针具ＨＲＶ特异性，可检出１０ｐｇ的ＲＮＡ。应用该项技术检测了１２０份婴幼儿腹泻粪样标本，其阳性率为６５％，明显高于ＰＡＧＥ方法（４９．１％）的阳性率。结论ＰＣＲ方法直接制备地高辛素标记的ｃＤＮＡ探针方便、快速、特异性好、标记率高。     

Detection of Coxiella burnetti by DNA amplification using polymerase chain reaction.

The polymerase chain reaction (PCR) was used for the detection of Coxiella burnetti, an obligate intracellular bacterium and the etiologic agent of Q fever. A pair of primers derived from the C. burnetii superoxide dismutase gene served to amplify a targeted 257-bp fragment of genomic DNA. These primers were chosen on the basis of GenBank analysis, G + C ratio, and absence of secondary structure. This technique allowed the detection of as few as 10 C. burnetii organisms. C. burnetti was detected in tissue culture and in specimens from patients (heart valves). In all, 8 reference isolates and 22 new isolates of C. burnetii from France were successfully amplified. No amplification products were found when PCR was performed with 25 bacterial species that had been isolated in a clinical laboratory from patients with clinically similar infections. Amplification products of C. burnetii were confirmed by restriction enzyme digestion and dot blot hybridization. The method used here, a combination of PCR and restriction analysis, is a faster and more sensitive assay for C. burnetii than standard culture techniques.     

Specific detection of Campylobacter jejuni and Campylobacter coli by using polymerase chain reaction.

Development of a routine detection assay for Campylobacter jejuni and Campylobacter coli in clinical specimens was undertaken by using the polymerase chain reaction (PCR). An oligonucleotide primer pair from a conserved 5' region of the flaA gene of C. coli VC167 was used to amplify a 450-bp region by PCR. The primer pair specifically detected 4 strains of C. coli and 47 strains of C. jejuni; but it did not detect strains of Campylobacter fetus, Campylobacter lari, Campylobacter upsaliensis, Campylobacter cryaerophila, Campylobacter butzleri, Campylobacter hyointestinalis, Wolinella recta, Helicobacter pylori, Escherichia coli, Shigella spp., Salmonella spp., Vibrio cholerae, Citrobacter freundii, or Aeromonas spp. By using a nonradioactively labeled probe internal to the PCR product, the assay could detect as little as 0.0062 pg of purified C. coli DNA, or the equivalent of four bacteria. In stools seeded with C. coli cells, the probe could detect between 30 and 60 bacteria per PCR assay. The assay was also successfully used to detect C. coli in rectal swab specimens from experimentally infected rabbits and C. jejuni in human stool samples.     

Detection of Mycobacterium tuberculosis in clinical samples by using polymerase chain reaction and a nonradioactive detection system.

A test based on the polymerase chain reaction (PCR) was developed for the detection of the Mycobacterium tuberculosis complex in clinical samples. In this test, a 245-bp sequence of the insertion element IS986 was amplified and detected by agarose gel electrophoresis in the presence of ethidium bromide and by Southern blot and dot blot hybridization by using a 188-bp digoxigenin-labeled probe. We tested clinical specimens from 227 patients suspected of having tuberculosis. These included 102 cerebrospinal fluid, 48 sputum, 18 pleural fluid, 5 bronchoalveolar lavage, 18 blood, 7 pus, 8 bone marrow, and 6 urine samples and 15 tissue biopsy specimens. We also tested sputum samples from 75 patients with diseases other than tuberculosis. Sputum samples were first decontaminated, and all samples were treated with proteinase K-detergent solution to extract the DNA. Part of each sample was spiked with M. tuberculosis to provide a semiquantitative assay and to control for the loss of mycobacteria or interference with the PCR which may cause false-negative results. One femtogram of M. tuberculosis DNA could be detected. PCR was positive for all 32 culture-positive (for M. tuberculosis) and Ziehl-Neelsen staining (ZN)-positive samples, 10 of 12 culture-positive and ZN-negative samples, and all 4 culture-negative and ZN-positive samples. PCR detected M. tuberculosis complex bacteria in 35 of 178 culture- and ZN-negative samples. Clinical data supported the diagnosis of tuberculosis in the majority of the 35 patients from whom those samples were obtained.     

Detection of Mycoplasma pneumoniae by polymerase chain reaction and nonradioactive hybridization in microtiter plates.

In order to improve the diagnosis of a Mycoplasma pneumoniae infection, we developed a polymerase chain reaction (PCR)-based assay. The gene encoding elongation factor Tu (tuf) was selected as the target sequence. Oligonucleotides derived from variable stretches of the tuf gene were able to prime the amplification of a 950-bp fragment exclusively when M. pneumoniae DNA was used as the template. The sensitivity of the assay was increased 10-fold when the amplification products were hybridized with an internal M. pneumoniae-specific oligonucleotide. The use of three to four genome copies for PCR was sufficient for obtaining a hybridization signal. In addition, we substituted radioactive filter hybridization with a microtiter plate assay. Via a biotin moiety of one PCR primer, the amplification products were immobilized on streptavidin-coated microtiter plates. Subsequent hybridization with a digoxigenin-labeled oligonucleotide resulted in the same sensitivity and specificity as those obtained by filter hybridization. Clinical application of the assay was performed on 102 throat swab specimens from patients with respiratory tract infections. Of 21 culture-positive samples, 19 were confirmed to be positive in the PCR-based assay (sensitivity, 90%). Furthermore, 14 of 19 seropositive but culture-negative samples gave a positive hybridization signal. Of 62 culture-negative and seronegative specimens, 60 gave a negative result in our assay (specificity, 97%). Of the 33 samples that were positive in our PCR-based assay, 5 samples initially gave false-negative results because of the presence of inhibitory substances in those specimens. Inhibition of Taq polymerase in these five cases was prevented by an additional step of phenol extraction and subsequent ethanol precipitation.     

Detection of Trypanosoma cruzi by DNA amplification using the polymerase chain reaction.

The polymerase chain reaction was used to amplify a 188-base pair (bp) segment of the repetitive 195-bp nuclear DNA sequence of Trypanosoma cruzi that is the most abundant sequence in this organism. The reaction amplified this repetitive element in four T. cruzi isolates from widely separated geographic regions. No amplification of the 188-bp fragment occurred when DNAs extracted from Leishmania spp., African trypanosomes, or blood samples from mice and humans were used. Amplification of one-half of the DNA from a single T. cruzi parasite produced an amount of the 188-bp element that was readily visible in a gel stained with ethidium bromide. Hybridization of a radiolabeled probe to membrane-bound amplification products increased the sensitivity to a level at which 1/200 of the DNA in a single parasite could be detected. T. cruzi DNA was readily detected in DNA extracted from the abdominal contents of infected insect vectors reared in the laboratory. No parasite DNA was detected in the blood samples of two individuals known to be infected with T. cruzi, possibly because in such patients the number of circulating parasites are extremely low or because parasitemias are intermittent. These results represent a considerable increase in sensitivity over previously reported methods for the detection of T. cruzi infections. Polymerase chain reaction amplification can be used to evaluate large numbers of samples in a single day and thus should be useful in large-scale studies of the prevalence of T. cruzi in both insect vectors and mammalian hosts.     

Construction of a DNA probe and detection of Actinobacillus pleuropneumoniae by using polymerase chain reaction.

A 1.5-kb Actinobacillus pleuropneumoniae 4074 DNA fragment from a genomic library was found to hybridization. No cross-hybridization hybridization. No cross-hybridization was detected with DNAs from hemolytic members of the family Pasteurellaceae. From the nucleotide sequence of the putative genomic probe, three primers were synthesized for use in polymerase chain reactions (PCRs), with 31 strains tested by using purified and crude DNA targets. PCR amplification products of 610 and 985 bp were observed in nucleic acids extracted from the 12 known serotypes and a biotype 2 strain. Template DNAs from other gram-negative and gram-positive bacteria, some of them found in the normal flora of swine and the upper respiratory tract, were not amplified by PCR. The only exception was an amplification of a similar 610- or 985-bp sequence in Actinobacillus lignieresii, a species that is closely related to A. pleuropneumoniae but that has never been isolated from swine. Amplification of specific A. pleuropneumoniae sequences by PCR directly from clinical specimens may find applications in the identification of asymptomatic carriers as well as in efforts to eradicate porcine pleuropneumonia.     

Detection of untreated mycobacteria by using polymerase chain reaction and specific DNA probes.

A method for specific identification of mycobacteria by using the polymerase chain reaction on organisms taken from liquid cultures, frozen suspensions, or colonies grown on Lowenstein-Jensen slants is presented. This direct detection of mycobacterial organisms has important implications for strain typing and diagnosis.     

Detection of HPV DNA in trichilemmomas by polymerase chain reaction

Paraffin sections of 11 formalin-fixed trichilemmomas were investigated for the presence of human papillomavirus (HPV) DNA by the polymerase chain reaction (PCR) with the degenerated consensus primer pairs. PCRs were conducted with different annealing temperatures. When the annealing temperature was reduced from 55°C to 50°C, amplification products of the expected size were obtained for all 11 cases investigated. Determination of the HPV type was performed by cloning and sequencing of the amplification products. The sequence analysis of the eleven cloned amplicons gave the following data: based on sequence comparison with published amino acid sequences, the best homology was found to epidermodysplasia verruciformis (EV)-associated HPVs (supergroup B). In four specimens an HPV type 23 related type was found; five specimens contained HPV sequences which did not match with one of the known HPV types, but had the closest homology to HPV types 15, 17, and 37. Three of the HPV variants which had not been characterised, displayed identical sequences. Two additional HPV amplification fragments displayed 100% homology to HPV-6b. These results demonstrate, for the first time, the presence of HPV DNA in trichilemmomas. The sequence data suggest that HPV variants or types in trichilemmoma are members of the EV-associated HPV supergroup B. J Med Virol 51:119–125, 1997. © 1997 Wiley-Liss, Inc.     

Detection of methicillin-resistant Staphylococcus aureus by polymerase chain reaction]

The low-affinity penicillin-binding protein (PBP 2') is associated with methicillin-resistance of Staphylococcus aureus and its structural gene (mecA) not present in methicillin-susceptible S. aureus could be detected by the polymerase chain reaction (PCR) method, in which a 533 bp region of mecA was amplified and detected by agarose gel electrophoresis. Survey for the mecA gene in 210 clinical isolates of S. aureus revealed that, while there was a gross correlation between the presence of the mecA gene and the resistance level to beta-lactams, three strains of mecA (+) tested showed beta-lactam susceptibility similar to those of mecA (-) strains. These three strains did not produce a detectable amount of PBP 2' constitutively nor inducibly, which was the cause of their high susceptibility to beta-lactams. One of them yielded a typical methicillin-resistant variant at a low frequency with a concomitant recovery of PBP 2' production when the bacterial cells of high density were spread onto an agar plate containing 10 micrograms/ml of oxacillin. These findings suggested that typical methicillin resistant S. aureus occurred during chemotherapy with beta-lactam antibiotics even when resistant strains could not be detected by the susceptibility test and thus all mecA (+) strains including those with high susceptibility should be precisely detected.     

Detection of human parvovirus B19 DNA by using the polymerase chain reaction.

The polymerase chain reaction (PCR) was investigated for detecting human parvovirus B19 (B19) DNA in sera. Three pairs of oligonucleotides were evaluated as primers. The best oligonucleotide pair spanned 699 nucleotides, including the region common to VP1 and VP2. After PCR amplification of B19 DNA in serum, a 699-nucleotide DNA fragment was detected on agarose gels. This DNA fragment was B19 DNA, because after Southern transfer it hybridized to a 19-nucleotide internal probe and contained a single PstI cleavage site. Dot blot hybridization with a radiolabeled cloned portion of the B19 genome as a probe was compared with PCR. PCR was 10(4) times more sensitive than dot blot hybridization and, with an internal radiolabeled probe, 10(7) times more sensitive than dot blot hybridization. Of 29 serum specimens from 18 patients with proven B19 infections, 24 were PCR positive. None of 20 serum samples from uninfected controls were positive. Of 22 serum samples positive for immunoglobulin M to B19, PCR detected B19 DNA in 17. Seven serum samples lacking immunoglobulin M were PCR positive. PCR detected B19 DNA in urine, amniotic fluid, pleural fluid, ascites, and leukocyte extracts. PCR is a rapid and simple method for diagnosing infections with human parvovirus B19 but must be combined with serologic tests for immunoglobulin M to B19, especially when testing only a single serum sample.     

Identification and classification of Campylobacter strains by using nonradioactive DNA probes

Acetylaminofluorene-labeled genomic DNA probes were used for the identification and classification of Campylobacter strains. Relationships among 17 well-known strains of Campylobacter species and subspecies were studied by comparing acetylaminofluorene- or 32P-labeled probes. Results obtained with both methods were closely correlated and were in agreement with those already reported. In an identification experiment, hybridization with nonradioactive probes was performed on 60 strains isolated from stool samples after subculturing and quick DNA extraction; conventional biochemical tests were conducted in parallel. A good correlation was found between the results obtained by nonradioactive hybridization and by biochemical tests. Thus, the acetylaminofluorene-labeled genomic DNA probe method is an interesting alternative for laboratories without access to radioisotopes for the identification and classification of bacteria.     

人喉癌组织中人乳头瘤病毒DNA的检测

目的为探讨喉癌与人乳头瘤病毒（ＨＰＶ）感染的关系和ＨＰＶ在喉癌中基因组型的分布与表达。方法应用聚合酶链反应技术（ＰＣＲ）制备非放射性探针标记物－地高辛标记ＨＰＶ共有引物探针,对１４６例喉不同病变的新鲜组织标本（喉癌６８例,喉其它病变４８例,正常喉组织３０例）,进行ＨＰＶ６,１１,１６,１８,３１,３３,３５,４２,５８共９型ＨＰＶＤＮＡ感染的检测;阳性者用多重引物ＰＣＲ方法分型。结果喉癌ＨＰＶ感染阳性率４５．６％（３１／６８）,喉癌颈转移淋巴结组织阳性率２０．０％（３／１５）,喉癌前病变阳性率１１．８％（２／１７）,声带息肉阳性率６．３％（１／１６）,１５例癌旁及１５例癌周正常喉组织均为ＨＰＶＤＮＡ阴性。ＨＰＶＤＮＡ型别分布在喉癌中以ＨＰＶ１６、１８型为主,喉良性病变中以ＨＰＶ６、１１型为主。结论喉癌发生与ＨＰＶ感染有关。     

Detection of pseudorabies virus DNA sequences by the polymerase chain reaction

Summary Genomic sequences of pseudorabies virus, a porcine herpesvirus, were amplified by the polymerase chain reaction from cells of infected cultures, nasal cells and organs from acutely diseased as well as from organs of latently infected pigs.On leave from: Department of Epizootiology, University of Veterinary Sciences, Budapest, Hungary.On leave from: Department of Agricultural Chemical Technology, Technical University, Budapest, Hungary.     

Detection of schistosomes polymerase chain reaction amplified DNA by oligochromatographic dipstick

The applications of highly specific and sensitive molecular techniques based on polymerase chain reaction (PCR) have constituted a valuable tool for the diagnosis of schistosomiasis and also for the detection of schistosome infections in the snail intermediate hosts. The common method of detecting PCR amplicons is gel electrophoresis in the presence of ethidium bromide, a carcinogen, which is followed by UV transillumination. Other methods, which are available for detecting PCR products, are real-time PCR, PCR-enzyme-linked immunosorbent assay (PCR-ELIZA) and mass spectrometry but they are cumbersome while they are sometimes complex and expensive. Therefore, a simple method of PCR product detection would be a welcome idea and a most valuable tool particularly in disease endemic countries with limited research facilities and resources. In this study, we applied a simple and rapid method for the detection of Schistosoma haematobium and Schistosoma mansoni PCR amplified DNA products using oligochromatographic (OC) dipstick. The amplicons are visualized by hybridization with a gold conjugated probe, while a control for the chromatographic migration is incorporated in the assay. The lower detection limit observed was 10fg of genomic DNA from each of the two species, while the dipstick was also specific for each of the species used in this study.     

Detection of chicken anaemia virus by DNA hybridization and polymerase chain reaction

A clone containing the complete genome of chicken anaemia virus (CAV) was used in hybridizations with DNA from various field isolates of CAV. CAV DNA from all field isolates was detected in a polymerase chain reaction with oligonucleotides derived from the sequence of the cloned CAV DNA as primers. By way of Southern blot analysis with (32)P-labelled DNA probes derived from cloned CAV DNA, all field isolates were shown to contain DNA molecules of about 2.3 kb, i.e. the size of cloned CAV DNA. In a dot-blot assay it was demonstrated that non-radioactively-labelled cloned CAV DNA hybridized specifically to DNA from field isolates. The cloned CAV DNA is highly similar to the DNA of field isolates, as borne out by restriction-enzyme mapping. We conclude that our cloned CAV genome is representative for CAV in the field. The described PCR and hybridization techniques, may, therefore, be used for research and diagnosis of CAV infections.     

Detection of Rickettsia rickettsii DNA in clinical specimens by using polymerase chain reaction technology.

A polymerase chain reaction (PCR) procedure for detecting rickettsial DNA was developed and shown to be specific for Rickettsia rickettsii and R. conorii, the etiologic agents of Rocky Mountain spotted fever (RMSF) and Boutonneuse fever, respectively. Blood clots were obtained from nine confirmed RMSF patients and six controls and analyzed for the presence of rickettsial DNA by the PCR method. A defined region of the rickettsial genome was successfully amplified from seven of the nine clinical specimens tested; all six control specimens gave negative results. These findings indicate that R. rickettsii can be detected early after the onset of RMSF, possibly facilitating the decision regarding appropriate antibiotic therapy for some patients. Further refinement of PCR technology could make this procedure a mainstay in the clinical laboratory.