The polymerase chain reaction: miracle or mirage? A critical review of its uses and limitations in diagnosis and research

Prevalence and genotypes of Chlamydia psittaci in pet birds of Hong Kong

Psittacosis, or parrot fever, is a zoonotic disease caused by Chlamydia species associated with birds. One of the causative agents of the disease is Chlamydia psittaci, which is commonly carried by psittacine and other bird species, can be highly pathogenic and virulent to humans. In Hong Kong, a city with high population density, psittacosis is a notifiable disease with over 60% of cases in the last decade resulting in hospitalization. However, the sources of transmission of C. psittaci and its prevalence in pet birds in Hong Kong are currently unknown. To evaluate the risks of psittacosis transmission through pet birds, we tested the presence of C. psittaci and determined its genotypes in samples obtained from 516 captive birds from households, pet shops, and a veterinary hospital in Hong Kong. Results revealed that five samples (0.97%), collected from budgerigars and cockatiels, were C. psittaci-positive, while four (80%) of them were obtained from pet shops. Our phylogenetic analysis revealed that all identified strains belonged to Genotype A and showed high similarity to other sequences of this genotype obtained from various geographical locations and host species, including mammals. Our findings provide evidence for the presence of Chlamydia psittaci and shed light on its sources in captive birds in Hong Kong. They highlight the potential zoonotic risks associated with this pathogen, which can affect both humans and wild birds.

Focused upon hybridization: rapid and high sensitivity detection of DNA using isotachophoresis and peptide nucleic acid probes

We present a novel assay for rapid and high sensitivity detection of nucleic acids without amplification. Utilizing the neutral backbone of peptide nucleic acids (PNA), our method is based on the design of low electrophoretic mobility PNA probes, which do not focus under isotachophoresis (ITP) unless bound to their target sequence. Thus, background noise associated with free probes is entirely eliminated, significantly improving the signal-to-noise ratio while maintaining a simple single-step assay requiring no amplification steps. We provide a detailed analytical model and experimentally demonstrate the ability to detect targets as short as 17 nucleotides (nt) and a limit of detection of 100 fM with a dynamic range of 5 decades. We also demonstrate that the assay can be successfully implemented for detection of DNA in human serum without loss of signal. The assay requires 15 min to complete, and it could potentially be used in applications where rapid and highly sensitive amplification-free detection of nucleic acids is desired.

Development of an allele-specific PCR assay for simultaneous sero-typing of avian pathogenic Escherichia coli predominant O1, O2, O18 and O78 strains

Systemic infections by avian pathogenic Escherichia coli (APEC) are economically devastating to poultry industries worldwide. E. coli strains belonging to serotypes O1, O2, O18 and O78 are preferentially associated with avian colibacillosis. The rfb gene cluster controlling O antigen synthesis is usually various among different E. coli serotypes. In present study, the rfb gene clusters of E. coli serotypes O1, O2, O18 and O78 were characterized and compared. Based on the serotype-specific genes in rfb gene cluster, an allele-specific polymerase chain reaction (PCR) assay was developed. This PCR assay was highly specific and reliable for sero-typing of APEC O1, O2, O18 and O78 strains. The sensitivity of the assay was determined as 10 pg DNA or 10 colony forming units (CFUs) bacteria for serotypes O2 and O18 strains, and 500 pg DNA or 1,000 CFUs bacteria for serotypes O1 and O78 strains. Using this PCR system, APEC isolates and the infected tissue samples were categorized successfully. Furthermore, it was able to differentiate the serotypes for the samples with multi-agglutination in the traditional serum agglutination assay. Therefore, the allele-specific PCR is more simple, rapid and accurate assay for APEC diagnosis, epidemiologic study and vaccine development.

Prevalence of enteroaggregative Escherichia coli and its virulence-related genes in a case-control study among children from north-eastern Brazil

Enteroaggregative Escherichia coli (EAEC) is an important agent that causes endemic and epidemic diarrhoeal diseases worldwide. Several EAEC virulence-related genes (VRGs) have been described but their role in the clinical outcome of infection is not completely defined. This study investigated the prevalence of EAEC and potential associations of its VRGs with risk of or protection from diarrhoeal diseases in children from urban communities in north-eastern Brazil. The case-control study included 166 children, who had their stools evaluated for the EAEC diagnostic genes (aaiC and aatA) using PCR. Positive samples were further analysed by multiplex PCR and identified 18 VRGs. EAEC was found in the same proportion in both groups (41%). The plasmid-borne gene encoding a hexosyltransferase homologue (capU) was the most frequently detected (89.6%), followed by dispersin protein (aap, 58.2%) and EAEC HilA homologue (eilA, 57.8%). The AAF/III fimbrial subunit (agg3A) gene was observed at lower frequency (1.5%). Plasmid-encoded toxin (pet) or AAF/II fimbrial subunit (aafA) was associated significantly with disease. AAF/IV fimbrial subunit (agg4A) or hypothetical plasmid-encoded haemolysin (orf61) was detected significantly more in controls than in children with diarrhoea. In addition, one set of genes in combination, aaiC and agg3/4C but lacking agg4A and orf61, was associated with diarrhoea cases; and another one, orf61 in the absence of pet and aafA, was correlated with control children. These data confirm a high prevalence, endemicity and heterogeneity of EAEC strains in the developing urban areas of north-eastern Brazil. Statistical correlation between cases and controls was seen with either isolated or combined sets of genes, suggesting that the pathophysiology of EAEC infection involves a complex and dynamic modulation of several VRGs.

Reverse transcription and polymerase chain reaction: principles and applications in dentistry

Various molecular biology techniques have become available in the last few years. One of the most revolutionary of these techniques regarding nucleic acid analysis is the polymerase chain reaction (PCR), which was first described in 1985. This method relies on the exponential amplification of specific DNA fragments, resulting in millions of copies that can serve as templates for different kinds of analyses. PCR can be preceded by a reverse transcription (RT) reaction in order to produce cDNA from RNA (RT-PCR). RT-PCR provides the possibility to assess gene transcription in cells or tissues. PCR and RT-PCR techniques have been instrumental in dental research, and show potential to be used for diagnosis as well as for treatment and prevention of many diseases (dental caries, periodontal disease, endodontic infections and oral cancer). Compared to other traditional methodologies, PCR and RT-PCR show many advantages including high specificity, sensitivity, and speed. Since PCR and RT-PCR are relatively new techniques and are not available to most students and professionals involved with dentistry, the aim of this work is to present the details of these techniques as well as dental literature reports in which they were used.

A display module implemented by the fast high-temperatue response of carbon nanotube thin yarns

Suspending superaligned multiwalled carbon nanotube (MWCNT) films were processed into CNT thin yarns, about 1 μm in diameter, by laser cutting and an ethanol atomization bath treatment. The fast high-temperature response under a vacuum was revealed by monitoring the incandescent light with a photo diode. The thin yarns can be electrically heated up to 2170 K in 0.79 mS, and the succeeding cool-down time is 0.36 mS. The fast response is attributed to the ultrasmall mass of the independent single yarn, large radiation coefficient, and improved thermal conductance through the two cool ends. The millisecond response time makes it possible to use the visible hot thin yarns as light-emitting elements of an incandescent display. A fully sealed display with 16 × 16 matrix was successfully fabricated using screen-printed thick electrodes and CNT thin yarns. It can display rolling characters with a low power consumption. More applications can be further developed based on the addressable CNT thermal arrays.

Novel genomic tools for specific and real-time detection of biothreat and frequently encountered foodborne pathogens

The bacterial genera Escherichia, Salmonella, Shigella, Vibrio, Yersinia, and Francisella include important food safety and biothreat agents. By extensive mining of the whole genome and protein databases of diverse, closely and distantly related bacterial species and strains, we have identified novel genome regions, which we utilized to develop a rapid detection platform for these pathogens. The specific genomic targets we have identified to design the primers in Francisella tularensis subsp. tularensis, F. tularensis subsp. novicida, Shigella dysenteriae, Salmonella enterica serovar Typhimurium, Vibrio cholerae, Yersinia pestis, and Yersinia pseudotuberculosis contained either known genes or putative proteins. Primer sets were designed from the target regions for use in real-time PCR assays to detect specific biothreat pathogens at species or strain levels. The primer sets were first tested by in silico PCR against whole-genome sequences of different species, subspecies, or strains and then by in vitro PCR against genomic DNA preparations from 23 strains representing six biothreat agents (Escherichia coli O157:H7 strain EDL 933, Shigella dysenteriae, S. enterica serovar Typhi, F. tularensis subsp. tularensis, V. cholerae, and Y. pestis) and six foodborne pathogens (Salmonella Typhimurium, Salmonella Saintpaul, Shigella sonnei, F. tularensis subsp. novicida, Vibrio parahaemolyticus, and Y. pseudotuberculosis). Each pathogen was specifically identifiable at the genus and species levels. Sensitivity assays performed with purified DNA showed the lowest detection limit of 128 fg of DNA/μl for F. tularensis subsp. tularensis. A preliminary test to detect Shigella organisms in a milk matrix also enabled the detection of 6 to 60 CFU/ml. These new tools could ultimately be used to develop platforms to simultaneously detect these pathogens.

Campylobacter jejuni and Campylobacter coli in children from communities in Northeastern Brazil: molecular detection and relation to nutritional status

This study determined the prevalence of Campylobacter jejuni/coli and its relation with nutritional status in children from Northeastern Brazil. This was a case-control study design. Stool samples were evaluated for hipO (C. jejuni), ask (C. coli), and cdtABC (C. jejuni's cytolethal distending toxin) genes. The nutritional status from these children was assessed by anthropometric measures and z-scores. C. jejuni and C. coli were detected in 9.6% (8/83) and 6.0% (5/83) in the diarrhea group and in 7.2% (6/83) and 1.2% (1/83) of the nondiarrhea group, respectively. Children with positive molecular detection of C. jejuni showed significantly lower z-scores than children without C. jejuni. The cdtABC operon was found in 57% of hipO(+) samples. C. jejuni/coli prevalence was similar in diarrhea and nondiarrhea groups. There was a significant association of C. jejuni infection with lower nutritional status.

Validation of a blood plasma separation system by biomarker detection

A microfluidic system was developed for blood plasma separation at high flow rate. This system uses only hydrodynamic forces to separate plasma from whole blood. The microfluidic network features a series of constrictions and bifurcations to enhance the product yield and purity. A maximum purity efficiency of 100% is obtained on blood with entrance hematocrit level up to 30% with a flow rate of 2 mL h(-1). Flow cytometry was performed on the extracted plasma to evaluate the separation efficiency and to assess cell damage. A core target of this study was the detection of cell-free DNA from the on-chip extracted plasma. To this effect, PCR was successfully carried out off-chip on the cell-free DNA present in the plasma extracted on-chip. A house-keeping gene sequence (GAPDH) was amplified without the need for a purification after the separation, thereby showing the high quality of the plasma sample. The resulting data suggests that the system can be used as a preliminary module of a total analysis system for cell-free DNA detection in human plasma.

A multiplex PCR method to detect 14 Escherichia coli serogroups associated with urinary tract infections

Urinary tract infections (UTIs) are one of the most common bacterial infections and are predominantly caused by uropathogenic Escherichia coli (UPEC). E. coli strains belonging to 14 serogroups, including O1, O2, O4, O6, O7, O8, O15, O16, O18, O21, O22, O25, O75 and O83, are the most frequently detected UPEC strains in a diverse range of clinical urine specimens. In the current study, the O-antigen gene clusters of E. coli serogroups O1, O2, O18 and O75 were characterized. A multiplex PCR method based on O-antigen-specific genes was developed for the simultaneous detection of all 14 E. coli serogroups. The multiplex PCR method was shown to be highly specific and reproducible when tested against 186 E. coli and Shigella O-serogroup reference strains, 47 E. coli clinical isolates and 10 strains of other bacterial species. The sensitivity of the multiplex PCR method was analyzed and shown to detect O-antigen-specific genes in samples containing 25 ng of genomic DNA or in mock urine specimens containing 40 colony-forming units (CFUs) per ml. Five urine specimens from hospital were examined using this multiplex PCR method, and the result for one sample was verified by the conventional serotyping methods. The multiplex PCR method developed herein can be used for the detection of relevant E. coli strains from clinical and/or environmental samples, and it is particularly useful for epidemiologic analysis of urine specimens from patients with UTIs.

Comparison of broad-range bacterial PCR and culture of cerebrospinal fluid for diagnosis of community-acquired bacterial meningitis

Appropriate, rapid and reliable laboratory tests are essential for the diagnosis and optimal antibiotic therapy of acute bacterial meningitis. Broad-range bacterial PCR, combined with DNA sequencing, was compared with culture-based methods for examining cerebrospinal fluid (CSF) samples from patients with suspected meningitis. In total, 345 CSF specimens from 345 patients were analysed, with acute community-acquired bacterial meningitis being diagnosed in 74 patients. The CSF of 25 patients was positive by both PCR and culture; 26 patients had CSF specimens positive by PCR only, and 14 patients had specimens positive by culture only. The sensitivity of PCR and culture for clinically relevant meningitis was 59% (44/74) and 43% (32/74), respectively, while the specificity was 97% (264/271) and 97% (264/271), respectively. The commonest bacterial rRNA gene sequences detected by PCR only were those of Streptococcus pneumoniae and Neisseria meningitidis (n = 12). PCR failed to detect the bacterial rRNA gene in seven specimens from patients with symptoms compatible with acute bacterial meningitis. Overall, the results demonstrated that PCR in conjunction with sequencing may be a useful tool in the diagnosis of bacterial meningitis. PCR is particularly useful for analysing CSF from patients who have been treated with antibiotics before lumbar puncture.

Reverse transcription-polymerase chain reaction: an overview of the technique and its applications

The polymerase chain reaction (PCR) has galvanized molecular biologists by virtue of its ability to provide them with large quantities of any desired fragment (up to 11kb) of DNA. This power combined with its flexibility has also inspired many useful applications, including new methods of DNA sequencing, cloning and mutagenesis. One logical variation of PCR has been its application to the detection and analysis of messenger RNA by the addition of a reverse transcription step prior to performing PCR. Due to the exquisite sensitivity of PCR, reverse transcription-PCR (RT-PCR) has been used to characterize mRNAs previously undetectable by established methods of RNA analysis such as Northern hybridization and RNase protection assays. Furthermore, its capacity as a method of quantitative analysis is currently being developed. RT-PCR has also been used to diagnose the presence of certain diseases. Recently, RT-PCR has been employed to identify and isolate genes that are differentially expressed in different cells or environmental conditions.

Accuracy of the serological ELISA test compared with the polymerase chain reaction for the diagnosis of cytomegalovirus infection in pregnancy

CONTEXT

The most frequently used methods for detecting antibodies are the indirect immunofluorescence test and the enzymatic immunoassay (ELISA). The polymerase chain reaction is a molecular biology technique in which the production of large amounts of specific DNA fragments is induced from very low concentrations of complex substrates aloowing the detection of very low amounts of viral particles.

OBJECTIVE

To assess the accuracy of serological/ELISA tests in comparison with the polymerase chain reaction in maternal blood to diagnose cytomegalovirus infection.

DESIGN

A descriptive study was performed.

SETTING

High-risk outpatient clinic of Campinas University (Unicamp).

PARTICIPANTS

We selected 243 pregnant women. All of them had been indicated for blood sampling because of suspicions of cytomegalovirus infection and also because of other infections.

MAIN MEASUREMENTS

The group was tested for cytomegalovirus. Serological tests were run and compared to the polymerase chain reaction, which was considered to be the gold standard. Status analyses were done using Fisher's exact test, via the SAS software.

RESULTS

The previous cytomegalovirus infection rate was 94.6%. The main reasons for inclusion in the study were fetal nervous system malformation (25.5%), maternal toxoplasmosis (25.5%) and Rh isoimmunization (14.8%). Only two women were included because of positive serological immunoglobulin M test for cytomegalovirus. The sensitivity and specificity of the serological tests were 94% and 6% for immunoglobulin G.

CONCLUSION

Serological tests had lower sensitivity in comparison with the polymerase chain reaction test when diagnosing cytomegalovirus infection. The consequences of positive polymerase chain reaction and negative immunoglobulin M in women remain unknown.

Novel amplification of DNA in a hairpin structure: towards a radical elimination of PCR errors from amplified DNA

Errors introduced during PCR amplification set a selectivity limit for microsatellite analysis and molecular mutation detection methods since polymerase misincorporations invariably get confused with genuine mutations. Here we present hairpin-PCR, a new form of PCR that completely separates genuine mutations from polymerase misincorporations. Hairpin-PCR operates by converting a DNA sequence to a hairpin following ligation of oligonucleotide caps to DNA ends. We developed conditions that allow a DNA hairpin to be efficiently PCR-amplified so that, during DNA synthesis, the polymerase copies both DNA strands in a single pass. Consequently, when a misincorporation occurs it forms a mismatch following DNA amplification, and is distinguished from genuine mutations that remain fully matched. Error-free DNA can subsequently be isolated using one of many approaches, such as dHPLC or enzymatic depletion. We present feasibility for the main technical steps involved in this new strategy, conversion of a sequence to a hairpin that can be PCR-amplified from human genomic DNA, exponential amplification from picogram amounts, conversion of misincorporations to mismatches and separation of homoduplex from heteroduplex hairpins using dHPLC. The present hairpin-PCR opens up the possibility for a radical elimination of PCR errors from amplified DNA and a major improvement in mutation detection.

Automation of fluorescence-based PCR for confirmation of meningococcal disease

A fluorescence-based PCR method was developed, fully automated, and used to confirm infection with Neisseria meningitidis by detection of the meningococcus-specific ctrA gene. The method provided a highly sensitive, high-throughput assay that was reproducible and less labor-intensive than manual methods.

In situ detection of specific p53 mutations in cultured cells using the amplification refractory mutation system polymerase chain reaction

Accurate molecular detection of genetic mutations involved in tumorigenesis has been based predominantly on analysis of extracted DNA, but this does not provide detailed information on the location, number, type or clonal distribution of mutated cells and their precise anatomic location and clonal distribution. This study has used a sensitive and specific application of the amplification refractory mutation system (ARMS)-polymerase chain reaction (PCR) in situ, combined with in situ hybridization to localize and identify cells with defined p53 mutations. The ARMS-PCR was performed in situ in SW480 cells in suspension and in cells either cultured or cytospun onto glass slides. Amplified mutant DNA PCR products were detected in SW480 cells using digoxigenin-labeled probes, visually identifying cells harboring specific mutations in the p53 gene. In situ hybridization alone of the mutant cells without the amplification step was negative. Normal human fibroblasts or endothelial cells were refractory to in situ amplification. This reaction was mutation-specific as CEM cells with different p53 mutations reacted negatively. Mutant messenger RNA (mRNA) in tumor cells was also selectively amplified in situ by ARMS-PCR following reverse transcription (RT). This study demonstrates the potential of in situ ARMS-PCR or RT-ARMS-PCR for mutation analysis in situ and could have useful clinical applications.

Antigenic and genetic characterization of twenty-six strains of human respiratory syncytial virus (subgroup A) isolated during three consecutive outbreaks in Havana city, Cuba

Twenty-six human respiratory syncytial virus strains (subgroup A) isolated from three outbreaks in Havana City during the period 1994/95, 1995/96 and 1996/97 were analyzed to determine their antigenic and genetic relationships. Analyses were performed by monoclonal antibodies and restriction mapping (N gene) following amplification of the select region of the virus genome by polymerase chain reaction. All isolated strains were classified as subgroup A by monoclonal antibodies and they showed a restriction pattern NP4 that belonged to subgroup A. Thus the results obtained in this work, showed a close relation (100%) between antigenic and genetic characterization of the isolated strains in our laboratory. These methods permit the examination of large numbers of isolates by molecular techniques, simplifying the researchs into the molecular epidemiology of the virus.

Lymphoma cells associated with bone marrow stromal cells in culture exhibit altered growth and survival

The detection of clonal populations of lymphoma cells in histologically negative bone marrow using culture techniques is a predictor of poor outcome for patients undergoing high dose therapy and autologous transplantation. In positive cultures, lymphoma cells were observed as outgrowths in association with adherent stromal cells, whilst only stromal cells were observed in negative long-term cultures. This study developed an experimental model to further study the interactions occurring between lymphoma cells and stromal cells. Using random dot graticule analysis, 86% and 74%, respectively, of patient lymphoma cells grew in association with stromal cells in leukapheresis and bone marrow harvest cultures with the formation of cobblestone areas at sites of interaction between lymphoma cells and stromal cells. Secondary cultures showed that individual stromal cells were able to support the growth of a small number of lymphoma cells. Coculture of the human lymphoma cell lines with a murine bone marrow stromal cell line, MS-5 also resulted in the formation of cobblestone areas, which corresponded with the suppression of nonadherent cell production by the lymphoma cell lines. Upon interacting with MS-5 cells, the lymphoma cell lines formed pseudopodia and underwent pleiomorphic nuclear changes. Contiguous linear homotypic associations between lymphoma cells were evident, as opposed to focal contacts occurring in the heterotypic interactions between lymphoma cells and MS-5 cells. An increasing proportion of supernatant lymphoma cells underwent apoptosis as time in culture increased. These results demonstrate that bone marrow stromal cells alter the pattern of growth of lymphoma cells and may have an important role in the maintenance of occult lymphoma by inhibiting apoptosis.

Nested polymerase chain reaction and in situ hybridization for diagnosis of canine herpesvirus infection in puppies

The usefulness of two nucleic acid detection systems in suspected cases of spontaneous canine herpesvirus (CHV) infection in puppies was evaluated. Formalin-fixed, paraffin-embedded tissues from seven 1-3-week-old naturally infected puppies with lesions characteristic of CHV infection were investigated in a retrospective study. Nested polymerase chain reaction (PCR) and nonradioactive in situ hybridization (ISH) were used to detect nucleotide sequences of the CHV thymidine kinase (TK) gene. According to the original necropsy reports, CHV was isolated in four of the seven puppies using primary canine lung and/or kidney cells. In all seven puppies, gross and histologic lesions consisted of disseminated focal necroses and hemorrhages predominantly in kidneys, lung, liver, and spleen. In addition, few small amphophilic intranuclear inclusion bodies were detected by light microscopy mainly in epithelial cells of kidney, lung, and liver. ISH was performed with a 111-base-pair (bp) digoxigenin-labeled double-stranded DNA probe. Viral DNA was detected in the nuclei of cells near and within lesions. Various cell types, including bronchiolar and alveolar epithelial cells, hepatocytes, renal tubular epithelial cells, neurons, fibrocytes, cardiac myocytes, and endothelial cells, were positive for viral DNA. PCR amplification products of the expected length of 168 bp containing the expected cleavage site for the restriction enzyme EcoRI, derived from paraffin blocks containing lung, kidney, and liver tissues, were detected in all seven puppies. The specificity of the obtained amplicon was further confirmed by Southern blot analysis. ISH and PCR are both useful methods for diagnosing CHV infection in formalin-fixed, paraffin-embedded tissues and are highly specific and sensitive methods for further investigations of the pathogenesis of CHV-induced lesions.

Molecular characterization of an outbreak of respiratory syncytial virus (subgroup A) in Havana, Cuba, by monoclonal antibodies and restriction mapping (N gene)

Twenty-one respiratory syncytial virus (RSV) strains isolated from one outbreak in Havana, Cuba (1994 to 1995), were analyzed to determine their relatedness. All isolated strains were classified as subgroup A by monoclonal antibodies. Of 21 RSV strains examined, 20 were classified as having restriction pattern NP4 and only 1 was classified as having restriction pattern NP5.

Analysis of respiratory syncytial virus in clinical samples by reverse transcriptase-polymerase chain reaction restriction mapping

The aim of this study was to develop a polymerase chain reaction (PCR) for the detection of respiratory syncytial virus (RSV) genomes. The primers were designed from published sequences and selected from conserved regions of the genome encoding for the N protein of subgroups A and B of RSV. PCR was applied to 20 specimens from children admitted to the respiratory ward of "William Soler" Pediatric Hospital in Havana City with a clinical diagnosis of bronchiolitis. The PCR was compared with viral isolation and with an indirect immunofluorescence technique that employs monoclonal antibodies of subgroups A and B. Of 20 nasopharyngeal exudates, 10 were found positive by the three assayed methods. In only two cases, samples that yielded positive RNA-PCR were found negative by indirect immunofluorescence and cell culture. Considering viral isolation as the "gold standard" technique, RNA-PCR had 100% sensitivity and 80% specificity. RNA-PCR is a specific and sensitive technique for the detection of the RSV genome. Technical advantages are discussed.

Identification of genetic variants of hepatitis A virus

Although detection of hepatitis A virus (HAV) has been greatly aided by the development of polymerase chain reaction (PCR) technology, identification of genetic variants requires sequencing PCR products, which necessarily limits the length of the HAV genome (typically 2%) that can be analyzed. From a regulatory standpoint, identification of the specific strain detected by PCR is a prerequisite not only to overrule contamination of test samples in the diagnostic laboratory, but also to possibly locate the origin of the virus detected by PCR. We explored alternatives to sequencing PCR products to achieve these goals. The findings indicate that restriction fragment length polymorphism (RFLP) analysis of PCR products from two noncontiguous regions of the HAV genome encompassing 765 nucleotides (approximately 10% of the genome) by the restriction endonucleases HinfI and AluI, which cut frequently within the HAV genome, can distinguish the common tissue culture adapted strains of HAV from stool isolates. The resolution can be greatly enhanced by combining single strand conformation polymorphism (SSCP) analysis with restriction enzyme digestion, when most of the seventeen strains analyzed could be identified.

Achalasia is not associated with measles or known herpes and human papilloma viruses

Achalasia is an esophageal motility disorder of unknown etiology. Several studies suggest possible herpes or measles virus etiology, but results are inconclusive. The aim of this study was to test whether herpesvirus (HV), measles (MV), or human papilloma virus (HPV) sequences could be detected in myotomy specimens from a wide spectrum of achalasia patients, using the polymerase chain reaction (PCR) technique. Myotomy specimens from 13 achalasia patients, esophagectomy specimens from nine esophageal cancer patients, and autopsy specimens from six fetuses were studied with the PCR technique. Paired oligonucleotide primers of HV (HSV-1 and 2, CMV, EBV, VZV, and HHV-6), MV and HPV sequences and exon 3 of the HPRT gene were used for the PCR DNA amplification. Amplified products were resolved on agarose gels and stained with ethidium bromide. All specimens yielded the appropriate-sized products for exon 3 of the HPRT and viral controls. No amplified products were seen in the achalasia specimens or controls corresponding to any of the virus sequences tested. The absence of HV, MV, and HPV sequences suggests that these viruses are not associated with achalasia but does not exclude the possibility of a previously unidentified virus as a causal agent. Further studies aimed at identifying an unknown viral agent as a cause for achalasia are warranted.

Molecular diagnosis of Helicobacter pylori

H. pylori infection can be diagnosed with many different tests. If the patient is undergoing endoscopy with gastric biopsies, culture and histology remain the diagnostic methods of choice. Indirect tests include rapid urease tests, urea breath tests, and serology. Molecular methods such as PCR offer marginal improvements when done on biopsy material, but has the advantage of being able to accurately identify H. pylori in areas outside the stomach where cultures usually fail. PCR can detect low numbers of organisms in gastric juice, bile, stool and oral secretions. Because of its high sensitivity it can also be used for epidemiologic investigations of environmental sources. However, the largest role for PCR may be in molecular fingerprinting. Arbitrary Primer PCR (RAPD) on the whole bacterial genome can reliably and accurately distinguish between isolates. PCR-based RFLP analysis can separate isolates based on restriction fragment sizes in a smaller amplified genome segment. REP-PCR can group isolates into clusters that appear to have different clinical expressions. These methods promise to shed new light on the transmission and pathogenicity of H. pylori.

False-positive polymerase chain reaction results for human papillomavirus in lichen planus. Potential laboratory pitfalls of this procedure

BACKGROUND

The polymerase chain reaction (PCR) is a common tool in laboratory evaluation of tissue samples. It has been particularly useful in testing for nucleic acids of infectious organisms implicated in the pathogenesis of cutaneous diseases.

OBJECTIVE

Our purpose was to evaluate archival biopsy material (paraffin-embedded) of lichen planus for human papillomavirus (HPV) DNA with PCR and in situ hybridization (ISH).

METHODS

Tissue sections were obtained from 13 specimens of lichen planus and 10 control tissues. Standard methods for PCR and ISH were used to evaluate the presence of HPV DNA. RESULTS. Initial PCR results demonstrated HPV DNA in 11 of 13 specimens and in none of the control tissue. However, testing for specific HPV types revealed nucleic acid contamination. ISH was negative in all specimens.

CONCLUSION

Accurate evaluation of tissue with PCR is difficult because of the procedure's profound sensitivity. Positive results reported in the literature should be viewed with caution. Potential causes for false-positive and false-negative results should be considered.

Technical report: Part 2. Basic requirements for designing optimal PCR primers

Designing optimal polymerase chain reaction (PCR) primer sequences is one of the critical factors for successful PCR with sensitive, specific, and assay-to-assay reproducible results. In this review, all the requirements of PCR primer sequences are summarized, such as location, size of amplicon, length of primers, nucleotide composition, Tm, 3' terminal hybridization strength and frequency, hairpin formation energy, primer-to-primer interaction, specificity, and location of mismatches to sequences of cross-hybridization. The report also discusses how to explore these various types of information for more advanced PCR applications, which include nested PCR, multiplex PCR, competitive PCR, long PCR, point mutation detection, degenerate primers, and PCR cloning.

Direct hybridization and amplification applications for the diagnosis of infectious diseases

We are entering an exciting new era of molecular diagnostics in the clinical microbiology laboratory. A number of perspectives are presented in this review. First presented was a discussion of molecular diagnostics for detection of the bacterium, Chlamydia trachomatis. This is especially relevant since the tests available for this organism represent the forefront of commercial systems. Also, these tests exemplify the difficulties and advantages inherent to future molecular diagnostics for all types of disease processes. Next, a discussion of the techniques thus far employed in the field of clinical microbiology is presented. Obvious overlap exists with other areas of molecular pathology. However, the emphasis is on which techniques have proven most useful in identifying infectious agents. Finally, the features of a successful clinical microbiology diagnostics laboratory are presented, including test component requirements, laboratory personnel, quality assurance techniques, and physical laboratory setting. It is hoped that helpful advice and references are provided that will assist individual clinical laboratories as they enter the field of molecular diagnostics of infectious diseases.

A multiplex polymerase chain reaction for distinguishing Mycobacterium tuberculosis from Mycobacterium tuberculosis complex

A multiplex polymerase chain reaction has been developed which is able to distinguish Mycobacterium tuberculosis from other members of the M. tuberculosis complex. The assay is based on the simultaneous amplification of two different targets: a 396bp region from the mtp40 species-specific gene sequence of M. tuberculosis and a 245bp fragment from the M. tuberculosis complex insertion sequence IS986. Results have been obtained for 54 mycobacterial strains including five non-M. tuberculosis complex isolates. All 49 strains of the M. tuberculosis complex were positive for IS986 but only the 27 M. tuberculosis isolates were positive for both IS986 and mtp40.

Characterization of crystals of the thermostable DNA polymerase I from Thermus aquaticus

Thermus aquaticus DNA polymerase I is an enzyme that is of both physiological and technological interest. It carries out template-directed polymerization of DNA at elevated temperatures and is widely used in polymerase chain reaction (PCR). We have obtained crystals of the enzyme that diffracts X-rays to at least 3.0 A resolution in a cubic space group. Determination of the three-dimensional structure of the native enzyme along with those of relevant complexes will greatly enhance our knowledge of molecular events involved in DNA replication, will permit improvements in PCR, and will add to our knowledge of the structural bases of thermostability in proteins.

Monoclonal antibodies for the direct detection of influenza-A virus by ELISA in clinical specimens from patients with respiratory infections

BACKGROUND

Monoclonal antibody technology provides antibody reagents of known specificity, high titres and unlimited availability, that form ideal reference antibodies for use in specific viral antigen-detection methods.

OBJECTIVES

To produce mouse monoclonal antibodies against antigenic sites of influenza-A virus, and evaluate their use as diagnostic reagents in a sandwich ELISA.

STUDY DESIGN

(1) Production and characterization of monoclonal antibodies against influenza-A virus; (2) application of these antibodies in an ELISA method for direct antigen detection; and (3) evaluation of the ELISA as routine procedure.

RESULTS

Four monoclonal antibodies (A1-A4) from mice immunized intranasally with influenza-A virus were selected according to their specific reactivity with either nucleoprotein or matrix protein antigens as demonstrated by Western blot analysis. These antibodies lacked haemagglutination inhibition and neutralization properties and recognized both H1N1 and H3N2 strains of influenza-A virus equally. A sandwich ELISA using unlabelled antibodies for antigen capture and biotin-labelled antibodies for antigen detection was used to analyse nasopharyngeal secretions or nasal swabs from culture-confirmed influenza-A-infected patients and comparable specimens from patients with other viral respiratory infections. Only influenza-A virus (strains H1N1 and H3N2) could be detected in samples from patients with known influenza-A and influenza-B infections, and also after re-isolation of such viruses in conventional cultures of MDCK cells or embryonated hens' eggs. The antigen-detection assay showed a diagnostic sensitivity of 100% and a specificity of 98.3% compared with conventional culture methods.

CONCLUSION

The reported ELISA appears to be a rapid and inexpensive method for diagnosis and epidemiological studies of influenza-A infections.

The use of the polymerase chain reaction in the diagnosis of B-cell lymphomas from formalin-fixed paraffin-embedded tissue

In this study the use of the polymerase chain reaction (PCR) to detect monoclonality in B-cell lymphoid proliferations in archival formalin-fixed paraffin-embedded tissue was assessed. Using consensus primers against the framework 3 (FR 3) region of the immunoglobulin heavy chain gene (IgH), PCR analysis was performed on 29 low grade B-cell non-Hodgkin's lymphomas. Cases of benign lymphoid hyperplasia served as polyclonal controls. Sequenced cases of acute lymphoblastic leukaemia served as positive controls. In the lymphomas, monoclonality could be demonstrated in 18 of 29 (62%) cases. Only five of 11 (45%) follicle centre cell lymphomas were positive by this method whilst the success rate for the remainder was 13 of 18 (72%). None of the polyclonal controls gave false positive results although occasional non-specific dominant bands were present which disappeared on repeating the experiments. These results show that this method will identify monoclonality in 62% of low grade B-cell non-Hodgkin's lymphomas in archival material. The success rate is increased to 72% if follicle centre cell lymphomas are excluded. Thus, this method is a useful adjunctive test to aid diagnosis in lymphoid infiltrates when standard morphology and immunohistochemistry are equivocal.

Detection of Epstein-Barr virus and human papillomavirus in nasopharyngeal carcinoma by the polymerase chain reaction technique

We used the PCR technique to detect the Epstein-Barr virus (EBV) and human papillomavirus (HPV) DNA in paraffin-embedded tissues from Greek patients with nasopharyngeal carcinoma (NPC). The oligonucleotide primers used for the detection of EBV amplify a 375-bp long sequence from the EcoRI B fragment of the viral genome, whereas for HPV the primers amplify a 151-bp long sequence of the viral genome. The PCR products were analysed by agarose gel electrophoresis and visualised by UV illumination after staining with ethidium bromide. Sixty-three specimens were examined. EBV specific sequence was amplified in 20 (32%) and HPV in 12 (19%) out of the 63 samples. There was no co-infection with EBV and HPV. Although there is a high correlation of EBV infection with poorly differentiated NPC in patients from Southern China and South-East Asia, the restricted distribution suggests genetic or environmental cofactors in the development of the neoplasm. Our results confirm this suggestion since there was only a 32% correlation of EBV with NPC in Greece. HPV may also be involved in the carcinogenesis of EBV-negative squamous cell nasopharyngeal carcinomas.

Use of a multiplex PCR to detect and identify Mycobacterium avium and M. intracellulare in blood culture fluids of AIDS patients

The presence of mycobacteria in blood culture fluids (BACTEC) of AIDS patients with positive growth indices (GIs, > 20 U) was investigated by using a multiplex PCR to detect and identify members of the genus Mycobacterium, M. avium, M. intracellulare, and M. tuberculosis. Three different methods of extracting mycobacterial DNA from blood culture fluid were compared for use with the multiplex PCR. Mycobacterial cells were pelleted from a small aliquot of blood culture fluid by centrifugation, and the DNA was extracted from cells by heat lysis or a sodium iodide-isopropanol or a phenol-chloroform method. DNAs of different sizes were amplified from a region of the MPB70 gene of M. tuberculosis (372 bp) and from a region of the 16S rRNA gene of members of the genus Mycobacterium (1,030 bp), M. intracellulare (850 bp), or M. avium (180 bp) as a multiplex PCR in a single tube. The amplified DNA products were detected by agarose gel electrophoresis and ethidium bromide staining in all 41 (100%) positive cultures after sodium iodide-isopropanol extraction, in 18 (44%) after heat lysis, and in 5 (12%) after phenol-chloroform extraction. Of the 41 positive cultures, 38 were identified as M. avium and 2 were identified as M. intracellulare by both routine methods and multiplex PCR. The remaining mycobacterium was identified as M. intracellulare by routine methods and as M. avium by the multiplex PCR. Another six blood cultures that were negative for the presence of acid-fast bacilli after Ziehl-Neelson staining were also negative by PCR. The study shows that the multiplex PCR is a useful method for the detection and identification of either M. avium or M. intracellulare in small samples of cultured BACTEC 13A fluid with positive GIs ranging from 21 to 999 U. The average time to positive GI was 18 days (median, 13 days) and ranged between 8 and 42 days. The multiplex PCR may permit cultured mycobacteria to be identified at an earlier stage than the routine methods which have been adapted for use with the BACTEC system. The results also show that the method selected for extracting mycobacterial DNA from blood culture fluids is crucial for providing sensitive and accurate PCR results.

Effect of cellular physiology on PCR amplification efficiency

Culture conditions, and other variables that modulate a cell's physiology, can bias a polymerase chain reaction (PCR) amplification against generating a representative population profile. Two Pseudomonas putida nahR alleles were constructed in pUC19 that differ solely in a 31-bp internal segment whose sequence has been inverted. After PCR amplification, the products could be distinguished on the basis of a change in a unique restriction site. When an Escherichia coli strain carrying one nahR allele is submitted to different growth conditions, the consequences of such variations on the relative PCR amplification of whole cells can be ascertained through coamplification with a strain carrying the other allele and subsequent restriction analysis. Cells in stationary phase displayed improved amplifiability while cells grown at 42 degrees C were equally amplifiable as compared to cells grown at 37 degrees C. However, sublethal levels of tetracycline or growth in minimal medium made the PCR target in these cells relatively less amplifiable. When cells are completely lysed and the plasmid DNA is purified beforehand, the coamplification bias is eliminated. These results suggest that mixed populations containing cells in different physiological states may not be representatively amplified by PCR unless a DNA extraction step is included.

General primer-mediated polymerase chain reaction for simultaneous detection and typing of human papillomavirus DNA in laryngeal squamous cell carcinomas

The aim of this study was to investigate the prevalence of different human papillomavirus (HPV) types in laryngeal squamous cell carcinomas using general primer-mediated polymerase chain reaction (PCR). Tumour sections from 42 patients with laryngeal carcinomas were investigated. For HPV DNA amplification, consensus primers were used which were directed to the L1 coding region of the HPV genome. Analysis of the PCR products was done using 2% agarose gel electrophoresis followed by restriction enzyme analysis to identify different HPV types. Amplification of the human TGF-beta 1 DNA was successfully performed in 36/42 (85.7%) of samples confirming the presence of sufficient DNA for viral amplification. HPV DNA was detected in 8/36 (22.2%) of the tumours examined (three HPV-6, two HPV-16, one HPV-11, two unknown HPV types). HPV DNA was not detected in any of the non-neoplastic laryngeal mucosa which was used as control (n = 15). Fifty per cent of women had HPV-positive tumours compared with 8% of men (chi2 = 5.8, P < 0.05). Our data indicate that while the overall prevalence of HPV in laryngeal carcinomas is fairly high (22.2%), the frequency of high-risk types (HPV-16 & HPV-18) is low (5.5%). HPV probably acts as a promoter in the multistep process of carcinogenesis in squamous mucosal cells of the larynx.

The impact of the PCR plateau phase on quantitative PCR

The quantitative use of the polymerase chain reaction (PCR) is often compromised by the variability of the amplification. The most useful system for quantitation by PCR involves the use of controls which are almost identical to the target and which can be amplified using the same primers as the sequences of interest. In this paper, we use a model system consisting of differently sized targets amplifiable with varying primers to demonstrate the effects of the plateau phase of PCR on quantitation by PCR. This model confirms two commonly observed results: (i) when varying amounts of a single target are amplified, a constant maximum level of product is obtained and (ii) coamplification of different concentrations of different targets results in retention of the initial proportions. The inherent contradiction in these results is examined by replacement of the key elements of the reaction including enzyme, dNTPs or primers, none of which have an effect on the plateau. Pyrophosphate is found to exert no inhibitory effect on the reaction, nor does the exonuclease action of the enzyme cause the plateau. Levels of amplification attained during amplification are both theoretically and empirically defined as being insufficient to lead to the plateau due to competition between self-annealing of product DNAs and primer binding. We conclude that, pending further biochemical enquiry into the enzyme(s) used in the PCR, none of reasons conventionally proposed for the plateau phase of the PCR are sufficient to explain the phenomenon. This being so, we define the plateau as being a feature of the reaction as a whole and, since the onset of this phase is simultaneous for all amplicons, quantitation using the internal control system need not require exponential amplification. This therefore greatly simplifies the quantitative application of PCR.

Application of polymerase chain reaction to detect animals latently infected with agents of malignant catarrhal fever

Oligonucleotide primers derived from alcelaphine herpesvirus 1 (AHV-1) isolate WC11 DNA, the first identified agent of malignant catarrhal fever (MCF), were used to assay blood lymphocyte DNA using the polymerase chain reaction (PCR). Multiple species of exotic ruminants were examined to determine the suitability of this technique for detecting animals that may be latently infected. To correlate the PCR results with those of serology, serum samples were obtained from each animal concurrently with lymphocyte collection and subjected to an AHV-1 virus-neutralization assay (VNA). A total of 86 MCF-susceptible animals were tested, and the results of the VNA and PCR assays were compared. PCR results were positive for 44 animals. Of these, 13 were positive by VNA. Animals positive by both VNA and PCR were all wildebeest, the asymptomatic carriers of AHV-1, confirming the ability of the primers to amplify AHV-1 sequence. Positive PCR results from species other than wildebeest may represent sequence amplified from viruses related to AHV-1, which may not induce antibodies capable of neutralizing the WC11 isolate used in the VNA. This study demonstrates that PCR is capable of detecting the presence of MCF agents in various populations of captive ruminants prior to the appearance of clinical MCF so that the sources of infection can be more reliably ascertained.

Diagnosis and epidemiology of bovine tuberculosis using molecular biological approaches

Conventional methods for diagnosis and epidemiological studies of bovine tuberculosis and other mycobacterial diseases are far from ideal. In the last twelve years, molecular biology has provided new approaches which have enabled detailed studies to be made of the molecular characteristics of Mycobacterium bovis, the causative organism of bovine tuberculosis. These characteristics have been investigated for their potential use in diagnosis and epidemiological studies. Restriction fragment analysis of genomic DNA from isolates of M. bovis has provided a highly discriminatory typing system which has been used extensively for epidemiological studies. DNA elements in M. bovis have been investigated for their potential use in diagnostic assays based on the polymerase chain reaction. Individual antigens of M. bovis and their reactive epitopes have been identified and investigated for their usefulness in both serological and T cell assays of animal infection. Serological assays have proven disappointing and the full potential of T cell assays has yet to be determined. Currently, T cell assays based on recombinant antigens have not been as sensitive as those based on natural antigens.

Polymerase chain reaction: basic concepts and clinical applications in dermatology

The polymerase chain reaction (PCR) has been extensively used in basic science research, and the clinical potential of PCR is only now beginning to be realized. The PCR is based on the fundamental DNA replication process that occurs in every living cell. PCR is essentially an in vitro adaptation of the in vivo DNA copying process. Because PCR is so efficient at amplifying even picogram quantities of DNA, contamination with even trace amounts of nucleic acids can lead to the generation of unwanted DNA sequences and false-positive test results. Despite this, there has been rapid growth in the use of PCR in biomedical research and clinical diagnostics. PCR is the most sensitive test for herpes simplex virus, varicella-zoster virus, and human papillomavirus infections. Other diagnostic uses, including tests for genetic diseases, cancers, and other infectious diseases, are evolving.

A technique for the sequential isolation of RNA and DNA from embryos developed for screening for viruses

A technique has been developed to detect RNA or DNA viruses in single embryos. This technique is based on sequential RNA and DNA isolation from the embryo and analysis of this nucleic acid by polymerase chain reaction. A constitutively expressed embryo gene (alpha subunit ATPase) is also analysed as an internal standard. Extraction of RNA was more efficient than that of DNA, however, positive results were obtained for the internal standard gene for 84% (RNA) and 30% (DNA) of embryos tested.

A comparison of the polymerase chain reaction with standard laboratory methods for the detection of EHV-1 and EHV-4 in archival tissue samples

A detection system incorporating the polymerase chain reaction was compared with the use of histopathology and virus isolation to determine the presence of equid herpesvirus type 1 or equid herpesvirus type 4 in equine tissues submitted to a diagnostic laboratory. When the polymerase chain reaction was performed, these tissues had been stored for up to 3 years. Thirty-eight tissues representing 14 cases had been stored embedded in paraffin wax. Analysis of these tissues using the PCR gave predictive values of 1.0 and 0.91 for a positive and negative result respectively, and sensitivity and specificity values of 75% and 100% respectively. Fifty-three tissues representing 28 cases had been stored immersed in 10% formalin. Analysis of these tissues gave predictive values of 0.44 and 0.42 for a positive and negative result respectively, and sensitivity and specificity values of 28% and 57% respectively. The poor results obtained with this group of tissues was attributed to contamination of the samples during wax embedding. Viral DNA could not be amplified from older tissues. These results indicate that under appropriate conditions the polymerase chain reaction is reliable when applied to tissues collected for routine diagnosis. However, it is less reliable when samples for analysis are handled collectively. Also, storage of tissues in wax blocks for 14 or more years inhibits later amplification of viral DNA from these tissues. The implications of these results to the application of the polymerase chain reaction to routine laboratory diagnosis are discussed.