[Cerebral hydatic cyst in children: apropos of 6 cases].
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Brain Diseases↗
Biomedical subjects
H Jalal
Publications and source records attributed to H Jalal.
The superiority of polymerase chain reaction over an amplified enzyme immunoassay for the detection of genital chlamydial infections.
BACKGROUND/OBJECTIVES: The polymer conjugate enhanced enzyme immunoassay (IDEIA) and Cobas Amplicor polymerase chain reaction Chlamydia trachomatis (CT) (Amplicor PCR) are two commonly used assays for the diagnosis of CT infection. The performance of these assays was compared for the diagnosis of genital CT infection among 1000 consecutive patients attending a genitourinary medicine (GUM) clinic. Confirmation of positive results and the clinical significance of the absence of cryptic plasmid in chlamydia on the diagnosis of infection by Amplicor PCR were also investigated. METHODS: IDEIA, Amplicor PCR, and two nested in-house PCR assays targeting cryptic plasmid and omp1 gene were performed on all samples. DNA from Amplicor PCR negative samples was pooled for in-house PCR assays. Each pool contained DNA from seven Amplicor PCR negative samples. RESULTS: Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and efficiency of IDEIA in the diagnosis of genital CT infection were 80%, 97%, 80%, 97%, and 95%, respectively. Sensitivity, specificity, PPV, NPV and efficiency of Amplicor PCR were 99%, 98%, 89%, 100%, and 98%, respectively. 16 (11%) of 144 Amplicor PCR positive results were identified as false positive by in-house PCR assays. No isolate of plasmid free CT was detected among the study population. CONCLUSIONS: IDEIA should not be used for the diagnosis of CT infection because of its poor sensitivity. Although the analytic specificity of Amplicor PCR was 98%, because of the adverse medical, social, and psychological impact of false positive results for patients, confirmation of Amplicor PCR positive results by a different assay with comparable sensitivity is essential. Amplification assays targeting cryptic plasmid are appropriate for the diagnosis of genital CT infections.
Adolescent↗
Mumps epididymo-orchitis with prolonged detection of virus in semen and the development of anti-sperm antibodies.
Epididymo-orchitis is the most common complication of mumps in post-pubertal men. A case of MMR vaccine failure, in whom mumps and mumps-associated unilateral epididymo-orchitis developed, is presented in this article. Mumps virus was isolated from the semen 14 days after onset and mumps RNA was detected in semen for up to 40 days using RT-PCR. Epididymo-orchitis was associated with transient but significant reduction in sperm count and severe abnormalities in sperm morphology. It also led to the appearance of anti-sperm antibodies, which may have potential long-term adverse effects on the patient's fertility. Sequencing of the SH gene of the virus showed this to be a new mumps genotype distinct from the virus circulating currently in the UK.
Adolescent↗
Detection of bacteraemia in patients with fever and neutropenia using 16S rRNA gene amplification by polymerase chain reaction.
Episodes of fever and neutropenia are common complications of treatment for cancer. The use of prophylactic and early empirical antibiotics has reduced mortality but decreases the sensitivity of diagnostic tests based on culture. The aim of this study was to determine the potential of a broad diagnostic approach (eubacterial) based on 16S rRNA gene amplification and sequencing to augment cultural methods of diagnosis of bacteraemia in patients with fever and neutropenia in a regional paediatric oncology centre. One hundred eleven patient-episodes of fever and neutropenia were evaluated during the study period, 17 of which were associated with positive blood cultures, as follows: Staphylococcus epidermidis (n = 6 episodes), Enterococcus faecium (n = 2), Streptococcus sanguis (n = 3), Streptococcus mitis (n = 3), Staphylococcus aureus (n = 1), Micrococcus spp. (n = 1), and Stenotrophomonas maltophilia (n = 1). Eubacterial polymerase chain reaction (PCR) detected bacterial DNA in nine of 11 blood culture-positive episodes for which a sample was available for PCR; the species identified by sequence analysis were identical to those derived from the conventional identification of the cultured isolates. Bacterial DNA was detected in 20 episodes (21 bacterial sequences) associated with negative blood cultures, 18 of which occurred in patients who were receiving antibiotics at the time of sample collection. The species presumptively identified by partial 16S rRNA gene sequencing were as follows: Pseudomonas spp. (n = 6 episodes), Acinetobacter spp. (n =5 ); Escherichia spp. (n = 3); Moraxella spp. (n = 3); Staphylococcus spp. (n = 2); Neisseria spp. (n = 1); and Bacillus spp. (n = 1). The results of this study suggest that molecular techniques can augment cultural methods in the diagnosis of bacteraemia in patients who have been treated with antibiotics.
Bacteremia↗
Eubacterial approach to the diagnosis of bacterial infection.
Computed tomography revealed a frontal empyema in an 8 month old boy who presented with a prolonged convulsion. Before admission he had received oral antibiotics and all specimens were negative on culture. The presence of bacteria in cerebrospinal and empyema fluid was demonstrated using the polymerase chain reaction (PCR) with 16S rRNA gene primers. A presumptive identification of Streptococcus pneumoniae was made by comparison of PCR products with those derived from known bacteria using denaturing gradient gel electrophoresis.
DNA, Bacterial↗
Determination of penicillin susceptibility of Streptococcus pneumoniae using the polymerase chain reaction.
AIM: To develop a polymerase chain reaction (PCR) based method to detect penicillin susceptibility in isolates of Streptococcus pneumoniae (SP). METHOD: PCR primers were designed to amplify differential nucleotide sequences of the penicillin-binding protein (PBP) genes 2b, 2x, and 1a in penicillin susceptible and resistant strains of SP. Primers derived from the PBP 2x and 2b genes were designed to amplify products from penicillin susceptible S pneumoniae (PSSP), whereas primers derived from the PBP 1a gene were designed to amplify gene sequences of penicillin resistant S pneumoniae (PRSP). RESULTS: Two hundred and thirty clinical isolates of SP from the USA, UK, Kenya, Romania, and the Kingdom of Saudi Arabia were tested. Of the isolates, 116 were penicillin susceptible, 65 were intermediately resistant, and 49 were highly resistant. PCR identified 108 (93%) of 116 of PSSP isolates, 55 (85%) of 65 intermediately resistant isolates, and all of the 49 highly resistant isolates of SP. The susceptibility of 16 (7%) isolates could not be determined using PCR. All of these 16 isolates had a minimum inhibitory concentration (MIC) of penicillin < 1 mg/l. None of the highly resistant isolates was identified as penicillin susceptible by PCR, although two of the isolates with intermediate resistance (MIC = 0.125 mg/l) were. CONCLUSION: Using primers that differentially identify the genotypes of susceptible and resistant strains of SP, PCR provides a rapid method for determining the penicillin susceptibility of SP isolates and could potentially be used for testing clinical samples.
Bacterial Proteins↗
Changes in Bcl-2 and p53 expression in recurrent B-cell lymphomas.
The aim of this study was to investigate the changes involved in the evolution of nine cases of recurrent B-cell lymphomas. Using the polymerase chain reaction (PCR) on formalin-fixed, paraffin-embedded tissue from both the primary and the recurrent lymphoma of each case, monoclonality was demonstrated in every tumour. In all nine cases, the recurrent lymphoma was shown to belong to the same clone as the primary lymphoma. Eight of these cases were then investigated by immunohistochemistry for changes in Bcl-2 and p53 expression. Five out of eight of the primary lymphomas showed Bcl-2 overexpression. Two of the three cases initially negative for Bcl-2 expression became positive in the recurrence. One out of eight of the primary lymphomas was positive for p53 expression. Of the seven negative cases, one became positive for p53 expression in the recurrence. Both of the p53-positive cases showed high-grade histology. This study shows that Bcl-2 overexpression is probably an important early event in the development of B-cell lymphomas, although it may occur as a post-neoplastic event. p53 mutation is probably more important as a late event and may be associated with high-grade transformation.
Gene Expression Regulation, Neoplastic↗
Application of 16S rRNA gene PCR to study bowel flora of preterm infants with and without necrotizing enterocolitis.
The purpose of the present study was to determine the extent to which bacteria not detected by culture contribute to the microbial flora of the bowel of preterm infants with and without neonatal necrotizing enterocolitis (NEC). Fecal samples from 32 preterm infants in special care baby units including samples from 10 infants with NEC were examined by culture and PCR amplification of the 16S rRNA gene (rDNA). The 16S rDNA V3 region was amplified with eubacterial primers, and the amplification products derived from the fecal sample DNA were compared with the products from individual cultured isolates by PCR and denaturing gradient gel electrophoresis (PCR-DGGE), allowing the DNA from uncultured bacteria to be identified. For the 22 infants without NEC weekly samples were examined for a mean of 5.3 postnatal weeks. The total number of types detected by culture combined with PCR-DGGE was 10.1 per infant, of which PCR-DGGE contributed 10.4% of the types identified. Additional types detected by PCR-DGGE were found in 14 (63.6%) of the 22 infants. The majority of the sequences associated with uncultured bacteria showed > 90% 16S rDNA sequence identity with sequences from culturable human enteric flora, and all were found in single infants with the exception of sequences indistinguishable by DGGE from seven infants. These sequences showed > 90% sequence identity with the 16S rDNA of Streptococcus salivarius and may have been derived from upper gastrointestinal or respiratory tract flora. In the present study uncultured bacteria detected by PCR-DGGE were no more frequent in fecal samples from infants with NEC than in samples from infants without NEC, although these findings do not exclude the possibility of unrecognized bacteria associated with the mucosa of the small intestine of infants with NEC.
Bacteria↗
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.
Base Sequence↗
Comparison of random amplified polymorphic DNA with restriction fragment length polymorphism as epidemiological typing methods for Mycobacterium tuberculosis.
Aim-To compare restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) methods for the epidemiological typing of Mycobacterium tuberculosis.Methods-Thirty one M tuberculosis cultures originating from patients in the Canton of Berne in Switzerland, which had previously been typed by RFLP, were subjected to RAPD analysis. Cultures were coded so that the investigators were blind to the RFLP results until RAPD analysis was complete.Results-The 31 cultures of M tuberculosis were divided into nine groups by RFLP and eight groups by RAPD. Generally there was good correlation between the groups identified by the two techniques, with the exception of strains that had only one copy of IS6110. Both methods subdivided isolates that were placed in a single group by the other method.Conclusions-RAPD analysis is quick, simple, and useful for the comparison of small numbers of isolates. RFLP is more reproducible and therefore better suited for the accumulation of RFLP fingerprints for long term local surveillance and large epidemiological studies.
Journal Article↗
Randomly amplified polymorphic DNA typing: a useful tool for rapid epidemiological typing of Klebsiella pneumoniae.
Discriminatory typing methods are invaluable in the investigation of outbreaks of infectious diseases. Single primers were used to generate randomly amplified polymorphic DNA (RAPD) profiles from Klebsiella pneumoniae isolates of various serotype and K. pneumoniae isolates from cases of sepsis at a Malaysian hospital and two English hospitals. RAPD profiles of acceptable reproducibility, a maximum of three minor band variations, were produced using a rapid DNA extraction method. RAPD typing of K. pneumoniae was shown to be as discriminatory as restriction fragment length polymorphism analysis using pulsed field gel electrophoresis yet quicker and less costly. The findings suggest that RAPD typing may be a useful tool for the epidemiological typing of K. pneumoniae.
Bacterial Typing Techniques↗
Rapid discrimination of Mycobacterium tuberculosis strains by random amplified polymorphic DNA analysis.
Investigations of the epidemiology of tuberculosis have been hampered by the lack of strain-specific markers that can be used to differentiate isolates of Mycobacterium tuberculosis. We report the development of a rapid protocol for random amplified polymorphic DNA analysis which included the use of a commercially available DNA extraction kit (GeneReleaser). This was applied to 14 strains of M. tuberculosis, including strains associated with temporal and geographical clusters of tuberculosis in the United Kingdom and those from India, Africa, and Saudi Arabia. Strains of M. tuberculosis could be discriminated in about 8 h by this method, which is therefore a rapid and simple alternative to restriction fragment length polymorphism analysis.
Africa↗
Absence of Mycobacterium tuberculosis DNA in synovial fluid from patients with rheumatoid arthritis.
OBJECTIVES: To determine whether Mycobacterium tuberculosis DNA can be detected in synovial fluid of patients with rheumatoid arthritis (RA). METHODS: The polymerase chain reaction was applied to cellular components of synovial fluid. RESULTS: No evidence of M tuberculosis DNA was found in synovial fluid from 31 patients with RA and 13 control patients. CONCLUSION: The findings do not support a role for persistent M tuberculosis infection in the pathogenesis of RA.
Adolescent↗
Detection of Epstein-Barr virus and human papillomavirus type 16 DNA in hairy leukoplakia by in situ hybridisation and the polymerase chain reaction.
Demonstration of Epstein-Barr virus (EBV) is considered desirable for the accurate diagnosis of hairy leukoplakia (HL). Previous studies have reported possible associations with human papillomavirus (HPV) infection although this is not a universal finding. Presence of EBV and HPV 16 was examined in biopsy specimens from 18 cases of HL and ten control specimens by in situ hybridisation using digoxigenin-labelled synthetic oligonucleotide probes and by the polymerase chain reaction (PCR). The presence of EBV was demonstrated in 12 cases by both techniques. Of the remaining six cases EBV could be detected in three by in situ hybridisation but not by PCR; EBV was not detected by either method in a further three cases. All samples were negative for HPV 16 by both techniques under conditions of high stringency, although when stringency of in situ hybridisation was reduced, four samples appeared to harbour HPV DNA sequences. This study provides further evidence to support the role of EBV in the pathogenesis of HL and suggests that HPV 16 is not regularly encountered.
DNA Probes↗
Detection of human papilloma virus type 16 DNA in oral squames from normal young adults.
We have employed the polymerase chain reaction (PCR) to detect Human Papillomavirus (HPV) type 16 in oral squames and mononuclear cells from 62 healthy young adult volunteers. Two groups were screened for the presence of this virus, but in not all cases was DNA obtained from the scrapes. In the first (n = 30), the results show that 43% of normal individuals harbour HPV 16 (a genital type) in their buccal mucosa, epithelium of dorsum of tongue and hard palate. In the second group (n = 18), 44% of individuals were positive for HPV 16 in their oral epithelial scrapes, while only 6% were positive for the same virus in mononuclear cells. Interestingly, in 2 cases, peripheral blood lymphocyte DNA gave a positive reaction with the HPV 16 primers. To investigate possible HPV infection of lymphocytes, a further 42 lymphocyte samples, taken from the same age group as the epithelial study group, were analysed. None of these lymphocytes were positive for the presence of HPV 16 DNA.
Adult↗
[Specific forms of cholecystitis: contribution of radiology. 2. Xanthogranulomatous cholecystitis].
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Cholecystitis↗