Detection of Toxoplasma gondii in cerebrospinal fluid from AIDS patients by polymerase chain reaction.

The polymerase chain reaction (PCR) was used to detect Toxoplasma gondii DNA in cerebrospinal fluid (CSF) from 14 patients with AIDS by amplification of the repetitive B1 gene. Positive PCRs were obtained in CSF from four of nine patients with toxoplasmic encephalitis. CSF samples from five control patients were negative for T. gondii DNA by PCR.     

Sensitive detection of Treponema pallidum by using the polymerase chain reaction.

We have developed a sensitive assay for Treponema pallidum subsp. pallidum (T. pallidum), the agent of veneral syphilis, based upon the polymerase chain reaction (PCR). A 658-bp portion of the gene encoding the 47-kDa membrane immunogen was amplified, and the PCR products were probed by DNA-DNA hybridization with a 496-bp fragment internal to the amplitifed DNA. The assay detected approximately 0.01 pg of purified T. pallidum DNA, and positive results were obtained routinely from suspensions of treponemes calculated to contain 10 or more organism and from some suspensions calculated to contain a single organism. Specific PCR products were obtained for the closely related agent of yaws, Treponema pallidum subsp. pertenue, but not with human DNA or DNAs from other spirochetes (including Borrelia burgdoferi), skin microorganisms, sexually transmitted disease pathogens, and central nervous system pathogens. T. pallidum DNA was detected in serum, cerebrospinal fluids, and amniotic fluids from syphilis patients but not in in nonsyphilitic controls. T. pallidum DNA was also amplified from paraffin-embedded tissue. The diagnosis of syphillis by using PCR may become a significant addition to the diagnostic armamentarium and a valuable technique for the investigation of syphilis pathogenesis.     

Detection of lymphotropic herpesvirus DNA by polymerase chain reaction in cerebrospinal fluid of AIDS patients with neurological disease

Cerebrospinal fluid (CSF) samples from 49 acquired immunodefficiency disease syndrome (AIDS) patients with a central nervous system (CNS) disease were examined by polymerase chain reaction (PCR) to evaluate the association between the positivity for cytomegalovirus (CMV) and Epstein-Barr virus (EBV), and clinical diagnosis of a CNS disease. Frequency and clinical relevance of detection of DNA of human herpesviruses 6 (HHV-6), 7 (HHV-7) and 8 (HHV-8) were also determined. DNA of one or more of the following viruses was found in 26 of 49 patients (53%): CMV in 16 (33%), EBV in 13 (27%), human herpesvirus 6 (HHV-6) in 2 (4%), human herpesvirus 7 (HHV-7) in 1 (2%), and human herpesvirus 8 (HHV-8) in 1 (2%). The CMV detection was significantly associated with encephalitis and peripheral neuropathy (7/16 vs. 2/33, p = 0.003), while EBV with primary CNS lymphoma (P-CNSL) (8/13 vs. 0/36, p < 0.0001). HHV-6 DNA was found in CSF of two patients with neuroradiological features suggestive of cerebral lesions. HHV-8 or HHV-7 DNA was detected in the CSF of patients with unexplained neurological symptoms. This study confirms that the PCR analysis of CSF is a valid tool for the diagnosis of neurological diseases associated with CMV and EBV. On the other hand, HHV-6, HHV-7 and HHV-8, instead, were rarely detected in CSF of AIDS patients and have certainly no correlation with the CNS disease found.     

Detection of Borrelia burgdorferi in cerebrospinal fluid by the polymerase chain reaction

The polymerase chain reaction (PCR) was used to amplify specific DNA sequences from different clinical isolates of Borrelia burgdorferi and from cerebrospinal fluid (CSF) of two patients with Lyme disease of the central nervous system. The amplification products were separated by polyacrylamide gel electrophoresis and visualised by ethidium bromide staining. The definitive identification of amplified DNA as a part of the B. burgdorferi flagellin gene was achieved by hybridisation to a 40-base oligonucleotide probe complementary to a part of the spirochaetal gene but not to the primers. Attempts to cultivate borreliae from either patient were unsuccessful and one patient had no serological marker in serum or CSF to indicate borreliosis. Clinical symptoms of both patients regressed with antibiotic therapy. The PCR system is a powerful and rapid technique to amplify flagellin gene sequences from CSF of patients with neuroborreliosis. Only one-tenth of the time needed for cultivation was required from CSF sampling to diagnosis. Gene amplification might, for the first time, allow effective monitoring of therapy for patients with Lyme disease of the central nervous system.     

Use of polymerase chain reaction and rabbit infectivity testing to detect Treponema pallidum in amniotic fluid, fetal and neonatal sera, and cerebrospinal fluid.

The diagnosis of congenital syphilis continues to pose a difficult clinical challenge. Because the serodiagnosis of congenital syphilis has significant limitations, the direct detection of Treponema pallidum in suspect neonatal tissues or body fluids represents a desirable alternate diagnostic strategy. We developed and applied the polymerase chain reaction (PCR) for the detection of T. pallidum in clinical material relevant to the diagnosis of congenital syphilis but which typically contain factors inhibitory for the PCR. Four methods of specimen processing were examined to circumvent PCR inhibition; clinical materials included amniotic fluids, neonatal sera, and neonatal cerebrospinal fluids. The PCR was 100% specific for T. T. pallidum compared with the sensitive rabbit infectivity test (RIT) for all clinical materials tested. For amniotic fluids, the PCR was 100% sensitive when correlated with the RIT but had a lesser sensitivity when applied to sera or cerebrospinal fluids, which typically contain few treponemes. The combined sensitivity of the PCR for all clinical samples was 78%. Positive PCR results also were obtained among some clinical specimens for which RIT was not performed; these results correlated well with either stigmata or risk factors for congenital syphilis. The combined results suggest that the PCR can be a useful adjunct to the diagnosis and clinical management of congenital syphilis and that it will provide a valuable tool for investigations of the pathogenesis of the disorder.     

Detection of JC virus by polymerase chain reaction in cerebrospinal fluid from two patients with progressive multifocal leukoencephalopathy

The polymerase chain reaction (PCR) was used to identify JC virus (JCV) in the cerebrospinal fluid of two patients with progressive multifocal leukoencephalopathy confirmed by brain biopsy. In addition, JCV viremia was demonstrated by PCR in one case. JCV detection in spinal fluid by PCR may be the first non-invasive technique available for the diagnostic confirmation of progressive multifocal leukoencephalopathy.     

Detection of Borrelia burgdorferi DNA in urine samples and cerebrospinal fluid samples from patients with early and late Lyme neuroborreliosis by polymerase chain reaction.

A polymerase chain reaction (PCR) was developed for use in the identification of a 248-bp fragment of the Borrelia burgdorferi flagellin gene in urine and cerebrospinal fluid (CSF) from patients with Lyme neuroborreliosis. The specificities of the PCR products were confirmed by DNA-DNA hybridization with an internal probe. The assay had a detection limit of 10 in vitro-cultivated B. burgdorferi. The PCR assay seemed to be species wide as well as species specific, since DNA from all 21 B. burgdorferi isolates from humans tested but not from Borrelia hermsii or Treponema pallidum could be amplified. We tested 10 consecutively diagnosed patients with untreated neuroborreliosis. There was lymphocytic pleocytosis and intrathecal B. burgdorferi-specific antibody synthesis in the CSF of all patients. Urine and CSF samples were investigated by PCR before, during, and up to 8.5 months after therapy. B. burgdorferi DNA was detected in urine samples from nine patients; five patients, including two patients with chronic neuroborreliosis, were PCR positive prior to treatment, whereas urine samples from the remaining four patients obtained 3 to 6 days after the onset of therapy became PCR positive. All urine samples obtained greater than 4 weeks after therapy were negative by PCR. PCR of CSF was less sensitive, and samples from only four patients, including one with chronic neuroborreliosis, were positive. We conclude that urine is a more suitable sample source than CSF for use in B. burgdorferi DNA detection by PCR. Normalization of inflammatory CSF changes and the negative PCR results during follow-up even in patients with chronic neuroborreliosis do not point to a persistent infection. The future role of PCR as a diagnostic tool for Lyme neuroborreliosis is still uncertain.     

Detection of Haemophilus influenzae in cerebrospinal fluids by polymerase chain reaction DNA amplification

Two primer sets were chosen for the detection of Haemophilus influenzae in cerebrospinal fluid by polymerase chain reaction (PCR) DNA amplification. One primer set was selected from sequences encoding a capsulation-associated protein and reacted with target DNA from all 15 capsulate H. influenzae strains (all serotypes) examined. The other primer set was selected from the DNA sequence of a gene encoding for outer-membrane protein P6 and reacted with the 15 capsulate and 10 non-capsulate strains of H. influenzae tested. This primer set also reacted with the closely related species H. haemolyticus and H. aegyptius, and with two of nine H. parainfluenzae strains. In reconstruction experiments, PCR DNA amplification was able to detect as few as five H. influenzae cells when 40 cycles of amplification were used. Two hundred cerebrospinal fluid (CSF) samples collected consecutively from patients suffering from meningitis were investigated by PCR; 40 were culture-positive for H. influenzae and 39 of these were also clearly positive in the PCR test with both primer sets. Contamination occurred to some extent with 40 cycles of amplification but was completely eliminated when the number of cycles was reduced to 35. We conclude that the two primer sets are appropriate for the detection of H. influenzae by PCR, each having its own specificity. When these two primer sets are used, PCR is a technique of equivalent sensitivity to culture for the detection of H. influenzae in CSF.     

Detection of varicella-zoster virus DNA by polymerase chain reaction in the cerebrospinal fluid of patients suffering from neurological complications associated with chicken pox or herpes zoster.

The polymerase chain reaction (PCR) was used to detect varicella-zoster virus (VZV) DNA in the cerebrospinal fluid of patients with VZV infection associated with neurological symptoms. Positive results were obtained in three of five children with post-chicken pox cerebellitis and in seven of seven herpes zoster patients with neurological symptoms. The PCR thus provides a useful tool for the early diagnosis of VZV-associated neurological disease.     

Detection of Treponema pallidum subsp. pallidum from skin lesions, serum, and cerebrospinal fluid in an infant with congenital syphilis after clindamycin treatment of the mother during pregnancy

We report here a case of congenital syphilis in a newborn after clindamycin treatment in pregnancy. Using PCR detection of tmpC (TP0319) and DNA sequencing of the genes TP0136 and TP0548, DNA sequences identical to Treponema pallidum subsp. pallidum strain SS14 were detected in the infant's skin lesions, serum, and cerebrospinal fluid.     

Detection of Treponema pallidum in early syphilis by DNA amplification.

By using experimentally infected rabbits as a model for early syphilis, the applicability of in vitro DNA amplification was explored for detection of Treponema pallidum. It was determined that whole blood in heparin or EDTA (but not serum), lesion exudate, and punch biopsy as well as swabs of lesions are useful specimens for examination by the polymerase chain reaction. Swabs do not require special diluents, and the specimens, whether kept at room temperature or frozen, are well suited for use in the polymerase chain reaction.     

Detection of staphylococcal genes directly from cerebrospinal and peritoneal fluid samples using a multiplex polymerase chain reaction

A multiplex polymerase chain reaction (PCR) that can simultaneously detect eubacterial isolates and the methicillin-susceptibility of staphylococcal isolates from cerebrospinal and peritoneal fluid samples was compared to conventional microbiological methods. Using conventional methods, bacteria were isolated from 8% (29/350) of the cerebrospinal fluid samples and from 5% (3/60) of the peritoneal fluid samples. All isolates except twoStaphylococcus epidermidis isolates were also detected using the multiplex PCR. Coagulase-negative staphylococci andStaphylococcus aureus were correctly identified using both methods. The multiplex PCR can rapidly and simultaneously detect eubacteria, and the methicillin susceptibility of staphylococci from samples containing 10² cfu/ml of bacteria.     

Diagnosis of herpes encephalitis via Southern blotting of cerebrospinal fluid DNA amplified by polymerase chain reaction

Herpes simplex virus thymidine kinase gene specific polymerase chain reaction (PCR) amplification of DNA extracted from lumbar cerebrospinal fluid (CSF) and Southern blotting (SB) were evaluated as a method for the diagnosis of herpes simplex encephalitis (HSE). Positive PCR-SB results were obtained with CSF samples from 9 of 10 patients (11 of 12 CSF specimens) with proven herpes encephalitis as early as 2 days after onset of neurological illness. Our data support the suggestion that PCR techniques may provide a clinically relevant "non-invasive" method for the diagnosis of HSE.     

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 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.     

Detection of Toxoplasma gondii in venous blood from AIDS patients by polymerase chain reaction.

Detection of Toxoplasma gondii in blood by means of the polymerase chain reaction (PCR) may facilitate the diagnosis and follow-up of cerebral toxoplasmosis in patients with AIDS. We evaluated this approach with seven patients with tissue culture-proven parasitemia, 14 patients with presumptive cerebral toxoplasmosis, and 17 healthy human immunodeficiency virus-positive controls. Each sample of blood was assayed on three different occasions by a PCR assay based on detection of the gene encoding the P30 surface protein. A positive PCR diagnosis required positivity in at least two of the three PCR tests. None of the controls had a positive PCR diagnosis, but six of the seven patients with parasitemia did. Cerebral toxoplasmosis was confirmed in 13 of the 14 patients with a presumptive diagnosis; diagnosis by PCR was positive before treatment for 9 of these 13 patients, whereas tissue culture was positive for only 1 patient. During treatment, blood samples were taken from 14 patients at regular intervals until day 12. PCR diagnosis became negative on ethidium-stained gels, but persistent signals were observed after hybridization, in some cases, for up to 12 days after initiation of therapy. PCR on venous blood could thus be a sensitive and noninvasive method for the diagnosis of cerebral and disseminated toxoplasmosis in AIDS patients and could be a potential tool for monitoring the effects of treatment.     

Detection of Mycoplasma pneumoniae in clinical samples from pediatric patients by polymerase chain reaction.

The polymerase chain reaction (PCR) technique was used to detect Mycoplasma pneumoniae DNA in clinical samples (nasopharyngeal aspirations or bronchoalveolar lavages) obtained from 100 children, 1 month to 16 years old. PCR allowed the detection of M. pneumoniae DNA from 20 out of the 100 patients studied. In 16 cases, PCR positivity was associated with acute respiratory symptomatology. For five PCR-positive patients, a positive culture or a serological response evidenced acute M. pneumoniae infections. A lack of antibody response was observed particularly with immunocompromised children and infants less than 12 months old. The amount of M. pneumoniae DNA in the PCR was estimated in a semiquantitative way by comparison of its hybridization signal with those obtained for 100, 10, and 1 color-changing unit (CCU) of the M. pneumoniae FH strain. Small amounts (less than or equal to 10(2) CCU/ml) of M. pneumoniae were found in samples from asymptomatic patients, while larger amounts (greater than or equal to 10(2) to greater than or equal to 10(4) CCU/ml) were found for 8 out of 10 patients with acute pneumonia.     

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.     

Detection of human papillomavirus DNA in formalin-fixed tissues by in situ hybridization after amplification by polymerase chain reaction.

The authors describe the detection of human papillomavirus (HPV) 16 DNA in paraffin-embedded, formalin-fixed tissues of cervical squamous intraepithelial lesions (SILs) by in situ hybridization after amplification by the polymerase chain reaction (PCR). Using conventional in situ hybridization and a biotin-labeled probe, variable numbers of superficial cells and none of the basal cells in the SILs showed detectable HPV 16 DNA. When the in situ assay was done after amplification, increased numbers of superficial cells had detectable HPV DNA, and the hybridization signal was much more intense. HPV DNA was also detected in basal and parabasal cells at the site of the lesion whereas not detectable in directly adjacent, normal squamous epithelium. Amplified HPV DNA was demonstrated in formalin-fixed SiHa cells using a biotin-labeled probe, demonstrating the ability to detect one copy of HPV 16 DNA. This technique should allow for direct visualization in cells of other DNA sequences of low copy number from achival specimens otherwise undetectable by conventional in situ hybridization analysis.