Petra Apfalter

Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens

ABSTRACT The reported rate of detection of Chlamydia pneumoniaeDNA within atherosclerotic lesions by PCR varies between 0 and 100%. In this study, identical sets of coded experimental atheroma samples (n = 15) and spiked controls (n = 5) were analyzed by 16 test methods in nine centers by means of PCR. The positive controls were correctly identified to levels of 1, 0.1, and 0.01 inclusion bodies of C. pneumoniae/ml of tissue homogenate by 16 (100%), 11 (69%), and 3 (19%) of the test methods, respectively. Three out of 16 negative controls (19%) were rated positive. Positivity rates for atheroma samples varied between 0 and 60% for the different test methods, with the maximum concordant result for positivity being only 25% for one carotid artery sample. There was no consistent pattern of positive results among the various laboratories, and there was no correlation between the detection rates and the sensitivity of the assay used.

In-House Nucleic Acid Amplification Assays in Research: How Much Quality Control Is Needed before One Can Rely upon the Results?

Over the last 20 years, nucleic acid amplification tests (NAATs) have become a major tool for detection of microorganisms, for diagnostic testing, and for research purposes in the field of infectious diseases. NAATs offer significant sensitivity and speed compared to culture and do not require viable organisms. However, validated, commercially available, U.S. Food and Drug Administration-cleared assays exist for the following microorganisms: Mycobacterium tuberculosis, Chlamydia trachomatis, Neisseria gonorrhoeae, methicillin-resistant Staphylococcus aureus, group B streptococcus, Legionella pneumophila, human immunodeficiency virus, hepatitis B virus, and hepatitis C virus. Some of these tests are for very limited indications, for example, the methicillin-resistant Staphylococcus aureus assay is intended only for use with nasopharyngeal

Comparison of a New Quantitative ompA-Based Real-Time PCR TaqMan Assay for Detection of Chlamydia pneumoniae DNA in Respiratory Specimens with Four Conventional PCR Assays

ABSTRACT Chlamydia pneumoniae, an important respiratory pathogen, is difficult to culture, and detection rates by conventional PCRs vary considerably. A new quantitative ompA-based real-time PCR assay based on TaqMan technology for detection of C. pneumoniae in respiratory samples is described, and its performance in terms of sensitivity and reproducibility is compared with those of four published conventional PCRs (one single-step PCR targeting a cloned PstI fragment; two nested PCRs, one targeting the 16S rRNA gene followed by hybridization and the other targeting the ompA gene; and a touchdown enzyme time-release [TETR] PCR also targeting the 16S rRNA gene). Both ompA-based PCRs showed the best analytical sensitivity. All five assays could detect even lower target levels from spiked sputum, with the 16S rRNA assays performing better than the ompA-based nested PCR (10−6 inclusion-forming units [IFU] were detected in four of four and two of four replicates by the 16S rRNA TETR PCR and the 16S rRNA nested PCR, respectively). In general, the ompA-based real-time protocol produced the most consistent positive results for all replicates tested down to 10−6 IFU. Eight of 45 patient sputum specimens (18%) were C. pneumoniae DNA positive in at least one of four replicates tested by at least one assay. Without taking into consideration the analytical sensitivity or the reproducibility of the test results, the numbers of C. pneumoniae DNA-positive sputum specimens (n = 8) were four, three, two, two, and one for the 16S rRNA TETR assay, the PstI-based single-step PCR, the ompA-based real-time PCR, the ompA-based nested touchdown PCR, and the 16S rRNA-based nested PCR, respectively. However, the overall rate of concordance of positive results was low. Only one cell culture-positive sputum specimen was positive by four of five assays (14 of 16 replicates; mean cycle threshold value, 25; 108 particles/ml of sputum). Thirty-seven specimens were C. pneumoniae negative by all five assays for all replicates tested, as were all negative controls (n = 65 to 100 per testing panel). No PCR inhibitors were detected by real-time PCR or by the 16S rRNA-based nested assay. We confirm that the analytical sensitivity of an assay for the detection of C. pneumoniae does not necessarily predict its ability to detect its target in sputum. A quantitative, fast, and easy-to-handle diagnostic approach such as the ompA-based real-time TaqMan PCR described here might improve the detection of C. pneumoniae in respiratory samples.

Reliability of Nested PCR for Detection of Chlamydia pneumoniae DNA in Atheromas: Results from a Multicenter Study Applying Standardized Protocols

ABSTRACT The present multicenter study was designed to find explanations for the discrepancies in the reported rates of detection of Chlamydia pneumoniae DNA in endarterectomy specimens. Coded identical sets of (i) a C. pneumoniae DNA dilution series (panel 1; n = 10), (ii) spiked control tissue specimens (panel 2; n = 10 specimens, including 5 negative controls), and (iii) endarterectomy specimens (panel 3; 15 atheromas, 5 negative controls) were analyzed at four laboratories by three standardized DNA extraction methods in each laboratory and a nested touchdown PCR protocol targeting the ompA gene of C. pneumoniae. Panel 1 samples were correctly identified as positive to levels of 0.3 inclusion-forming units (IFU)/PCR mixture (100%) and 0.03 IFU/PCR mixture (50%). All negative controls were correctly reported as negative. Panel 2 samples were identified as C. pneumoniae positive to levels of 0.01 IFU/PCR mixture (100%) and 0.005 IFU/PCR mixture (91%), independent of the DNA extraction method used, and only one false-positive result was reported. For panel 3 samples, 5 of 240 (2%) analyses (in which DNA extractions and PCR were performed at the same laboratory) were positive; the positive specimens were from three endarterectomy specimens and two negative controls. After exchange of DNA extracts between laboratories, 13 of 15 atheroma samples were C. pneumoniae DNA positive in at least 1 of a series of 48 analyses per atheroma sample; however, the overall positivity rate did not exceed 5% (33 of 720 analyses) and therefore was lower than that for the negative controls (8%; 19 of 240 analyses). Not a single positive result could be achieved when all panel 3 extracts (n = 240 analyses) were reamplified by a 16S rRNA PCR followed by hybridization with a C. pneumoniae-specific probe. Statistical analyses demonstrated that positive results did not occur in an independent and random fashion and could most likely be explained by amplicon carryover at the nested PCR level as well as amplicon introduction during DNA extraction, but not by the patterns of distribution of very low target levels or a certain DNA extraction protocol. The results of studies by nested PCR for detection of the prevalence of C. pneumoniae will always be questionable.

Detection and Identification of Fungi from Fungus Balls of the Maxillary Sinus by Molecular Techniques

ABSTRACT The aim of this study was to find a reliable method for the detection and identification of fungi in fungus balls of the maxillary sinus and to evaluate the spectrum of fungi in these samples. One hundred twelve samples were obtained from patients with histologically proven fungal infections; 81 samples were paraffin-embedded tissue sections of the maxillary sinus. In 31 cases, sinus contents without paraffin embedding were sent for investigation. PCR amplification with universal fungal primers for 28S ribosomal DNA and amplicon identification by hybridization with species-specific probes for Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus glaucus, Pseudallescheria boydii, Candida albicans, and Candida glabrata were performed for all samples. Furthermore, PCR products were sequenced. Fresh samples were also cultivated. Fungal DNA was detected in all of the fresh samples but only in 71 paraffin-embedded tissue samples (87.7%). Sequence analysis was the most sensitive technique, as results could be obtained for 28 (90.3%) fresh samples by this method in comparison to 24 (77.4%) samples by hybridization and 16 (51.6%) samples by culture. However, sequence analysis delivered a result for only 36 (50.7%) of the paraffin-embedded specimens. Hybridization showed reliable results for A. fumigatus, which proved to be the most common agent in fungus balls of the maxillary sinus. Other Aspergillus species and other genera were rarely found.

Isolation and continuous growth of Chlamydia pneumoniae from arterectomy specimens.

Abstract For the purpose of collecting Chlamydia pneumoniae strains of vascular origin that could be grown continuously in vitro, a cell culture system has been established. Using different types of vascular specimens obtained from 38 patients, Chlamydia pneumoniae could be isolated in three (7.9%) cases. The strains were obtained from specimens of the carotid artery, the femoral artery and an infrarenal aneurysm of the abdominal aorta of three male atherosclerosis patients. Thus, viable Chlamydia pneumoniae strains are also present in vascular regions other than those hitherto described.

Evaluation of a protocol for molecular broad-range diagnosis of culture-negative bacterial infections in clinical routine diagnosis

Aim:  Introduction of a protocol for broad‐range diagnosis of bacterial infections, which remain negative in culture.

No Evidence of Involvement of Chlamydia pneumoniae in Severe Cerebrovascular Atherosclerosis by Means of Quantitative Real-Time Polymerase Chain Reaction

Background and Purpose— All studies reporting high numbers of Chlamydia pneumoniae DNA positives in stroke patients published to date have used polymerase chain reaction (PCR) techniques highly prone to generate false-positive results. The aim of this study was to analyze the prevalence of C. pneumoniae DNA in plaques of the carotid artery as well as in peripheral blood by means of a new, closed, real-time PCR system. Methods— Carotid endarterectomy specimens and preoperative peripheral blood mononuclear cells (PBMC) of 75 individuals with severe cerebrovascular atherosclerosis were analyzed by means of a C. pneumoniae-specific quantitative omp A-based real-time PCR TaqMan system. Plaques were also cultured onto HEp-2 cells. Before the surgical intervention, C. pneumoniae-specific IgM, IgG, and IgA as well as C-reactive protein (CRP) levels were determined. Results— 89% of all patients studied had C. pneumoniae- specific antibodies, but the pathogen was not detected in a single carotid atheroma by real-time PCR and cell culture. However, C. pneumoniae DNA was detected in 4 PBMC samples (5.3%) at very low levels (<1 inclusion/6 mL EDTA blood). No statistical significance was found between symptomatic/asymptomatic patients, C. pneumoniae PCR, results and CRP values after correction for multiplicity-of-test adjustment. Conclusions— By means of a closed, highly sensitive, and specific real-time PCR, C. pneumoniae was not detected in cerebrovascular atherosclerosis. PCR on PBMC was not predictive for endovascular chlamydia infection and most likely stem from previous C. pneumoniae respiratory tract infection in individual cases. (Stroke. 2004;35:2024-2028.)

Performance of a new chromogenic oxacillin resistance screen medium (Oxoid) in the detection and presumptive identification of methicillin-resistant Staphylococcus aureus

A new chromogenic Oxacillin Resistance Screen Agar (ORSA; Oxoid) for the presumptive detection of methicillin-resistant Staphylococcus aureus (MRSA) was compared to a phenyl-mannitol-salt-oxacillin medium (MS-Oxa), blood agar and brain heart-infusion (BHI) on 579 clinical specimens. After 24 h [48h] sensitivity and specificity for ORSA vs. MS-Oxa were 50.8% [68.2%] vs. 53.8% [65.7%] and 95.6% [94.5%] vs. 92.7% [91.8], respectively. Within 24 h, ORSA and MS-Oxa identified 51% and 54% MRSA. It is not feasible to omit BHI in MRSA-screening protocols since 33% MRSA grew in BHI only.

Disseminated Infection with Nattrassia mangiferae in an Immunosuppressed Patient

ABSTRACT Disseminated infection with the coelomycetous fungus Nattrassia mangiferae is a very rare disease affecting only the immunocompromised host. We report the first case of a disseminated infection with spondylodiscitis and granular skin lesions due to N. mangiferae in a renal transplant patient.