Relevance of nucleic acid amplification techniques for diagnosis of respiratory tract infections in the clinical laboratory

Clinical utility of an amplification test based on ligase chain reaction in pulmonary tuberculosis

We evaluated the sensitivity and specificity of a new semiautomated direct amplification test (DAT), the LCx-MTB, for the diagnosis of pulmonary tuberculosis (TB) and assessed its positive predictive value by focusing on patients with high clinical and radiologic suspicion of pulmonary TB. Respiratory tract specimens from 32 consecutive patients with high suspicion of active pulmonary TB (case patients) and from 204 control patients were cultured for Mycobacterium tuberculosis and tested by LCx-MTB. Sensitivity and specificity of LCx-MTB when compared with culture was, respectively, 80 and 98%. Pulmonary TB was confirmed in the 32 case patients without knowledge of the LCx results: 18 patients were smear- and culture-positive for M. tuberculosis, and all gave at least one specimen that was LCx-positive. Eight patients were smear-negative culture-positive, and seven gave at least one LCx-positive specimen. LCx-MTB was negative in all the specimens obtained from six patients with smear- and culture-negative TB. A positive LCx-MTB result in a smear negative specimen was 100% predictive that at least one of the case patients' specimens would yield M. tuberculosis. As a consequence, knowledge of the LCx-MTB results at the time of specimen collection could have hastened the start of the antituberculosis therapy in three (21%) smear-negative case patients and could have avoided unnecessary invasive diagnostic procedures in four (29%). We conclude that the sensitivity of LCx-MTB in detecting M. tuberculosis DNA in respiratory tract specimens is similar to other DATs, that LCx-MTB is a reliable test for confirmation of TB in smear-positive patients and that LCx-MTB could be beneficial as a diagnostic step in smear-negative patients with a high suspicion of pulmonary TB.

Evaluation of ligase chain reaction for direct detection of Mycobacterium tuberculosis in respiratory specimens

A new automated amplification method, Ligase Chain Reaction (LCx MTB), was evaluated for direct detection of Mycobacterium tuberculosis in respiratory specimens from 208 patients and its performance was compared with culture and direct smears. Out of 226 specimens, 28 LCx MTB and 15 cultures were found positive for M. tuberculosis. After resolution of clinical history, the sensitivity of LCx MTB and culture was respectively 89.3% and 53.6% with a specificity of 98.5% and 100%. However, samples coming from untreated patients presented similar results between culture and LCx MTB (sensitivity 75% and 83.3% for culture and LCx MTB).

Diagnostic value of the Amplicor PCR assay for initial diagnosis and assessment of treatment response for pulmonary tuberculosis

We evaluated the Amplicor PCR assay as an initial diagnostic tool on the basis of clinical diagnosis, and assessed this assay as a follow-up test for patients with pulmonary tuberculosis during chemotherapy. Of the 208 specimens from 155 patients who were bacteriologically and/or clinically diagnosed with active tuberculosis before chemotherapy, 144 were Amplicor PCR-positive (sensitivity, 69.2%), which was equal to the results of culturing. Among 89 specimens which showed positive results by smear and culturing, the Amplicor PCR assay detected 87 (97.8%), whereas among 55 specimens which showed smear-negative but culture-positive results, the Amplicor PCR assay detected 46 (83.6 %)(P= 0.003). No false positive results were found in the two systems (specificity, 100%, 120/120). The Amplicor PCR assay was also evaluated as a follow-up test using 926 specimens from 207 patients receiving active tuberculosis chemotherapy. Among 433 specimens which showed Amplicor-PCR positive, 222 (51.3%) were culture-negative. On the other hand, among 233 culture-positive specimens, only 12 (5.2%) were Amplicor PCR-negative. Therefore, this assay is useful for the rapid diagnosis of tuberculosis. The duration of Amplicor PCR-positive after culture-negative conversion was significantly associated with the presence of cavitary lesion, smear-positive specimens before treatment, and smear-positive specimens with negative cultures during chemotherapy.

Polymerase chain reaction in the detection of microbes in amniotic fluid

Intra-amniotic infection during pregnancy can be caused by bacteria, viruses or protozoa, Toxoplasma gondii for example. Bacterial intrauterine infections are connected with premature birth, premature rupture of fetal membranes, and infective complications of both the mother and the newborn. Viral infections and Toxoplasma gondii can cause fetal malformations and illness with serious sequelae to the infant or fetal death in utero. Determining the causative agent is important and often greatly affects the prognosis of the newborn. Amniotic fluid is in most cases easily and safely obtainable during the second and third trimester and can be used in several microbiological assays. These include bacterial and viral cultures, Gram staining, quantitative assays for immunoglobulins or cytokines, and polymerase chain reaction (PCR) for detecting microbial DNA. This review concentrates on broad-spectrum or universal bacterial PCR for detection of bacterial DNA in amniotic fluid and on PCR assays for certain clinically important viruses and for Toxoplasma gondii.

Comparison of immunofluorescence with monoclonal antibodies and RT-PCR for the detection of human coronaviruses 229E and OC43 in cell culture

Human coronaviruses, with two known serogroups named 229E and OC43, cause up to one third of common colds and may be associated with serious diseases such as nosocomial respiratory infections, enterocolitis, pericarditis and neurological disorders. Reliable methods of detection in clinical samples are needed for a better understanding of their role in pathology. As a first step in the design of such diagnostic procedures, the sensitivities and specificities of two viral diagnostic assays were compared in an experimental cell culture model: an indirect immuno-fluorescence assay using monoclonal antibodies and reverse transcriptase-polymerase chain reaction amplification of viral RNA from infected cells. Immunofluorescence detected human coronaviruses in cells infected at a MOI as low as 10(-2) (log TCID50/ml = 4.25 for HCV-229E and 2.0 for HCV-OC43; log PFU/ml = 4.83 for HCV-229E and 1.84 for HCV-OC43) versus 10(-3) (HCV-OC43) or 10(-4) (HCV-229E) for reverse transcriptase-polymerase chain reaction amplification (log TCID50/ml = 1.75 for HCV-229E and 1.5 for HCV-OC43; log PFU/ml = 2.3 for HCV-229E and 1.34 for HCV-OC43). There were no false positive signals with other human respiratory pathogens: influenza virus, respiratory syncytial virus and adenovirus. Moreover, each assay was coronavirus serogroup-specific. These results demonstrate the potential usefulness of immunofluorescence with monoclonal antibodies and reverse transcriptase-polymerase chain reaction RNA amplification for the rapid detection of human coronaviruses in infected cell cultures. Both methods could be applied to clinical specimens for the diagnosis of human infections.

Comparison of PCR, culture, and histopathology for diagnosis of tuberculous pericarditis

Nucleic acid amplification techniques for the diagnosis of tuberculosis (TB) are rapidly being developed. Scant work, however, has focused on pericardial TB. Using cryopreserved specimens from a prior study of pericarditis, we compared PCR to culture and histopathology for the diagnosis of tuberculous pericarditis in 36 specimens of pericardial fluid and 19 specimens of pericardial tissue from 20 patients. Fluid and tissue were cultured on Lowenstein-Jensen and Middlebrook solid media and in BACTEC radiometric broth. Tissue specimens were stained with hematoxylin-eosin, Ziehl-Neelsen, auramine O, and Kinyoun stains and were examined for granuloma formation and acid-fast bacilli. PCR was performed with both fluid and tissue with IS6110-based primers specific for the Mycobacterium tuberculosis complex by published methods. Sixteen of the 20 patients had tuberculous pericarditis and 4 patients had other diagnoses. TB was correctly diagnosed by culture in 15 (93%) patients, by PCR in 13 (81%) patients, and by histology in 13 of 15 (87%) patients. PCR gave one false-positive result for a patient with Staphylococcus aureus pericarditis. Considering the individual specimens as the unit of analysis, M. tuberculosis was identified by culture in 30 of 43 specimens (70%) from patients with tuberculous pericarditis and by PCR in 14 of 28 specimens (50%) from patients with tuberculous pericarditis (P > 0.15). The sensitivity of PCR was higher with tissue specimens (12 of 15; 80%) than with fluid specimens (2 of 13; 15%; P = 0.002). In conclusion, the overall accuracy of PCR approached the results of conventional methods, although PCR was much faster. Therefore, PCR merits further development in this regard. The sensitivity of PCR with pericardial fluid was poor, and false-positive results with PCR remain a concern.