Detection of Mycobacterium tuberculosis by PCR amplification with pan-Mycobacterium primers and hybridization to an M. tuberculosis-specific probe

Multidrug-resistant tuberculosis

One of predominant contributors to global mortality is tuberculosis (TB), an infection caused by Mycobacterium tuberculosis (MTB). Inappropriate and ineffectual treatment can lead to the development of drug-resistant TB. One of the most common forms of drug-resistant TB is multidrug-resistant tuberculosis (MDR-TB), caused by mutations in the rpoB and katG genes that lead to resistance to anti-TB drugs, rifampicin (RIF) and isoniazid (INH), respectively. Although culturing remains the gold standard, it is not rapid thereby delaying potential treatment and potentially increasing the incidence of MDR-TB. In contrast, molecular techniques provide a highly sensitive and specific alternative. This review discusses the classification of biomarkers used to detect MDR-TB, some of the commonly used anti-TB drugs, and DNA mutations in MTB that lead to anti-TB resistance. The objective of this review is to increase awareness of the need for rapid and precise detection of MDR-TB cases to decrease morbidity and mortality of this infectious disease worldwide.

Osteoarticular tuberculosis: A series of six cases diagnosed on fine-needle aspiration cytology

A few studies are dealing with the role of fine-needle aspiration cytology in diagnosing osteoarticular tuberculosis (TB). The present study was undertaken to study the cytomorphological features of six cases of osteoarticular TB throughout 1 year, diagnosed by fine-needle aspiration cytology. The Papanicolaou, Giemsa, Ziehl–Neelsen, and periodic acid–Schiff stains were used in each case. The sampled material was also cultured in Lowenstein– Jensen media for Mycobacterium species and polymerase chain reaction assay for Mycobacterium tuberculosis. Histopathological findings were correlated whenever available. There were four male and two female patients. The age of the patients ranged from 15 to 53 years, with a mean age of 37 years. Most cases involved small bones (4/6) and long bones of upper and lower limbs (2/6). Radiologically, the suspected lesions presented as osteolytic lesions, fractures, and joint destruction. The smears showed epithelioid cell granulomas in 5 out of 6 cases (83.3%), multinucleate and Langhans’ giant cells in 3 out of 6 cases (50%), and only necrosis in 1 case (16.7%). Inflammatory cells were seen in the background in 5 out of 6 cases (83.3%). AFB was positive in 3 cases (50%). Culture in Löwenstein–Jensen media, done in three cases, showed growth of M. tuberculosis. PCR showed positivity for M. tuberculosis in all six cases. Fine-needle aspiration cytology is an easy procedure that can be used for the diagnosis of osteoarticular tuberculosis. Cytomorphologically, smears show epithelioid cell granulomas, multinucleated and Langhan’s’ giant cells, and necrosis.

Detection of Mycobacterium tuberculosis on stool specimens by PCR among patients with pulmonary tuberculosis

Background:

To detect Mycobacterium tuberculosis on stool specimens by polymerase chain reaction (PCR) among patients with pulmonary tuberculosis. Detection of M. tuberculosis complex in sputum forms the basis of diagnosis of pulmonary tuberculosis. However, some patients tend to swallow sputum and some are unable to produce sputum. Based on the survival of M. tuberculosis in the gastric fluid, swallowed organisms may be detectable in stool samples.

Methods:

The study was carried out on 30 cases each in four groups: sputum smear-positive and sputum smear-negative adults, pediatric patients suspected of pulmonary tuberculosis along with healthy controls. The samples were processed for direct microscopy for acid-fast bacilli (AFB) and M. tuberculosis culture. Stool PCR was done on all 120 samples.

Results:

AFB was demonstrated in 42 and cultured in 39 out of 240 samples. PCR-targeting IS6110 gene showed positive results in 24 (20%) out of 120 stool samples. PCR in stool showed the highest positivity in sputum smear-positive samples followed by gastric aspirates and sputum smear-negative samples.

Conclusion:

Stool PCR is a potentially useful diagnostic method for pulmonary tuberculosis.

Calvarial tuberculosis in a paediatric patient: a diagnosis not to forget

We report the case of a 10-year-old boy that presented with a palpable, painless, frontal lesion. Laboratory assessments were unremarkable and the patient was asymptomatic. Initial investigation, with a skull radiograph and unenhanced CT scan, showed a lytic midline frontal lesion involving the inner and outer tables of the skull and a large subgaleal hypodense component. MRI further depicted communication with the epidural space and contact with the superior sagittal sinus (SSS). Subsequent evaluation by Doppler ultrasound and MR angiography excluded a sinus pericranii and showed normal patency of the SSS. Surgical biopsy revealed chronic granulomatous inflammation; PCR was positive for Mycobacterium sp. One year after surgical resection and antitubercular therapy, there are no signs of recurrence. Primary calvarial involvement by tuberculosis is rare, even in developing countries. Familiarity with the expected clinical and imaging features is required to avoid diagnostic delay.

Metastatic cholangiocarcinoma mimicking tuberculosis in a cow

Here we describe a metastatic hepatic cholangiocarcinoma (cholangiocellular carcinoma) in a 14-y-old Beefmaster cow that was euthanized because of depression and progressive weight loss. Gross changes included coalescing, white-to-yellow, firm-to-hard nodules with central areas of necrosis and mineralization that effaced much of the hepatic parenchyma, omentum, mesentery, ruminal serosa, and diaphragm. A fresh sample of a hepatic nodule was submitted for a modified acid-fast (MAF) stain during autopsy to rule out tuberculosis. The MAF stain was inconclusive, and the sample was subsequently submitted for a PCR assay for Mycobacterium spp. Histologically, all nodules consisted of a neoplastic proliferation of epithelial cells surrounded by extensive areas of desmoplasia, consistent with a metastatic cholangiocarcinoma. PCR for Mycobacterium spp. was negative. Although the histologic diagnosis in our case was metastatic hepatic cholangiocarcinoma, gross changes were strikingly similar to those described in cases of tuberculosis, highlighting the need to remain vigilant in the identification of zoonotic and suspected foreign animal diseases during autopsy to protect human health.

Differential Diagnosis of Fungal Pneumonias vs. Tuberculosis in AIDS Patients by Using Two New Molecular Methods

Opportunistic fungal pneumonias (OFP) are the main cause of death in AIDS patients worldwide. Diagnosis of these infections is often late as tuberculosis (TB) is frequently the first suspicion. In addition, diagnostic tools have limitations and are unavailable in disadvantaged regions. To perform the differential diagnosis of the main fungi causing OFP in AIDS patients (Histoplasma capsulatum, Cryptococcus neoformans/C. gattii and Pneumocystis jirovecii) vs. the Mycobacterium tuberculosis complex (MTBC), two new assays were developed: (i) a multiplex real-time PCR (MRT-PCR) and (ii) a simple and cost-effective method based on real-time PCR and the analysis of melting curves after amplification (MC-PCR). Both of the techniques were optimized and standardized “in vitro”, showing a suitable reproducibility (CV ranged between 1.84 and 3.81% and 1.41 and 4.83%, respectively), a 100% specificity and detection limits between 20 and 2 fg of genomic DNA per 20 µL of reaction. A validation study was performed by retrospectively using 42 clinical samples from 37 patients with proven fungal infection or TB, and 33 controls. The overall sensitivity for the MRT-PCR assay and the MC-PCR assay was 88% and 90.4%, respectively. Both techniques were fast, sensitive and reproducible, allowing for the detection of these pathogens and the performance of a differential diagnosis.

Repeated bouts of pulmonary tuberculosis in a hunting cat: reinfection or recrudescence?

CASE SUMMARY

A 7-year-old neutered male Siamese cat was referred for investigation of weight loss and hypercalcaemia (3.3 mmol/l; reference interval 2-3 mmol/l). Haematology, serum biochemistry, thoracic imaging, bronchoalveolar lavage (BAL), Ziehl-Neelsen staining of the BAL fluid and interferon gamma release assay (IGRA) were compatible with pneumonia caused by the less pathogenic member of the Mycobacterium tuberculosis complex, that is, M microti (the 'vole bacillus'), which is common in cats in the UK. Treatment with azithromycin, rifampicin and marbofloxacin was given for 2 months, followed by 4 months of azithromycin and marbofloxacin. Treatment recommendations for tuberculous pneumonia have since changed. The cat remained asymptomatic for 1 year but went on to develop M microti pneumonia on five other occasions, and was treated for 6-12 months on each occasion. The patient's clinical signs, hypercalcaemia and radiographic/CT pulmonary pathology always resolved completely, and the IGRA became negative, before antimycobacterial treatment was stopped. This suggests cure followed by reinfection owing to avid hunting behaviour. Alternatively, this could represent recrudescence of dormant disease. This case has previously been included in a study that described a series of cases of feline tuberculosis.

RELEVANCE AND NOVEL INFORMATION

This case shows that M microti infection in cats can present as recurrent episodes of pneumonia, even after prolonged treatment courses.

Role of Laparoscopy in the Diagnosis of Genital TB in Infertile Females in the Era of Molecular Tests

STUDY OBJECTIVE

To assess diagnostic value of polymerase chain reaction (PCR) in endometrial aspirates (EAs) in comparison with conventional tests for diagnosis of female genital tuberculosis (TB) and to find agreement between EA PCR done for endometrial TB and laparoscopic findings of pelvic TB in women with unexplained infertility.

DESIGN

Prospective observational cohort study.

SETTING

Tertiary care hospital.

PATIENTS

A total of 732 infertile females screened and 385 enrolled to undergo procedure to obtain EAs.

INTERVENTIONS

EAs were tested by conventional tests (histopathology, acid-fast bacilli, Lowenstein-Jensen staining, liquid culture) and PCR for Mycobacterium tuberculosis. Patients with positive conventional tests were started on antitubercular treatment (ATT). Patients with negative conventional tests underwent laparohysteroscopy irrespective of PCR results to assess changes of tubercular infection in the pelvis. Peritoneal washings were also sent for liquid culture and PCR for TB, and suspicious lesions were biopsied at laparohysteroscopy. Findings at laparoscopy upgraded the diagnosis in these women. EAPCR results were analyzed to find agreement with the findings at laparoscopy.

MEASUREMENTS AND MAIN RESULTS

Conventional tests were positive in 8 of 385 (2%) patients. PCR was positive in 58.1% (n = 224) of endometrial samples, with sensitivity of 62.5% (95% confidence interval [CI], 24.49-91.48), specificity of 41.91% (95% CI, 36.88-47.07), positive predictive value of 2.23% (95% CI, 1.31-3.78), negative predictive value of 98.14% (95% CI, 95.53-99.24), and a diagnostic accuracy of 42.34% (95% CI, 37.35-47.45) with conventional tests. A total of 265 patients underwent laparoscopy, of whom 165 were PCR positive and 100 were PCR negative. Laparoscopic findings suggestive of TB were found in 39.3% of patients who were PCR positive and 9% of patients who were PCR negative. Kappa agreement was 0.25, suggesting fair agreement between PCR and laparoscopy.

CONCLUSION

PCR as a stand-alone diagnostic test for endometrial TB is not justified to confirm diagnosis and initiate ATT. The addition of laparohysteroscopy improves diagnostic yield for genital TB. Referring patients with a suspicion of female genital TB to tertiary care for 1-time laparoscopy is better than initiating ATT solely on the basis of PCR results.

Importance of differential identification of Mycobacterium tuberculosis strains for understanding differences in their prevalence, treatment efficacy, and vaccine development

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a serious global health problem in the 21^st century because of its high mortality. Mtb is an extremely successful human-adapted pathogen that displays a multifactorial ability to control the host immune response and to evade killing by drugs, resulting in the breakdown of BCG vaccine-conferred anti-TB immunity and development of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb. Although genetic components of the genomes of the Mtb complex strains are highly conserved, showing over 99% similarity to other bacterial genera, recently accumulated evidence suggests that the genetic diversity of the Mtb complex strains has implications for treatment outcomes, development of MDR/XDR Mtb, BCG vaccine efficacy, transmissibility, and epidemiological outbreaks. Thus, new insights into the pathophysiological features of the Mtb complex strains are required for development of novel vaccines and for control of MDR/XDR Mtb infection, eventually leading to refinement of treatment regimens and the health care system. Many studies have focused on the differential identification of Mtb complex strains belonging to different lineages because of differences in their virulence and geographical dominance. In this review, we discuss the impact of differing genetic characteristics among Mtb complex strains on vaccine efficacy, treatment outcome, development of MDR/XDR Mtb strains, and epidemiological outbreaks by focusing on the best-adapted human Mtb lineages. We further explore the rationale for differential identification of Mtb strains for more effective control of TB in clinical and laboratory settings by scrutinizing current diagnostic methods.

Covalent modification of primers improves PCR amplification specificity and yield

We report a method for covalent modification of primers that enhances the specificity of PCR and increases the yield of specific amplification products at the end of PCR. The introduction of thermally stable covalent modifications, such as alkyl groups to the exocyclic amines of deoxyadenosine or cytosine residues at the 3'-ends of primers results in enhanced specificity of reactions. This higher specificity can result in greater sensitivity of detection by reducing competition with non-productive reactions. The reduction in the amplification of unintended byproducts is most apparent when both primers are modified at their respective 3'-ends. The T Ms of such modified primers are only slightly affected by the inclusion of these modifiers. The principal mode of action is believed to be driven by the poor enzyme extension of substrates with closely juxtaposed bulky alkyl groups, such as would result from the replication of primer dimer artifact.

Biosensor-based detection of tuberculosis

Tuberculosis (TB), caused byMycobacterium tuberculosis(M.tb.), is one of the most prevalent and serious infectious diseases worldwide with an estimated annual global mortality of 1.4 million in 2010.

Epidemiological Characterization of Drug Resistance among Mycobacterium tuberculosis Isolated from Patients in Northeast of Iran during 2012-2013

INTRODUCTION

Tuberculosis is still one of the most important health problems in developing countries and increasing drug resistance is the main concern for its treatment. This study was designed to characterize the drug resistant Mycobacterium tuberculosis isolated from patients suffering from pulmonary tuberculosis in northeast of Iran.

METHOD

In this cross-sectional study during 2012-2013, drug susceptibility testing was performed on Mycobacterium tuberculosis isolated in northeast of Iran using proportional method. Epidemiological data concerning these strains were also analyzed.

RESULTS

Among 125 studied isolates, 25 mycobacteria (20%) were diagnosed as nontuberculosis mycobacteria. Among the remaining 100 Mycobacterium tuberculosis isolates, the resistance rates were 7%, 7%, 3%, and 9% against isoniazid, rifampin, ethambutol, and streptomycin, respectively. Four isolates were resistant against both isoniazid and rifampin (MDR tuberculosis). The highest resistance rate was observed among 15-45-year-old patients. The MDR tuberculosis was much more prevalent among those who had previous history of treatment.

CONCLUSION

Considering these findings, DOTS strategy should be emphasized and promptly used in order to prevent further resistance. Regarding the high rate of nontuberculosis mycobacteria, it is recommended that confirmatory tests were performed before any therapeutic decision.

Evaluation of Cobas TaqMan MTB for direct detection of the Mycobacterium tuberculosis complex in comparison with Cobas Amplicor MTB

The Roche Cobas Amplicor MTB assay, recently replaced by the Roche Cobas TaqMan MTB assay, was one of the first commercially available assays for detection of the Mycobacterium tuberculosis complex based on nucleic acid amplification. We reported previously on the limited specificity of the Cobas Amplicor MTB assay, in particular for positive samples with an optical density at 660 nm (OD660) of <2.0. Using a selected set of respiratory samples, which were scored as false positive by the Cobas Amplicor test, we demonstrate here that the specificity of the Cobas TaqMan assay is significantly improved. In addition, our study of a set of 133 clinical samples revealed that the Cobas TaqMan MTB assay showed significantly less PCR inhibition than the Cobas Amplicor test. An overall concordance of 98.2% was observed between the two assays. In a subsequent prospective study, we evaluated the performance of the Roche Cobas TaqMan MTB assay on 1,143 clinical specimens, including respiratory (n = 838) and nonrespiratory (n = 305) specimens. Using culture as the gold standard, we found a sensitivity of 88.4% and a specificity of 98.8% for the 838 respiratory specimens, compared to a sensitivity of 63.6% and a specificity of 94.6% for the 305 nonrespiratory specimens. We conclude that the Cobas TaqMan MTB assay is a significantly improved tool for the direct detection of M. tuberculosis DNA in clinical specimens.

Detection of Mycobacterium avium subsp. paratuberculosis in bulk tank milk by combined phage-PCR assay: evidence that plaque number is a good predictor of MAP

Conventional culture and a rapid phage-PCR method were used to detect Mycobacterium avium subsp. paratuberculosis (MAP) in bulk tank milk (BTM) samples. Only two of 225 samples (0.9%) were found to contain MAP by culture whereas 50 (22%) MAP-positive samples were identified using the phage-PCR assay, including both samples that were MAP-culture positive. Results using the phage-based method for independently tested duplicate samples indicated that the assay is very reproducible (r(2)=0.897), especially when low levels of mycobacteria are present. A relationship was established between plaque number and the presence of MAP in a sample. A cut-off value was determined allowing identification of MAP-positive samples based on plaque number alone (90% sensitivity, 99% specificity; area under the curve=0.976). These results indicate that the assay is a robust method for screening BTM, providing results within 24 h.

Comparison of smear microscopy, culture, and real-time PCR for quantitative detection of Mycobacterium tuberculosis in clinical respiratory specimens

BACKGROUND

As a rapid diagnostic technique, the real-time polymerase chain reaction (PCR) can detect Mycobacterium tuberculosis with a high sensitivity and specificity. However, further studies are needed to confirm it as a standard method. In this study, we evaluated the cyp141 gene for the detection and quantification of M. tuberculosis in respiratory specimens and compared the results with direct microscopy and culture.

METHODS

Sputum samples (n = 247) were collected from patients of the different provinces of Iran. DNA was extracted from clinical specimens and H37Rv strain. After measuring the standard strain DNA concentration by NanoDrop and using the Avogadro number, the DNA was diluted 6 times in order to obtain 1 × 10(6) to 10 template copies. A Taqman probe was designed for detection of the target in a real-time PCR using the specific primers.

RESULTS

Of 247 samples, 135 (55%) were culture-negative. Of 112 (45%) culture-positive samples, 88 were positive by both smear and culture and 24 were smear-negative but culture-positive. The real-time PCR enumerated 1.5E + 02 to 4.3E+ 03, 8.5E + 03 to 5.5E + 04, 7.2E + 04 to 1.1E + 06, and 1.2E + 06 to 8.1E + 07 M. tuberculosis cells in the specimens with smear-negative, 1-plus, 2-plus, and 3-plus codes, respectively. The overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the real-time PCR were 90.2% (101/112), 97.8% (132/135), 97.1%, and 92.3%, respectively.

CONCLUSIONS

The overall sensitivity and specificity, the results in comparison with those of the Xpert MTB/RIF kit, and the good correlation with molecular and phenotypic methods, show that cyp141 could be a good target for the quantification of M. tuberculosis in sputum and possibly other clinical specimens.

Is real-time PCR better than conventional PCR for Mycobacterium tuberculosis complex detection in clinical samples?

Cobas Amplicor MTB and later Cobas TaqMan MTB were used to test a very large series of consecutive specimens received for tuberculosis diagnosis. Performance parameters were estimated and compared overall and for separate specimen categories. Both systems showed excellent specificity, and that of TaqMan was the higher. The sensitivities were similar but satisfactory only with respiratory specimens and smear-positive samples.

Strengths and weaknesses of FDA-approved/cleared diagnostic devices for the molecular detection of respiratory pathogens

The rapid, sensitive, and specific identification of the microbial etiological characteristics of respiratory tract infections enhances the appropriate use of both antibiotics and antiviral agents and reduces the risk of nosocomial transmission. This article reviews the current nucleic acid amplification tests approved by the U.S. Food and Drug Administration (FDA) for the detection of respiratory pathogens. In addition, Emergency Use Authorization tests for the detection of 2009 influenza A H1N1 are discussed. The advantages and limitations of the current FDA-approved/cleared tests are reviewed.

Panniculitis attributable to Mycobacterium goodii in an immunocompetent dog in Georgia

CASE DESCRIPTION

A 5-year-old 38.3-kg (84.5-lb) mixed-breed dog was examined because of acute onset of lethargy and anorexia. Four days later, a raised, firm, warm 15 × 10-cm lesion was detected in the right caudal paralumbar area.

CLINICAL FINDINGS

Cephalexin treatment yielded a poor response. Formalin-fixed tissue and fluid samples from the cystic areas of the lesion were submitted for cytologic and histologic examinations, routine bacterial and mycobacterial culture, and genus identification and 16S partial sequencing via PCR assays. Cytologic examination revealed chronic pyogranulomatous inflammation. Histologic examination by use of routine, Giemsa, silver, acid-fast, and modified acid-fast stains revealed multifocal nodular granulomatous panniculitis without identifiable organisms. Mycobacteria were initially identified via PCR assay and mycobacterial culture within 3 days. Mycobaterium goodii was speciated by use of partial 16S RNA sequence analysis.

TREATMENT AND OUTCOME

The lesion resolved after long-term treatment with a combination of rifampin and clarithromycin and insertion of a Penrose drain. There has been no recurrence of the condition.

CLINICAL RELEVANCE

M goodii is an environmental rapidly growing mycobacterium and is a zoonotic pathogen. Infections have not been previously reported in domestic animals in North America, although there are rare reports of infection in humans associated with surgery, especially surgical implants. Domestic animals are a potential sentinel for this non-tuberculous mycobacterial infection in humans, although lack of speciation in infections of domestic animals likely underestimates the potential public health importance of this pathogenic organism. Current microbiological molecular methods allow for a rapid and inexpensive diagnosis.

PCR-linked reverse DNA hybridization using oligonucleotide-specific probes of rpoB for identification of Mycobacterium avium and Mycobacterium intracellulare

A PCR-linked reverse DNA hybridization method using two different specific rpoB DNA probes (Avp and Intp) of Mycobacterium avium and Mycobacterium intracellulare, respectively, were evaluated for the differentiation and identification of M. avium and M. intracellulare culture isolates. Among the 504 culture isolates tested by this method, 48 strains showed positive results for M. avium and 60 strains showed positive results for M. intracellulare. The other 396 culture isolates showed negative results for both M. avium and M. intracellulare. These results were consistent with those obtained from partial rpoB (306 bp) sequence analysis and biochemical tests. The negative strains obtained by this DNA hybridization method were identified as M. tuberculosis (366 strains), M. peregrinum (11 strains), M. abscessus (9 strains), M. fortuitum (8 strains), and M. flavescens (2 strains) by rpoB DNA sequence analysis. Due to the high sensitive and specific result obtained by this assay, we suggest that this PCR-linked reverse DNA hybridization method using two different specific rpoB DNA probes of M. avium and M. intracellulare would be used for the rapid and precise method for differentiation and identification of M. avium and M. intracellulare.

Detection and identification of Mycobacterium spp. in clinical specimens by combining the Roche Cobas Amplicor Mycobacterium tuberculosis assay with Mycobacterium genus detection and nucleic acid sequencing

We have recently developed a PCR assay for detection of Mycobacterium spp. at the genus level based on the Cobas Amplicor platform. The sensitivities for smear-positive and smear-negative specimens were found to be 100% and 47.9%, respectively. The specificity was 97.7%, the positive predictive value 84.6%, and the negative predictive value 93.1%. In a follow-up study, we have systematically evaluated the Mycobacterium genus assay in parallel with the Cobas Amplicor Mycobacterium tuberculosis assay on 2,169 clinical specimens, including respiratory and nonrespiratory specimens. Based on the genus assay, nontuberculous mycobacteria were readily detected and identified to the species level by PCR-mediated sequencing. In addition, our data point to a limited specificity of the Cobas Amplicor M. tuberculosis assay.

Development and evaluation of a molecular assay for detection of nontuberculous mycobacteria by use of the cobas amplicor platform

We have developed and evaluated a semiautomated assay for detection of nontuberculous mycobacteria (NTM) from clinical samples based on the Cobas Amplicor Mycobacterium tuberculosis test (Roche Diagnostics, Switzerland). A capture probe, specific for mycobacteria at the genus level, was linked to magnetic beads and used for the detection of amplification products obtained by the Cobas Amplicor M. tuberculosis assay. We demonstrate that the analytical sensitivity of the genus assay is similar to that of Cobas Amplicor M. tuberculosis detection. Four hundred sixteen clinical specimens were evaluated for the presence of NTM DNA. Sensitivities for smear-positive and smear-negative specimens were found to be 100% and 47.9%, respectively. Specificity was 97.7%, the positive predictive value 84.6%, and the negative predictive value 93.1%. The genus assay is easy to perform, produces reliable results, and was found to be a valuable diagnostic tool for rapid diagnosis of infections with NTM. The genus assay has the potential to detect NTM not routinely recovered by culture and to discover new mycobacterial species.

Microbiological diagnostic procedures in respiratory infections: mycobacterial infections

This article will review traditional and newer microbiological techniques for the diagnosis of mycobacterial respiratory infections. It will concentrate on the diagnosis of infections due to Mycobacterium tuberculosis, the main mycobacterium causing respiratory infections of clinical and public health importance. The diagnosis of respiratory disease associated with non-tuberculous mycobacteria (NTM), particularly in children with underlying airway pathology such as cystic fibrosis (CF) or bronchiectasis, will be briefly discussed. With respect to the diagnosis of tuberculosis (TB), the review will concentrate on the diagnosis of patients with symptoms and/or signs of clinical disease, rather than the detection of exposure or asymptomatic infection. It will not specifically address the assessment of pre-test probability based on clinical or epidemiological factors, the use of radiological investigations or the investigation of extrathoracic lymph node disease or chest wall disease. The role of newer diagnostic modalities including nucleic acid detection (NAD) and gamma-interferon assays in paediatric practice will be reviewed, and suggestions made as to how they may fit into contemporary diagnostic algorithms.

Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis

BACKGROUND

Even though commercial nucleic acid amplification tests (NAATs) have become the most frequently used molecular tests for laboratory diagnosis of pulmonary tuberculosis (TB), published studies report variable estimates of their diagnostic accuracy. We analysed the accuracy of commercial NAATs for the diagnosis of pulmonary TB in smear positive and smear negative respiratory samples using culture as a reference standard.

METHODS

English language studies reporting data sufficient for calculating sensitivity and specificity of commercial NAATs on smear positive and/or smear negative respiratory samples were included. Meta-regression was used to analyse associations with reference test quality, the prevalence of TB, sample and test type. Predictive values for different levels of pre-test probability were quantified using Bayes' approach.

RESULTS

Sixty three journal articles published between 1995 and 2004 met the inclusion criteria. Pooled sensitivity and specificity were 0.96 and 0.85 among smear positive samples and 0.66 and 0.98 among smear negative samples. The number of culture media used as reference test, the inclusion of bronchial samples, and the TB prevalence were found to influence the reported accuracy. The test type had no effect on the diagnostic odds ratio but seemed to be correlated with sensitivity or specificity, probably via a threshold effect.

CONCLUSIONS

Commercial NAATs can be confidently used to exclude TB in patients with smear positive samples in which environmental mycobacteria infection is suspected and to confirm TB in a proportion of smear negative cases. The methodological characteristics of primary studies have a considerable effect on the reported diagnostic accuracy.

Bioaerosol mass spectrometry for rapid detection of individual airborne Mycobacterium tuberculosis H37Ra particles

Single-particle laser desorption/ionization time-of-flight mass spectrometry, in the form of bioaerosol mass spectrometry (BAMS), was evaluated as a rapid detector for individual airborne, micron-sized, Mycobacterium tuberculosis H37Ra particles, comprised of a single cell or a small number of clumped cells. The BAMS mass spectral signatures for aerosolized M. tuberculosis H37Ra particles were found to be distinct from M. smegmatis, Bacillus atrophaeus, and B. cereus particles, using a distinct biomarker. This is the first time a potentially unique biomarker was measured in M. tuberculosis H37Ra on a single-cell level. In addition, M. tuberculosis H37Ra and M. smegmatis were aerosolized into a bioaerosol chamber and were sampled and analyzed using BAMS, an aerodynamic particle sizer, a viable Anderson six-stage sampler, and filter cassette samplers that permitted direct counts of cells. In a background-free environment, BAMS was able to sample and detect M. tuberculosis H37Ra at airborne concentrations of >1 M. tuberculosis H37Ra-containing particles/liter of air in 20 min as determined by direct counts of filter cassette-sampled particles, and concentrations of >40 M. tuberculosis H37Ra CFU/liter of air in 1 min as determined by using viable Andersen six-stage samplers. This is a first step toward the development of a rapid, stand-alone airborne M. tuberculosis particle detector for the direct detection of M. tuberculosis bioaerosols generated by an infectious patient. Additional instrumental development is currently under way to make BAMS useful in realistic environmental and respiratory particle backgrounds expected in tuberculosis diagnostic scenarios.

Diagnosis of major salivary gland tuberculosis: experience of eight cases and review of the literature

CONCLUSIONS

Tuberculosis of the salivary gland is mostly a medically curable disease entity but early diagnosis is very important to ensure complete remission. In cases with a high index of suspicion, reliable diagnostic methods such as polymerase chain reaction (PCR) should always be considered before surgical intervention to enable differential diagnosis of a salivary gland tumor.

OBJECTIVES

To investigate the clinical characteristics of major salivary gland tuberculosis and to review the literature relating to its diagnosis.

MATERIAL AND METHODS

Eight patients diagnosed as having major salivary gland tuberculosis between 1994 and 2004 were treated at one of three tertiary referral centers. Medical records, including imaging findings and the results of microbiological tests, Mycobacterium tuberculosis PCR and histopathology, were retrospectively retrieved and the literature was reviewed.

RESULTS

The parotid and submandibular glands were involved in 5 (62.5%) and 3 cases (37.5%), respectively. Neck CT demonstrated typical findings of salivary gland tuberculosis in 3 patients (37.5%). Fine-needle aspiration cytology revealed chronic inflammation in 6/7 patients (85.7%), 2 of whom (33.3%) showed caseous necrosis, strongly suggesting tuberculosis. Five of the 8 patients (62.5%) required resection of the affected gland and 3 (37.5%) received open biopsy. PCR was performed in half of the cases and was affirmative in every case. No significant differences were found between the surgically resected and non-resected groups in terms of treatment results or morbidity. All patients received anti-tuberculous chemotherapy for 8-12 months, with no disease recurrence.

Comparison of an internally controlled, large-volume LightCycler assay for detection of Mycobacterium tuberculosis in clinical samples with the COBAS AMPLICOR assay

We present a sensitive and specific assay for reliable and flexible detection of members of the Mycobacterium tuberculosis complex (MTBC) in clinical samples. This real-time PCR assay, which uses the LightCycler 2.0 instrument and 100-mul glass capillaries, can provide a result within 1 h after DNA extraction. The primers amplify a 206-bp fragment of the MTBC 16S rRNA gene. The sensor hybridization probe targets a region highly specific to members of the MTBC. The assay also includes a novel type of internal control that monitors the function of the reaction components and can detect potential inhibitors. Template DNA was extracted by the same procedure used for the COBAS AMPLICOR M. tuberculosis assay, so the LightCycler assay could be directly compared to the COBAS AMPLICOR assay. The LightCycler assay was evaluated with 146 clinical samples of various types. Very good agreement (100% sensitivity, 98.6% specificity) could be shown between the LightCycler and COBAS AMPLICOR assays. Specificity was checked with a panel of nontuberculous mycobacteria, as well as a large panel of bacterial and fungal organisms.

The diagnosis of tuberculosis

Diagnostic testing for tuberculosis has remained unchanged for nearly a century, but newer technologies hold the promise of a true revolution in tuberculosis diagnostics. New tests may well supplant the tuberculin skin test in diagnosing latent tuberculosis infection in much of the world. Tests such as the nucleic acid amplification assays allow more rapid and accurate diagnosing of pulmonary and extrapulmonary tuberculosis. The appropriate and affordable use of any of these tests depends on the setting in which they are employed.

First isolation of Mycobacterium microti (Llama-type) from a dog

We report the first isolation of Mycobacterium microti from a dog with lesions of acute peritonitis. The isolate was demonstrated to be M. microti of Llama-Type by spoligotyping. Epidemiological implications of the isolation of this possibly zoonotic agent from a dog are discussed.

Molecular genetic methods for diagnosis and antibiotic resistance detection of mycobacteria from clinical specimens

Mycobacteria comprise a diverse group of bacteria that are widespread in nature, some of which cause significant disease in humans. Members of the Mycobacterium tuberculosis complex (MTBC) are the most important human pathogens of the genus Mycobacterium. Traditional methods for detection and identification of mycobacteria include microscopy, culture and phenotypic tests. These methods either lack sensitivity, specificity, or are time consuming. Advances in the field of molecular biology have provided rapid diagnostic tools that have reduced the turnaround times for detecting MTBC and drug resistance in cultures and directly in clinical specimens from weeks to days. This review discusses the molecular genetic techniques for detecting and identifying MTBC as well as drug resistance of mycobacteria in clinical specimens.

Disseminated tuberculosis following reduced-intensity cord blood transplantation for adult patients with hematological diseases

Allogeneic hematopoietic stem cell transplantation (allo-SCT) recipients are prone to infections. The incidences of mycobacterial infections after allo-SCT in several case series vary from less than 0.1-5.5%. However, no study has been published on tuberculosis following unrelated cord blood transplantation (UCBT). We retrospectively reviewed medical records of 113 adult patients with a median age of 54 years who underwent reduced-intensity UCBT (RI-UCBT) at Toranomon Hospital from March 2002 to May 2004. Mycobacterium tuberculosis infections were diagnosed in three patients (2.7%), of these two patients developed primary infection and one patient developed reactivation of latent tuberculosis. The interval between RI-UCBT and the diagnosis of tuberculosis was 34, 41 and 61 days. All the patients had disseminated disease at diagnosis. Histological examination showed the lack of granuloma in caseous necrosis. Combination antituberculous treatments showed limited efficacy, and two patients died immediately after diagnosis. M. tuberculosis caused life-threatening illness, rapidly progressing in RI-UCBT recipients. The lack of granuloma in caseous necrosis suggests the impaired T-cell function in early post transplant phase of RI-UCBT. We should consider M. tuberculosis in the differential diagnoses of fever of unknown source after RI-UCBT.

Identification of Mycobacterium tuberculosis by PCR-linked reverse hybridization using specific rpoB oligonucleotide probes

A reverse probe hybridization method using two different Mycobacterium tuberculosis-specific rpoB DNA probes in combination was evaluated for the identification of M. tuberculosis culture isolates. Among the 384 isolates tested, 354 strains were identified as M. tuberculosis, which included 37 rifampin-resistant strains, and 30 were nontuberculous mycobacteria (NTM). This result was in accord with partial rpoB sequence analysis and IS6110 polymerase chain reaction (PCR) results, but not with the results of biochemical testing, which produced two false negative results. Because of its high level of sensitivity and specificity, we suggest that M. tuberculosis-specific rpoB probes immobilized on micro-titer well plates or on other solid matrixes can be used efficiently for the rapid and convenient identification of M. tuberculosis.

Assessment by meta-analysis of PCR for diagnosis of smear-negative pulmonary tuberculosis

We conducted a meta-analysis to assess the performance of PCR for the diagnosis of smear-negative pulmonary tuberculosis (SPT) and to identify factors that account for differences in the diagnostic accuracy of different studies. Studies published before February 2002 were included if sensitivity and specificity of PCR in smear-negative respiratory or gastric-aspirate specimens could be calculated. Analysis was conducted by using summary receiver operating characteristics models. Sensitivity and specificity ranged from 9 to 100% and from 25 to 100%, respectively. Fewer than 40% of the 50 studies reported results by number of patients, reported clinical characteristics of patients, or used as a reference standard combined culture and clinical criteria. Studies that included bronchial specimens showed higher accuracy than studies that evaluated only sputum specimens or included gastric aspirates. Studies that did not report that tests were applied blindly showed higher accuracy than those reporting blind testing. Increased sensitivity due to the use of DNA purification methods was associated with decreased specificity. Studies published after 1995, using Amplicor or dUTP-UNG, were associated with an increase in specificity at the expense of lower sensitivity. We concluded that PCR is not consistently accurate enough to be routinely recommended for the diagnosis of SPT. However, PCR of bronchial specimens could be useful in highly suspicious SPT cases. Studies not reporting blind testing are likely to overestimate accuracy of PCR. Future evaluation of PCR accuracy should be conducted by patient and type of respiratory specimen, blindly, by using a reference standard that combines culture and clinical criteria and addresses the issue of how patient characteristics affect PCR accuracy.

Rapid diagnosis of extrapulmonary tuberculosis by PCR: impact of sample preparation and DNA extraction

In cases of suspected extrapulmonary tuberculosis, rapid and accurate laboratory diagnosis is of prime importance, since traditional techniques of detecting acid-fast bacilli have limitations. The major difficulty with mycobacteria is achieving optimal cell lysis. Buffers used in commercial kits do not allow this complete lysis in a number of clinical specimens. A comparison of two sample preparation methods, pretreatment with proteinase K (PK-Roche) and complete DNA purification (cetyltrimethylammonium bromide [CTAB]-Roche), was conducted on 144 extrapulmonary specimens collected from 120 patients to evaluate the impact on the Cobas-Amplicor method. Thirty patients were diagnosed with tuberculosis, with 15 patients culture positive for Mycobacterium tuberculosis. Amplification and detection of the amplicons were impaired by a high number of inhibitory specimens (39 to 52%). CTAB-Roche allowed the detection of more culture-positive specimens by PCR than PK-Roche. Comparison with the final diagnoses of tuberculosis confirmed that CTAB-Roche produced the best sensitivity (53.8%) compared to culture (43.3%), PK-Roche (16%), and smear (13%). However, the specificity of the PCR assay with CTAB-Roche-extracted material was always lower (78.8%) than those with culture (100%) and PK-Roche (96.5%). False-positive specimens were lung biopsy material, lymph node biopsy material and aspirate, or bone marrow aspirate, mainly from immunocompromised patients. Despite the efficiency of complete DNA extraction for the rapid diagnosis by PCR of extrapulmonary tuberculosis, the false-positive results challenge our understanding of PCR results.

Polymerase chain reaction based detection of Mycobacterium tuberculosis in tissues showing granulomatous inflammation without demonstrable acid-fast bacilli

BACKGROUND

Cutaneous tuberculosis is especially difficult to distinguish from other granulomatous dermatoses. We used polymerase chain reaction (PCR) to evaluate the incidence of cutaneous tuberculosis and atypical mycobacterial infection in formalin-fixed, paraffin-embedded tissues with unspecified granulomatous inflammation and negative results for acid-fast bacilli (AFB), and analyzed the pattern of cutaneous tuberculosis in this group of patients.

METHODS

A total of 38 specimens which had been collected from 36 patients and fulfilled the criteria for tissues described above were used in this study. Two different primer pairs targeting the gene encoding for 16S ribosomal RNA (common to all mycobacteria) and the insertion sequence IS6110 (specific for M. tuberculosis complex) were used in the PCR assays. The clinical characteristics, histopathologic findings, and culture results of the patients were also analyzed.

RESULTS

Four specimens were excluded from the analysis due to the lack of internal control testing. Of the remaining 34 specimens, 22 were PCR positive for the 16S rRNA gene. Among them, 18 specimens were PCR positive for both the 16S rRNA gene and IS6110. Cutaneous tuberculosis could be diagnosed in these 18 cases (56.2%). Out of the 18 cases, there were 8 women and 10 men. The age range was 15-77 years (mean: 44.2 years). After reviewing their clinical presentation, 11 cases were considered as tuberculosis verrucosa cutis, 6 cases as lupus vulgaris, and 1 case as erythema induratum. The remaining 4 cases (12.5%) positive only for 16S rRNA gene were considered as possible atypical mycobacteria infection.

CONCLUSIONS

These results show that in paucibacillary form of cutaneous tuberculosis with unclassical clinical and histological presentation, this PCR system provides rapid and sensitive detection of M. tuberculosis DNA in formalin-fixed, paraffin-embedded specimens. Cutaneous tuberculosis represents a significant proportion in specimens showing granulomatous inflammation. In areas like Taiwan, where prevalence of pulmonary tuberculosis is still high, tuberculosis verrucosa cutis and lupus vulgaris are common forms of cutaneous tuberculosis and are seen more frequently than atypical mycobacterial infection.

Sensitivity of acid-fast staining for Mycobacterium tuberculosis in formalin-fixed tissue

Microscopic examination of tissue sections of mycobacterial lesions frequently results in few or no bacilli seen, even if the lesions appear active histologically. This might be due to the effects of the fixative fluid and/or organic solvent, both of which are conventionally used to make tissue sections for histopathology, on the acid-fast staining of bacteria. The present study was performed to examine how formalin and xylene lower the sensitivity of acid-fast staining for Mycobacterium tuberculosis and to clarify the meaning of the staining result in tissue sections. Microscopic observation of mycobacteria smeared on glass slides revealed that both of these agents greatly reduced the sensitivity of acid-fast staining. Moreover, the number of bacilli was calculated in 30 samples of paraffin-embedded granulomatous lesions using acid-fast microscopy and real-time polymerase chain reaction. The numbers of bacilli present that were estimated by real-time polymerase chain reaction were considerably higher than those counted with a microscope. These results suggest that the bacilli are frequently missed or underestimated with acid-fast microscopy on formalin-fixed, paraffin-embedded tissue.

Rapid-cycle PCR and fluorimetry for detection of mycobacteria

In this study we used LightCycler PCR amplification and product detection by fluorescence resonance energy transfer probes to identify mycobacteria and differentiate between Mycobacterium tuberculosis complex, Mycobacterium avium, and other nontuberculous mycobacteria. Targeting the 16S rRNA gene, three different probes specific for mycobacteria, M. tuberculosis complex, and M. avium were constructed. As few as five genome copies of target nucleic acid were detected by the probes, illustrating the high sensitivity of the system. All 33 mycobacterial species tested but none of the closely related actinomycetes and other bacteria produced a specific fluorescence signal. A specificity of 100% was also demonstrated for the M. tuberculosis complex-specific probe and the M. avium-specific probe. Within 45 min, the LightCycler method correctly detected mycobacteria and specifically identified M. tuberculosis complex and M. avium without any post-PCR sample manipulation. In view of future clinical studies, we also constructed and tested an internal control which could be used to assure successful amplification and detection of mycobacteria. Monitoring of PCR inhibition will be essential for evaluation of this system for direct detection of mycobacteria in clinical specimens. Finally, we tested our system on sputum seeded with mycobacteria and were able to detect as few as 10 organisms. At present, this system is the fastest available method for identification and differentiation of mycobacteria from culture-positive specimens and offers an excellent alternative to previously established nucleic acid amplification-based techniques for the diagnostic mycobacterial laboratory.

Molecular genetic and traditional methods for detection of Mycobacterium tuberculosis complex (discrepancy analysis)

In the past six and half years, 862 different clinical samples [sputum, bronchoalveolar lavage, thorax puncture, cerebrospinal fluid and skin samples] were tested by Gen-probe amplified Mycobacterium tuberculosis direct test (MTD) or ligase chain reaction (LCR) or polymerase chain reaction (PCR). 239 parallel clinical samples were cultivated, and some samples were stained with Ziehl-Neelsen staining. 1-4 samples were tested per patient. 29 (12.13%) samples were positive and 177 (74.05%) samples were negative with both cultivation and molecular genetic methods. 2 (0.83%) samples were positive only on cultivation, and 31 (12.97%) samples were positive only with the molecular diagnostic methods. The differences are undoubtedly explained by the sensitivity of the molecular diagnostic methods.

Comparison of in-house polymerase chain reaction method with the Roche Amplicor technique for detection of Mycobacterium tuberculosis in cytological specimens

Two techniques have been approved by the United States FDA for diagnosis of tuberculosis in smear positive sputa: LCX M. tuberculosis, a ligase chain reaction procedure manufactured by Abbott Laboratories, and Amplicor, a polymerase chain reaction (PCR) procedure manufactured by Roche. However, these commercial methods are expensive and beyond the reach of laboratories in most developing countries. We compared the Roche Amplicor kit with an in-house PCR using a primer set for Mycobacterium tuberculosis/bovis directed at MPB 64 protein gene. It was able to distinguish between M. tuberculosis, M. avium, M. gordonii, M. intracellularae, and M. kansasii. Fifty-seven cytological samples were submitted to the laboratory for molecular diagnosis of M. tuberculosis. Both procedures were run on every sample submitted and the two methods agreed completely. The custom-made method is less expensive than the commercial technique.

Clinical evaluation of Amplicor Mycobacterium detection system for the diagnosis of pulmonary mycobacterial infection using sputum

SETTING

The Amplicor Mycobacterium detection kit was evaluated for the diagnosis of active pulmonary mycobacterial infection using sputum.

OBJECTIVE

To assess the clinical usefulness of the Amplicor Mycobacterium kit for the diagnosis of pulmonary tuberculosis and non-tuberculous mycobacterial infection in the country of medium prevalence.

DESIGN

All the patients were diagnosed with bacterial, histopathological, and clinical 'gold standard'. The sensitivity and specificity for diagnosing clinically active pulmonary tuberculosis and Mycobacterium avium and Mycobacterium intracellulare infections were evaluated comparing Amplicor results and clinical diagnosis.

RESULTS

A total of 1088 sputum specimens were collected from 780 in and out patients. Mycobacteria were recovered from 339 specimens by culture. The sensitivity and specificity of conventional culture method for the diagnosis of pulmonary tuberculosis were 60.2% and 99.8% respectively based on the number of patients. The figures for Amplicor were 61.8% and 97.4% respectively. There was no statistical significant difference between these methods. In rapidity, the Amplicor was significantly superior to the microscopy method in sensitivity.

CONCLUSION

Patients with Amplicor positive and conventional negative result had mostly mycobacteria related diseases. The Amplicor positive result indicated mostly active mycobacterial infection and was clinically useful for rapid diagnosis.

Multicenter evaluation of a pathogenic mycobacterium screening probe

The introduction of nucleic acid amplification assays into the clinical laboratory has reduced the time needed to diagnose diseases caused by members of the Mycobacterium tuberculosis complex (MTBC). However, several mycobacterial species other than those of the MTBC are known to cause disease, especially in immunocompromised individuals. A screening assay has been developed for the detection of the major pathogenic mycobacterial species. The assay utilizes pan-genus primers to amplify mycobacterial DNA and a screening probe (KY493) that detects all major pathogenic mycobacteria. A multicenter European study was conducted to assess the performance of the screening probe in the clinical laboratory. The screening probe was evaluated against individual probes specific for M. tuberculosis, M. avium, and M. intracellulare, a genus-specific probe with broader species coverage, and culture. The screening probe had a sensitivity equivalent to that of the species-specific probes; all specimens positive with any of the species-specific probes were also positive with the screening probes. Compared to culture, the sensitivity of the screening probe was 89% (154 of 173) for all culture-positive specimens tested. This value was 89.6% for the genus-specific probe. The screening probe was more specific than the genus-specific probe. Specificity was 93.9% (661 of 704) compared to culture results alone. The comparable specificity value for the genus-specific probe was 84.8%. When clinical data were taken into consideration, the sensitivity of the screening assay was similar to that of culture (81% versus 76.2%) but the positive predictive value of the test was lower (76.2% versus 100% for culture). However, the screening probe was more sensitive than smear and may be a useful tool in the rapid diagnosis of mycobacterial disease.