Large-scale use of polymerase chain reaction for detection of Mycobacterium tuberculosis in a routine mycobacteriology laboratory

Varying clinical presentations of nontuberculous mycobacterial disease : Similar to but different from tuberculosis

The incidence rate of pulmonary nontuberculous mycobacterial disease (PNTMD) in Japan is the highest among major industrialized nations. Although the typical clinical course and radiological manifestations of PNTMD are different from those of pulmonary tuberculosis (TB), confusion about these mycobacterial diseases leads to a diagnostic pitfall. Diagnostic challenges include the coexistence of Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM), false positives for NTM in MTB nucleic acid amplification tests, microbial substitution, and abnormal radiological manifestations caused by NTM. Features of extrapulmonary NTM diseases, such as pleurisy, vertebral osteomyelitis, and disseminated disease, are different from the corresponding tuberculous diseases. Moreover, the immunological background of the patient (status of human immunodeficiency virus infection with or without antiviral therapy, continuation or discontinuation of immunosuppressive therapy, use of immune checkpoint inhibitor, pregnancy and delivery, etc.) influences the pathophysiology of mycobacterial diseases. This review describes the varying clinical presentations of NTM disease with emphasis on the differences from TB. J. Med. Invest. 68 : 220-227, August, 2021.

Evaluation of the performance of an in-house duplex PCR assay targeting the IS6110 and rpoB genes for tuberculosis diagnosis in Cameroon

Background

Tuberculosis (TB) remains a major public health concern in many low-income countries accounting for approximately two-thirds of deaths in people living with human immunodeficiency virus (HIV) infection. With prompt, accurate and appropriate treatment, almost all TB disease can be cured. The present study was to evaluate the diagnostic performance of an in-house duplex PCR (D-PCR) using IS1610 and rpoB specific primers in sputum samples from TB suspected patients.

Methods

A hospital-based cross-sectional study was conducted at the Limbe and Buea Regional Hospitals of the South West Region of Cameroon from June 2016 to April 2017. Sputum samples, decontaminated with hypertonic saline/sodium hydroxide solution were centrifuged and pellets processed for smear microscopy, culture and DNA extraction. Suspected inhibition was resolved by serial dilution of genomic DNA. Results were compared to culture as gold standard as well as a Composite Reference Standard (CRS).

Results

A total of 129 participants aged between 5 to 82 years were enrolled in to the study. The median age of the participants was 37 years (interquartile range, IQR: 27–50 years), with 54.3% being male. Forty-seven samples (36.4%) were positive by direct sputum microscopy, 49 (38%) by microscopy after concentration, 51 (39.5%) by culture and 62 (40.1%) by D-PCR. PCR inhibition was resolved in 85.7% (18/21) of the samples that had inhibition. The overall sensitivity, specificity, positive and negative predictive values, positive and negative likelihood ratios and area under the curve AUC) of the D-PCR was 93.5, 94, 94, 94%, 15.6, 0.005 and 89.0% respectively using CRS as reference. The sensitivities of D-PCR observed among different sample categories were 95.7, 87.5 and 87.5% for smear-and culture-positives, smear-negative/culture-positive, and clinically diagnosed cases respectively.

Conclusion

IS1610 and rpoB duplex PCR using relatively cheap decontamination and DNA extraction methods in addition to simple serial dilutions to resolve PCR inhibition shows high sensitivity in the diagnosis of paucibacillary tuberculosis.

A systemic review on tuberculosis

Tuberculosis (TB), which is caused by bacteria of the Mycobacterium tuberculosis complex, is one of the oldest diseases known to affect humans and a major cause of death worldwide. Tuberculosis continues to be a huge peril disease against the human population and according to WHO, tuberculosis is a major killer of the human population after HIV/AIDS. Tuberculosis is highly prevalent among the low socioeconomic section of the population and marginalized sections of the community. In India, National strategic plan (2017-2025) has a national goal of elimination of tuberculosis by 2025. It requires increased awareness and understanding of Tuberculosis. In this review article history, taxonomy, epidemiology, histology, immunology, pathogenesis and clinical features of both pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB) has been discussed. A great length of detailed information regarding diagnostic modalities has been explained along with diagnostic algorithm for PTB and EPTB. Treatment regimen for sensitive, drug resistant and extensive drug resistant tuberculosis has been summarized along with newer drugs recommended for multi drug resistant tuberculosis. This review article has been written after extensive literature study in view of better understanding and to increase awareness regarding tuberculosis, as a sincere effort that will help eliminate tuberculosis off the face of the earth in near future.

Prospective Cohort Study on Performance of Cerebrospinal Fluid (CSF) Xpert MTB/RIF, CSF Lipoarabinomannan (LAM) Lateral Flow Assay (LFA), and Urine LAM LFA for Diagnosis of Tuberculous Meningitis in Zambia

Tuberculous meningitis (TBM) is a devastating infection of the central nervous system lacking an adequate point-of-care diagnostic test. We conducted a prospective cohort study of 550 Zambian adults with suspected TBM to determine the diagnostic accuracy of cerebrospinal fluid (CSF) Xpert MTB/RIF, CSF lipoarabinomannan (LAM), urine LAM, CSF total protein, and CSF glucose compared with the gold standard of CSF culture. We categorized patients with a positive CSF tuberculosis (TB) culture as definite TBM. We also assessed inpatient and 1-year mortality on definite TBM patients when CSF Xpert MTB/RIF results were available in real time to treating physicians relative to a historical comparison cohort in whom Xpert results were not available in real time. Of the 550 patients, 474 (86.2%) were HIV-infected and 105/550 (19.1%) had definite TBM based on a positive CSF culture. The sensitivity/specificity of the diagnostic tests were CSF Xpert MTB/RIF, 52.9%/94.2%; CSF LAM, 21.9%/94.2%; urine LAM, 24.1%/76.1%; and CSF glucose <40 mg/dl, and total protein, >100 mg/dl, 66.3%/90%. A model including CSF Xpert MTB/RIF, CSF LAM, CSF glucose, and CSF total protein demonstrated an area under the receiver operating curve of 0.90. The inpatient and 1-year mortality for definite TBM was 43% and 57%, respectively. There was low sensitivity for the diagnosis of TBM across all diagnostics tests. CSF Xpert MTB/RIF and CSF LAM are highly specific for the diagnosis of TBM. Despite the use of Xpert MTB/RIF for diagnostic purpose in real time, TBM was still associated with a high mortality in Zambian patients.

Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example

BACKGROUND

The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we aimed to explain this method with the example of Mycobacterium tuberculosis complex and investigate its efficacy in a diagnostic test.

METHODS

A specific target was identified using modified genome comparison method and an in-house PCR test was designed. To determine the analytical sensitivity and specificity, 10 standard specimens were used. Also, 230 specimens were used to determine the clinical sensitivity and specificity.

RESULTS

The identity and query cover of our new diagnostic target (5KST) were ≥ 90% with M. tuberculosis complex. The 5KST-PCR sensitivity was 100% for smear-positive, culture-positive and 85.7% for smear-negative, culture-positive specimens. All of 100 smear-negative, culture-negative specimens were negative in 5KST-PCR (100% clinical specificity). Analytical sensitivity of 5KST-PCR was approximately 1 copy of genomic DNA per microliter.

CONCLUSIONS

Modified genome comparison method is a confident way to find specific targets for use in diagnostic tests. Accordingly, the 5KST-PCR designed in this study has high sensitivity and specificity and can be replaced for conventional TB PCR tests.

Vulvar Tuberculosis Cutis Orificialis Concomitant to Pulmonary Tuberculosis: A Case Report

Tuberculosis (TB) is a common condition with increasing incidence worldwide. Cutaneous TB represents a small portion of extrapulmonary TB. Health care professionals must be aware of cutaneous forms of TB to avoid delay in diagnosis and treatment. We present a case of a 59-year-old woman with vulvar TB cutis orificialis in association with pulmonary TB without any other involvement of genitourinary system. We discuss epidemiological aspects, classification, treatment, range of histopathological patterns, and use of ancillary techniques for diagnosis.

Recent technological advancements in tuberculosis diagnostics - A review

Early diagnosis and on-time effective treatment are indispensable for Tuberculosis (TB) control - a life threatening infectious communicable disease. The conventional techniques for diagnosing TB normally take two to three weeks. This delay in diagnosis and further increase in detection complexity due to the emerging risks of XDR-TB (Extensively drug Resistant-TB) and MDR-TB (Multidrug Resistant-TB) are evoking interest of researchers in the field of developing rapid TB detection techniques such as biosensing and other point-of-care (POC) techniques. Biosensing technologies along with the collaboration with nanotechnology have enormous potential to boost the MTB detection and for overall management in clinical diagnosis. A diverse range of portable, sensitive and rapid biosensors based on different signal transducer principles and with different biomarkers detection capabilities have been developed for TB detection in the early stages. Further, a lot of progress has been achieved over the years in developing various point-of-care diagnostic tools including non-molecular methods and molecular techniques. The objective of this study is to present a succinct review of the available TB detection techniques that are either in use or under development. The focus of this review is on the current developments occurred in nano-biosensing technologies. A synopsis of ameliorations in different non-molecular diagnostic tools and progress in the field of molecular techniques along with the role of emerging Lab-on-Chip technology for diagnosing and mitigating the TB consequences have also been presented.

Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments

Background

Control of the global burden of tuberculosis is obstructed due to lack of simple, rapid and cost effective diagnostic techniques that can be used in resource poor-settings.

To facilitate the early diagnosis of TB directly from clinical specimens, we have standardized and validated the use of nested multiplex PCR, targeting gene fragments IS6110, MTP40 and 32kD α-antigen encoding genes specific for Mycobacterium tuberculosis complex and non-tubercular mycobacteria (NTM), in comparison to smear microscopy, solid culture and single step multiplex PCR. The results were evaluated in comparison to a composite reference standard (CRS) comprising of microbiological results (smear and culture), clinical, radiological and cytopathological findings, clinical treatment and response to anti-tubercular therapy.

Methods

The nested multiplex PCR (nMPCR) assay was evaluated to test its utility in 600 (535 pulmonary and 65 extra-pulmonary specimens) clinically suspected TB cases. All specimens were processed for smear, culture, single step multiplex PCR and nested multiplex PCR testing.

Results

Out of 535 screened pulmonary and 65 extra-pulmonary specimens, 329 (61.5 %) and 19 (29.2 %) cases were culture positive for M. tuberculosis. Based on CRS, 450 patients had “clinical TB” (definitive-TB, probable-TB and possible-TB). Remaining 150 were confirmed “non-TB” cases. For culture, the sensitivity was low, 79.3 % for pulmonary and 54.3 % for extra-pulmonary cases. The sensitivity and specificity results for nMPCR test were evaluated taken composite reference standard as a gold standard. The sensitivity of the nMPCR assay was 97.1 % for pulmonary and 91.4 % for extra-pulmonary TB cases with specificity of 100 % and 93.3 % respectively.

Conclusion

Nested multiplex PCR using three gene primers is a rapid, reliable and highly sensitive and specific diagnostic technique for the detection and differentiation of M. tuberculosis complex from NTM genome and will be useful in diagnosing paucibacillary samples. Nested multiplex PCR assay was found to be better than single step multiplex PCR for assessing the diagnosis of TB.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1450-1) contains supplementary material, which is available to authorized users.

Fast and efficient detection of tuberculosis antigens using liposome encapsulated secretory proteins of Mycobacterium tuberculosis

PURPOSE

A rapid and efficient diagnostic test was developed for the detection of Mycobacterium tuberculosis antigens in serum samples of active tuberculosis (TB) and extrapulmonary TB patients via a liposomal agglutination-based method.

METHODS

A rapid card test has been developed to facilitate the recognition of high-affinity binding rabbit raised purified culture filtrate protein antibodies coupled on the surface of activated liposomal preparation. In the presence of TB antigens, the polyclonal antibodies bound to the liposomal particles demonstrate a visible agglutination reaction.

RESULTS

The developed assay was simple, rapid, reliable, sensitive, and specific as a diagnostic test for the detection of antigens in serum samples of clinically confirmed cases of TB within 4-5 minutes' duration. The test was evaluated at different hospitals, medical colleges, and pathology centers, and involved 1483 participants. This investigation was conducted to detect the presence of these antigens during the period of active growth of the microorganism in serum samples for pulmonary TB and processed tissue biopsy for other extrapulmonary TB. Results obtained using this test were compared with acid-fast bacilli smear and culture results.

CONCLUSION

Our study demonstrated that the newly developed liposome tuberculosis antigen card test detected antigens in our study population with approximately 97.48% sensitivity and 95.79% specificity. This is the first study to report the liposomal encapsulation of culture filtrate proteins from M. tuberculosis for diagnostic application.

Efficacy of Induced Sputum for the Diagnosis of Pulmonary Tuberculosis in Adults Unable to Expectorate Sputum

Background

Induced sputum (IS) has been used to collect airway secretions in subjects who have inadequate sputum production. The aim of this study was to investigate the efficacy of IS for the diagnosis of pulmonary tuberculosis (PTB) in adults unable to expectorate sputum.

Methods

Medical records of 39 PTB patients who underwent IS due to absence of spontaneous sputum production between January 2011 and March 2014 at a tertiary hospital in South Korea were reviewed. Results of acid fast bacilli smear, Mycobacterium tuberculosis culture and polymerase chain reaction assay for M. tuberculosis (TB-PCR) of IS specimens from these patients were analyzed. Clinical and high-resolution computed tomography (HRCT) characteristics were also analyzed to find characteristics associated with IS culture positivity.

Results

Of the 39 IS specimens from PTB patients, 7 (17.9%) were smear positive and 31 (79.5%) were culture positive. Twenty-four IS specimens were tested for TB-PCR and 13 (54.2%) were positive on TB-PCR. Multivariate analysis showed that younger age (p=0.04) and presence of tree-in-bud appearance on HRCT (p=0.03) were independent predictors of IS culture positivity.

Conclusion

IS is useful for the diagnosis of PTB in adults unable to expectorate sputum. Younger age and tree-in-bud appearance on HRCT were associated with IS culture positivity in these patients.

Diagnostic yield of sputum microbiological analysis in the diagnosis of pulmonary tuberculosis in a period of 10 years

INTRODUCTION

Pulmonary tuberculosis (TB) requires an early diagnosis for prompt introduction of treatment and prevention of transmission. Definitive diagnosis is obtained by microbiological culture and identification of Mycobacterium tuberculosis in respiratory specimens, mostly sputum samples.

MATERIALS AND METHODS

Retrospective data analysis of all patients suspected of pulmonary TB that submitted three consecutive sputum samples to the Pulmonology Diagnostic Center (PDC) Laboratory between 2004 and 2013. Extrapulmonary TB cases were excluded. Four microbiological analyses were executed on each specimen: two smears with Ziehl-Neelsen staining, direct and concentrate; and two culture examinations, one in liquid and one in solid medium. Statistical analysis was performed by SPSS.

RESULTS

A total of 694 patients were enrolled in this study (65% men, mean age 48.5±18.6 years, 97% Portuguese), most of them exhibiting TB-related complaints. Pulmonary TB was diagnosed in 41% of the patients; 54% had non-specific radiological changes and 34% had pulmonary cavitation. The cumulative sensitivity rates of each of the three smears were 24.6%, 27.7% and 28.8% for concentrated samples and 19.3%, 20.4% and 22.5% for direct samples. The cumulative sensitivities of sputum culture were 33.3%, 37.9% and 41.8% for solid medium, and 43.9%, 51.6% and 55.4% for liquid medium. Pondering all forms of microbiological analysis, the cumulative sensitivities of each sample were 51.2%, 59.6% and 63.2%. There was an incremental yield of 8.4% for the second specimen and 3.5% for the third specimen. All sensitivity rates were higher among patients with pulmonary cavitation.

CONCLUSIONS

This study showed an incremental yield with more than one sputum sample. However, overall sensitivity remained low, suggesting a need for new diagnostic strategies and novel and better diagnostic tools.

Standardization of a TaqMan-based real-time PCR for the detection of Mycobacterium tuberculosis-complex in human sputum

Real-time polymerase chain reaction (qPCR) was optimized for detecting Mycobacterium tuberculosis in sputum. Sputum was collected from patients (N = 112) with suspected pulmonary tuberculosis, tested by smear microscopy, decontaminated, and split into equal aliquots that were cultured in Löwenstein-Jensen medium and tested by qPCR for the small mobile genetic element IS6110. The human ERV3 sequence was used as an internal control. 3 of 112 (3%) qPCR failed. For the remaining 109 samples, qPCR diagnosed tuberculosis in 79 of 84 patients with culture-proven tuberculosis, and sensitivity was greater than microscopy (94% versus 76%, respectively, P < 0.05). The qPCR sensitivity was similar (P = 0.9) for smear-positive (94%, 60 of 64) and smear-negative (95%, 19 of 20) samples. The qPCR was negative for 24 of 25 of the sputa with negative microscopy and culture (diagnostic specificity 96%). The qPCR had 99.5% sensitivity and specificity for 211 quality control samples including 84 non-tuberculosis mycobacteria. The qPCR cost ∼5US$ per sample and provided same-day results compared with 2-6 weeks for culture.

Use of endo-ovarian tissue biopsy and pelvic aspirated fluid for the diagnosis of female genital tuberculosis by conventional versus molecular methods

BACKGROUND

Til date, none of the diagnostic techniques available for the detection of female genital tuberculosis (FGTB) are 100% accurate. We therefore, proposed to use the endometrial tissue biopsies (ETBs), ovarian tissue biopsies (OTBs) and pelvic aspirated fluids (PAFs) for the diagnosis of FGTB among infertile women by conventional versus molecular methods.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 302 specimens were collected both from 202 infertile women highly suspected of having FGTB on laparoscopy examination and 100 control women of reproductive age. Out of 302 specimens, 150 (49.67%) were ETBs, 95 (31.46%) were OTBs and 57 (18.87%) were PAFs. All specimens were tested by conventional techniques, later compared with multi-gene PCR for the detection of Mycobacterium tuberculosis (MTB) and correlated with laparoscopic findings. The presence of MTB DNA was observed in 49.5% of ETBs, 33.17% of OTBs and 5.44% of PAF specimens collected from highly suspected FGTB patients. All women of control group were confirmed as negative for tuberculosis. The conventional methods showed 99% to 100% specificity with a low sensitivity, ranging from 21.78% to 42.08% while hematoxylin and eosin staining showed a sensitivity of 51.48%. Multi-gene PCR was found to have much higher sensitivity of 70.29% with MTB64 gene, 86.63% with 19 kDa antigen gene at species and TRC4 element at regional MTB complex and 88.12% with 32 kDa protein gene at genus level. The specificity of multi-gene PCR was 100%. Compared with culturing and Ziehl-Neelsen's staining, multi-gene PCR demonstrated improvement in the detection of FGTB (χ2 = 214.612, 1 df, McNemar's test value <0.0001).

CONCLUSIONS SIGNIFICANCE

We suggest site specific sampling, irrespective of sample type and amplification of the 19 kDa antigen gene in combination with TRC4 element as a successful multi-gene PCR for the diagnosis of FGTB and differentiation of mycobacterial infection among endo-ovarian tissue biopsies and PAFs taken from infertile women.

Tuberculous lymphadenitis in Northern Ethiopia: in a public health and microbiological perspectives

Background

The actual burden and causative agent of tuberculous lymphadenitis (TBLN) cases is not well known due to lack of strong surveillance system and diagnostic facilities in Ethiopia. This study was conducted to determine the prevalence of TBLN, its causative agent and risk factors for acquiring this infection.

Methods

A cross-sectional study was conducted from April to May 2012 at four main hospitals and one diagnostic clinic located in northern Ethiopia. Fine needle aspirates (FNAs) from TBLN suspects were taken for acid fast bacilli (AFB) microscopy, culture and molecular typing.

Results

Among 437 aspirates, culture yielded AFB in 226 (51.7%) of cases. Sixty one culture negative cases (30.5% of 200 cases) were positive by Xpert MTB/RIF test. Moreover, a rifampicin resistant AFB was detected from culture negative cases. The overall prevalence of FNAs positive TBLN cases was 65.8 %. The BacT/AlerT 3D system proved to be a more rapid method with higher recovery rate than Lowenstein-Jensen (L-J) and/or Gottsacker media (P<0.0001). Molecular typing identified all culture positive isolates as M.tuberculosis. The main risk factors for TBLN were pediatric age (OR 2.8, 95% CI, 1.09- 7.05) and cough (OR 2, 95%CI, 1.09-3.7).

Conclusions

The results of this study revealed a high prevalence of TBLN in the study sites and that pediatric age and cough are key predictors of the disease. TBLN is an important public health problem that needs to be addressed in the area. It is important to note that MDR strains of TB could be involved and aetiological confirmation and drug sensitivity testing of TBLN isolates should be expanded. Further studies on the M.tuberculosis lineages, circulating strains and transmission dynamics, are recommended.

Rapid detection of Mycobacterium tuberculosis in clinical samples by multiplex polymerase chain reaction (mPCR)

Although the multi-copy and specific element IS6110 provides a good target for the detection of Mycobacterium tuberculosis complex by PCR techniques, the emergence of IS6110-negative strains suggested that false negative may occur if IS6110 alone is used as the target for detection. In this report, a multiplex polymerase chain reaction (mPCR) system was developed using primers derived from the insertion sequence IS6110 and an IS-like elements designated as B9 (GenBank accession no. U78639.1) to overcome the problem of detecting negative or low copy IS6110 containing strains of M. tuberculosis. The mPCR was evaluated using 346 clinical samples which included 283 sputum, 19 bronchial wash, 18 pleural fluid, 9 urine, 7 CSF, 6 pus, and 4 gastric lavage samples. Our results showed that the sensitivity (93.1 %) and specificity (89.6 %) of the mPCR system exceeds that of the conventional method of microscopy and culture. The mPCR assay provides an efficient strategy to detect and identify M. tuberculosis from clinical samples and enables prompt diagnosis when rapid identification of infecting mycobacteria is necessary.

Adenosine deaminase activity in cerebrospinal fluid and serum for the diagnosis of tuberculous meningitis

OBJECTIVE

To evaluate the usefulness of serum and CSF adenosine deaminase (ADA) activity for the diagnosis of tuberculous meningitis (TBM) from other meningitis.

METHODS

We studied CSF and serum ADA activity for 83 cases of TBM, 148 of bacterial meningitis (BM), and 262 of viral or aseptic meningitis.

RESULTS

The mean ADA activities (IU/L) in CSF and serum were higher in TBM (11.80 ± 2.50, 30.28 ± 7.30) than in other types of meningitis (8.52 ± 3.60, 17.90 ± 9.20 in BM; 5.26 ± 1.90, 8.56 ± 5.9 in viral or aseptic meningitis). When we accepted a serum ADA activity cut-off value of 15 IU/L for the differential diagnosis of TBM and non-TBM with ROC analysis, the sensitivity was 84% and specificity was 82%. Combining CSF (≥ 10) and serum (≥ 15) ADA activity significantly increased overall specificity from 92% to 97% for the diagnosis of TBM.

CONCLUSIONS

The determination of CSF and serum ADA activity is a simple and reliable test for differentiating TBM from other types of meningitis.

Multi-drug resistance tuberculosis (MDR-TB) in Kassala State, Eastern Sudan

This study investigates the prevalence of drug resistance and mutations in rpoB gene among Mycobacterium tuberculosis isolates from Kassala State, Sudan. In a cross-sectional study during 2011, sputum specimens (n = 90) were examined microscopically and grown cultures were identified by analysing IS6110 insertion sequence. Antimicrobial sensitivity and mutations in the rpoB gene were determined. Of the 90 specimens found which were positive for acid-fast bacilli (AFB), 65 (72.2%) showed growth of mycobacteria. Sixty (66.7%) of these were M. tuberculosis, 5 (5.6%) were rapidly growing mycobacteria and 10 (11.1%) revealed no growth. Of the 60 M. tuberculosis, 31 (51.7%) were drug resistant, including 18 multidrug resistant TB (30%), and 15 (83.3%) demonstrated mutations in the rpoB gene. Isoniazid and rifampicin revealed the highest resistance rates (64.5%, 61.3%, respectively). In conclusion, drug resistance M. tuberculosis in Kassala State was high (30%) and was found to be mainly (83.3%) due to mutations in the rpoB gene.

Novel multi-targeted polymerase chain reaction for diagnosis of presumed tubercular uveitis

Background

The objective of this study was to report the use of multi-targeted polymerase chain reaction (PCR) in the diagnosis of presumed tubercular uveitis. Multi-targeted PCR using three targets specific for Mycobacterium tuberculosis, i.e., IS6110, MPB64, and protein b, was performed on intraocular fluid samples of 25 subjects. Nine had presumed tubercular uveitis, six had intraocular inflammation secondary to a nontubercular etiology (disease controls), and ten had no evidence of intraocular inflammation (normal controls). As described previously, response to antitubercular therapy was considered as the gold standard.

Results

Multi-targeted PCR was positive in seven out of nine patients with presumed tubercular uveitis and negative in all normal and disease controls. The sensitivity and specificity were 77.77% and 100%, respectively. For the diagnosis of presumed tubercular uveitis, multi-targeted PCR had a positive predictive value of 100% and a negative predictive value of 88.88%.

Conclusion

Multi-targeted PCR can be a valuable tool for diagnosing presumed tubercular uveitis.

Rapid diagnosis of Mycobacterium tuberculosis with Truenat MTB: a near-care approach

Background

Control of the global Tuberculosis (TB) burden is hindered by the lack of a simple and effective diagnostic test that can be utilized in resource-limited settings.

Methods

We evaluated the performance of Truenat MTB™, a chip-based nucleic acid amplification test in the detection of Mycobacterium tuberculosis (MTB) in clinical sputum specimens from 226 patients with suspected pulmonary tuberculosis (TB). The test involved sputum processing using Trueprep-MAG™ (nanoparticle-based protocol run on a battery-operated device) and real-time PCR performed on the Truelab Uno™ analyzer (handheld, battery-operated thermal cycler). Specimens were also examined for presence of MTB using smear microscopy, liquid culture and an in-house nested PCR protocol. Results were assessed in comparison to a composite reference standard (CRS) consisting of smear and culture results, clinical treatment and follow-up, and radiology findings.

Results

Based on the CRS, 191 patients had “Clinical-TB” (Definite and Probable-TB). Of which 154 patients are already on treatment, and 37 were treatment naïve cases. Remaining 35 were confirmed “Non-TB” cases which are treatment naïve cases. The Truenat MTB test was found to have sensitivity and specificity of 91.1% (CI: 86.1–94.7) and 100% (CI: 90.0–100) respectively, in comparison to 90.58% (CI: 85.5–94.3) and 91.43% (CI: 76.9–98.2) respectively for the in-house nested PCR protocol.

Conclusion

This preliminary study shows that the Truenat MTB test allows detection of TB in approximately one hour and can be utilized in near-care settings to provide quick and accurate diagnosis.

Immunocytochemistry versus nucleic acid amplification in fine needle aspirates and tissues of extrapulmonary tuberculosis

Background:

Immunocytochemistry (ICC) is an established routine diagnostic adjunct to cytology and histology for tumor diagnosis but has received little attention for diagnosis of tuberculosis.

Aims:

To have an objective method of direct visualization of mycobacteria or their products in clinical extrapulmonary tuberculosis (EPTB) specimens, immunocytochemical localization of M. tuberculosis antigen by staining with species specific monoclonal antibody to 38-kDa antigen of Mycobacterium tuberculosis complex.

Materials and Methods:

Immunostaining with specific monoclonal antibody to 38-kDa antigen of Mycobacterium tuberculosis complex was done in fresh and archival fine needle aspirates and tissue granulomata of 302 cases of extrapulmonary tuberculosis and was compared with the molecular diagnostic i.e., nucleic amplification and conventional [Cytomorphology, Ziehl Neelsen (ZN) staining and culture] tests and 386 controls.

Results:

Diagnostic indices by Bayesian analysis for all types of archival and fresh material varied from 64 to 76% in nucleic acid amplification (NAA) and 96 to 98% in ICC. There was no significant difference in the diagnostic indices of ZN staining and/ or ICC in fresh or archival material whereas the sensitivity of NAA differed significantly in fresh versus archival material both in cytology (71.4% vs 52.1%) and histology (51.1% vs 38.8%). ICC can be easily used on archival smears and formalin-fixed paraffin-embedded tissue sections with almost equal sensitivity and specificity as with fresh material, in contrast to NAA which showed significant difference in test results on archival and fresh material.

Conclusions:

Low detection sensitivity of MTB DNA in archival material from known tuberculous cases showed the limitation of in-house NAA-based molecular diagnosis. ICC was found to be sensitive, specific and a better technique than NAA and can be used as an adjunct to conventional morphology and ZN staining for the diagnosis of EPTB in tissue granulomas.

Direct molecular detection of Mycobacterium tuberculosis complex from clinical samples - An adjunct to cultural method of laboratory diagnosis of tuberculosis

Background:

Tuberculosis, a communicable disease with significant morbidity and mortality, is the leading cause of death in the world from bacterial infectious disease. Because of its public health importance, there is need for rapid and definitive method of detecting the causative organism. Several approaches have been attempted, but the molecular methods, especially Polymerase Chain Reaction assays are the most promising for rapid detection of Mycobacterium tuberculosis complex from clinical samples.

Aim:

This study was aimed at using Polymerase Chain Reaction for detection of Mycobacterium tuberculosis complex from clinical samples using universal sample processing methodology.

Subjects and Methods:

Two hundred clinical samples sent to Tuberculosis laboratories in Ibadan and Osogbo, Nigeria, were enrolled in this study. The samples were processed by universal sample processing methodology for PCR; smear microscopy was carried out on sputum samples by Ziehl Nelseen staining technique; and cultured on Middlebrook agar medium containing oleic acid albumin dextrose complex supplement after decontamination of samples.

Results:

Ninety six (48%) samples were detected positive for M. tuberculosis complex by polymerase chain reaction using the combination of boiling and vortexing and microscopy detected 72 (36%) samples positive for acid fast bacilli. Using culture method as gold standard, it was found that polymerase chain reaction assay was more sensitive (75.5%) and specific (94.8%) than microscopy (sensitivity of 48.5% and specificity of 85.7%) in detecting M. tuberculosis complex from clinical samples. There was significant difference in detecting M. tuberculosis from clinical samples when compared to microscopy (p<0.05).

Conclusion:

The study recommends that direct molecular detection of M. tuberculosis complex is sensitive and specific and polymerase chain reaction method should be used as an adjunct to other methods of laboratory diagnosis of tuberculosis.

Detection of 123 bp fragment of insertion element IS6110 Mycobacterium tuberculosis for diagnosis of extrapulmonary tuberculosis

PURPOSE

Extrapulmonary tuberculosis (EPTB) is emerging problem in developing and developed countries. The diagnosis of EPTB in its different clinical presentations remains a true challenge. IS6110-based polymerase chain reaction (PCR) is used for rapid identification and positivity rate of the Mycobacterium tuberculosis complex in clinical isolates of different sites of EPTB. The present study was carried out to study the prevalence of M. tuberculosis complex in clinical isolates of EPTB at tertiary care centres in Lucknow.

MATERIALS AND METHODS

Seven hundred fifty-six specimens were collected from the suspected cases of EPTB which were processed for Mycobacteria by Ziehl Neelson (ZN) staining and BACTEC culture. All the specimens were also processed for IS6110-based PCR amplification with primers targeting 123 bp fragment of insertion element IS6110 of the M. tuberculosis complex.

RESULTS

Of these 756 specimens, 71(9.3%) were positive for acid fast bacilli (AFB) by ZN staining, 227(30.1%) were positive for mycobacteria by BACTEC culture and IS6110 PCR were positive for M. tuberculosis complex in 165 (20.7%) isolates. We found a significant difference in sensitivities of different tests (P<0.05).

CONCLUSIONS

This study reveals the positivity of M. tuberculosis complex in clinical isolates of EPTB case in tertiary care hospitals in Northern India. 72.7% of M. tuberculosis complex was confirmed by IS6110-PCR in culture isolates from different sites of EPTB. The high prevalence of the M. tuberculosis complex was seen in lymph node aspirate and synovial fluid. However, utility of PCR may play a potentially significant role in strengthening the diagnosis of EPTB especially targeting IS6110.

Assessment of Status of rpoB Gene in FNAC Samples of Tuberculous Lymphadenitis by Real-Time PCR

Introduction. Multidrug resistance tuberculosis (MDR TB), the combined resistance of Mycobacterium tuberculosis to isoniazid (INH) and rifampin (RFM) is a major public health problem in India as it ranks second among the MDR-TB high burden countries worldwide. WHO recommends RFM resistance as a “surrogate marker” for detecting MDR. FNAC is the most widely used noninvasive investigative technique for TB lymphadenitis. Real-time polymerase chain reaction, an extremely versatile technique can be used for the timely detection and treatment of MDR TB by assessing RFM resistance status in the FNAC samples of TB lymphadenitis. Aim. To assess the status of rpoB gene by real-time PCR in FNAC samples of TB lymphadenitis. Materials and Methods. Thirty FNAC samples from patients with persistent LAP or appearance of new LAP after 5 months or more of Anti Tubercular Treatment were assessed for status of rpoB gene by Real-Time PCR using probe covering the “hot spot resistance” region of the rpoB gene. Result. By using probe covering codons 531 and 526 of rpoB gene, we could detect 17 of 30 (56.7%) rifampin resistant isolate. The PCR could detect Mtb DNA in 100% of cases. Conclusion. Use of molecular methods like Real-Time PCR for detection of MDR-TB in FNAC samples is time saving, logical and economical approach over the culture based method.

Sample preparation of Mycobacterium tuberculosis extracts for nuclear magnetic resonance metabolomic studies

Mycobacterium tuberculosis is a major cause of mortality in human beings on a global scale. The emergence of both multi- (MDR) and extensively-(XDR) drug-resistant strains threatens to derail current disease control efforts. Thus, there is an urgent need to develop drugs and vaccines that are more effective than those currently available. The genome of M. tuberculosis has been known for more than 10 years, yet there are important gaps in our knowledge of gene function and essentiality. Many studies have since used gene expression analysis at both the transcriptomic and proteomic levels to determine the effects of drugs, oxidants, and growth conditions on the global patterns of gene expression. Ultimately, the final response of these changes is reflected in the metabolic composition of the bacterium including a few thousand small molecular weight chemicals. Comparing the metabolic profiles of wild type and mutant strains, either untreated or treated with a particular drug, can effectively allow target identification and may lead to the development of novel inhibitors with anti-tubercular activity. Likewise, the effects of two or more conditions on the metabolome can also be assessed. Nuclear magnetic resonance (NMR) is a powerful technology that is used to identify and quantify metabolic intermediates. In this protocol, procedures for the preparation of M. tuberculosis cell extracts for NMR metabolomic analysis are described. Cell cultures are grown under appropriate conditions and required Biosafety Level 3 containment, harvested, and subjected to mechanical lysis while maintaining cold temperatures to maximize preservation of metabolites. Cell lysates are recovered, filtered sterilized, and stored at ultra-low temperatures. Aliquots from these cell extracts are plated on Middlebrook 7H9 agar for colony-forming units to verify absence of viable cells. Upon two months of incubation at 37 °C, if no viable colonies are observed, samples are removed from the containment facility for downstream processing. Extracts are lyophilized, resuspended in deuterated buffer and injected in the NMR instrument, capturing spectroscopic data that is then subjected to statistical analysis. The procedures described can be applied for both one-dimensional (1D) H NMR and two-dimensional (2D) H-(13)C NMR analyses. This methodology provides more reliable small molecular weight metabolite identification and more reliable and sensitive quantitative analyses of cell extract metabolic compositions than chromatographic methods. Variations of the procedure described following the cell lysis step can also be adapted for parallel proteomic analysis.

Recent advances in the diagnosis of Mycobacterium tuberculosis

Molecular technologies offer the greatest potential for laboratories in resource-rich countries because they have the highest sensitivity and specificity. Continued use of new technologies will be crucial in elucidating the true epidemiology and pathogenesis of a disease, including the less well studied diseases. Continued development of affordable, sensitive, and specific diagnostic tools will be required for use in resource-poor settings, where the incidence of disease is highest.

Controversies and unresolved issues in tuberculosis prevention and control: a low-burden-country perspective

Despite declining incidence in most high-income countries, tuberculosis shows no signs of disappearing in the near future. Although surveillance data from most Western European countries show relatively stable declines in the rate of tuberculosis over the past several decades, some have reported either an increasing rate or a decelerating pace of reduction in recent years. The burden of disease now disproportionately affects high-risk groups such as migrants, homeless persons, and prisoners. In view of the concentration of cases in urban areas and high-risk deprived groups, interventions that may not be efficient when applied to the general population may be highly cost effective when targeted at high-risk groups. In this article, we examine some controversial elements of tuberculosis prevention and control in low-burden countries and recommend issues for further research. In particular, we assess current evidence on the duration of protection by BCG vaccine, the screening of migrants and hard-to-reach groups, and the use of preventive therapy for contacts of cases of infectious multidrug-resistant tuberculosis. This analysis is presented from the perspective of low-tuberculosis-burden, high-income countries attempting to eliminate tuberculosis.

Can tissue PCR augment the diagnostic accuracy in genitourinary tract tuberculosis?

PURPOSE

Conventional methods like smear and culture for Mycobacterium tuberculosis are of limited sensitivity and specificity. Histopathological examination (HPE) for the tissues obtained gives inconclusive diagnosis in the absence of caseous necrosis or stained acid-fast bacilli. This study was conducted to determine the utility of tissue PCR for diagnosing tuberculosis of the genitourinary tract (GUTB) and its comparative evaluation with HPE.

PATIENTS AND METHODS

A prospective study was conducted from January 2006 to August 2009 with 78 tissue specimens (renal, prostate, epididymis, penile and soft tissue) from patients with clinically suspected GUTB. All the samples were processed for both PCR and histopathology.

RESULTS

In 68 (87.1%) samples, results for both PCR and HPE were coinciding. False positivity and false negativity was observed in 5.1% (4/78) and 7.6% (6/78) samples, respectively. With HPE as the gold standard, PCR has shown sensitivity of 87.5% (95% CI 80.1; 91.9) and specificity of 86.7% (95% CI 74.9; 93.8) and positive agreement between two tests was observed as significant (0.7). PCR results were obtained within a mean period of 3.4 days while those of HPE were obtained in 7.2 days.

CONCLUSIONS

Tissue PCR is a sensitive and specific method for obtaining early and timely diagnosis of GUTB. Application of tissue PCR results can augment the diagnostic accuracy in histopathologically labelled granulomatous inflammations.

Sensitivity and specificity of immunocytochemical staining of mycobacterial antigens in the cytoplasm of cerebrospinal fluid macrophages for diagnosing tuberculous meningitis

The sensitivity and specificity of immunocytochemical staining of mycobacterial antigens in the cytoplasm of cerebrospinal fluid (CSF) macrophages for diagnosis of tuberculous meningitis (TBM) was prospectively compared with Ahuja criteria from 393 consecutive CSF specimens. The assay can play an important role for the diagnosis of TBM, with sensitivity of 73.5% and specificity of 90.7%.

Assessment of the quality of dna extracted by two techniques from Mycobacterium tuberculosis for fast molecular identification and genotyping

We report a comparative study of two DNA extraction techniques, thermolysis and chemical lysis (CTAB), for molecular identification and genotyping of M. tuberculosis. Forty DNA samples were subjected to PCR and the results demonstrated that with thermolysis it is possible to obtain useful data that enables fast identification and genotyping.

Multiplex PCR for rapid diagnosis of tuberculous meningitis

Rapid and specific diagnosis of tubercular meningitis is of paramount importance to decrease morbidity and mortality. The aim of the study was to evaluate multiplex PCR using protein b, MPB 64, and IS6110 primers directed against M. tuberculosis complex for the diagnosis of tuberculous meningitis (TBM). Multiplex PCR was performed on 18 TBM confirmed cases (culture was positive), 92 clinically suspected TBM cases and 100 non-TBM (control group) patients. Multiplex PCR had a sensitivity of 94.4% for confirmed cases and specificity of 100% for confirmed TBM cases. In 92 clinically diagnosed but unconfirmed TBM cases, multiplex PCR was positive in 84.78% cases. The overall sensitivity of microscopy, culture and multiplex cases were 1.81, 16.73, and 86.63% and specificity was 100, 100, and 100% respectively. Multiplex PCR using protein b, MPB 64, and IS6110 primers has a high sensitivity and specificity in diagnosis of tubercular meningitis.

Evaluation of Cobas TaqMan MTB PCR for detection of Mycobacterium tuberculosis

Nucleic acid-based amplification tests allow the rapid detection of Mycobacterium tuberculosis. Recently, a real-time PCR assay for M. tuberculosis complex, the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), was introduced. We performed a prospective study to evaluate the diagnostic performance of the Cobas TaqMan MTB test system. A total of 406 specimens collected from 247 patients were simultaneously tested by conventional culture, Cobas Amplicor MTB PCR, and TaqMan MTB PCR. The cross-reactivity with other Mycobacterium species and the detection limit were also evaluated. Among 406 specimens, a total of 24 specimens (5.9%) were culture positive: 14 specimens were positive by both TaqMan and Amplicor MTB PCRs, while 5 specimens were positive by only TaqMan PCR. The remaining five specimens were negative by both PCR methods. Seven specimens with negative culture results were positive by TaqMan PCR, but five of these were negative by Amplicor MTB PCR. The sensitivity, specificity, and positive (PPV) and negative (NPV) predictive values were 79.1%, 98.2%, 73.1%, and 98.7% for TaqMan and 58.3%, 99.5%, 87.5%, and 97.4% for the Amplicor MTB PCR test, respectively. There was no cross-reactivity with M. tuberculosis and nontuberculous mycobacterial species. The detection limit for the Cobas TaqMan MTB PCR test was 4.0 copies/μl. The Cobas TaqMan MTB PCR test showed higher sensitivity for detection of the M. tuberculosis complex without disturbing the specificity and NPV than the Amplicor MTB PCR test.

Severe extensive bone marrow necrosis from miliary tuberculosis without granulomas and pulmonary presentations

Bone marrow necrosis (BMN) is a rare clinicopathologic entity caused by hypoxemia after failure of the microcirculation, which frequently manifests with bone pain, fever, and peripheral cytopenia. In most reported cases of BMN resulting from miliary tuberculosis (TB), the presence of marrow granulomas, pulmonary infiltrates and/or extrapulmonary involvement is common. We report a female patient with extensive BMN from miliary TB, whose initial presentation was only severe peripheral cytopenia with extensive marrow necrosis, with neither evident pulmonary manifestations nor granulomas in the marrow biopsy. Serial Ziehl-Neelsen stains and Mycobacterium tuberculosis cultures were negative. The diagnosis of suspected miliary TB was made by consecutive positive results from polymerase chain reaction analysis for TB of marrow samples at 2 separate examination time points and a good treatment response to anti-TB therapy. Magnetic resonance imaging showed a geographic pattern of multiple signal abnormalities, indicating bone infarcts over the bilateral iliac bones and T-L-spine vertebral bodies, compatible with extensive BMN. The unusual presentation of extensive BMN with severe peripheral cytopenia in the absence of granulomas or pulmonary presentations should alert clinical physicians in epidemic areas. We discuss the use of polymerase chain reaction analysis for TB and magnetic resonance imaging for diagnosis of these patients.

Sternal osteomyelitis caused by infection with Mycobacterium tuberculosis

We report the case of a 74-year-old male patient with a one-year history of chest pain in the suprasternal notch associated with erythema, edema and drainage of purulent material from a fistulous lesion. The patient was HIV-negative with no history of TB. A CT scan of the chest showed an osteolytic lesion in the sternum, and a biopsy revealed caseous granuloma, which, in the microbiological evaluation, was negative for fungi and acid-fast bacilli. The diagnosis of sternal osteomyelitis caused by Mycobacterium tuberculosis was confirmed using PCR.

Evaluation of a simplified IS6110 PCR for the rapid diagnosis of Mycobacterium tuberculosis in an area with high tuberculosis incidence

PURPOSE

To assess the diagnostic yield of a simplified IS6110-PCR in an area with high tuberculosis incidence.

METHODS

Pulmonary (218) and extrapulmonary (121) samples were collected from 236 patients including smearpositive leprosy patients. All samples were processed to detect acidfast bacilli by microscopy, culture on solid media and PCR. To remove PCR inhibitors, three washing steps of the decontaminated pellet were included before mycobacterial cell lysis by heat treatment. No detergents, enzymes, or chelating agents were used. From the 339 samples, 34 were selected basing on their large volume and were tested by the commercial kit GenoType Mycobacteria Direct (GTMD) (VER 4, Hain Lifescience, Germany) in addition to the tests cited above.

RESULTS

The overall sensitivity and specificity of PCR were 93.8 and 98.6% for pulmonary samples, 63.6 and 100% for extrapulmonary samples, respectively. The assay detected MTC in 94.2% of smear positive samples with a positive predictive value of 100%. No inhibition was found among seven samples that were PCR negative but bacteriological confirmed as containing Mycobacterium tuberculosis. No false positive result occurred with samples from leprosy patients. The sensitivities for PCR and GTMD were 81.8 and 75%, respectively.

CONCLUSION

PCR could efficiently complement conventional bacteriological tools for the rapid diagnosis of tuberculosis but cannot replace them.

Tuberculosis of paranasal sinuses

Nasal tuberculosis is very rare but much rarer is tuberculosis of paranasal sinuses. It involves especially the maxillary sinus and is usually unilateral. We report an unusual case of tuberculosis of frontal and maxillary sinus in a 68 years old male, who presented with a swelling above left medial canthus, with no other eye or nasal complaints. Clinical and radiological findings on our initial evaluation suggested that the patient had left frontal mucocoele with bilateral maxillary haziness. Diagnosis was established on FNAC report and subsequent Ziehl - Neelsen staining of nasal swabs and tuberculin skin test. Later chest x-ray examination was suggestive of pulmonary tuberculosis, which was the primary cause. Patient responded well to antituberculosis drug therapy.

Evaluation of the IS6110 PCR assay for the rapid diagnosis of tuberculous meningitis

Background

Tuberculous meningitis (TBM) is one of the common clinical manifestations of extra-pulmonary tuberculosis. It is difficult to diagnose due to a lack of rapid, sensitive, and specific tests. Newer methods, which are easy and reliable, are required to diagnose TBM at an early stage. Thus our aim was to evaluate the polymerase chain reaction (PCR) technique, using primers directed against the IS6110 gene, for the detection of Mycobacterium tuberculosis in the CSF, for the diagnosis of TBM patients.

Methods

An in-house IS6110 PCR method using a specific pair of primers designed to amplify the insertion sequence, IS6110, in the M. tuberculosis genome was used to analyze CSF. A total of 80 CSF samples from different groups of patients were studied (confirmed TBM n = 35, clinically suspected TBM n = 16, non-TBM infectious meningitis n = 12, non infectious neurological diseases n = 17).

Results

PCR gave a sensitivity of 91.4% and specificity of 75.9% for the diagnosis of TBM in patients with TBM confirmed by culture. In 16 clinically diagnosed, but unconfirmed, TBM cases PCR was positive in 10 (62.5%) cases. There were seven (24.1%) PCR-positive cases among the 29 patients with non-TBM and non-infectious neurological disease.

Conclusion

We conclude that the performance of an in-house IS6110 PCR assay is valuable in the rapid diagnosis of tuberculous meningitis.

Eight cases of nasal tuberculosis

OBJECTIVE

To elucidate the clinical characteristics of nasal tuberculosis and to discuss its diagnostic difficulties.

STUDY DESIGN

Retrospective clinical analysis.

RESULTS

A total of eight patients presented with nasal tuberculosis during the study period (from January 1989 through December 2006). Six were female and two were male. The patient age varied from 17 to 51 years, with a mean of 31 years. The most commonly involved site was the nasal septum (7 of 8). Perforation of the nasal septum was observed in three cases. Sinus invasion was observed in two cases and required sinus surgery. Six of the cases were a result of primary infections, while two were secondary disease manifestations. All patients were treated with anti-tuberculosis medications, with subsequent improvement with regard to clinical symptoms and physical signs.

CONCLUSIONS

We present the largest number of nasal tuberculosis cases reported in the medical literature from a single institute. Diagnosing nasal tuberculosis requires a high index of suspicion and occasionally the use of experimental drug treatment options.