Molecular diagnostics in tuberculosis

Fluorescein-switching-based lateral flow assay for the detection of microRNAs

Lateral flow assays (LFAs) are a cost-effective and rapid colorimetric technology that can be effectively used for nucleic acid tests (NATs) in various fields such as medical diagnostics and biotechnology. Given their importance, developing more diverse LFAs that operate through novel working mechanisms is essential for designing highly selective and sensitive NATs and providing insights for designing various practical point-of-care testing (POCT) systems. Herein we report a new type of lateral flow assay (LFA) based on fluorescein-switching, enabled by nucleic acid-templated photooxidation of reduced fluorescein by riboflavin tetraacetate (RFTA). The LFA design leverages the fact that a reduced form of fluorescein, which weakly binds to gold nanoparticle (GNP)-conjugated anti-fluorescein antibodies, is oxidized in the presence of target nucleic acids to yield its native state, which then strongly binds to the antibodies. The study involved designing and optimizing probe sequences to detect miR-6090 and miR-141, which are significant markers for prostate cancer. To minimize background signals of LFAs, sodium borohydride (NaBH4) was specifically introduced as a reducing agent, and detailed procedures were established. The developed LFA system accurately identified low fmol levels of target microRNAs with minimal false positives, all detectable with the naked eye, making the system a promising tool for point-of-care diagnostics.

Development of the novel gene chip and restriction fragment length polymorphism (RFLP) methods for rapid detection of Mycobacterium tuberculosis complex in broth culture

BACKGROUND

Tuberculosis (TB) is a major global public health issue. Prompt and accurate TB diagnosis is crucial for starting appropriate treatments and preventing the disease's spread. Current diagnostic techniques are either slow or expensive. This study aimed to create and evaluate a new, fast, highly reliable, and cost-effective TB detection method using a gene chip and Restriction Fragment Length Polymorphism (RFLP) analysis on Mycobacteria Growth Indicator Tubes (MGIT) specimens.

METHODS

We assessed the effectiveness of a novel gene chip and RFLP methods targeting the 16S rRNA gene of Mycobacterium tuberculosis in 2000 MGIT culture-positive specimens. RFLP analysis identified the AfeI restriction site within the M. tuberculosis complex (MTBC) genome. Discrepancies were investigated through extensive sequencing and Cobas TaqMan PCR analysis, along with reviewing patient profiles.

RESULTS

Both methods showed high efficacy in detecting MTBC in broth cultures, with the gene chip method achieving a sensitivity of 99.27 %, specificity of 98.35 %, and the RFLP method showing a sensitivity of 98.18 %, specificity of 99.31 %. False negatives in two isolates were due to a mutation in the AfeI site. Additionally, five cases showed MTBC presence when nontuberculous Mycobacterium species grew in cultures.

CONCLUSION

Our novel gene chip and RFLP methods are effective for rapid highly-reliable and cost-effective M. tuberculosis detection in MGIT specimens. Both gene chip and RFLP methods are suitable for resource-limited settings, offering an economical advantage. These methods have significant potential to improve clinical TB diagnosis.

Ocular tuberculosis associated with Epstein-Barr virus myelitis: A case report

Ocular tuberculosis (OTB) is a chronic eye infection caused by Mycobacterium tuberculosis. Some cases of myelitis are associated with Epstein-Barr virus (EBV), with 1-5% of EBV infections leading to neurologic complications. We describe a 34-year-old Iranian woman with OTB and EBV coinfection. Despite initial success with anti-TB agents, the disease progressed, necessitating enucleation. Mycobacterium tuberculosis was detected by a tuberculin coagulation test, and EBV was confirmed via polymerase chain reaction. MRI showed plaques in the spinal cord and brain. The patient was treated with anti-TB and antiretroviral agents. Recognizing TB in the differential diagnosis of EBV myelitis is crucial.

Lineage classification and antitubercular drug resistance surveillance of Mycobacterium tuberculosis by whole-genome sequencing in Southern India

IMPORTANCE

Studies mapping genetic heterogeneity of clinical isolates of M. tuberculosis for determining their strain lineage and drug resistance by whole-genome sequencing are limited in high tuberculosis burden settings. We carried out whole-genome sequencing of 242 M. tuberculosis isolates from drug-sensitive and drug-resistant tuberculosis patients, identified and collected as part of the TB Portals Program, to have a comprehensive insight into the genetic diversity of M. tuberculosis in Southern India. We report several genetic variations in M. tuberculosis that may confer resistance to antitubercular drugs. Further wide-scale efforts are required to fully characterize M. tuberculosis genetic diversity at a population level in high tuberculosis burden settings for providing precise tuberculosis treatment.

Recovery rates of mycobacterium from suspected extra-pulmonary tuberculosis patients using liquid culture at a tertiary referral centre of India

Tuberculosis still remains a serious public health problem in developing countries. Rapid isolation of mycobacteria is critical for accurate diagnosis and management of tuberculosis. In the present study BACTEC MGIT 960 system was evaluated against Lowenstein Jensen (LJ) medium for isolation of mycobacteria from different extra-pulmonary specimens (N = 371). The samples were processed using NaOH-NALC method and inoculated in BACTEC MGIT and on LJ medium. The BACTEC MGIT 960 system detected 93 (25.06%) samples positive for acid fast bacilli and by LJ only 38 samples (10.24%) was positive. Furthermore, total 99 (26.68%) samples were detected positive by both the culture methods. The mean turnaround time to detection of mycobacteria by MGIT 960 were significantly less (12.4 days) as compared with LJ (22.76 days). In conclusion, BACTEC MGIT 960 system is more sensitive and rapid culture system for isolation of mycobacteria. However LJ culture method also suggested to further increase the detection rate of EPTB cases.

Point-of-care nucleic acid tests: assays and devices

The COVID-19 pandemic (caused by the SARS_CoV_2 virus) has emphasized the need for quick, easy-to-operate, reliable, and affordable diagnostic tests and devices at the Point-of-Care (POC) for homes/fields/clinics. Such tests and devices will contribute significantly to the fight against the COVID-19 pandemic and any future infectious disease epidemic. Often, academic research studies and those from industry lack knowledge of each other's developments. Here, we introduced DNA Polymerase Chain Reaction (PCR) and isothermal amplification reactions and reviewed the current commercially available POC nucleic acid diagnostic devices. In addition, we reviewed the history and the recent advancements in an effort to develop reliable, quick, portable, cost-effective, and automatic point-of-care nucleic acid diagnostic devices, from sample to result. The purpose of this paper is to bridge the gap between academia and industry and to share important knowledge on this subject.

Primary Breast Tuberculosis Concealed Behind Granulomatous Mastitis

Granulomatous mastitis is an inflammatory disease that often affects women with a history of breastfeeding. The pathogenesis is still unclear and several factors have been incriminated, such as trauma, metabolic and hormonal disorders, infections, and autoimmunity. This poses a diagnostic issue, given that there are several different diagnoses, particularly carcinomatous mastitis. We report the case of a 32-year-old woman, with a history of breastfeeding, who presented with inflammatory left breast. The physical examination has objectified a 10/10 cm painless mass and a 3 cm homolateral axillary lymphadenopathy. A sonomammography revealed inflammatory left breast infiltration with multiple collections associated with homolateral axillary lymphadenopathies. A Trucut biopsy was performed, revealing granulomatous mastitis without signs of malignancy. Interferon-gamma measurement and Koch Bacillus (BK) search by polymerase chain reaction (PCR) in the breast collection were all negative. The patient was put on non-specific antibiotics with no response and clinical worsening; therefore, we were obliged to start bacillary treatment. The evolution was marked by a total drought and the disappearance of inflammatory signs within a few weeks. Mammary tuberculosis poses a diagnostic issue given the difficulty to identify the bacteria in the samples. This is why tuberculosis should never be excluded despite negative results, especially in endemic countries.

Investigation of species distribution of nontuberculosis mycobacteria isolated from sputum samples in patients with suspected pulmonary tuberculosis

Aims

Rapid and accurate identification of mycobacteria is important for the species-specific treatment of the disease. The aim of this study was the identification at the species level of 34 nontuberculous mycobacteria strains isolated from respiratory tract samples and 14 reference strains as by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.

Materials and Methods

Isolates derived from clinical specimens were subcultured in the Lowenstein-Jensen medium. Deoxyribonucleic acid isolation was carried out using the boiling method. PCR amplification was performed using primers specific to the hsp65 gene region. The PCR products were digested BstEII and HaEIII enzymes. All samples were studied comparatively by two different centers.

Results

In our study, the most common species were found to be Mycobacterium intracellulare in 23.52% (8/34). The performance of the PCR-RFLP method in detecting mycobacteria was found to be 82.35%.

Conclusions

The PCR-RFLP method is a rapid, cheap, and practical method for the identification of mycobacteria.

Revisiting the methods for detecting Mycobacterium tuberculosis: what has the new millennium brought thus far?

Tuberculosis (TB) affects around 10 million people worldwide in 2019. Approximately 3.4 % of new TB cases are multidrug-resistant. The gold standard method for detecting Mycobacterium tuberculosis, which is the aetiological agent of TB, is still based on microbiological culture procedures, followed by species identification and drug sensitivity testing. Sputum is the most commonly obtained clinical specimen from patients with pulmonary TB. Although smear microscopy is a low-cost and widely used method, its sensitivity is 50-60 %. Thus, owing to the need to improve the performance of current microbiological tests to provide prompt treatment, different methods with varied sensitivity and specificity for TB diagnosis have been developed. Here we discuss the existing methods developed over the past 20 years, including their strengths and weaknesses. In-house and commercial methods have been shown to be promising to achieve rapid diagnosis. Combining methods for mycobacterial detection systems demonstrates a correlation of 100 %. Other assays are useful for the simultaneous detection of M. tuberculosis species and drug-related mutations. Novel approaches have also been employed to rapidly identify and quantify total mycobacteria RNA, including assessments of global gene expression measured in whole blood to identify the risk of TB. Spoligotyping, mass spectrometry and next-generation sequencing are also promising technologies; however, their cost needs to be reduced so that low- and middle-income countries can access them. Because of the large impact of M. tuberculosis infection on public health, the development of new methods in the context of well-designed and -controlled clinical trials might contribute to the improvement of TB infection control.

Menstrual Blood versus Endometrial Biopsy in Detection of Genital Tuberculosis by Using Nested Polymerase Chain Reaction in an Endemic Region

Aim

The aim of this study is to compare the results of nested polymerase chain reaction (PCR) for early detection of genital tuberculosis (GTB) using menstrual blood (MB) and endometrial tissue (ET) as samples in females presenting as infertility.

Methods

The ET and MB samples were collected from a total of 194 females, enrolled in this study. DNA isolation from samples was done using standard, phenol-chloroform method. Heat shock protein gene (hsp65/groEL2) of Mycobacterium tuberculosis was targeted and amplified, and the final products were analyzed.

Results

Overall, 126 (65%) cases of infertility were positive for M. tuberculosis complex by nested PCR. The detection rates in the two samples were statistically insignificant. The combined positivity rate of ET and MB, when compared with positivity rate in MB showed a positive predictive value, negative predictive value, and accuracy of 100%, 68.7%, and 84%, respectively. The results of nested PCR using MB as sample alone showed good agreement with the nested PCR results of the combined samples.

Conclusions

The hsp65 Nested PCR of MB can be used as a noninvasive screening test for early diagnosis of GTB.

Delays in the Diagnosis and Treatment of Tuberculous Lymphadenitis in Low-Incidence Countries: A Systematic Review

Early detection and treatment of tuberculosis (TB) is essential to achieve the goals appointed in the WHO End TB Strategy. Tuberculous lymphadenitis (TBLA) is the most common manifestation of extrapulmonary TB, but the diagnosis can be challenging in low-incidence countries due to sparse and inconsistent clinical features, resulting in delay. We aimed to summarize and discuss the current literature on patient delay, health care delay, and total delay (i.e., time to first health care contact, diagnosis, and treatment) in patients with TBLA in TB low-incidence countries. A systematic review using PubMed was conducted, searching for studies set in TB low-incidence countries (defined as <20 per 100,000 citizens) that reported on health care seeking behaviour, patient delay, health care delay, and/or total delay. Studies were categorized by type of delay and compared. We identified 11 heterogeneous studies with highly variable observations. Mean patient delay varied from 55 to 154 days (range, 14-1,461), mean health care delay from 44 to 94 days (range, 7-224) and median total delay from 77.5 to 122 days (range, 0-2,820). Evidently, more comprehensive insights into the diagnostic pathway and delay in TBLA patients are warranted.

Clinical Aspects and Principles of Management of Tuberculosis

Tuberculosis over the ages, has killed more people than any other infection has. Notwithstanding the advances in modern science, clinical diagnosis sometimes remains elusive, owing principally to the frequent paucibacillary occurrence of the disease and the slow doubling time of the organism; empiric treatment is often fraught with risks in the era of increasing drug resistance.

This chapter attempts to provide an overview of the disease, beginning with the pathogenesis and its protean clinical presentations. It also discusses the recent evolution of molecular methods that have lately provided an impetus to early diagnosis with a clear opportunity to unmask drug resistance before initiating “blind”, potentially ineffective, and sometimes harmful treatment with standard therapy.

The chapter also provides insight into tuberculosis in special situations, and discusses briefly the treatments in uncomplicated cases as well as in special situations, and in instances of drug resistance. Preventive methods including current and upcoming vaccines are mentioned.

Finally, a short discussion of the sequelae of tuberculosis—which have the potential to be confused with active disease—is presented.

Autoimmune keratitis in mycobacterium tuberculosis

Purpose

To report a case of autoimmune keratitis in a patient with mycobacterium tuberculosis (MBT).

Methods

An 84-year-old male with pulmonary tuberculosis (TB) was admitted with chronic, non-healing bilateral ulcerations of the inferior peripheral cornea associated with stromal and subconjunctival nodules.

Results

Clinical examination revealed circumscribed peripheral corneal ulceration with whitish nodules in adjacent stromal and subconjunctival tissue. Microbiological cultures of the corneal tissue were negative for MBT and other microbial pathogens; however, enzyme-linked immunosorbent assay (ELISA) of blood and corneal samples showed significantly elevated levels of IgM and IgA against MBT. In addition to systemic anti-tuberculosis therapy, the patient was treated topically with Polyspectran^® eye drops, Dexamethasone eye drops, and Bepanthen^® ointment, for 2 weeks. Both eyes showed dramatic improvement after 2 weeks.

Conclusion

The present report demonstrates that MBT is able to initiate delayed autoimmune response within the corneal tissue during an intensive phase of anti-tuberculosis treatment.

Practice Guidelines for Clinical Microbiology Laboratories: Mycobacteria

Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.

Molecular Diagnosis of Tuberculosis

Tuberculosis (TB) is one of the leading causes of adult death in the Asia-Pacific Region, including Indonesia. As an infectious disease caused by Mycobacterium tuberculosis (MTB), TB remains a major public health issue especially in developing nations due to the lack of adequate diagnostic testing facilities. Diagnosis of TB has entered an era of molecular detection that provides faster and more cost-effective methods to diagnose and confirm drug resistance in TB cases, meanwhile, diagnosis by conventional culture systems requires several weeks. New advances in the molecular detection of TB, including the faster and simpler nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have resulted in a shorter time for diagnosis and, therefore, faster TB treatments. In this review, we explored the current findings on molecular diagnosis of TB and drug-resistant TB to see how this advancement could be integrated into public health systems in order to control TB.

Performance of Mycobacterium Growth Indicator Tube BACTEC 960 with Lowenstein-Jensen method for diagnosis of Mycobacterium tuberculosis at Ethiopian National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia

BACKGROUND

Bacteriological confirmed active case detection remains the corner stone for diagnosing tuberculosis. Non-radiometric liquid culture system Mycobacterium Growth Indicator Tube with automated interface had been recommended by expert groups in addition to conventional solid culture media such as Lowenstein-Jensen. However in high burden resource limited countries advanced non-radiometric based tuberculosis diagnostic methods such as MGIT 960 is limited. Therefore we have evaluated the performance of MGIT 960 system compared to LJ for recovery of Mycobacterium complex (MTBC) from clinical specimens.

METHODS

A cross sectional study was conducted from a total of 908 samples between January 1st, 2013 to December 31st, 2014. Clinical specimens were processed following standard procedures and the final suspension was inoculated to MGIT tubes and LJ slant. Identification and confirmation of MTBC was done by ZN staining and SD Bioline test. Data was analyzed by SPSS version 20. The sensitivity, specificity, recovery rate and the average turnaround time to recover the organism was computed.

RESULTS

From a total of 908 clinical specimens processed using both LJ and BACTEC MGIT liquid culture methods the recovery rate for LJ and MGIT, for smear positive samples was 66.7% (74/111) and 87.4% (97/ 111) respectively while for smear negative samples was 13.4% (108/797) and 17.4% (139/797) for LJ and MGIT methods respectively. The overall recovery rate for MGIT is significantly higher than LJ methods [26% (236/908; vs. 20%, 182/908, P = 0.002)]. The average turnaround time for smear positive samples was 16 and 31 days for MGIT and LJ respectively. Turnaround time for smear negative samples was 20 and 36 days for MGIT and LJ respectively. The overall agreement between MGIT and LJ was fairly good with Kappa value of 0.59 (P < 0.001). In the present study the contamination rate for MGIT is higher than the LJ methods, 15 and 9.3% respectively.

CONCLUSIONS

The BACTEC MGIT liquid culture system has better MTBC recovery rate with shorter turnaround time for both smear positive and negative clinical specimens compared to Conventional LJ method. However, efforts should be made in order to reduce the high contamination rate in BACTEC MGIT system and to lesser extent to LJ methods.

Official American Thoracic Society/Infectious Diseases Society of America/Centers for Disease Control and Prevention Clinical Practice Guidelines: Diagnosis of Tuberculosis in Adults and Children

BACKGROUND

Individuals infected with Mycobacterium tuberculosis (Mtb) may develop symptoms and signs of disease (tuberculosis disease) or may have no clinical evidence of disease (latent tuberculosis infection [LTBI]). Tuberculosis disease is a leading cause of infectious disease morbidity and mortality worldwide, yet many questions related to its diagnosis remain.

METHODS

A task force supported by the American Thoracic Society, Centers for Disease Control and Prevention, and Infectious Diseases Society of America searched, selected, and synthesized relevant evidence. The evidence was then used as the basis for recommendations about the diagnosis of tuberculosis disease and LTBI in adults and children. The recommendations were formulated, written, and graded using the Grading, Recommendations, Assessment, Development and Evaluation (GRADE) approach.

RESULTS

Twenty-three evidence-based recommendations about diagnostic testing for latent tuberculosis infection, pulmonary tuberculosis, and extrapulmonary tuberculosis are provided. Six of the recommendations are strong, whereas the remaining 17 are conditional.

CONCLUSIONS

These guidelines are not intended to impose a standard of care. They provide the basis for rational decisions in the diagnosis of tuberculosis in the context of the existing evidence. No guidelines can take into account all of the often compelling unique individual clinical circumstances.

Epidemiology, Diagnosis and Management of Extra-Pulmonary Tuberculosis in a Low-Prevalence Country: A Four Year Retrospective Study in an Australian Tertiary Infectious Diseases Unit

OBJECTIVES

Extra-pulmonary tuberculosis (EPTB) is relatively neglected and increasing in incidence, in comparison to pulmonary tuberculosis (PTB) in low-burden settings. It poses particular diagnostic and management challenges. We aimed to determine the characteristics of EPTB in Western Sydney, Australia, and to conduct a quality assurance investigation of adherence to guidelines among Infectious Diseases (ID) practitioners managing EPTB cases.

METHODS

All adult EPTB cases managed by a large ID service during 01/01/2008-31/12/2011 were eligible for inclusion in the retrospective review. Data were extracted from patient medical records on demographic, diagnostic, clinical and management details, and on clinician adherence to local and international TB guidelines.

RESULTS

129 cases managed by the ID service were identified, with files available for 117. 98 cases were managed by the Respiratory service and were excluded. 98.2%(112/114) had been born in a country other than Australia. HIV status was tested or previously known in 97 people, and positive in 4 (4%). Microbiological confirmation was obtained in 68/117 (58.1%), an additional 24 had histopathological findings considered confirmatory (92/117, 78.6%), with the remainder diagnosed on clinical and/or radiological grounds. Median time to diagnosis post-migration from a high TB-burden country was 5 years (range 0-41). 95 cases were successfully treated, 11 cases defaulted, refused therapy or transferred, 2 cases relapsed and outcomes unknown or pending in 9 cases. No deaths occurred in the sample analysed. Clinician adherence to guidelines was high, but with scope for improvement in offering testing for co-infections, performing eye checks, monitoring blood glucose in patients receiving adjunctive corticosteroids, and considering drug interactions.

CONCLUSIONS

Despite excellent TB outcomes in this setting, the low proportion of cases with susceptibility data is worrying in this era of increasing drug resistance, and illustrates the diagnostic difficulties faced even in a well-resourced setting. Vigilance for EPTB needs to remain high in those moving from high prevalence countries to Australia, even decades after immigration.

[Tuberculosis and immigration]

The incidence of tuberculosis worldwide is declining. However, in Western countries this decline is slower due to the impact of immigration. Tuberculosis in the immigrant population is related to health status in the country of origin and with overcrowding and poverty conditions in the host country. Immigrants with tuberculosis are younger, have a higher prevalence of extrapulmonary forms, greater proportion of drug resistance and higher treatment default rates than those of natives. New molecular techniques not only reduce diagnostic delay time but also allow the rapid identification of resistances and improve knowledge of transmission patterns. It is necessary to implement measures to improve treatment compliance in this population group like facilitating access to health card, the use of fixed-dose combination drugs, the participation of cultural mediators and community health workers and gratuity of drugs.

Respiratory Infections in the U.S. Military: Recent Experience and Control

This comprehensive review outlines the impact of military-relevant respiratory infections, with special attention to recruit training environments, influenza pandemics in 1918 to 1919 and 2009 to 2010, and peacetime operations and conflicts in the past 25 years. Outbreaks and epidemiologic investigations of viral and bacterial infections among high-risk groups are presented, including (i) experience by recruits at training centers, (ii) impact on advanced trainees in special settings, (iii) morbidity sustained by shipboard personnel at sea, and (iv) experience of deployed personnel. Utilizing a pathogen-by-pathogen approach, we examine (i) epidemiology, (ii) impact in terms of morbidity and operational readiness, (iii) clinical presentation and outbreak potential, (iv) diagnostic modalities, (v) treatment approaches, and (vi) vaccine and other control measures. We also outline military-specific initiatives in (i) surveillance, (ii) vaccine development and policy, (iii) novel influenza and coronavirus diagnostic test development and surveillance methods, (iv) influenza virus transmission and severity prediction modeling efforts, and (v) evaluation and implementation of nonvaccine, nonpharmacologic interventions.

Breast Tuberculosis

Tuberculosis affects over a billion people worldwide. There is a raise in incidence of extrapulmonary tuberculosis in recent years. Mammary tuberculosis has been estimated to be 0.1 % of breast lesions examined histologically, and it constitutes about 3-4.5 % of surgically treated breast diseases in developing countries. Breast tuberculosis is paucibacillary and routine diagnostic tests such as microscopy, culture, and nucleic acid amplification tests such as polymerase chain reaction techniques do not have the same diagnostic utility as they do in pulmonary tuberculosis. Also, the histology resembles various other granulomatous mastitis. The coexistence of carcinoma and breast tuberculosis adds challenge to diagnosis. Correct diagnosis of tuberculous mastitis is important as the treatment of differential disease varies from steroid to surgery which can have devastating consequences in patients suffering from breast tuberculosis.

Comparison of AdvanSure TB/NTM PCR and COBAS TaqMan MTB PCR for Detection of Mycobacterium tuberculosis Complex in Routine Clinical Practice

The AdvanSure tuberculosis/non-tuberculous mycobacterium (TB/NTM) PCR (LG Life Science, Korea) and COBAS TaqMan Mycobacterium tuberculosis (MTB) PCR (Roche Diagnostics, USA) are commonly used in clinical microbiology laboratories. We aimed to evaluate these two commercial real-time PCR assays for detection of MTB in a large set of clinical samples over a two-year period. AdvanSure TB/NTM PCR and COBAS TaqMan MTB PCR were performed on 9,119 (75.2%) and 3,010 (24.8%) of 12,129 (9,728 respiratory and 2,401 non-respiratory) MTB specimens, with 361 (4.0%) and 102 (3.4%) acid-fast bacilli (AFB)-positive results, respectively. In MTB culture, 788 (6.5%) MTB and 514 (4.2%) NTM were identified. The total sensitivity and specificity of the AdvanSure assay were 67.8% (95% confidence interval [CI], 63.9-71.6) and 98.3% (95% CI, 98.0-98.6), while those of the COBAS TaqMan assay were 67.2% (95% CI, 60.0-73.8) and 98.4% (95% CI, 97.9-98.9), respectively. The sensitivities and specificities of the AdvanSure and COBAS TaqMan assays for AFB-positive and AFB-negative samples were comparable. Furthermore, the AdvanSure assay showed fewer invalid results compared with the COBAS TaqMan assay (5.0 vs. 20.4 invalid results/1,000 tests, P<0.001). AdvanSure assay represents a comparable yet more reliable method than COBAS TaqMan for the identification of mycobacteria in routine clinical microbiology.

Detection of Mycobacterium tuberculosis complex by nested polymerase chain reaction in pulmonary and extrapulmonary specimens

OBJECTIVE:

To compare the performance of nested polymerase chain reaction (NPCR) with that of cultures in the detection of the Mycobacterium tuberculosis complex in pulmonary and extrapulmonary specimens.

METHODS:

We analyzed 20 and 78 pulmonary and extrapulmonary specimens, respectively, of 67 hospitalized patients suspected of having tuberculosis. An automated microbial system was used for the identification of Mycobacterium spp. cultures, and M. tuberculosis IS6110 was used as the target sequence in the NPCR. The kappa statistic was used in order to assess the level of agreement among the results.

RESULTS:

Among the 67 patients, 6 and 5, respectively, were diagnosed with pulmonary and extrapulmonary tuberculosis, and the NPCR was positive in all of the cases. Among the 98 clinical specimens, smear microscopy, culture, and NPCR were positive in 6.00%, 8.16%, and 13.26%, respectively. Comparing the results of NPCR with those of cultures (the gold standard), we found that NPCR had a sensitivity and specificity of 100% and 83%, respectively, in pulmonary specimens, compared with 83% and 96%, respectively, in extrapulmonary specimens, with good concordance between the tests (kappa, 0.50 and 0.6867, respectively).

CONCLUSIONS:

Although NPCR proved to be a very useful tool for the detection of M. tuberculosis complex, clinical, epidemiological, and other laboratory data should also be considered in the diagnosis and treatment of pulmonary and extrapulmonary tuberculosis.

Evaluation of in-house loop-mediated isothermal amplification (LAMP) assay for rapid diagnosis of M. tuberculosis in pulmonary specimens

BACKGROUND

Loop-mediated isothermal amplification (LAMP) assay has come forward as a rapid, cost-effective molecular technique for diagnosis of tuberculosis (TB) in developing countries. This study evaluated Mycobacterium tuberculosis-specific in-house LAMP assay targeting 16s rRNA and compared it with other conventional tests and nucleic acid amplification assay (IS6110 PCR).

METHODS

A total of 133 sputum specimens (103 from suspected pulmonary TB cases and 30 from non-TB controls) were subjected to conventional tests, IS6110 PCR and 16s rRNA LAMP assay.

RESULTS

Of the 103 patients, the maximum number of cases were found to be positive by LAMP assay, that is, in 87 (84.5%) patients, followed by culture positive in 78 (75.7%), IS6110 PCR in 74 (71.8%), and smear positive in 70 (67.9%) patients. Of the 83 smear positive and/or culture positive cases, LAMP detected 77 (92.77%) cases, and was found to be superior to IS6110 PCR, which could detect 69 (83.1%) cases; a concordance of 0.6 was obtained between the two tests using kappa statistics.

CONCLUSION

Overall, LAMP was simple and efficacious for early diagnosis of smear positive, culture positive cases as well as for confirmation of smear negative, culture negative cases, and was found to be superior to IS6110 PCR.

Molecular methods for detection of invasive fungal infections and mycobacteria and their clinical significance in hematopoietic stem cell transplantation

Infection remains an important source of morbidity and mortality in patients who undergo hematopoietic stem cell transplantation (HSCT). In the immune reconstitution period after transplantation, HSCT recipients are most likely to have bacterial or fungal infections. Invasive fungal infections (IFIs) and mycobacterial infections (MBIs) are among the complications of HSCT, with high morbidity and mortality rates. Early diagnosis of both is crucial in order to manipulate the disease and to avoid fulminant outcomes. This chapter reviews the current knowledge on the molecular diagnosis of IFIs and MBIs in HSCT recipients, describing two different polymerase chain reaction (PCR)-based methods, one commercial (qPCR, Roche) and one in-house IS6110-based protocol.

Tuberculosis of the genitourinary system-Urinary tract tuberculosis: Renal tuberculosis-Part II

This article reviews the computed tomography and magnetic resonance imaging (MRI) features of renal tuberculosis (TB), including TB in transplant recipients and immunocompromised patients. Multi detector computed tomography (MDCT) forms the mainstay of cross-sectional imaging in renal TB. It can easily identify calcification, renal scars, mass lesions, and urothelial thickening. The combination of uneven caliectasis, with urothelial thickening and lack of pelvic dilatation, can also be demonstrated on MDCT. MRI is a sensitive modality for demonstration of features of renal TB, including tissue edema, asymmetric perinephric fat stranding, and thickening of Gerota's fascia, all of which may be clues to focal pyelonephritis of tuberculous origin. Diffusion-weighted MR imaging with apparent diffusion coefficient (ADC) values may help in differentiating hydronephrosis from pyonephrosis. ADC values also have the potential to serve as a sensitive non-invasive biomarker of renal fibrosis. Immunocompromised patients are at increased risk of renal TB. In transplant patients, renal TB, including tuberculous interstitial nephritis, is an important cause of graft dysfunction. Renal TB in patients with HIV more often shows greater parenchymal affection, with poorly formed granulomas and relatively less frequent findings of caseation and stenosis. Atypical mycobacterial infections are also more common in immunocompromised patients.

Amplified Mycobacterium tuberculosis direct test for diagnosing tuberculous pleurisy--a diagnostic accuracy study

BACKGROUND

The study was designed to investigate the clinical usefulness of Amplified Mycobacterium Tuberculosis Direct (AMTD) tests for diagnosing TB pleurisy.

METHODS

One hundred and fifty-two patients for whom the exclusion of tuberculous pleural effusion was necessary were retrospectively analyzed.

RESULTS

The sensitivity of AMTD in diagnosing pleural TB was 36.4% (20 of 55). Combining sputum and pleural effusion AFB smear, pleural biopsy, and AMTD test of pleural effusion increased sensitivity to 82.5% (33/40). There were significantly higher percentages of neutrophils in the pleural effusion in the positive than in the negative AMTD group (38.0 ± 6.7% vs. 11.1 ± 3.7%, p<0.001). Patients with symptom duration <18 days prior to pleural effusion studies had more positive AMTD tests than those with symptom >18 days (70% vs. 31.4%; OR 5.09; 95% CI 1.54-16.79; p = 0.011).

CONCLUSIONS

Combining AMTD tests with conventional diagnostic methods offer good sensitivity for pleural TB diagnosis. Patients in the early course of the disease are better candidates for AMTD tests.

Detection of IS6110 and HupB gene sequences of Mycobacterium tuberculosis and bovis in the aortic tissue of patients with Takayasu's arteritis

BACKGROUND

Takayasu's arteritis (TA) is a chronic inflammatory disease affecting the large arteries and their branches; its etiology is still unknown. In individuals suffering from TA, arterial inflammation progresses to stenosis and/or occlusion, leading to organ damage and affecting survival. Relation of TA with Mycobacterium tuberculosis has been known, but there have been only a few systematic studies focusing on this association. The IS6110 sequence identifies the Mycobacterium tuberculosis complex and the HupB establishes the differences between M. tuberculosis and M. bovis. Our objective was to search the presence of IS6110 and HupB genes in aorta of patients with TA.

METHODS

We analyzed aorta tissues embedded in paraffin from 5760 autopsies obtained from our institution, we divided the selected samples as cases and controls;

CASES

aortic tissues of individuals with Takayasu's arteritis. Control positive: aortic tissues (with tuberculosis disease confirmed) and control negative with other disease aortic (atherosclerosis).

RESULTS

Of 181 selected aorta tissues, 119 fulfilled the corresponding criteria for TA, TB or atherosclerosis. Thus 33 corresponded to TA, 33 to tuberculosis (TB) and 53 to atherosclerosis. The mean age was 22 ± 13, 41 ± 19, and 57 ± 10, respectively. IS6110 and HupB sequences were detected in 70% of TA tissues, 82% in tuberculosis, and in 32% with atherosclerosis. Important statistical differences between groups with TA, tuberculosis versus atherosclerosis (p = 0.004 and 0.0001, respectively) were found.

CONCLUSION

We identified a higher frequency of IS6110 and HupB genes in aortic tissues of TA patients. This data suggests that arterial damage could occur due to previous infection with M. tuberculosis.

Diagnosis of extrapulmonary tuberculosis by PCR

During the last two decades, the resurgence of tuberculosis (TB) has been documented in both developed and developing nations, and much of this increase in TB burden coincided with human immunodeficiency virus (HIV) epidemics. Since then, the disease pattern has changed with a higher incidence of extrapulmonary tuberculosis (EPTB) as well as disseminated TB. EPTB cases include TB lymphadenitis, pleural TB, TB meningitis, osteoarticular TB, genitourinary TB, abdominal TB, cutaneous TB, ocular TB, TB pericarditis and breast TB, although any organ can be involved. Diagnosis of EPTB can be baffling, compelling a high index of suspicion owing to paucibacillary load in the biological specimens. A negative smear for acid-fast bacilli, lack of granulomas on histopathology and failure to culture Mycobacterium tuberculosis do not exclude the diagnosis of EPTB. Novel diagnostic modalities such as nucleic acid amplification (NAA) can be useful in varied forms of EPTB. This review is primarily focused on the diagnosis of several clinical forms of EPTB by polymerase chain reaction (PCR) using different gene targets.

Evaluation of real-time polymerase chain reaction for detection of the 16S ribosomal RNA gene of Mycobacterium tuberculosis and the diagnosis of cervical tuberculous lymphadenitis in a country with a high tuberculosis incidence

BACKGROUND

Tuberculous lymphadenitis (TBL) is the most common form of extrapulmonary tuberculosis. Currently, the standard diagnostic test for TBL is culture, which takes more than several weeks to yield results. We studied a real-time polymerase chain reaction (PCR) for rapid detection of Mycobacterium tuberculosis in cervical lymph node specimens obtained from patients in a country where the tuberculosis incidence is high.

METHODS

Patients with cervical lymphadenopathy were prospectively enrolled between April 2009 and March 2010. Clinical specimens obtained through fine-needle aspiration (FNA) and excisional biopsy were tested for M. tuberculosis by the COBAS TaqMan MTB Test, a real-time PCR assay for detecting the 16S ribosomal RNA gene of M. tuberculosis. Mycobacterial culture and histopathological findings from tissue biopsy specimens were used as a reference standard for sensitivity and specificity calculations.

RESULTS

Of 73 patients, 41 received a diagnosis of TBL. For biopsy specimens, the sensitivity of real-time PCR was 63.4%, and the specificity was 96.9%. For FNA specimens, the sensitivity was 17.1%, and the specificity was 100%. The sensitivity of real-time PCR of biopsy specimens was comparable to that of tissue culture but significant lower than that of histopathological examination (P < .01).

CONCLUSIONS

Real-time PCR did not increase the yield for rapid diagnosis of TBL.

Rapid and effective diagnosis of tuberculosis and rifampicin resistance with Xpert MTB/RIF assay: a meta-analysis

OBJECTIVES

Xpert MTB/RIF (Cepheid) assay has been introduced for the diagnosis of tuberculosis (TB) and RIF-resistance. The meta-analysis was used to establish the overall accuracy of Xpert MTB/RIF assay for diagnosing TB and RIF-resistance.

METHODS

Based on comprehensive searches of the Pubmed and Embase, we identified outcome data from all articles estimating diagnostic accuracy with Xpert MTB/RIF assay. A summary estimation for sensitivity, specificity, diagnostic odds ratios (DOR) and the area under the summary ROC curve (AUC) was calculated by using the bivariate random-effects approach.

RESULTS

The meta-analysis included 18 studies (10,224 suspected specimens). The summary estimate was 90.4% (95%CI 89.2%-91.4%) for sensitivity, 98.4% (95%CI 98.0%-98.7%) for specificity and 328.3/0.9822 for DOR/AUC in pulmonary tuberculosis (PTB). The sensitivity, specificity and DOR/AUC of detecting RIF-resistance were 94.1%, 97.0% and 177.8/0.9832, respectively. For extrapulmonary tuberculosis, the overall pooled sensitivity was 80.4% and specificity was 86.1%. The findings in subgroup analysis were as follows: the accuracy of Xpert MTB/RIF assay is higher in smear-positive specimens and the sensitivity of diagnosing PTB in adults was higher than that in children (90.8% versus 74.3%).

CONCLUSIONS

TB and RIF-resistance can be rapidly and effectively diagnosed with Xpert MTB/RIF assay.

Brain tuberculoma (Mycobacterium africanum): high index of suspicion helps in avoiding biopsy/surgery

Partial seizures can be due to a growing cerebral lesion, which may be tumoral or inflammatory/infectious in nature. The differential diagnosis is obviously important; increasing immigration to Europe from Africa is leading to an increase of infectious disease involving also the central nervous system. The authors report imaging the a case of a brain tuberculoma due to Mycobacterium africanum mimicking brain tumor, in which diagnosis was possible by inoculum in guinea-pig of material obtained by mediastinal biopsy of enlarged lymph nodes. Specific treatment led to marked reduction in the size of the brain lesion.

Three cases of primary inoculation tuberculosis as a result of illegal acupuncture

Primary inoculation tuberculosis results from the direct inoculation of Mycobacterium tuberculosis into the skin of a person who has no natural or artificially acquired immunity to the organism. The pathogenesis requires a break in the skin from an abrasion or injury that allows entry of the tubercle bacilli. We report 3 cases of primary inoculation tuberculosis resulting from illegal acupuncture. Three patients over 70 years old presented with erythematous, ulcerative, indurated plaques on the back. Skin lesions had developed at the acupuncture sites 1 or 2 weeks after a session of acupuncture, which was intended to relieve back pain. An unlicensed, non-medically trained person conducted each session. The patients' past medical and family histories were unremarkable. Granulomatous inflammatory infiltration and acid-fast bacilli were observed histologically. M. tuberculosis was identified by mycobacterial culture and polymerase chain reaction. Nine months after the initiation of antituberculosis medication, skin lesions improved, and no evidence of recurrence or other organ involvement was observed at the 1-year follow-up visit.

Fluorescent nanoparticle-based indirect immunofluorescence microscopy for detection of Mycobacterium tuberculosis

A method of fluorescent nanoparticle-based indirect immunofluorescence microscopy (FNP-IIFM) was developed for the rapid detection of Mycobacterium tuberculosis. An anti-Mycobacterium tuberculosis antibody was used as primary antibody to recognize Mycobacterium tuberculosis, and then an antibody binding protein (Protein A) labeled with Tris(2,2-bipyridyl)dichlororuthenium(II) hexahydrate (RuBpy)-doped silica nanoparticles was used to generate fluorescent signal for microscopic examination. Prior to the detection, Protein A was immobilized on RuBpy-doped silica nanoparticles with a coverage of ∼5.1×102 molecules/nanoparticle. With this method, Mycobacterium tuberculosis in bacterial mixture as well as in spiked sputum was detected. The use of the fluorescent nanoparticles reveals amplified signal intensity and higher photostability than the direct use of conventional fluorescent dye as label. Our preliminary studies have demonstrated the potential application of the FNP-IIFM method for rapid detection of Mycobacterium tuberculosis in clinical samples.

Multicenter evaluation of a transcription-reverse transcription concerted assay for rapid detection of mycobacterium tuberculosis complex in clinical specimens

A European multicenter study was performed to evaluate the performance of a new method, based on the transcription-reverse transcription concerted reaction (TRC-2), which enabled one-step amplification and real-time detection of the Mycobacterium tuberculosis 16S rRNA target directly in clinical specimens. A total of 633 respiratory and nonrespiratory specimens were tested, and the results were compared with those from smears and cultures. A total of 129 patients (Paris center) were followed up in order to evaluate the clinical performance of TRC-2. By using M. tuberculosis complex strains to inoculate sterile sputa, the detection limit of TRC-2 was found to be 30 to 50 CFU/ml. A total of 548 respiratory specimens and 59 extrapulmonary specimens were assessable. For pulmonary specimens, the sensitivities of TRC-2 and acid-fast smear were 86.8% and 50.4%, respectively (P = 0.002). The specificities were 97.5% and 100%, respectively. For extrapulmonary specimens, the sensitivities of TRC-2 and acid-fast smear were 83.3% and 8.3% (P < 0.0001), and the specificities were 95.8% and 100%, respectively. Fifteen of 129 patients were diagnosed with pulmonary tuberculosis (TB). The sensitivities of culture and TRC-2 were 80% (12/15) and 86.7% (13/15) (P = 0.16), and the specificities were 100% and 93.9%, respectively. Based on an 11.6% incidence of TB in our population, the positive predictive values of TRC-2 and culture were 81.3% and 100%, respectively, and the negative predictive values were 98.2% and 97.4%, respectively. These results demonstrated that detection of M. tuberculosis complex in clinical specimens by TRC-2 with ready-to-use reagents was an efficient and rapid method for the diagnosis of pulmonary and extrapulmonary TB.

Rapid diagnosis of tuberculosis directly from clinical specimens using a gene chip

The aim of this study was to explore a gene chip capable of detecting the presence of Mycobacterium tuberculosis isolates directly in clinical sputum specimens and to compare it with current molecular detection techniques. At first, we selected 13 M. tuberculosis-specific target genes to construct a gene chip for rapid diagnosis. Using the membrane array method, we diagnosed M. tuberculosis by gene chip directly from 246 sputum specimens from patients suspected of having tuberculosis. Among 80 M. tuberculosis complex (MTBC) culture-positive sputum specimens, the MTBC detection rate was 62.5% (50/80) by PCR-restriction fragment length polymorphism (RFLP), 70% (56/80) by acid-fast staining, and 85% (68/80) by the membrane array method. Furthermore, subspecies showed different gene expression patterns in the membrane array. In conclusion, MTBC could be detected directly in sputum by the membrane array method. The rapidity of detection and the capability of differentiating subspecies could make this method useful in the control and prevention of tuberculosis.

Recent advances in the diagnosis and treatment of multidrug-resistant tuberculosis

Tuberculosis (TB) is a major infectious disease killing nearly two million people, mostly in developing countries, every year. The increasing incidence of resistance of Mycobacterium tuberculosis strains to the most-effective (first-line) anti-TB drugs is a major factor contributing to the current TB epidemic. Drug-resistant strains have evolved mainly due to incomplete or improper treatment of TB patients. Resistance of M. tuberculosis to anti-TB drugs is caused by chromosomal mutations in genes encoding drug targets. Multidrug-resistant (resistant at least to rifampin and isoniazid) strains of M. tuberculosis (MDR-TB) evolve due to sequential accumulation of mutations in target genes. Emergence and spreading of MDR-TB strains is hampering efforts for the control and management of TB. The MDR-TB is also threatening World Health Organization's target of tuberculosis elimination by 2050. Proper management of MDR-TB relies on early recognition of such patients. Several diagnostic methods, both phenotypic and molecular, have been developed recently for rapid identification of MDR-TB strains from suspected patients and some are also suitable for resource-poor countries. Once identified, successful treatment of MDR-TB requires therapy with several effective drugs some of which are highly toxic, less efficacious and expensive. Minimum treatment duration of 18-24 months is also long, making it difficult for health care providers to ensure adherence to treatment. Successful treatment has been achieved by supervised therapy with appropriate drugs at institutions equipped with facilities for culture, drug susceptibility testing of MDR-TB strains to second-line drugs and regular monitoring of patients for adverse drug reactions and bacteriological and clinical improvement.

Early diagnosis of extrapulmonary tuberculosis by a new procedure combining broth culture and PCR

The diagnosis of extrapulmonary tuberculosis is difficult because of the paucibacillary nature of these infections. We developed a culture-enhanced PCR assay combining a preliminary step of broth culture in BacT/Alert MP bottles with the subsequent detection of Mycobacterium tuberculosis using the GenoType Mycobacteria Direct test. First, the procedure was applied to 10-fold-diluted suspensions of M. tuberculosis prepared in vitro. These experiments showed that a 15-day incubation time was required to detect bacilli in the suspension, with the lowest inoculum size yielding a single colony on Lowenstein-Jensen slants. The efficacy of culture-enhanced PCR at day 15 was subsequently evaluated with 225 nonrespiratory specimens from 189 patients with suspected tuberculosis. All these specimens were smear negative, and 31 (13.8%) from 27 patients were culture positive. The result of culture-enhanced PCR at day 15 was consistent with final culture results in all specimens tested. Compared to culture results, the sensitivity, specificity, positive predictive value, and negative predictive value were 100%. Four patients with a negative culture and a negative PCR result were diagnosed as having tuberculosis on the basis of histological findings or therapeutic response. When using a positive diagnosis of tuberculosis as a gold standard, the sensitivity, specificity, positive predictive value, and negative predictive value were 88.6%, 100%, 100%, and 97.9%, respectively. These results indicate that culture-enhanced PCR is a highly sensitive and specific method for the early detection of M. tuberculosis in extrapulmonary specimens.

Molecular analysis of Mycobacterium isolates from extrapulmonary specimens obtained from patients in Mexico

Background

Little information is available on the molecular epidemiology in Mexico of Mycobacterium species infecting extrapulmonary sites in humans. This study used molecular methods to determine the Mycobacterium species present in tissues and body fluids in specimens obtained from patients in Mexico with extrapulmonary disease.

Methods

Bacterial or tissue specimens from patients with clinical or histological diagnosis of extrapulmonary tuberculosis were studied. DNA extracts from 30 bacterial cultures grown in Löwenstein Jensen medium and 42 paraffin-embedded tissues were prepared. Bacteria were cultured from urine, cerebrospinal fluid, pericardial fluid, gastric aspirate, or synovial fluid samples. Tissues samples were from lymph nodes, skin, brain, vagina, and peritoneum. The DNA extracts were analyzed by PCR and by line probe assay (INNO-LiPA MYCOBACTERIA v2. Innogenetics NV, Gent, Belgium) in order to identify the Mycobacterium species present. DNA samples positive for M. tuberculosis complex were further analyzed by PCR and line probe assay (INNO-LiPA Rif.TB, Innogenetics NV, Gent, Belgium) to detect mutations in the rpoB gene associated with rifampicin resistance.

Results

Of the 72 DNA extracts, 26 (36.1%) and 23 (31.9%) tested positive for Mycobacterium species by PCR or line probe assay, respectively. In tissues, M. tuberculosis complex and M. genus were found in lymph nodes, and M. genus was found in brain and vagina specimens. In body fluids, M. tuberculosis complex was found in synovial fluid. M. gordonae, M. smegmatis, M. kansasii, M. genus, M. fortuitum/M. peregrinum complex and M. tuberculosis complex were found in urine. M. chelonae/M. abscessus was found in pericardial fluid and M. kansasii was found in gastric aspirate. Two of M. tuberculosis complex isolates were also PCR and LiPA positive for the rpoB gene. These two isolates were from lymph nodes and were sensitive to rifampicin.

Conclusion

1) We describe the Mycobacterium species diversity in specimens derived from extrapulmonary sites in symptomatic patients in Mexico; 2) Nontuberculous mycobacteria were found in a considerable number of patients; 3) Genotypic rifampicin resistance in M. tuberculosis complex infections in lymph nodes was not found.