Utility of multiplex real-time PCR in the diagnosis of extrapulmonary tuberculosis

Nanopore-based targeted next-generation sequencing of tissue samples for tuberculosis diagnosis

Objective

Diagnosing tuberculosis (TB) can be particularly challenging in the absence of sputum for pulmonary tuberculosis cases and extrapulmonary TB (EPTB). This study evaluated the utility of nanopore-based targeted next-generation sequencing (tNGS) for diagnosing TB in tissue samples, and compared its efficacy with other established diagnostic methods.

Methods

A total of 110 tissue samples from clinical cases were examined. The sensitivity and specificity of tNGS were benchmarked against a range of existing diagnostic approaches including hematoxylin and eosin (HE) staining in conjunction with acid-fast bacilli (AFB) detection, HE staining combined with PCR, HE staining paired with immunohistochemistry (IHC) using anti-MPT64, and the Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF) assay.

Results

The sensitivity and specificity of tNGS were 88.2 and 94.1%, respectively. The respective sensitivities for HE staining combined with AFB, HE staining combined with PCR, HE staining combined with IHC using anti-MPT64, and Xpert MTB/RIF were 30.1, 49.5, 47.3, and 59.1%. The specificities for these methods were 82.4, 88.2, 94.1, and 94.1%, respectively. Analysis of drug resistance based on tNGS results indicated that 10 of 93 TB patients (10.75%) had potential drug resistance.

Conclusion

Targeted next-generation sequencing achieved higher accuracy than other established diagnostic methods, and can play a crucial role in the rapid and accurate diagnosis of TB, including drug-resistant TB.

Diagnosis of extra pulmonary tuberculosis: An update on novel diagnostic approaches

Tuberculosis (TB) remains a major global public health problem worldwide. Though Pulmonary TB (PTB) is mostly discussed, one in five cases of TB present are extrapulmonary TB (EPTB) that manifests conspicuous diagnostic and management challenges with respect to the site of infection. The diagnosis of EPTB is often delayed or even missed due to insidious clinical presentation, pauci-bacillary nature of the disease, and lack of laboratory facilities in the resource limited settings. Culture, the classical gold standard for the diagnosis of tuberculosis, suffers from increased technical and logistical constraints in EPTB cases. Other than culture, several other tests are available but their feasibility and effciacy for the detection of EPTB is still the matter of interest. We need more specific and precise test/s for the various forms of EPTB diagnosis which can easily be applied in the routine TB control program is required. A test that can contribute remarkably towards improving EPTB case detection reducing the morbidity and mortality is the utmost requirement. In this review we described the scenario of molecular and other noval methods available for laboratory diagnosis of EPTB, and also discussed the challenges linked with each diagnostic method. This review will make the readers aware of new emerging diagnostic techniques in the field of EPTB diagnosis. They can make an informed decision to choose the appropriate one according to the test availability, their clinical settings and financial considerations.

Agreement Test of Histopathology in the Diagnosis of Extrapulmonary Tuberculosis with Gold Standard Polymerase Chain Reaction Technique: A Step to Overcome False Diagnosis

BACKGROUND: Tuberculosis (TB) is global health problem which is caused by Mycobacterium tuberculosis (M. tuberculosis) bacteria. One-quarter of the world’s populations is infected by M. tuberculosis and only 10–15% of those develop the disease, while the remaining 85–95% of the population are carrying the bacteria and cannot transmit the disease to the others. M. tuberculosis bacteria affects the lungs, but any organ in the body can be affected by the bacteria. About 15% of M. tuberculosis infections are of in the extrapulmonary type. The diagnosis of extrapulmonary TB (EPTB) is very challenging because most sites are inaccessible and paucibacillary nature of the bacteria in these sites. The need for rapid and more sensitive and specific tests for the diagnosis of EPTB in comparison to culture and histopathology is increasing. The molecular methods for the detection of M. tuberculosis gene(s) in the provided sample are now promising. PATIENT AND METHODS: A cross-sectional descriptive study at AL-Kindy Teaching Hospital at Al-Resaffa part of Baghdad city, Iraq. Data collection has been done in three months duration (July, August, and September) 2015. A total of 74 formalin-fixed paraffin-embedded samples from suspected EPTB cases was collected, both Polymerase Chain reaction test for M. tuberculosis and histopathological examination was done for each sample. RESULTS: A total of 74 patients (18 males, 56 females), mean age 29.72 suspected to had extrapulmonary TB underwent biopsies from different tissue types. The biopsies from the 74 patients were taken from different tissues according to the site of lesion, 49 (66.2%) biopsies were taken from lymph node, 12 biopsies (16.2%) was taken from mass in the axilla, 6 (8.1%) from abscess, 4 (5.4%) from the intestine, 3 (4.1%) from fistula. Of the 74 studied patients 57 (77%) showed positive polymerase chain reaction (PCR) and 17 (23%) showed negative PCR results. Regarding to the histopathological reports of the biopsies, there were 54 (73%) patients had positive histopathological (granuloma) result and 20 (27%) patients had negative results (nongranuloma). The sensitivity of histopathological examination of the biopsies was 91.02%, the specificity 88.2%, and the kappa was 0.748 (p = 0.00) which is mean good agreement between histopathological examination of the biopsies and the polymerase chain reaction test. CONCLUSIONS: The sensitivity, specificity, and the positive predictive value of histopathology examination of biopsies were 91.02%, 88.2%, and 96%, respectively. The kappa was 0.748 (p = 0.00) which is mean good agreement between histopathological examination of the biopsies and the polymerase chain reaction test.

Molecular detection of Mycobacterium tuberculosis in pulmonary and extrapulmonary samples in a hospital-based study

OBJECTIVE

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a deadly infectious disease. India contributes to one-third of the global TB burden. However, no studies have been carried out in the Telangana (Hyderabad) population using real-time polymerase chain reaction (RT-PCR). Therefore, the current study evaluated the role of RT-PCR as a rapid and non-invasive test to diagnose TB by testing for pulmonary tuberculosis (PTB) and extrapulmonary tuberculosis (EPTB).

MATERIALS AND METHODS

This hospital-based study examined 1670 samples (900 EPTB; 770 PTB) comprising tissue (n = 537), peritoneal fluid (n = 420), sputum (n = 166), bronchial fluid (n = 126), cerebrospinal fluid (n = 145), ascetic fluid (n = 76), sputum pus (n = 78), urine (n = 79), and bronchoalveolar fluid (n = 43) samples. DNA from samples was separated using specific isolation kits and subjected to RT-PCR.

RESULTS

In this study, we enrolled 1670 subjects and categorized 54.4% as females and 45.6% as males. The collected samples were categorized as 48.5% of fluid samples, followed by tissue (32.2%), sputum (9.9%), urine (4.7%), and pus-swab (4.6%). RT-PCR analysis revealed that 4.7% patients were positive for Mtb. Our results revealed that 61% of the affected patients were male and 39% were female. Among the specimen types, tissue samples gave the highest proportion of positive results (36.3%).

CONCLUSION

The results showed that RT-PCR should be implemented and given top priority in TB diagnosis to save time and facilitate a definitive diagnosis. Tissue samples are highly recommended to screen the Mtb through the technique RTPCR. Future studies should extend the technique to the global population and exome sequencing analysis should be performed to identify TB risk markers.

Mycobacterium tuberculosis concealed by enterococcal sacroiliitis

A 77-year-old African American female with rheumatoid arthritis presented with fever and unsteady gait. She was started on broad-spectrum antimicrobials due to CT evidence for sacroiliitis and psoas abscess and underwent partial excision of her sacroiliac bone and drainage of the abscess. One of four blood cultures grew Enterococcus faecalis and the patient was sent home with intravenous ampicillin for 6 weeks. Two days after antimicrobial completion, the patient presented with night sweats and weakness. Chest x-ray revealed new right upper lobe pulmonary infiltrates, and the AFB culture sent during her prior admission returned positive for TB. RIPE therapy with moxifloxacin was initiated. Although she responded well to treatment, she retained functional immobility. We report a case of musculoskeletal TB initially misdiagnosed as enterococcus sacroiliitis, resulting in a delayed initiation of anti-tuberculous therapy. A high index of suspicion and rapid detection with TB-PCR testing should be considered to avoid delayed diagnosis.

Use of Digital Technology to Enhance Tuberculosis Control: Scoping Review

Background

Tuberculosis (TB) is the leading cause of death from a single infectious agent, with around 1.5 million deaths reported in 2018, and is a major contributor to suffering worldwide, with an estimated 10 million new cases every year. In the context of the World Health Organization’s End TB strategy and the quest for digital innovations, there is a need to understand what is happening around the world regarding research into the use of digital technology for better TB care and control.

Objective

The purpose of this scoping review was to summarize the state of research on the use of digital technology to enhance TB care and control. This study provides an overview of publications covering this subject and answers 3 main questions: (1) to what extent has the issue been addressed in the scientific literature between January 2016 and March 2019, (2) which countries have been investing in research in this field, and (3) what digital technologies were used?

Methods

A Web-based search was conducted on PubMed and Web of Science. Studies that describe the use of digital technology with specific reference to keywords such as TB, digital health, eHealth, and mHealth were included. Data from selected studies were synthesized into 4 functions using narrative and graphical methods. Such digital health interventions were categorized based on 2 classifications, one by function and the other by targeted user.

Results

A total of 145 relevant studies were identified out of the 1005 published between January 2016 and March 2019. Overall, 72.4% (105/145) of the research focused on patient care and 20.7% (30/145) on surveillance and monitoring. Other programmatic functions 4.8% (7/145) and electronic learning 2.1% (3/145) were less frequently studied. Most digital health technologies used for patient care included primarily diagnostic 59.4% (63/106) and treatment adherence tools 40.6% (43/106). On the basis of the second type of classification, 107 studies targeted health care providers (107/145, 73.8%), 20 studies targeted clients (20/145, 13.8%), 17 dealt with data services (17/145, 11.7%), and 1 study was on the health system or resource management. The first authors’ affiliations were mainly from 3 countries: the United States (30/145 studies, 20.7%), China (20/145 studies, 13.8%), and India (17/145 studies, 11.7%). The researchers from the United States conducted their research both domestically and abroad, whereas researchers from China and India conducted all studies domestically.

Conclusions

The majority of research conducted between January 2016 and March 2019 on digital interventions for TB focused on diagnostic tools and treatment adherence technologies, such as video-observed therapy and SMS. Only a few studies addressed interventions for data services and health system or resource management.

Multiplex Polymerase Chain Reaction for diagnosis of gastrointestinal tuberculosis

Background and Aim

To evaluate the role of multiplex polymerase chain reaction (PCR) for diagnosis of gastrointestinal tuberculosis (GITB).

Methods

This was a prospective observational study conducted from July 2015 to November 2016 at a tertiary care teaching institution in north India. Fifty individuals with clinically suspected GITB and older than 18 years of age were recruited. Patients underwent radiological investigations, esophagogastroduodenoscopy, or colonoscopy as clinically indicated. Multiple biopsies for tissue diagnosis and PCR were taken. All specimens were subjected to Ziehl Neelsen staining, histopathology, and multiplex PCR using specific primers for genes IS6110, MPB64, and Protein b. The performance of the assay was assessed using a composite reference standard for diagnosis of tuberculosis. It comprised a combination of clinical characteristics and microbiological methods, including smear, Bactenecin (BACTEC) culture, histopathology, and response to antitubercular therapy.

Results

A final diagnosis of tuberculosis was made in 32 cases (Duodenal‐4, Ileo‐colonic‐28). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of histopathology for the diagnosis of tuberculosis was 28.12, 100, 100, and 43.9%, respectively. The sensitivity, specificity, PPV and NPV of BACTEC Mycobacteria Growth Indicator Tube (MGIT) culture for the diagnosis of tuberculosis was 9.3, 100, 100, and 38.29%, respectively. The sensitivity, specificity, PPV, and NPV of multiplex PCR for the diagnosis of tuberculosis was 87.5, 100, 100, and 86.2%, respectively.

Conclusion

Multiplex PCR using specific primers for genes IS6110, MPB64, and Protein b had a higher sensitivity compared to conventional techniques for the diagnosis of GITB.