Tuberculosis-targeted next-generation sequencing and machine learning: An ultrasensitive diagnostic strategy for paucibacillary pulmonary tuberculosis and tuberculous meningitis

BACKGROUND

Existing diagnostic approaches for paucibacillary tuberculosis (TB) are limited by the low sensitivity of testing methods and difficulty in obtaining suitable samples.

METHODS

An ultrasensitive TB diagnostic strategy was established, integrating efficient and specific TB targeted next-generation sequencing and machine learning models, and validated in clinical cohorts to test plasma cfDNA, cerebrospinal fluid (CSF) DNA collected from tuberculous meningitis (TBM) and pediatric pulmonary TB (PPTB) patients.

RESULTS

In the detection of 227 samples, application of the specific thresholds of CSF DNA (AUC = 0.974) and plasma cfDNA (AUC = 0.908) yielded sensitivity of 97.01 % and the specificity of 95.65 % in CSF samples and sensitivity of 82.61 % and specificity of 86.36 % in plasma samples, respectively. In the analysis of 44 paired samples from TBM patients, our strategy had a high concordance of 90.91 % (40/44) in plasma cfDNA and CSF DNA with both sensitivity of 95.45 % (42/44). In the PPTB patient, the sensitivity of the TB diagnostic strategy yielded higher sensitivity on plasma specimen than Xpert assay on gastric lavage (28.57 % VS. 15.38 %).

CONCLUSIONS

Our TB diagnostic strategy provides greater detection sensitivity for paucibacillary TB, while plasma cfDNA as an easily collected specimen, could be an appropriate sample type for PTB and TBM diagnosis.

Diagnostic value of tNGS vs Xpert MTB/RIF in childhood TB

Objectives

To evaluate the diagnostic value of targeted next generation sequencing (tNGS) in childhood tuberculosis (TB) and compare the accuracy with Xpert MTB/RIF method.

Methods

Children aged ≤18 years with symptoms suggestive of TB during July 2021 to December 2022 at Beijing Children's Hospital were included, and the performances of tNGS and Xpert were evaluated.

Results

A total of 103 children with suspected TB were recruited, including 72 discharge diagnosis of TB and 31 non-TB cases. The mean age was 7.37 ± 4.77 years, and 62.1 % were male. The most common type of specimens was gastric aspirate (GA) (59, 57.3 %). Among all the 72 TB patients, tNGS showed higher sensitivity than Xpert, but the difference was not significant (34.7 %, 25/72 vs 20.8 %, 15/72; P = 0.063). The specificities of tNGS and Xpert were 87.1 % (27/31) and 96.8 % (30/31), respectively (P = 0.162). Among different types of specimen, the highest sensitivity of tNGS on sputum and pus was observed (80.0 %, 4/5), followed by pleural effusion (50.0 %, 2/4). One rifampin resistance and one protionamide resistance were detected in bacteriologically confirmed TB by tNGS.

Conclusion

tNGS had a higher sensitivity but lower specificity compared to Xpert in diagnosis of children TB. tNGS yielded higher sensitivity than Xpert on gastric aspirate and sputum and pus.

Comparison of Conventional Methods with Newer Diagnostic Modalities to Detect Genital Tuberculosis in Infertile Women

Background

Genital tuberculosis is one of the leading causes of female infertility. Paucibacillary nature of the disease in the female genital system often makes its diagnosis difficult. No single test has been able to accurately diagnose genital tuberculosis. In this study we aim to compare conventional diagnostic tests for tuberculosis like Acid Fast Bacilli (AFB) Staining, Lowenstein Jensen (LJ) Culture and Histopathology with newer tests like PCR, MGIT 960, GeneXpert.

Methods

This study included 67 infertile women from Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi. They were subjected to detailed history and routine investigations, namely Haemogram, ESR, Mantoux test, Chest X-ray and pelvic ultrasound to look for the findings of tuberculosis. A premenstrual endometrial aspirate was taken and was subjected to the AFB Staining, LJ Culture, Histopathology, PCR, MGIT 960, Gene Xpert, and the test results were compared.

Result and Conclusion

35.8% (24/67) of women were diagnosed with genital tuberculosis using the diagnostic criteria. With culture as the gold standard, the positivity of genital TB was 19.4% (13/67). Majority of infertile patients with low index of suspicion clinically were positive for genital tuberculosis. Therefore, all the patients of infertility should be routinely evaluated for genital tuberculosis. PCR and MGIT 960 have shown promising results in the newer methods. LJ culture and histopathology are still the most reliable and available diagnostic methods. The usefulness of AFB Staining and GeneXpert remains questionable.

Updates in Pediatric Tuberculosis in International Settings

Childhood tuberculosis (TB) has been underreported and underrepresented in TB statistics across the globe. Contributing factors include health system barriers, diagnostic barriers, and community barriers leading to an underdetected epidemic of childhood tuberculosis. Despite considerable progress in childhood TB management, there is a concerning gap in policy and practice in high-burden countries leading to missed opportunities for active case detection, early diagnosis and treatment of TB exposure, and infection and disease in children regardless of human immunodeficiency virus status. Bridging this gap requires multisectoral coordination and political commitment along with an eye to research and innovation with potential to scale.

Utility of EBUS-TBNA in diagnosing mediastinal tuberculous lymphadenitis in East London

OBJECTIVES

To characterise and describe the diagnostic utility of Endobronchial ultrasound-transbronchial needle aspiration (EBUS-TBNA) in intrathoracic tuberculosis in a cohort of patients with mediastinal lymphadenopathy of unknown aetiology.

METHODS

Consecutive patients with intrathoracic lymphadenopathy undergoing EBUS-TBNA between 2012 and 2016 were identified. Demographic data, biopsy cytopathology and mycobacteriology results, HIV and vitamin D status, susceptibility results and final diagnoses were recorded. Pre- and post-procedure probability scores were assigned to each case to reflect the probability of tuberculosis.

RESULTS

315 cases were identified; 54 (17.1%) had tuberculosis and 261 (82.9%) had a non-tuberculosis diagnosis. amongst TB cases, the sensitivity of EBUS-TBNA was 59.3% (95% CI 45.06-72.14), specificity 100% (95% CI 98.19-100) and the negative predictive value (NPV) was 92.23% (95% CI 88.31-94.95). 19/54 (35%) TB cases were confirmed by EBUS mycobacterial culture and 13/54 (24.1%) by cytopathology.  33 (61.1%) of the TB cases, had a low to medium pre-test probability score assigned prior to EBUS-TBNA. Amongst EBUS culture-confirmed cases, we found a resistance rate of 10.5% to one or more first line TB drugs, with one case of multi-drug resistant TB.

CONCLUSIONS

We confirmed the utility of EBUS-TBNA in the diagnosis of intrathoracic tuberculosis in an undifferentiated cohort of patients with mediastinal lymphadenopathy of unknown aetiology and advocate sending samples for mycobacterial culture in all cases in high tuberculosis incidence areas.

Xpert MTB/RIF Ultra improved the diagnosis of paucibacillary tuberculosis: A prospective cohort study

OBJECTIVES

We assessed the diagnostic performance of Xpert MTB/RIF Ultra (Xpert Ultra) in comparison to Xpert MTB/RIF (Xpert) for the detection of paucibacillary tuberculosis (TB).

METHODS

Smear-negative sputum, pleural fluid and cerebrospinal fluid (CSF) were collected from TB suspects at Beijing Chest Hospital (Beijing, China) and were examined using smear, Xpert and culture. Xpert Ultra was tested using specimens stored at -80 °C. Drug susceptibility testing (DST) was conducted for all of the isolates recovered. The performances of Xpert Ultra and Xpert were evaluated using composite reference standard (CRS) as gold standard, which included clinical, laboratory, histopathological, radiological and follow-up features.

RESULTS

Totally 689 cases were included. The direct head-to-head diagnostic performance comparison showed higher sensitivity of Xpert Ultra in contrast with Xpert among 292 smear-negative pulmonary TB (PTB) (70.89% vs 57.88%, P = 0.001), 108 tuberculous pleurisy (61.11% vs 34.26%, P<0.001), and 43 tuberculous meningitis (44.19% vs 18.60%, P = 0.011). The percentage of definite PTB, tuberculous pleurisy and tuberculous meningitis increased from 67.12% to 78.77%, 61.11% to 69.44% and 23.26% to 51.16%, respectively after integrating Xpert Ultra outcomes. The specificity of Xpert Ultra and Xpert was 96.75% (238/246) and 98.37% (242/246), respectively. Xpert Ultra and Xpert performed similarly in detecting rifampicin resistance.

CONCLUSION

Xpert Ultra has higher sensitivity but relatively reduced specificity compared with Xpert in diagnosis of paucibacillary TB. Performing Xpert Ultra would improve the definite diagnosis of smear-negative pulmonary tuberculosis, tuberculous pleurisy and tuberculous meningitis.

A Study of Selenium in Leprosy

INTRODUCTION

Leprosy is a chronic infection caused by Mycobacterium leprae. Selenium, on the other hand, is a substance, which is needed for its protective role against microorganism infection.

AIM

This study aims to know the association between selenium serum levels with bacteriological index.

METHODS

This is an analytical cross-sectional study model. Sampling was done with consecutive sampling method in Pirngadi General Hospital, Lau Simomo Leprosy Hospital and H. Adam Malik General Hospital. Samples were taken from patients' venous blood serum then selenium levels were measured.

RESULTS

This study found 30 leprosy patients consisted of 19 patients with paucibacillary (PB) leprosy and 11 patients with multibacillary (MB) leprosy. Selenium serum levels of patients with PB leprosy (mean = 97.16 µg/dL) were found to be significantly higher than MB leprosy (mean = 77.27 µg/dL) with p = 0.008 using t-test. The negative correlation between selenium serum levels with bacterial index in patients with leprosy was also found in this study using Spearman's rho test (r = - 0.499, p = 0.005).

CONCLUSIONS

Selenium serum levels of patients with PB leprosy are higher than patients with MB leprosy, and high bacteriological index in patients with leprosy were correlated with low selenium serum levels.

Expression of inflammatory cytokine and inducible nitric oxide synthase genes in the small intestine and mesenteric lymph node tissues of pauci- and multibacillary sheep naturally infected with Mycobacterium avium ssp. paratuberculosis

OBJECTIVE/BACKGROUND

Paratuberculosis (Johne's disease) is a chronic infectious granulomatous enteritis, primarily affecting ruminants, and caused by Mycobacterium avium ssp. paratuberculosis (MAP). The disease is widely prevalent throughout the world with significant economic losses. MAP has also been implicated with human Crohn's disease. There exists a strong correlation between the immune response and development of various types of pathologies in ruminants. The polarization of the immune response, which is critical to clinical outcome of the paratuberculosis infection, is controlled by the differential expression of certain cytokines and inducible nitric oxide synthase (iNOS) in Johne's disease. In previous studies, the role of different cytokines (Th1 and Th2) has been occasionally studied in sheep paratuberculosis. In the present study, we studied differential expression of interferon (IFN)-γ, interleukin (IL)-1α, IL-10, transforming growth factor (TGF)-β, iNOS, and TRAF1 genes in MAP-infected sheep and established relationship with distinct pathologies.

METHODS

Tissue sections (small intestine, ileocecal junction, and mesenteric lymph nodes) were collected from sheep suspected for Johne's disease and appropriately preserved for RNA extraction, polymerase chain reaction (PCR) analysis, and histopathology. Pathologic grading was done on the basis of nature and extent of cellular infiltration, granuloma formation and abundance of acid-fast bacilli. Six sheep each with pauci (PB)- and multibacillary (MB) lesions and six healthy control sheep were selected for cytokine studies. MAP in tissue extracted genomic DNA of sheep was quantified by a quantitative PCR assay. Tissue extracted RNA was reversed transcribed to prepare c-DNA from which quantitative reverse transcription PCR (qRT-PCR) was performed to amplify IFN-γ, IL-1β, IL-10, TGF-β, β-actin, TRAF1, and iNOS with Quantitect SYBR Green Master Mix. qRT-PCR data were analyzed using 2^-ΔΔCT method using β-actin gene as a control. All qRT-PCR results were compared by using one-way analysis of variance (least significance difference and Duncan tests) for p-value using SPSS (version 7.5) for expression of each gene in tissues from infected and control sheep.

RESULTS

In the small intestine, PB sheep showed significant enhancements in the expression of IL-10, TGF-β, iNOS, and IFN-γ in comparison to similar tissues from uninfected control sheep. IL-1α expression was significantly reduced (p<0.01). The expression of IL-10 in the mesenteric lymph node (MLN) tissue of PB sheep was significantly increased (p<0.01) as compared with the control sheep. MB sheep revealed significantly enhanced expression of TGF-β mRNA and reduction in the expression of IL-1α in comparison to control sheep. In the MLN of MB sheep, the expressions of IL-10 and TGF-β were significantly (p<0.01) increased, and IFN-γ was significantly downregulated in comparison to uninfected control sheep. When the cytokine expression was compared between two distinctly infected groups, the MB sheep showed highly significant decrease (p<0.01) in the expression of iNOS and IFN-γ in the small intestine and IFN-γ in the MLN tissues.

CONCLUSION

The present study indicated that IFN-γ and iNOS were found to play important role in the induction of Th1 type immune response in PB sheep. MB sheep had significant reduction in expression of IFN-γ and iNOS and elevation of IL-10 and TGF-β, which was typical of Th2 cytokine pattern. Elevated expression of IL-10 and TGF-β in PB cases possibly suggests the role of T-regulatory cells and may follow an independent mechanism not typical of Th1 pattern. In view of significantly reduced expression in both forms of the disease, IL-1α may not be an important cytokine in ovine paratuberculosis.

Utility of Bacillary Index in Slit Skin Smears in Correlation with Clinical and Histopathological Alterations in Hansen's Disease: An Attempt to Revive a Simple Useful Procedure

Leprosy, a relatively common chronic contagious disease having diverse modes of clinical presentation, can mimic a variety of unrelated diseases. For proper and adequate treatment, the diagnosis must be made accurately with subtyping which should be done with the help of bacillary index, histopathological features, and clinical correlation. This is extremely important in patient care as paucibacillary and multibacillary types have different modes of treatment. Our aim is to categorize leprosy into various types based on bacillary index, morphological findings both in slit skin smears, and biopsy along with clinical correlation.

Leprosy. An update: definition, pathogenesis, classification, diagnosis, and treatment

Leprosy is a chronic granulomatous disease caused by the bacillus Mycobacterium leprae. It primarily affects the skin and peripheral nerves and is still endemic in various regions of the world. Clinical presentation depends on the patient's immune status at the time of infection and during the course of the disease. Leprosy is associated with disability and marginalization. Diagnosis is clinical and is made when the patient has at least 1 of the following cardinal signs specified by the World Health Organization: hypopigmented or erythematous macules with sensory loss; thickened peripheral nerves; or positive acid-fast skin smear or skin biopsy with loss of adnexa at affected sites. Leprosy is treated with a multidrug combination of rifampicin, clofazimine, and dapsone. Two main regimens are used depending on whether the patient has paucibacillary or multibacillary disease.