Xpert MTB/RIF ultra for rapid diagnosis of extrapulmonary tuberculosis in a high-income low-tuberculosis prevalence setting

Optimal processing of tongue swab samples for Mycobacterium tuberculosis detection by the Xpert MTB/RIF Ultra assay

Tongue swabs represent a potential alternative to sputum as a sample type for detecting pulmonary tuberculosis (TB) using molecular diagnostic tests. The methods used to process tongue swabs for testing in the WHO-recommended Xpert MTB/RIF Ultra (Xpert Ultra) assay vary greatly. We aimed to identify the optimal method for processing diagnostic tongue swabs for subsequent testing by Xpert Ultra. We compared four methods for treating dry tongue swabs with Xpert Ultra sample reagent (SR) mixed with various concentrations of Tris-EDTA-Tween (TET), to treatment with SR alone or to a commonly used SR-free heat-inactivation protocol. In each condition, swabs obtained from volunteers without TB were placed into test buffer spiked with known amounts of Mycobacterium tuberculosis ( Mtb ) strain H37Rv-mc 2 6230. Swabs processed with 1:1 diluted SR buffer had the lowest Mtb limit of detection (LOD) at 22.7 CFU/700 µl (95% CI 14.2-31.2), followed by 2:1 diluted SR buffer at 30.3 CFU/700 µl (95% CI 19.9-40.7), neat SR at 30.9 CFU/700 µl (95% CI 21.5-40.3) and SR prefilled in the Xpert Ultra at 57.1 CFU/700 µl (95% CI 42.4-71.7). Swabs processed using the heat-based protocol had the highest LOD (77.6 CFU/700 µl; 95% CI 51.2-104.0). Similar findings were observed for LOD of RIF-susceptibility. Assay sensitivity using the 2:1 diluted SR buffer did not vary considerably in the presence of sputum matrix or phosphate buffer saline. Further studies are needed to assess the performance of this processing protocol in a clinical setting.

Importance

Xpert MTB/RIF Ultra (Xpert Ultra) is approved by the World Health Organization for the diagnosis of tuberculosis (TB). This test is typically performed using sputum specimens obtained from people with presumptive TB. In order to inactivate Mtb and aid liquefaction, sputum must be mixed with Xpert SR prior to transfer into the Xpert Ultra. However, some people under evaluation for TB are unable to produce sputum. Alternative sample types for TB diagnosis would therefore be of value. Oral-swabs, including tongue-swabs have shown promise, but there are technical challenges associated with sample processing. In this study, several new tongue swab processing conditions were evaluated, utilizing SR, either neat or diluted in buffer. The ability of Xpert Ultra to detect TB was improved under these conditions compared with the previously published heat-processing method (1-3), processing steps were simplified, and technical challenges were overcome.

Advancements in Tuberculosis Diagnostics: A Comprehensive Review of the Critical Role and Future Prospects of Xpert MTB/RIF Ultra Technology

Tuberculosis remains a persistent global health challenge, demanding swift and accurate diagnostic methods for effective treatment. The emergence of the Xpert MTB/RIF Ultra system marks a significant milestone in combating tuberculosis, streamlining the identification of Mycobacterium tuberculosis, and advancing our pursuit of eradicating the disease. Delving into the therapeutic landscape of tuberculosis and rifampicin resistance, this scientific narrative review offers a comprehensive exploration. It begins by delving into the historical backdrop and the hurdles encountered with traditional tuberculosis diagnostics. From there, it traces the journey of the Xpert MTB/RIF technology, underscoring its molecular underpinnings. In this narrative review, the performance of the Xpert MTB/RIF Ultra system undergoes thorough scrutiny, encompassing investigations into sensitivity, specificity, and comparisons with alternative diagnostic methods. The spotlight shines on its clinical applications across diverse scenarios, from diagnosing pulmonary and extrapulmonary tuberculosis to its pivotal role in identifying rifampicin resistance. The study also evaluates its clinical efficacy in enhancing patient outcomes and supporting global tuberculosis control initiatives. However, the review does not shy away from discussing the challenges and limitations associated with the Xpert MTB/RIF Ultra system. It meticulously addresses concerns regarding cost, infrastructure requirements, and potential diagnostic inaccuracies. Offering a panoramic view, the review assesses the system's impact in resource-constrained settings and its potential to bolster tuberculosis elimination endeavors worldwide. Peering into the future, it explores ongoing research avenues and potential enhancements in Xpert MTB/RIF Ultra technology, envisioning a landscape of improved performance, broader applications, and emerging diagnostic innovations in the realm of tuberculosis diagnostics.

Xpert MTB/RIF Ultra for the rapid diagnosis of extrapulmonary tuberculosis in a clinical setting of high tuberculosis prevalence country and interpretation of 'trace' results

To evaluate the diagnostic performance of Xpert MTB/RIF Ultra (Ultra) for the diagnosis of extrapulmonary tuberculosis (EPTB) from different types of extrapulmonary specimens in comparison with culture and composite microbiological reference standard (CRS). A total of 240 specimens were prospectively collected from presumptive EPTB patients between July 2021-January 2022 and tested by Ultra, Xpert, culture and acid-fast bacilli (AFB) smear microscopy. Out of 240 specimens, 35.8 %, 20.8 %, 11.3 %, and 7.1 % were detected as Mycobacterium tuberculosis complex by Ultra, Xpert, culture and AFB microscopy, respectively. An additional 15.0 % cases were detected by Ultra compared to Xpert MTB/RIF (Xpert) assay. A total of 28 (11.7 %) cases were identified as 'trace' category by Ultra with indeterminate rifampicin resistance result; of which 36.4 % were clinically confirmed as EPTB. Compared to culture, the sensitivity and specificity of Ultra and Xpert were 100 % and 72.3 %; 92.6 % and 88.3 %, respectively. In comparison with CRS, these were respectively: 98.9 % and 100 %; 57.5 % and 100 %. For individual category of specimens, sensitivity of Ultra was 100 % with varying specificity. We found that Ultra was highly sensitive for the rapid diagnosis of EPTB and has extensive potential over current diagnostics in high TB burden countries, but 'trace' results should be interpreted with caution.

Usefulness of Xpert MTB/RIF Ultra for rapid diagnosis of extrapulmonary tuberculosis in Tunisia

Extrapulmonary tuberculosis (EPTB) remains a challenging diagnosis. The purpose of this study was to assess the accuracy of Xpert MTB/RIF Ultra (Cepheid, USA) for rapid diagnosis of EPTB in Tunisia. Eight hundred and forty-seven extrapulmonary samples collected from 2017 to 2021, were subjected to Xpert MTB/RIF Ultra. Microscopy and culture were performed for all the specimens. The accuracy of Xpert Ultra was evaluated in comparison to the culture. Xpert Ultra diagnosed EPTB with a global sensitivity of 80.66% (74.3-85.75) and specificity of 70.87% (67.31-74.20). The molecular test was most accurate when performed in cerebrospinal fluids, bones and joints and cutaneous specimens showing a sensitivity of 100% and a specificity ranging from 70.60 to 91.11%. In lymph node samples comprising aspirates and biopsies, the sensitivity of Xpert Ultra was high 87.50% (77.23-93.53), however, the specificity was 51.08% (44.67-57.46). For pleural samples, the Xpert Ultra sensitivity was 77.50% (68.34-84.68) ranging from 71.43 to 80% in pleural biopsies and fluids respectively. The specificity in all pleural specimens was 79.56% (74.40-83.91). Xpert Ultra showed promise in the diagnosis of EPTB. The performances varied according to the site of the disease. The test may be more valuable if used in combination with other diagnostic modalities.

Higher Sensitivity of Xpert MTB/RIF Ultra Over Tuberculosis Culture for the Diagnosis of Spinal Tuberculosis With Open or Computed Tomography-Guided Biopsies

Background

Diagnostic specimens for spinal tuberculosis (STB) are mostly collected via open surgery. Percutaneous computed tomography (CT)-guided biopsies are used in times of limited surgical availability. However, poor diagnostic accuracy of Mycobacterium tuberculosis (Mtb) culture has been reported with this method, due to limited sample volume and the paucibacillary nature of STB. We evaluated Xpert MTB/RIF Ultra on open and CT-guided biopsies as compared with the gold standard Mtb culture and histopathology.

Methods

We conducted a prospective diagnostic accuracy study of Xpert Ultra, as compared with tuberculosis culture and histopathology, in adults with signs and symptoms of STB at a tertiary academic hospital in South Africa from November 2020 to December 2021. Diagnostic testing was performed on 31 patients with available samples.

Results

Xpert Ultra had a sensitivity of 94.7% (95% CI, 75.3%-99.7%) and specificity of 100% (95% CI, 75.7%-100.0%) against a reference standard of Mtb culture and histopathology. Xpert Ultra had high diagnostic accuracy in open and CT-guided biopsy samples with sensitivity and specificity of 100% and 100% (open) and 89% and 100% (CT), respectively. Mtb culture had limited specificity for CT-guided biopsies (43%; 95% CI, 15.8%-74.9%). HIV-1 coinfection did not affect Mtb abundance measures by Xpert Ultra or culture. Xpert Ultra was also superior to culture for STB diagnosis in patients concurrently treated for pulmonary tuberculosis.

Conclusions

Xpert Ultra detected more STB cases than culture for CT-guided biopsy samples. There was also no difference in sensitivity for open biopsies, irrespective of HIV-1 status, making it an important tool for rapid diagnosis, especially during times or in locations where open surgery is not possible or concurrent pulmonary tuberculosis treatment is initiated.

Evaluation of Xpert MTB/RIF Ultra for the Diagnosis of Extrapulmonary Tuberculosis: A Retrospective Analysis in Saudi Arabia

The incidence of extrapulmonary tuberculosis (EPTB) in low- and middle-income countries, as well as, high-income countries has increased over the last two decades. The acid-fast bacillus (AFB) smear test is easy to perform and cost-effective with a quick turnaround time but the test has low sensitivity. Culture remains the gold standard for detecting TB; however, it has low sensitivity and slow bacterial growth patterns, as it may take up to 6 to 8 weeks to grow. Therefore, a rapid detection tool is crucial for the early initiation of treatment and ensuring an improved therapeutic outcome. Here, the Xpert Ultra system was developed as a nucleic acid amplification technique to accelerate the detection of MTB in paucibacillary clinical samples and endorsed by the World Health Organization. From March 2020 to August 2021, Xpert Ultra was evaluated for its sensitivity and specificity against EPTB and compared with those of the routinely used Xpert, culture, and AFB tests in 845 clinical samples in Saudi Arabia. The results indicate the overall sensitivity and specificity of Xpert Ultra to be 91% and 95%, respectively, compared with the Xpert (82% and 99%, respectively) and AFB smear (18% and 100%, respectively) tests. The results also indicated that despite the low microbial loads that were categorized as trace, very low, or low on Xpert Ultra, yet, complete detection was achieved with some sample types (i.e., 100% detection). Consequently, Xpert Ultra has great potential to replace conventional diagnostic approaches as a standard detection method for EPTB.

GeneXpert Ultra in Urine Samples for Diagnosis of Extra-Pulmonary Tuberculosis

Extra-pulmonary tuberculosis (EPTB) continues to be difficult to diagnose. Novel biomarkers in biological specimens offer promise. Detection of Mycobacterium tuberculosis (Mtb) DNA in urine could prove useful in diagnosis of EPTB, possibly due to disseminated disease or micro-abscesses reported in kidneys. The current study was designed to detect Mtb DNA in stored urine samples from patients with EPTB. Diagnosis of EPTB was reached using Microbiological Reference Standards (MRS) on samples from the disease site using WHO Recommended Diagnostics (WRD), [smear microscopy, liquid culture (MGIT-960)] and GX (molecular WRD, mWRD) and Comprehensive reference standards [CRS, clinical presentation, microbiological reference standards, radiology, histopathology]. GX-Ultra was performed on urine samples stored in -80oC deep freezer, retrospectively. Of 70 patients, 51 (72.9%) were classified as confirmed TB, 11 (15.7%) unconfirmed TB, and 8 (11.4%) unlikely TB. GX-Ultra in urine samples demonstrated sensitivity of 52.9% and specificity of 57.9% against MRS, and higher sensitivity of 56.5% and specificity of 100% against CRS. The sensitivity and specificity of GX-Ultra in urine was 53.6% and 75% for pus sample subset and 52.2% and 53.3% for fluid sample subset. Urine being non-invasive and easy to collect, detection of Mtb DNA using mWRD in urine samples is promising for diagnosis of EPTB.

Diagnostic Efficacy of New Xpert Ultra for Extrapulmonary Tuberculosis Using Culture and Composite Reference Standard

Introduction

Xpert Ultra (Cepheid, USA) is recently introduced with an extra category of trace-positive results and higher sensitivity for tuberculosis (TB) diagnosis.

Objective

The objective of the study was to assess the diagnostic accuracy of Xpert Ultra for extrapulmonary samples using culture and composite reference standard (CRS) as the gold standard.

Materials and Methods

In a 1-year (March 2021-22) prospective observational study, samples of suspected extrapulmonary TB (EPTB) patients were subjected to Ziehl-Neelsen staining, culture, and Xpert Ultra (Cepheid, Sunnyvale, CA) tests. Relevant clinical and treatment information was noted. The diagnostic accuracy of Xpert Ultra compared with culture and CRS was calculated.

Results

Out of 1720 suspected patients of EPTB, 223 (13%), predominantly males 135 (60%), with a mean age of 41.46 ± 19.81 years, were diagnosed as TB positive following CRS criteria. The maximum cases were of pleural TB (35.4%), followed by central nervous system TB (17.9%), gastrointestinal TB (17.5%), and lymph node TB (12.1%). Of all samples, 150 (8.7%) were microbiologically confirmed, including 141 detected by Xpert ultra, 67 culture positive, and only 16 smear positive. Among the Xpert Ultra-positive samples, 35 showed trace results, including six false-positive results. Considering culture and CRS as the gold standard, the sensitivity (86.57%, 59.64%) and specificity (94.98%, 99.47%) of Xpert Ultra were calculated, respectively. Rifampicin resistance was detected in 1 (0.70%) sample.

Conclusion

Diagnosis of EPTB is a challenge and Xpert Ultra may detect TB at a very early stage. However, it is essential to rule out false-positive results. Additional studies are needed on Xpert Ultra to interpret trace results better.

Diagnosis of extrapulmonary tuberculosis by GeneXpert MTB/RIF Ultra assay

INTRODUCTION

Diagnosis of extrapulmonary tuberculosis (EPTB) is an arduous task owing to different anatomical locations, unusual clinical presentations, and sparse bacillary load in clinical specimens. Although GeneXpert® MTB/RIF is a windfall in TB diagnostics including EPTB, it yields low sensitivities but high specificities in many EPTB specimens. To further improve the sensitivity of GeneXpert®, GeneXpert® Ultra, a fully nested real-time PCR targeting IS6110, IS1081 and rpoB (Rv0664) has been endorsed by the WHO (2017), wherein melt curve analysis is utilized to detect rifampicin-resistance (RIF-R).

AREA COVERED

We described the assay chemistry/work design of Xpert Ultra and evaluated its performance in several EPTB types, that is, TB lymphadenitis, TB pleuritis, TB meningitis, and so on, against the microbiological reference standard or composite reference standard. Notably, Xpert Ultra exhibited better sensitivities than Xpert, but mostly at the compensation of specificity values. Moreover, Xpert Ultra exhibited low false-negative and false-positive RIF-R results, compared with Xpert. We also detailed other molecular tests, that is, Truenat MTBTM/TruPlus, commercial real-time PCR, line probe assay, and so on, for EPTB diagnosis.

EXPERT OPINION

A combination of clinical features, imaging, histopathological findings, and Xpert Ultra are adequate for definite EPTB diagnosis so as to initiate an early anti-tubercular therapy.

Genital tuberculosis, infertility and assisted reproduction

PURPOSE OF REVIEW

The goal of this review is to familiarize a global readership on the subtilities of clinical presentation and the mayhem that a missed diagnosis of genital tuberculosis (GTB) is capable of inflicting on the health and wellbeing of infertile women with untreated GTB attempting to conceive with assisted reproductive technology (ART).

RECENT FINDINGS

Emerging and recent literature relating to the epidemiology and clinical presentation of GTB and reporting of unique risks of ART for maternal and fetal morbidity in untreated cases of GTB are reviewed. Evidence relating to a broadening spectrum of screening methodologies for GTB detection of GTB is additionally considered.

SUMMARY

Genital TB must be considered as a mechanism for couple's infertility in at-risk populations. Attempting to treat female GTB-related infertility with in-vitro fertilization poses unique and potentially life-threatening risks, both to the mother and to the conceptus; these risks can be avoided through vigilance, appropriate screening and timely treatment prior to proceeding with IVF.

Utility of anti-Mycobacterium tuberculosis antibody (ab905) for detection of mycobacterial antigens in formalin-fixed paraffin-embedded tissues from clinically and histologically suggestive extrapulmonary tuberculosis cases

Background

The detection of acid-fast bacilli in extrapulmonary tissue samples is challenging due to its paucibacillary nature. The present study assessed the utility of immunohistochemistry (IHC) using anti-Mycobacterium tuberculosis antibody (ab905) for detecting the presence of mycobacterial antigens in archived formalin-fixed paraffin-embedded (FFPE) tissues.

Methods

FFPE tissues [surgical biopsies (n = 32) and post-mortem tissues (n = 8)] from clinically and histologically suggestive extrapulmonary tuberculosis (EPTB) cases at the Korle Bu Teaching Hospital, Accra, Ghana from 2015 to 2020 were stained with IHC (anti-Mycobacterium tuberculosis antibody) and Ziehl-Neelsen (ZN) stain. The staining outcomes of IHC and ZN were compared, and their sensitivity and specificity determined against histopathology as reference standard.

Results

Lymph nodes were about 40% (16/40) of the samples analyzed. IHC stained positive in 43.8% (7/16) biopsies and 87.5% (4/5) post-mortem samples ranging from 43.8% (7/16) in lymph nodes to 80% (4/5) in gastrointestinal organs. The overall sensitivity for IHC was 52.50% (95% CI: 36.13%-68.49%) and 0% (95% CI: 0.00%-8.81%) for ZN. Specificity was 72.50% (95% CI: 56.11%-85.40%) and 75% (95% CI: 58.80-87.31%) for IHC and ZN respectively.

Conclusions

IHC using anti-Mycobacterium tuberculosis antibody (ab905) can detect mycobacterial antigens in diverse range of paucibacillary extrapulmonary tissue sections. It is potentially a useful tool for the diagnosis of EPTB in FFPE tissues in a routine pathology laboratory.

Xpert MTB/RIF Ultra versus Xpert MTB/RIF for diagnosis of tuberculous pleural effusion: A systematic review and comparative meta-analysis

Objective

We compared diagnostic accuracy of pleural fluid Xpert MTB/RIF (Xpert) and Xpert MTB/RIF Ultra (Ultra) assays for diagnosing tuberculous pleural effusion (TPE), through systematic review and comparative meta-analysis.

Methods

We searched PubMed and Embase databases for publications reporting diagnostic accuracy of Xpert or Ultra for TPE. We used bivariate random-effects modeling to summarize diagnostic accuracy information from individual studies using either mycobacterial culture or composite criteria as reference standard. We performed meta-regression through hierarchical summary receiver operating characteristic (HSROC) modeling to evaluate comparative performance of the two tests from studies reporting diagnostic accuracy of both in the same study population.

Results

We retrieved 1097 publications, and included 74 for review. Summary estimates for sensitivity and specificity for Xpert were 0.52 (95% CI 0.43–0.60, I² 82.1%) and 0.99 (95% CI 0.97–0.99, I² 85.1%), respectively, using culture-based reference standard; and 0.21 (95% CI 0.17–0.26, I² 81.5%) and 1.00 (95% CI 0.99–1.00, I² 37.6%), respectively, using composite reference standard. Summary estimates for sensitivity and specificity for Ultra were 0.68 (95% CI 0.55–0.79, I² 80.0%) and 0.97 (95% CI 0.97–0.99, I² 92.1%), respectively, using culture-based reference standard; and 0.47 (95% CI 0.40–0.55, I² 64.1%) and 0.98 (95% CI 0.95–0.99, I² 54.8%), respectively, using composite reference standard. HSROC meta-regression yielded relative diagnostic odds ratio of 1.28 (95% CI 0.65–2.50) and 1.80 (95% CI 0.41–7.84) respectively in favor of Ultra, using culture and composite criteria as reference standard.

Conclusion

Ultra provides superior diagnostic accuracy over Xpert for diagnosing TPE, mainly because of its higher sensitivity.

Accuracy of Xpert MTB/RIF Ultra for the diagnosis of tuberculosis in adult patients: a retrospective cohort study

OBJECTIVES

The value of the "trace" result in Xpert Ultra for diagnosing active tuberculosis (TB) remains unclear. Our study evaluated the diagnostic accuracy of Xpert MTB/RIF Ultra (Xpert Ultra) (Cepheid, Sunnyvale, USA) over Xpert MTB/RIF (Xpert) (Cepheid, Sunnyvale, USA) and mycobacterial culture when compared with a composite reference standard (CRS).

METHODS

A retrospective single-center observational study was conducted in a tertiary care hospital in South India. Over three months, patients (aged ≥15 years) data on Xpert Ultra tests and mycobacterial culture of pulmonary and extrapulmonary samples were extracted from their electronic medical records. Patients were defined as TB cases based on the CRS criteria. Sensitivity, specificity, positive and negative predictive values of diagnostic tests were calculated by comparing them to the CRS.

RESULTS

Xpert Ultra was more sensitive (87.8%) than Xpert (72.1%) and culture (44.1%). The specificity of Xpert Ultra was lower (98.1%) than those of Xpert (100%) and culture (100%). The sensitivity (92%) and specificity (100%) of Xpert Ultra were highest when performed on pus samples.

CONCLUSIONS

Xpert Ultra with the trace category is superior to the conventional Xpert, and mycobacterial culture in identifying TB.

Diagnosis of urogenital tuberculosis by multiplex-nested PCR targeting mpt64 (Rv1980c) and IS6110: comparison with multiplex PCR and GeneXpert® MTB/RIF

A multiplex-nested PCR (M-nested PCR) targeting mpt64 (Rv1980c) + IS6110 was designed to detect Mycobacterium tuberculosis (Mtb) DNA within urine (n = 35), endometrial biopsies (n = 22) and menstrual blood (n = 3) of male/female UGTB patients, and results were compared with M-PCR using the same targets. Detection limit of the purified Mtb DNA was found to be 1 fg by M-nested PCR, which was 10⁶ -fold lower than M-PCR. Moreover, sensitivities of 100% and 81·8% were obtained in confirmed (n = 5) and clinically suspected UGTB (n = 55) cases, respectively, by M-nested PCR, with a specificity of 97·1% (n = 70). Sensitivities attained by M-nested PCR were significantly higher (p < 0·05) than M-PCR in both clinically suspected and total UGTB (n = 60) cases. To confirm the true PCR-negative results, an internal amplification control, that is, human β-globin gene (hbb) was incorporated in the M-nested PCR/M-PCR assays, wherein all the clinical specimens (positive/negative for mpt64/IS6110) were found to be positive for hbb. Some UGTB specimens (n = 35) were also subjected to GeneXpert® MTB/RIF assay that revealed a significantly lower (p < 0·001) sensitivity (17·1 vs 88·6%) than M-nested PCR, although high specificity (100%) was attained with GeneXpert. After validating the results in a higher number of UGTB specimens, our M-nested PCR may be translated into an attractive diagnostic kit.

Rapid Molecular Diagnosis of Extra-Pulmonary Tuberculosis by Xpert/RIF Ultra

Rapid detection of Mycobacterium tuberculosis complex and determination of drug resistance are essential for early diagnosis and treatment of tuberculosis (TB). Xpert MTB/RIF Ultra (Xpert Ultra), a molecular test that can simultaneously identify M. tuberculosis complex and resistance to rifampicin directly on clinical samples, is currently used. Xpert Ultra represents a helpful tool for rapid pulmonary TB diagnosis, especially in patients with paucibacillary infection. The aim of this review is to provide an overview of the diagnostic performance of Xpert Ultra in detection of extra-pulmonary tuberculosis.

Evaluating the efficacy of stool sample on Xpert MTB/RIF Ultra and its comparison with other sample types by meta-analysis for TB diagnostics

Precise and timely detection of tuberculosis (TB) is crucial to reduce transmission. This study aims to assess the accuracy of Xpert MTB/RIF Ultra on stool samples and systematically review the performance of Xpert MTB/RIF Ultra with different sample types by meta-analysis. Stool samples of smear-negative pulmonary TB (PTB), cervical lymph node TB, and abdominal TB patients were tested on the Xpert MTB/RIF Ultra system. Meta-analysis was performed on a set of 44 studies. Data were grouped by sample type, and the pooled sensitivity and specificity of Xpert MTB/RIF Ultra were calculated. The sensitivity of Xpert MTB/RIF Ultra with stool samples was 100% for smear-negative PTB, 27.27% for cervical lymph node TB, and 50% for abdominal TB patients, with 100% specificity for all included TB groups. The summary estimate for all PTB samples showed 84.2% sensitivity and 94.5% specificity, and EPTB samples showed 88.6% sensitivity and 96.4% specificity. Among all sample types included in our meta-analysis, urine showed the best performance for EPTB diagnosis. This pilot study supports the use of stool as an alternative non-invasive sample on Xpert MTB/RIF Ultra for rapid testing, suitable for both PTB and EPTB diagnosis.

Tuberculous meningitis: progress and remaining questions

Tuberculous meningitis is a devastating brain infection that is caused by Mycobacterium tuberculosis and is notoriously difficult to diagnose and treat. New technologies characterising the transcriptome, proteome, and metabolome have identified new molecules and pathways associated with tuberculous meningitis severity and poor outcomes that could offer novel diagnostic and therapeutic targets. The next-generation GeneXpert MTB/RIF Ultra assay, when used on CSF, offers diagnostic sensitivity for tuberculous meningitis of approximately 70%, although it is not widely available and a negative result cannot rule out tuberculous meningitis. Small trials indicate that clinical outcomes might be improved with increased doses of rifampicin, the addition of linezolid or fluoroquinolones to standard antituberculosis therapy, or treatment with adjunctive aspirin combined with corticosteroids. Large phase 3 clinical trials are underway worldwide to address these and other questions concerning the optimal management of tuberculous meningitis; these studies also form a platform for studying pathogenesis and identifying novel diagnostic and treatment strategies, by allowing the implementation of new genomic, transcriptomic, proteomic, and metabolomic technologies in nested substudies.

First patient in the Iranian Registry with novel DOCK2 gene mutation, presenting with skeletal tuberculosis, and review of literature

Background

Dedicator of cytokinesis 2 (DOCK2) deficiency is an inborn error of immunity characterized by cellular and humoral immunological abnormalities leading to early-onset infections.

Case presentation

We reported a novel case of a 27 months old girl presenting with recurrent pneumonia and a history of skeletal tuberculosis at the age of 19-month-old. Her immunological workup revealed persistent lymphopenia and low CD4 + T cell count along with elevated levels of CD19 +, CD20 +, CD16 +, and CD56 + cells. Furthermore, she had a high level of immunoglobulin (Ig) E and a slightly reduced IgM level with a non-protective antibody titer against diphtheria. The whole-exome sequencing (WES) analysis identified a homozygous frameshift deletion mutation (c.1512delG, p.I505Sfs*28) in exon 16 of the DOCK2 gene. We also conducted electronic searches in PubMed, Web of Science, and Scopus databases and reviewed the articles reporting patients with DOCK2 deficiency. The literature search yielded 14 DOCK2-deficient patients suffering from both cellular and humoral immune defects leading to early-onset infections, particularly human herpesvirus (HHV) infection.

Conclusion

DOCK2 deficiency should be considered in the context of severe or unusual early-onset infections, especially HHV infections, in a patient with a probable clinical diagnosis of combined immunodeficiency. We also recommended that DOCK2-deficient patients might benefit from T-cell receptor excision circle (TREC) assay as part of the routine newborn screening program.

Performances of single tube nested polymerase chain reaction and GeneXpert ultra on Formalin fixed paraffin embedded tissues in the diagnosis of tuberculous spondylodiscitis

INTRODUCTION

Tuberculous Spondylodiscitis is the most common form of musculoskeletal tuberculosis. Molecular techniques on fresh tissues are proved to improve the diagnosis of tuberculous spondylodiscitis and to allow a rapid diagnosis to initiate the treatment and prevent neurological complications.

OBJECTIVES

The objective of the present study was to assess the diagnostic performances of single tube nested PCR and GeneXpert ultra in the diagnosis of tuberculous spondylodiscitis on formalin fixed paraffin embedded tissues.

METHODS

This study included 63 tuberculous spondylodiscitis cases collected from June 2014 to January 2020 and corresponding to 27 definite tuberculous spondylodiscitis with positive microbiology, and 36 probable tuberculous spondylodiscitis, with histopathological, clinical and radiological findings consistent with tuberculous spondylodiscitis but with negative microbiology. The sensitivity, specificity, positive predictive value and negative predictive value of nested PCR and GeneXpert ultra were determined with reference to microbiology.

RESULTS

Nested PCR was positive in 47 (75%) cases: 26/27 definite tuberculous spondylodiscitis and 21/36 probable tuberculous spondylodiscitis. GeneXpert ultra was positive in only 6 (10%) cases corresponding to definite tuberculous spondylodiscitis. The sensitivity, specificity, positive predictive value and negative predictive value of nested PCR on formalin fixed paraffin embedded tissues were 96%, 100%, 100%, 83% respectively. For GeneXpert ultra, these rates were 22%, 100%, 100% and 25% respectively.

CONCLUSION

Nested PCR and GeneXpert ultra on formalin fixed paraffin embedded tissues are useful tools for the diagnosis of tuberculous spondylodiscitis, especially for cases where microbiological investigations were not carried out. Both techniques have excellent specificity but single tube nested PCR is more sensitive. Key Points • Molecular techniques are routinely performed on fresh tissues • GeneXpert and nested PCR on formalin fixed paraffin embedded tissues are reliable for the diagnosis of tuberculous spondylodiscitis • Nested PCR is more sensitive than Genexpert for diagnosing tuberculous spondylodiscitis.

Extrapulmonary Tuberculosis—An Update on the Diagnosis, Treatment and Drug Resistance

Pathogenic Mycobacterium tuberculosis complex organisms (MTBC) primarily cause pulmonary tuberculosis (PTB); however, MTBC are also capable of causing disease in extrapulmonary (EP) organs, which pose a significant threat to human health worldwide. Extrapulmonary tuberculosis (EPTB) accounts for about 20–30% of all active TB cases and affects mainly children and adults with compromised immune systems. EPTB can occur through hematogenous, lymphatic, or localized bacillary dissemination from a primary source, such as PTB, and affects the brain, eye, mouth, tongue, lymph nodes of neck, spine, bones, muscles, skin, pleura, pericardium, gastrointestinal, peritoneum, and the genitourinary system as primary and/or disseminated disease. EPTB diagnosis involves clinical, radiological, microbiological, histopathological, biochemical/immunological, and molecular methods. However, only culture and molecular techniques are considered confirmatory to differentiate MTBC from any non-tuberculous mycobacteria (NTM) species. While EPTB due to MTBC responds to first-line anti-TB drugs (ATD), drug susceptibility profiling is an essential criterion for addressing drug-resistant EPTB cases (DR-EPTB). Besides antibiotics, adjuvant therapy with corticosteroids has also been used to treat specific EPTB cases. Occasionally, surgical intervention is recommended, mainly when organ damage is debilitating to the patient. Recent epidemiological studies show a striking increase in DR-EPTB cases ranging from 10–15% across various reports. As a neglected disease, significant developments in rapid and accurate diagnosis and better therapeutic interventions are urgently needed to control the emerging EPTB situation globally. In this review, we discuss the recent advances in the clinical diagnosis, treatment, and drug resistance of EPTB.

Current updates in diagnosis of male urogenital tuberculosis

Introduction: Urogenital tuberculosis (UGTB) is a common manifestation of extrapulmonary TB (EPTB), which affects both men and women in a ratio of 2:1. Similar to other EPTB types, diagnosis of UGTB is quite challenging owing to atypical clinical presentation and paucibacillary nature of specimens. This review is primarily focused on the current updates developed in the diagnosis of male UGTB.Area covered: Smear/culture, imaging, histopathology, and interferon-γ release assays are the main modalities employed for detecting male UGTB cases. Moreover, we described the utility of nucleic acid amplification tests (NAATs), including loop-mediated isothermal amplification, PCR, nested-PCR, and GeneXpert (MTB/RIF) assays. The possibility of using other novel modalities, such as immuno-PCR (I-PCR), aptamer-linked immobilized sorbent assay (ALISA), and identification of circulating cell-free DNA (cfDNA) by NAATs were also discussed.Expert opinion: The current methods used for the diagnosis of male UGTB are not adequate. Therefore, the latest molecular/immunological tools, i.e. Xpert Ultra, Truenat MTB^TM, I-PCR, ALISA, and cfDNA detection employed for the diagnosis of other EPTB forms and pulmonary TB may also be exploited for UGTB diagnosis. Reliable and timely diagnosis of male UGTB may initiate an early start of anti-tubercular therapy that would reduce infertility and other complications associated with disease.

Limited role of GeneXpert in peritoneal fluid in the diagnosis of genital tuberculosis in infertile women

Background and Objectives:

Genital tuberculosis (TB) is an important cause of infertility in women that poses many challenges in diagnosis. The study is done to understand the utility of GeneXpert test in peritoneal fluid in the diagnosis of genital TB in infertile women.

Methods:

All infertile women in postmenstrual phase who were planned for laparoscopy in study period were included. Women who were already on anti-TB therapy were excluded. Peritoneal fluid/washings were retrieved during laparoscopy to test for Mycobacterium tuberculosis by GeneXpert. A note was made of laparoscopy evidence of TB. Endometrial sample was sent for microbiological testing of mycobacterium on smear and liquid culture. Histopathological test of endometrium was also done to look for granulomas.

Results:

In a total of 57 women, 8 (14.03%) women were diagnosed with TB on the basis of laparoscopy or microbiological or histopathological tests. Six women had caseating tubercles in pelvis, of them two women had presence of mycobacterium on smear, one woman also had positive liquid culture. In two women endometrial smear was positive. None of the women had a positive GeneXpert test in peritoneal fluid.

Conclusion:

Genital TB is a clinical problem in infertile women. Even in women with confirmed genital TB the peritoneal fluid/washings were negative for mycobacterium. GeneXpert did not pick Mycobacterium in peritoneal fluid in women with genital TB. Hence, it is not a sensitive and good tool for the diagnosis of female genital TB.