The rapid molecular test Xpert MTB/RIF ultra: towards improved tuberculosis diagnosis and rifampicin resistance detection

Diagnostic yield of Xpert MTB/RIF, Xpert MTB/RIF Ultra, and Truenat MTB assays on non-pulmonary samples from suspected cases of extra-pulmonary tuberculosis (EPTB)

BACKGROUND

Extrapulmonary tuberculosis (EPTB) poses a diagnostic challenge due to its paucibacillary nature and low diagnostic yield of traditional methods. Molecular diagnostic tools like Xpert MTB/RIF, Xpert MTB/RIF Ultra, and Truenat MTB offer promising alternatives for the rapid and higher detection rates for pulmonary TB samples. However, the yield of these newly introduced molecular tests on extra-pulmonary samples requires country-specific evaluation and comparative analysis.

METHODOLOGY

This study evaluated the diagnostic performance of Xpert MTB/RIF, Xpert MTB/RIF Ultra, and Truenat MTB assays in detecting EPTB on 211 clinical specimens collected at a tertiary care centre of central India. The assays' sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPP) were compared against a composite reference standard.

RESULTS

Xpert MTB/RIF Ultra exhibited the highest sensitivity (50%) for EPTB detection, outperforming the standard GeneXpert MTB/RIF (29.4%) and Truenat MTB (35.3%), with comparable specificity across all three assays. Among the specimen types, pus samples demonstrated the highest (value) diagnostic yield. These findings highlight the superior diagnostic capabilities of Xpert MTB/RIF Ultra, particularly in paucibacillary cases.

CONCLUSION

Xpert Ultra demonstrates superior sensitivity for EPTB detection compared to Xpert MTB/RIF and Truenat MTB, making it a promising tool to enhance diagnostic accuracy in paucibacillary TB. Its adoption as a standard diagnostic method could significantly improve EPTB management. These findings advocate for integrating advanced molecular diagnostics into routine tuberculosis workflows to reduce diagnostic delays and improve patient outcomes.

CLINICAL TRAIL NUMBER

Not applicable.

The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics

The lung microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The present study aimed to characterize the lung microbiota in patients with pulmonary tuberculosis (PTB), and to explore the association between the abundance of Mycobacterium tuberculosis complex (MTBC) and the lung microbiota. This retrospective study included 190 patients with MTBC infection. The enrolled patients were classified into three groups based on the abundance results of bronchoalveolar lavage fluid (BALF) mNGS: low [reads per ten million (RPTM) = 1 ~ 1000], medium (RPTM = 1001 ~  10000) and high (RPTM > 10000). In the high-abundance group, there were more bilateral lobar involvement and symptoms of cavitation. In addition to mNGS, the highest positivity rates were T-spot (92.36%), GeneXpert (71.58%), culture (68.95%) and AFB smear (17.84%). The positive rates of culture, AFB smear and GeneXpert increased with the increase of MTBC abundance, and the positive rates were highest in the high-abundance MTBC group. Both the alpha and beta diversity showed significant difference between the three groups, with the high-abundance MTBC groups showed lowest alpha diversity. The increased abundance of MTBC positively associated with the longer time of hospital stay. To sum up, the lung microbiota of patients with PTB were significantly distinct between groups with different abundant levels of MTBC. Combined with imaging features, a high abundance of MTBC suggests the patient is more severely ill and has a poorer prognosis.

Nanobiosensors Enable High-Efficiency Detection of Tuberculosis Nucleic Acid

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), with a complex pathogenesis that poses a long-term threat to human health globally. Early and accurate diagnosis of TB provides a critical window for timely and effective treatment. The development of nucleic acid testing (NAT) based on polymerase chain reaction (PCR) has greatly improved the diagnostic efficiency of TB. However, balancing detection accuracy, efficiency, and cost in TB NAT remains challenging. Functionalized nanomaterials-based nanobiosensors have demonstrated exceptional performance in detecting TB nucleic acid by integrating their unique physicochemical properties with diverse biological probes that exploit Mtb characteristics to effectively amplify biological signals. Compared to traditional NAT, nanobiosensors simplify nucleic acid detection, improve accuracy, and reduce reliance on external conditions, thereby contributing to more immediate and accurate TB diagnosis. In this perspective, we provide a comprehensive summary and discussion on current strategies for detecting Mtb biomarkers using nucleic acid along with novel solutions for TB diagnosis. Additionally, we explore the advantages and challenges associated with applying nanotechnology to the clinical management of TB, particularly point-of-care testing (POCT).

A Comprehensive Review of the Diagnostics for Pediatric Tuberculosis Based on Assay Time, Ease of Operation, and Performance

Pediatric tuberculosis (TB) is still challenged by several diagnostic bottlenecks, imposing a high TB burden in low- and middle-income countries (LMICs). Diagnostic turnaround time (TAT) and ease of operation to suit resource-limited settings are critical aspects that determine early treatment and influence morbidity and mortality. Based on TAT and ease of operation, this article reviews the evolving landscape of TB diagnostics, from traditional methods like microscopy and culture to cutting-edge molecular techniques and biomarker-based approaches. We examined the benefits of efficient rapid results against potential trade-offs in accuracy and clinical utility. The review highlights emerging molecular methods and artificial intelligence-based detection methods, which offer promising improvements in both speed and sensitivity. The review also addresses the challenges of implementing these technologies in resource-limited settings, where most pediatric TB cases occur. Gaps in the existing diagnostic methods, algorithms, and operational costs were also reviewed. Developing optimal diagnostic strategies that balance speed, performance, cost, and feasibility in diverse healthcare settings can provide valuable insights for clinicians, researchers, and policymakers.

Strategic diagnosis- Unraveling Tuberculosis- A comprehensive approach

Tuberculosis, an airborne-infectious disease caused by Mycobacterium tuberculosis remains a perpetual threat globally. It claims over 1.4 million lives per year. Various diagnostic strategies including smear microscopy, culture methods, immunochromatographic assays and molecular methods have paved the way for tuberculosis diagnosis. The Government of India has introduced National Strategic Plan (NSP) for TB elimination, aiming to achieve a rapid decline in the incidence, morbidity, and mortality of TB by the year 2030. In its quest for TB elimination, the plan is structured around four strategic pillars: "Detect-Treat-Prevent-Build." To achieve these pillars and progress towards TB elimination, the government encourages adoption of novel point-of- care diagnostics techniques.

Prevalence and causes of rifampicin-resistance genotypic/phenotypic discrepancy detected on Xpert MTB/RIF in Singapore

The Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) (Cepheid, Sunnyvale, CA, US) has been pivotal in tuberculosis (TB) diagnostics, enabling the rapid detection of both TB and RIF resistance. Xpert, a nucleic acid amplification test (NAAT), is recommended by both the World Health Organization (WHO)1 and Singapore’s clinical management guidelines2 as a frontline diagnostic tool for TB and RIF resistance. With a high specificity rate (98%) in detecting RIF resistance, Xpert has a positive predictive value (PPV) exceeding 90% in settings where the prevalence of RIF resistance is above 15%.3 However, in Singapore, a country with medium-incidence of TB and low prevalence of RIF resistance (<1% among individuals born in Singapore), 4 the PPV of detecting RIF resistance via Xpert is substantially lower.3 Phenotypic-genotypic discrepant RIF resistance have been reported to result from technical errors, false-positive results in paucibacillary samples,5 silent mutations6 or disputed mutations where minimal inhibitory concentrations (MICs) fall below critical concentrations in phenotypic drug susceptibility testing (pDST) systems.7 We conducted a quality assessment of sputum samples which tested positive for TB and RIF resistance using point-of-care Xpert at the Singapore National Tuberculosis Care Centre (NTBCC) to determine the prevalence and causes of false-positive RIF resistance.

Impact of isoniazid monoresistance on overall and vulnerable patient populations in Taiwan

Isoniazid is an early bactericidal anti-tuberculosis (TB) agent and isoniazid mono-resistance TB is the most prevalent drug-resistant TB worldwide. Concerns exist regarding whether resistance to isoniazid would lead to delayed culture conversion and worst outcomes. From January 2008 to November 2017, adult culture-positive pulmonary TB patients receiving isoniazid, rifampicin, pyrazinamide, and ethambutol were identified through Taiwan Center for Disease Control database and were followed until the end of 2017. Primary outcomes included time to sputum culture conversion (SCC) within two months. Secondary outcomes included death and unfavourable outcomes at the end of 2nd month. A total of 37,193 drug-susceptible and 2,832 isoniazid monoresistant pulmonary TB patients were identified. Compared with no resistance, isoniazid monoresistance was not associated with a delayed SCC (HR: 0.99, 95% CI: 0.94─1.05, p = 0.8145), a higher risk of 2-month mortality (HR: 1.19, 95% CI: 0.92─1.53, p = 0.1884), and unfavourable outcomes at 2nd month (OR: 1.05, 95% CI: 0.97─1.14, p = 0.2427). Isoniazid monoresistance was associated with delayed SCC (HR: 0.90, 95% CI: 0.83─0.98, p = 0.0099) and a higher risk of unfavourable outcomes (OR:1.18, 95% CI: 1.05─1.32, p = 0.0053) in patients aged between 20 and 65, and delayed SCC in patients without underlying comorbidities (HR: 0.90, 95% CI: 0.81─0.98, p = 0.0237). Isoniazid mono-resistant TB had a comparable outcome with drug-susceptible TB at the end of the intensive phase. Healthy, and non-elderly patients were more likely to had culture persistence, raising concerns about disease transmission in these subgroups and warranting early molecular testing for isoniazid resistance.

Phenotypic and genotypic analysis of drug resistance in M. tuberculosis isolates in Gansu, China

Tuberculosis has posed a serious threat to human health. It is imperative to investigate the geographic prevalence of tuberculosis and medication resistance, as this information is essential for informing strategies for its prevention and treatment. Drug resistance was identified using a proportion method. Drug-resistant genes and pathways were predicted using whole genome sequencing. The drug resistance range of bedaquiline was identified using the microporous plate two-fold dilution method, and drug resistance genes were studied using sequencing. The study revealed that 19.99% of the tuberculosis cases had multidrug resistance. The genes of M. tuberculosis are predominantly involved in the synthesis of ABC transporters, two-component systems, and bacterial secretion systems, as well as in energy production and conversion, and lipid transport and metabolism. The genes encode for 82.45% of carbohydrate-related enzymes such as glycoside hydrolases, glycosyl transferases, and carbohydrate esterases. The minimum inhibitory concentration (MIC) of bedaquiline against clinical strains was approximately 0.06 μg/mL, with identified mutations in drug-resistant genes Rv0678, atpE, and pepQ, specifically V152A, P62A, and T222N, respectively. The multidrug resistance tuberculosis development was attributed to the strong medication resistance exhibited. It was concluded that tuberculosis had presented a high level of drug resistance. Phenotypic resistance was related to genes, existing potential genetic resistance in M. tuberculosis. Bedaquiline was found to possess effective antibacterial properties against M. tuberculosis.

A case of eosinophilic granulomatosis with polyangiitis combined with pulmonary tuberculosis: A case report

RATIONALE

Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare autoimmune disease that can affect multiple organ systems. The standard treatment mainly relies on glucocorticoids and immunosuppressive agents. In our study, we present an EGPA patient who had pulmonary tuberculous mycobacteria infection, such cases are rarely reported.

PATIENT CONCERNS

A 71-year-old male patient was diagnosed with EGPA (systemic type) and pulmonary tuberculosis simultaneously.

DIAGNOSES

The Five-Factor score indicated that the patient required glucocorticoids combined with immunosuppressive agents for induction therapy, however, the use of immunosuppressive agents would significantly inhibit antituberculosis treatment. Nowadays, treating active autoimmune disease in patients with infections remains a clinical challenge.

INTERVENTIONS

Considering the patient did not show life-threatening or severe organ involvement and reduced the effect of antituberculosis immunity, we used glucocorticoids alone.

OUTCOMES

Finally, the patient had no adverse events, the eosinophil counts were markedly decreased and symptoms of EGPA were relieved.

LESSONS

The patient of EGPA combined with pulmonary tuberculosis successfully treated with glucocorticoids alone may provide significant support in selecting the appropriate treatments for similar cases in the future.

A multi-AS-PCR-coupled CRISPR/Cas12a assay for the detection of ten single-base mutations

Single-nucleotide polymorphism (SNP) detection is critical for diagnosing diseases, and the development of rapid and accurate diagnostic tools is essential for treatment and prevention. Allele-specific polymerase chain reaction (AS-PCR) is widely used for detecting SNPs with multiplexing capabilities, while CRISPR-based technologies provide high sensitivity and specificity in targeting mutation sites through specific guide RNAs (gRNAs). In this study, we have integrated the high sensitivity and specificity of CRISPR technology with the multiplexing capabilities of AS-PCR, achieving the simultaneous detection of ten single-base mutations. As for Multi-AS-PCR, our research identified that competitive inhibition of primers targeting the same loci, coupled with divergent amplification efficiencies of these primers, could result in diminished amplification efficiency. Consequently, we adjusted and optimized primer combinations and ratios to enhance the amplification efficacy of Multi-AS-PCR. Finally, we successfully developed a novel nested Multi-AS-PCR-Cas12a method for multiplex SNPs detection. To evaluate the clinical utility of this method in a real-world setting, we applied it to diagnose rifampicin-resistant tuberculosis (TB). The limit of detection (LoD) for the nested Multi-AS-PCR-Cas12a was 102 aM, achieving sensitivity, specificity, positive predictive value, and negative predictive value of 100 %, 93.33 %, 90.00 %, and 100 %, respectively, compared to sequencing. In summary, by employing an innovative design that incorporates a universal reverse primer alongside ten distinct forward allele-specific primers, the nested Multi-AS-PCR-Cas12a technique facilitates the parallel detection of ten rpoB gene SNPs. This method also holds broad potential for the detection of drug-resistant gene mutations in infectious diseases and tumors, as well as for the screening of specific genetic disorders.

Evaluating Truenat Assay for the Diagnosis of Ocular Tuberculosis and Detection of Drug Resistance

BACKGROUND

Truenat MTB Plus assay was evaluated for diagnosing ocular tuberculosis (OTB) and detecting multi-drug resistant (MDR) and extremely-drug resistant (XDR) OTB.

METHODS

A total of 75 vitreous fluid specimens [five confirmed OTB, 40 clinically suspected OTB and 30 controls] were subjected to Truenat MTB Plus, multiplex PCR, and Xpert Ultra. Chips of Truenat were used for detecting rifampicin, isoniazid, fluoroquinolone and bedaquiline resistance. The performance was compared against culture, composite reference standard, and gene sequencing.

RESULTS

The overall sensitivity of TruePlus, MPCR, and Ultra in diagnosing OTB was 66.6%, 73.3%, and 55.5%, respectively. Out of six cases with mutations in rpoB gene, RifR was detected in five by TrueRif and four by Ultra. Three MDR and one XDR-OTB were reported by Truenat.

CONCLUSION

Truenat assay along with its strategic chips is a rapid and reliable tool for diagnosis of OTB and detection of drug resistance, including MDR and XDR-OTB.Abbreviations: OTB: Ocular tuberculosis; XDR: Extremely drug resistant; Ultra: Xpert MTB/RIF Ultra; Xpert: Xpert MTB/RIF; PCR: polymerase chain reaction; NAATs: Nucleic acid amplification tests; MDR: Multi Drug Resistant; NSP: National Strategic plan for elimination of tuberculosis; FqR: Fluoroquinolone resistant; BdqR: bedaquiline resistant; TrueRif: Truenat MTB Rif Dx; TruePlus: Truenat Plus; INH: Isoniazid; DST: Drug susceptibility testing; MGIT: Mycobacterial growth indicator tube; CRF: Composite reference standard; PPV: positive predictive value; NPV: negative predictive value; EPTB: extrapulmonary tuberculosis; VF: vitreous fluid; DNA: deoxyribonucleic acid; ATT: antitubercular therapy; RifR: Rifampicin resistance; RifS: Rifampicin susceptible; RifI: Rifampicin indeterminate.

Decoding drug resistance in Mycobacterium tuberculosis complex: genetic insights and future challenges

INTRODUCTION

Tuberculosis (TB), particularly its drug-resistant forms (MDR-TB and XDR-TB), continues to pose a significant global health challenge. Despite advances in treatment and diagnosis, the evolving nature of drug resistance in Mycobacterium tuberculosis (MTB) complicates TB eradication efforts. This review delves into the complexities of anti-TB drug resistance, its mechanisms, and implications on healthcare strategies globally.

AREAS COVERED

We explore the genetic underpinnings of resistance to both first-line and second-line anti-TB drugs, highlighting the role of mutations in key genes. The discussion extends to advanced diagnostic techniques, such as Whole-Genome Sequencing (WGS), CRISPR-based diagnostics and their impact on identifying and managing drug-resistant TB. Additionally, we discuss artificial intelligence applications, current treatment strategies, challenges in managing MDR-TB and XDR-TB, and the global disparities in TB treatment and control, translating to different therapeutic outcomes and have the potential to revolutionize our understanding and management of drug-resistant tuberculosis.

EXPERT OPINION

The current landscape of anti-TB drug resistance demands an integrated approach combining advanced diagnostics, novel therapeutic strategies, and global collaborative efforts. Future research should focus on understanding polygenic resistance and developing personalized medicine approaches. Policymakers must prioritize equitable access to diagnosis and treatment, enhancing TB control strategies, and support ongoing research and augmented government funding to address this critical public health issue effectively.

Development and clinical evaluation of a real-time multiple cross displacement amplification assay for rapid and sensitive detection of Mycobacterium tuberculosis

Molecular techniques of nucleic acid testing recommended by the World Health Organization (WHO) for the Mycobacterium tuberculosis (MTB) detection were considered to have the potential access to the accurate tuberculosis (TB) notifications. In this study, a new method, which coupled real-time (rt) fluorescence technique with multiple cross displacement amplification (MCDA), was developed for the rapid, sensitive and specific detection of MTB (termed MTB-rt-MCDA). According to the principle of the rt-MCDA test, a set of ten primers were designed for the MCDA reaction, of which one was engineered with a restrictive endonuclease recognition site, a fluorophore and a quencher for achieving the real-time fluorescence detection. MTB-rt-MCDA test was conducted under the optimized conditions (67 °C, 40 min) on the real-time fluorescence platform. The MTB-rt-MCDA assay accurately identified the MTB strains with no cross reaction with other bacteria. The lowest detectable genomic DNA concentration of the MTB-rt-MCDA assay was 25 fg/μl. We employed the genomic DNA templates extracted from sputum of clinical cases for validating the practical applicability of this assay, and the detection power of the MTB-rt-MCDA assay was comparable to that of the Xpert method and MCDA-based biosensor detection and superior to smear microscope method. The complete process of the MTB-rt-MCDA assay, including rapid extraction of DNA and rt-MCDA test, takes less than 1 h. In conclusion, the presented MTB-rt-MCDA assay provided an effective and simple option for the rapid screening of MTB infection.

Case report: Difficult diagnosis of Mycobacterium tuberculosis infection in patients after allogeneic hematopoietic stem cell transplantation: two case reports and a literature review

Background

Mycobacterium tuberculosis (MTB) is a relatively infrequent infection encountered during hematopoietic stem-cell transplantation (HSCT). The identification of MTB following HSCT remains a complex task, with delayed detection and misdiagnosis potentially resulting in unfavorable outcomes. Metagenomic next-generation sequencing (mNGS) represents a novel, highly sensitive, and rapid diagnostic tool in clinical settings for discerning intricate infections and detecting exceedingly rare pathogens.

Methods

With the aid of mNGS, we diagnosed MTB in the lymph nodes and lungs of two patients with hematological diseases following allogeneic peripheral blood hematopoietic stem cell transplantation. Both patients presented with a fever, localized symptoms, and clinical signs. Following inconclusive results from routine tests, impractical biopsy procedures, and unsuccessful responses to empirical treatments, mNGS was employed as a final recourse, revealing DNA fragments of MTB in blood samples.

Results

The diagnoses were ultimately confirmed in conjunction with additional clinical evidence. The application of mNGS in MTB cases after allogeneic HSCT has rarely been reported. The mNGS technique can provide a prompt and highly sensitive indication leading to the definitive diagnosis of MTB in complex post-transplant scenarios.

Diagnostic Role of Metagenomic Next-Generation Sequencing in Tubercular Orthopedic Implant-Associated Infection

Objective

The diagnosis of tubercular orthopedic implant-associated infection (TB-IAI) is challenging. This study evaluated the value of metagenomic next-generation sequencing (mNGS) for the diagnosis of TB-IAI and developed a standardized diagnostic procedure for TB-IAI.

Methods

The records of all patients with TB-IAI diagnosed and treated at our institution between December 2018 and September 2022 were retrospectively reviewed. Patient demographic characteristics, medical history, laboratory test, microbial culture, histopathology, and mNGS results, and time to diagnosis were recorded. The diagnostic efficiency of mNGS for TB-IAI was assessed by comparing the results and diagnostic time with that of other diagnostic modalities.

Results

Ten patients were included in the analysis, including eight with prosthetic joint infections and two with fracture-related infections. The mNGS positivity rate was 100% (10/10), which was higher than that of TB-antibody (11%, 1/9), real-time quantitative polymerase chain reaction (22%, 2/9), T-SPOT.TB (25%, 2/8), purified protein derivative (50%, 4/8), microbial culture (50%, 5/10), and histopathology (20%, 2/10). mNGS shortened the time to diagnosis of TB-IAI. A standardized diagnostic procedure for TB-IAI was developed based on the findings.

Conclusion

mNGS is useful for the diagnosis of TB-IAI. mNGS is recommended in cases where it is difficult to identify a pathogen using routine diagnostic tests. The standardized diagnostic procedure might improve TB-IAI diagnosis.

Importance

TB-IAI is a rare infection, which occurs after orthopedic surgery and hard to diagnose microbiologically. mNGS is a new detection technique not yet discussed in current literature as a means for TB-IAI diagnostics. Here we describe a cohort of patients with TB-IAI diagnosed by mNGS show high efficiency of mNGS for detection of this pathology and present a clinical algorithm supplementing conventional methods for TB-IAI assessment.

Evidence for Tuberculosis in Individuals With Xpert Ultra "Trace" Sputum During Screening of High-Burden Communities

BACKGROUND

"Trace" results on Xpert MTB/RIF Ultra ("Ultra"; Cepheid) -a molecular diagnostic test for tuberculosis (TB)-are often interpreted as an indication for TB treatment, but may also represent detection of nonviable bacilli or analytical error. In community-screening settings where individual TB risk is low, there is limited guidance on how to interpret Ultra-trace results.

METHODS

We conducted systematic Ultra TB screening of adults and adolescents (≥15 years) in Kampala, Uganda, through door-to-door and event-based sputum collection. We enrolled individuals with trace-positive sputum for detailed clinical, radiographic, and microbiological (including 2 sputum cultures, repeat Ultra, and for people with HIV, urine lipoarabinomannan) evaluation, and compared those findings with similar evaluations in controls with Ultra-negative and Ultra-positive (non-trace) sputum.

RESULTS

Of 21 957 people screened with Ultra, 211 (1.0%) tested positive, including 96 (46% of positives) with trace results. Of 92 people enrolled with trace-positive sputum; 12% (11/92) were HIV-positive and 14% (13/92) had prior TB. The prevalence of TB among participants with trace-positive sputum results was 14% (13/92) by culture, 24% (22/92) using broader microbiological criteria, and 26% (24/92) after accounting for clinical diagnosis. The prevalence of cough and of abnormal chest computed tomography (CT) findings were 32% and 26%, respectively, if Ultra-negative; 34% and 54% if trace-positive/non-microbiologically confirmed; 72% and 95% if trace-positive/microbiologically confirmed; and 71% and 93% if Ultra-positive (more than trace).

CONCLUSIONS

Most individuals with trace-positive sputum in Ugandan communities did not have microbiologically confirmed TB but had more symptoms and chest CT abnormalities than people with Ultra-negative sputum.

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.

Pooling sputum samples for the Xpert MTB/RIF assay: a practical screening strategy for highly infectious tuberculosis cases

The Xpert MTB/RIF test (Xpert) can help in the accurate screening of tuberculosis, however, its widespread use is limited by its high cost and lack of accessibility. Pooling of sputum samples for testing is a strategy to cut expenses and enhance population coverage but may result in a decrease in detection sensitivity due to the dilution of Mycobacterium tuberculosis (Mtb) by sample mixing. We investigated how the mixing ratio affected the detection performance of Xpert. We used frozen sputum samples that had been kept after individual Xpert assays of the sputa from Mtb-confirmed TB patients and non-TB patients. Our results showed that the overall sensitivity of the Xpert pooling assay remained higher than 80% when the mixing ratio was between 1/2 and 1/8. When the mixing ratio was raised to 1/16, the positive detection rate fell to 69.0%. For patients with either a high sputum Mtb smear score ≥ 2+, a time-to-positive culture ≤ 10 days, or an Xpert test indicating a high or medium abundance of bacteria, the pooling assay positivity rates were 93.3%, 96.8%, and 100% respectively, even at a 1/16 mixing ratio. For participants with cavities and cough, the pooling assay positivity rates were 86.2% and 90.0% at a 1/8 ratio, higher than for those without these signs. Our results show that the Xpert pooled assay has a high overall sensitivity, especially for highly infectious patients. This pooling strategy with lower reagent and labor costs could support TB screening in communities with limited resources, thereby facilitating reductions in the community transmission and incidence of TB worldwide.

Spatial spillover effect of environmental factors on the tuberculosis occurrence among the elderly: a surveillance analysis for nearly a dozen years in eastern China

BACKGROUND

In many areas of China, over 30% of tuberculosis cases occur among the elderly. We aimed to investigate the spatial distribution and environmental factors that predicted the occurence of tuberculosis in this group.

METHODS

Data were collected on notified pulmonary tuberculosis (PTB) cases aged ≥ 65 years in Zhejiang Province from 2010 to 2021. We performed spatial autocorrelation and spatial-temporal scan statistics to determine the clusters of epidemics. Spatial Durbin Model (SDM) analysis was used to identify significant environmental factors and their spatial spillover effects.

RESULTS

77,405 cases of PTB among the elderly were notified, showing a decreasing trend in the notification rate. Spatial-temporal analysis showed clustering of epidemics in the western area of Zhejiang Province. The results of the SDM indicated that a one-unit increase in PM2.5 led to a 0.396% increase in the local notification rate. The annual mean temperature and precipitation had direct effects and spatial spillover effects on the rate, while complexity of the shape of the greenspace (SHAPE_AM) and SO2 had negative spatial spillover effects.

CONCLUSION

Targeted interventions among the elderly in Western Zhejiang may be more efficient than broad, province-wide interventions. Low annual mean temperature and high annual mean precipitation in local and neighboring areas tend to have higher PTB onset among the elderly.

How has the municipal availability of the GeneXpert®MTB/RIF system affected the detection of drug-resistant tuberculosis in Brazil?

OBJECTIVE

To evaluate the association between the availability of GeneXpert®MTB/RIF in municipalities and the proportion of people who have access to this diagnostic technology for tuberculosis (TB), as well as the resistance detected by the surveillance system in Brazil.

METHODS

We analysed 4998 Brazilian municipalities that reported 432,937 new TB cases between 2015 and 2020. We compared municipalities with and without the availability of GeneXpert®MTB/RIF regarding the effective access to GeneXpert®MTB/RIF diagnosis and the prevalence of detected resistance.

RESULTS

Municipalities with at least one GeneXpert®MTB/RIF system had three times (95% CI 2.9-3.0) the access to diagnostic tests and 80.4% (95% CI 70.6%-90.2%) higher detection of resistance, compared with municipalities without this technology. We estimated that there have been 1890 cases of undetected resistance during this period in the country.

CONCLUSIONS

The availability of GeneXpert®MTB/RIF system in the municipality increased the sensitivity of the surveillance for detecting TB resistance.

PUBLIC HEALTH IMPLICATIONS

It is a priority to strengthen laboratory networks and narrow the gap in access to rapid diagnosis in remote areas to improve the detection and control of drug-resistant tuberculosis.

A novel chemokine biomarker to distinguish active tuberculosis from latent tuberculosis: a cohort study

BACKGROUND

Interferon-γ release assays (IGRAs), which are widely used to diagnose tuberculosis (TB), cannot effectively discriminate latent TB infection (LTBI) from active TB (ATB). This study aimed to identify potential antigen-specific biomarkers for differentiating LTBI cases from ATB cases.

METHODS

Ongoing recruitment was conducted of individuals meeting study inclusion criteria at Beijing Chest Hospital from May 2020 to April 2022; 208 participants were enrolled and assigned to three groups: HC (60 healthy controls), LTBI (52 subjects with LTBI) and ATB (96 ATB patients). After participants were assigned to the discovery cohort (20 or 21 subjects/group), all others were assigned to the verification cohort. Discovery cohort blood levels of 40 chemokines were measured using Luminex assays to identify chemokines that could be used to discriminate LTBI cases from ATB cases; candidate biomarkers were verified using enzyme-linked immunosorbent assay-based testing of validation cohort samples.

RESULTS

Luminex results revealed highest ATB group levels of numerous cytokines, growth factors and chemokines. Receiving operating characteristic curve-based analysis of 40 biomarkers revealed CCL8 (AUC = 0.890) and CXCL9 (AUC = 0.883) effectively discriminated between LTBI and TB cases; greatest diagnostic efficiency was obtained using both markers together (AUC = 0.929). Interpretation of CCL8 and CXCL9 levels for validation cohort IGRA-positive subjects (based on a 0.658-ng/ml cutoff) revealed ATB group CCL8-based sensitivity and specificity rates approaching 90.79% and 100.00%, respectively.

CONCLUSION

TB-specific chemokines hold promise as ATB diagnostic biomarkers. Additional laboratory confirmation is needed to establish whether CCL8-based assays can differentiate between ATB and LTBI cases, especially for bacteriologically unconfirmed TB cases.

Clinical utility of metagenomic next-generation sequencing in pathogen detection for lower respiratory tract infections and impact on clinical outcomes in southernmost China

Background

Today, metagenomic next-generation sequencing (mNGS) has emerged as a diagnostic tool for infections. However, since Hainan has a complicated pathogen spectrum, the diagnostic value and impact on patient outcomes of mNGS in Hainan are to be explored.

Methods

From April 2020 to October 2021, 266 suspected lower respiratory tract infections (LRTIs) patients in Hainan were enrolled, and specimens were collected before antibiotic treatment. Bronchoalveolar lavage fluid (BALF) samples were subjected to mNGS and culture to compare the diagnostic performance. Other conventional microbiological tests (CMT) were also performed. Patients' treatments and clinical outcomes were recorded, and the antibiotic resistance genes (ARGs) were detected via mNGS workflow.

Results

The positive rate of mNGS outperformed that of culture (87.55% vs. 39.30%, p<0.001) and CMT (87.12% vs. 52.65%, p<0.001). Specifically, mNGS detected more P. aeruginosa (12.03% vs 9.02%, p<0.05), H. influenzae (9.77% vs 2.26%, p<0.001), Aspergillus fumigatus (3.00% vs 0.75%, p<0.05), Candida albicans (26.32% vs 7.52%, p<0.001) and uncommon pathogens. It also demonstrated great diagnostic advantages in Mycobacterium tuberculosis with 80% sensitivity and 97.4% specificity. Over half of the patients (147, 55.26%) had modified empirical treatment according to mNGS results and 89.12% of them responded well. For three deaths with modified treatment, multiple drug resistance was predicted by mNGS and confirmed by antibiotic susceptibility test.

Conclusions

The application of mNGS can benefit clinics in pathogen identification and antimicrobial treatment stewardship. Physicians should be alert to some emerging uncommon pathogens, including Chlamydia Psittaci, Nocardia otitidiscaviarum, and rare NTM.

Evaluating the Sensitivity of Different Molecular Techniques for Detecting Mycobacterium tuberculosis Complex in Patients with Pulmonary Infection

This study aimed to evaluate the accuracy of detecting drug-resistant Mycobacterium tuberculosis complex (MTBC)-specific DNA in sputum specimens from 48 patients diagnosed with pulmonary tuberculosis. The presence of MTBC DNA in the specimens was validated using the GeneXpert MTB/RIF system and compared with a specific PCR assay targeting the IS6110 and the mtp40 gene sequence fragments. Additionally, the results obtained by multiplex PCR assays to detect the most frequently encountered rifampin, isoniazid, and ethambutol resistance-conferring mutations were matched with those obtained by GeneXpert and phenotypic culture-based drug susceptibility tests. Of the 48 sputum samples, 25 were positive for MTBC using the GeneXpert MTB/RIF test. Nevertheless, the IS6110 and mtp40 single-step PCR revealed the IS6110 in 27 of the 48 sputum samples, while the mtp40 gene fragment was found in only 17 of them. Furthermore, multiplex PCR assays detected drug-resistant conferring mutations in 21 (77.8%) of the 27 samples with confirmed MTBC DNA, 10 of which contained single drug-resistant conferring mutations towards ethambutol and two towards rifampin, and the remaining nine contained double-resistant mutations for ethambutol and rifampin. In contrast, only five sputum specimens (18.5%) contained drug-resistant MTBC isolates, and two contained mono-drug-resistant MTBC species toward ethambutol and rifampin, respectively, and the remaining three were designated as multi-drug resistant toward both drugs using GeneXpert and phenotypic culture-based drug susceptibility tests. Such discrepancies in the results emphasize the need to develop novel molecular tests that associate with phenotypic non-DNA-based assays to improve the detection of drug-resistant isolates in clinical specimens in future studies.

Comparative performance of microbiological methods for the detection of tuberculous meningitis pathogens in cerebrospinal fluid

The aim of this study was to comprehensively evaluate metagenomic next-generation sequencing (mNGS), Acid-fast bacillus stain (AFB), MGIT960 culture, polymerase-chain-reaction (PCR), and Xpert MTB/RIF in the diagnosis of tuberculous meningitis (TBM). A cohort of 280 patients who presented with suspected TBM (ie, headache or altered mental status with clinical signs of meningism) were analyzed. The sensitivities of the 5 assays for the diagnosis of TBM ranged from 10.0% to 70.0%. The AFB had the lowest sensitivity of 10.0% (0.5-45.9), while mNGS and PCR had the highest sensitivity, both at 70.0% (35.4-91.9). mNGS demonstrated a distinct advantage in identifying a wider array of pathogens, including viruses, in CSF samples. PCR was a cost-effective option with excellent sensitivity and specificity. However, no single method was statistically significantly better than any other in the diagnosis of TBM. New diagnostic techniques are urgently needed for the independent, rapid and accurate detection of Mycobacterium tuberculosis to guide the diagnosis of TBM.

Comparison of Xpert MTB/RIF Ultra with Xpert MTB/RIF for the detection of Mycobacterium tuberculosis and rifampicin resistance in a primary-level clinic in rural China

The Xpert MTB/RIF Ultra (Ultra) is not yet used for the diagnosis of tuberculosis (TB) in China. We compared the performance of the Xpert and Ultra for detecting Mycobacterium tuberculosis and rifampicin resistance in a primary-level clinic in rural China. Sputum samples from suspected pulmonary TB patients were collected and subjected to smear microscopy, liquid culture, Xpert and Ultra tests. We then compared the sensitivity and specificity of Xpert and Ultra for diagnosing TB against liquid culture. Whole-genome sequencing was performed to predict rifampicin resistance and the results were compared with the Xpert and Ultra tests. The sensitivities of Xpert and Ultra were 88.1% and 95.1%, and the specificities were 91.9% and 84.4%, respectively. Among the 61 smear-negative culture-positive patients, the sensitivities of Xpert and Ultra were 80.3% and 91.8%. All Xpert-positive patients were Ultra-positive. Among culture-negative Xpert or Ultra-positive patients, 69.6% were taking anti-TB drugs or had a previous history of TB. Of the samples that Ultra classified as trace, nearly 25% were probably false-positives. Both Xpert and Ultra accurately detected all rifampicin-resistant patients. In conclusion, Ultra was more sensitive than Xpert, especially for smear-negative patients but had decreased specificity with more false-positives, especially with Ultra trace results.

Time-to-detection in culture of Mycobacterium tuberculosis: performance for assessing index cases contact-positivity

OBJECTIVES

Time-to-detection (TTD) in culture on liquid media is inversely correlated to bacillary load and should be a contributing factor for assessing tuberculosis transmission. We wanted to assess if TTD was a better alternative than smear status to estimate transmission risk.

METHODS

From October 2015 to June 2022, we retrospectively studied a cohort of index cases (IC) with pulmonary tuberculosis (tuberculosis disease [TD]) from which samples were culture-positive before treatment. We studied the correlation between TTD and contact-positivity (CP) of IC contacts: CP was defined as CP = 1 (CP group) in case of TD or latent tuberculosis infection (LTI) in at least one screened contact of an IC, and CP = 0 otherwise (contact-negativity [CN] group). Univariate and multivariable analyses (logistic regression) were done.

RESULTS

Of the 185 IC, 122 were included, generating 846 contact cases of which 705 were assessed. A transmission event (LTI or TD) was identified in 193 contact cases (transmission rate: 27%). At day 9, 66% and 35% of the IC had their sample positive in culture for CP and CN groups, respectively. Age and TTD ≤9 days were independent criteria of CP (odds ratio 0.97, confidence interval [0.95-0.98], P = 0.002 and odds ratio 3.52, confidence interval [1.59-7.83], P = 0.001, respectively).

CONCLUSION

TTD was a more discriminating parameter than smear status to evaluate the transmission risk of an IC with pulmonary tuberculosis. Therefore, TTD should be considered in the contact-screening strategy around an IC.

Recent advances in microbiological and molecular biological detection techniques of tuberculous meningitis

Tuberculous meningitis (TBM) is the most common type of central nervous system tuberculosis (TB) and has the highest mortality and disability rate. Early diagnosis is key to improving the prognosis and survival rate of patients. However, laboratory diagnosis of TBM is often difficult due to its paucibacillary nature and sub optimal sensitivity of conventional microbiology and molecular tools which often fails to detect the pathogen. The gold standard for TBM diagnosis is the presence of MTB in the CSF. The recognised methods for the identification of MTB are acid-fast bacilli (AFB) detected under CSF smear microscopy, MTB cultured in CSF, and MTB detected by polymerase chain reaction (PCR). Currently, many studies consider that all diagnostic techniques for TBM are not perfect, and no single technique is considered simple, fast, cheap, and efficient. A definite diagnosis of TBM is still difficult in current clinical practice. In this review, we summarise the current state of microbiological and molecular biological diagnostics for TBM, the latest advances in research, and discuss the advantages of these techniques, as well as the issues and challenges faced in terms of diagnostic effectiveness, laboratory infrastructure, testing costs, and clinical expertise, for clinicians to select appropriate testing methods.

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.

What's new in childhood tuberculosis

PURPOSE OF REVIEW

The current review identifies recent advances in the prevention, diagnosis, and treatment of childhood tuberculosis (TB) with a focus on the WHO's updated TB management guidelines released in 2022.

RECENT FINDINGS

The COVID-19 pandemic negatively affected global TB control due to the diversion of healthcare resources and decreased patient care-seeking behaviour. Despite this, key advances in childhood TB management have continued. The WHO now recommends shorter rifamycin-based regimens for TB preventive treatment as well as shorter regimens for the treatment of both drug-susceptible and drug-resistant TB. The Xpert Ultra assay is now recommended as the initial diagnostic test for TB in children with presumed TB and can also be used on stool samples. Point-of-care urinary lipoarabinomannan assays are promising as 'rule-in' tests for children with presumed TB living with HIV. Treatment decision algorithms can be used to diagnose TB in symptomatic children in settings with and without access to chest X-rays; bacteriological confirmation should always be attempted.

SUMMARY

Recent guideline updates are a key milestone in the management of childhood TB, and the paediatric TB community should now prioritize their efficient implementation in high TB burden countries while generating evidence to close current evidence gaps.

Clinical application of metagenomic next-generation sequencing in tuberculosis diagnosis

Objective

The purpose of this study was to evaluate the clinical diagnostic value of metagenomic next-generation sequencing (mNGS) for tuberculosis (TB).

Methods

This retrospective study included 52 patients with suspected TB infection. mNGS, targeted PCR, acid-fast staining and, T-SPOT.TB assay were performed on the specimen. The positive rate of mNGS and traditional detection methods was statistically analyzed. Pathological tests were performed when necessary.

Results

In total, 52 patients with suspected of TB in this study were included in the analysis, and 31 patients were finally diagnosed with TB. Among 52 patients, 14 (26.9%) cases were positive for acid-fast staining. The positive rate of T-SPOT.TB assay in 52 patients was 73.1% (38/52). Among 52 patients, 39 (75%) were detected positive for Mycobacterium tuberculosis (MTB) by mNGS. Regarding the detection rate of MTB, mNGS were as high as 75% (39/52), whereas acid-resistant staining was only 26.9% (14/52), which showed a statistically significant difference (p&lt;0.05). The positive rates of T-SPOT.TB assay and mNGS were not statistically significant (p&gt;0.05). Of the 52 suspected TB patients, 24 had targeted PCR, of which 18 were PCR positive. In 24 patients, the positive rate of PCR was 75%, and the positive rate of mNGS was 100%, with statistical difference between them (p&lt;0.05).

Conclusions

The detection rate of MTB by mNGS was higher than that by conventional acid-fast staining and PCR, but not statistically significant compared with T-SPOT.TB assay. As an adjunctive diagnostic technology, mNGS can be combined with traditional detection methods to play a guiding role in the diagnosis and treatment of TB.

A case report about a child with drug-resistant tuberculous meningitis

BACKGROUND

Hematogenous disseminated tuberculosis predisposes to concurrent tuberculous meningitis (TBM), the most devastating and disabling form of tuberculosis. However, children often have atypical clinical symptoms, difficulty in specimen collection, low specimen content, and an increasing incidence of drug-resistant tuberculosis. Thus, the accurate diagnosis and timely treatment of childhood tuberculosis face monumental challenges.

CASE PRESENTATION

The 14-year-old female presented to the hospital with intermittent fever, headache, and blurred vision. Her cerebrospinal fluid (CSF) showed a lymphocytic pleocytosis, an elevated protein level, and a decreased chloride level. And her CSF tested positive for TB-RNA. Xpert MTB/RIF detected Mycobacterium tuberculosis in her CSF, but the rifampin resistance test was unknown. Subsequently, her CSF culture was positive for Mycobacterium tuberculosis. The drug sensitivity test (DST) revealed resistance to isoniazid, rifampin, and fluoroquinolones. A computed tomography (CT) of the chest showed diffuse miliary nodules in both lungs. Intracranial enhanced magnetic resonance imaging (MRI) showed "multiple intensified images of the brain parenchyma, cisterns, and part of the meninges." The final diagnosis is miliary pulmonary tuberculosis and pre-extensive drug-resistant TBM. After 19 months of an oral, individualized antituberculosis treatment, she recovered with no significant neurological sequelae.

CONCLUSION

For patients with miliary pulmonary tuberculosis, especially children, even if there are no typical clinical symptoms, it is necessary to know whether there is TBM and other conditions. Always look for the relevant aetiological basis to clarify whether it is drug-resistant tuberculosis. Only a rapid and accurate diagnosis and timely and effective treatment can improve the prognosis and reduce mortality and disability rates.

Value analysis of next-generation sequencing combined with Xpert in early precise diagnosis of pulmonary tuberculosis

The current study aims to investigate the value of combination of NGS with Xpert MTB/RIF in the diagnosis of early pulmonary tuberculosis (PTB). A total of 85 patients with suspected PTB were analyzed retrospectively. The positive detection rates of PTB by Xpert MTB/RIF, TBseq Ultra, TB-DNA, and TB-RNA were significantly higher than those by acid-fast staining. Xpert MTB/RIF, TBseq Ultra, TB-DNA, and TB-RNA possessed higher sensitivity and accuracy than acid-fast stained smears. Kappa agreement analysis showed good agreement between Xpert MTB/RIF and TBseq Ultra. Combined diagnosis improves the detection sensitivity compared with a single diagnostic method. ROC curve analysis showed that Xpert MTB/RIF combined with TBseq Ultra showed the highest area under the curve (0.886). In conclusion, the combined diagnosis of TBseq Ultra and Xpert MTB/RIF harbors the characteristics of short cycle, high specificity and accuracy, which demonstrated a promising application value in the early diagnosis of PTB.

Performance of microbiological tests for tuberculosis diagnostic according to the type of respiratory specimen: A 10-year retrospective study

Background

The microbial diagnosis of tuberculosis (TB) remains challenging and relies on multiple microbiological tests performed on different clinical specimens. Polymerase chain reactions (PCRs), introduced in the last decades has had a significant impact on the diagnosis of TB. However, questions remain about the use of PCRs in combination with conventional tests for TB, namely microscopy and culture. We aimed to determine the performance of microscopy, culture and PCR for the diagnosis of pulmonary tuberculosis according to the type of clinical specimen in order to improve the diagnostic yield and to avoid unnecessary, time and labor-intensive tests.

Methods

We conducted a retrospective study (2008-2018) on analysis (34'429 specimens, 14'358 patients) performed in our diagnostic laboratory located in the Lausanne University Hospital to compare the performance of microbiological tests on sputum, induced sputum, bronchial aspirate and bronchoalveolar lavage (BAL). We analysed the performance using a classical "per specimen" approach and a "per patient" approach for paired specimens collected from the same patient.

Results

The overall sensitivities of microscopy, PCR and culture were 0.523 (0.489, 0.557), 0.798 (0.755, 0.836) and 0.988 (0.978, 0.994) and the specificity were 0.994 (0.993, 0.995), 1 (0.999, 1) and 1 (1, 1). Microscopy displayed no significant differences in sensitivity according to the type of sample. The sensitivities of PCR for sputum, induced sputum, bronchial aspirate and BAL were, 0.821 (0.762, 0.871), 0.643 (0.480, 0.784), 0.837 (0.748, 0.904) and 0.759 (0.624, 0.865) respectively and the sensitivity of culture were, 0.993 (0.981, 0.998), 0.980 (0.931, 0.998), 0.965 (0.919, 0.988), and 1 (0.961, 1) respectively. Pairwise comparison of specimens collected from the same patient reported a significantly higher sensitivity of PCR on bronchial aspirate over BAL (p < 0.001) and sputum (p < 0.05) and a significantly higher sensitivity of culture on bronchial aspirate over BAL (p < 0.0001).

Conclusions

PCR displayed a higher sensitivity and specificity than microscopy for all respiratory specimens, a rational for a smear-independent PCR-based approach to initiate tuberculosis microbial diagnostic. The diagnosis yield of bronchial aspirate was higher than BAL. Therefore, PCR should be systematically performed also on bronchial aspirates when available.

Diagnostic performance of adenosine deaminase for abdominal tuberculosis: A systematic review and meta-analysis

Background and aim

Abdominal tuberculosis (TB) is a common type of extrapulmonary TB with an insidious onset and non-specific symptoms. Adenosine deaminase (ADA) levels increase rapidly in the early stages of abdominal TB. However, it remains unclear whether ADA serves as a diagnostic marker for abdominal TB.

Methods

We performed a systematic literature search for relevant articles published in PubMed, Web of Science, Cochrane Library, and Embase up to April 2022. First, we used the Quality Assessment of Diagnostic Accuracy Studies tool-2 (QUADAS-2), to evaluate the quality of the included articles. Bivariate and hierarchical summary receiver operating characteristic (HSROC) models were then utilized to analyze pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR) and area under the receiver operating characteristic curve (AUROC). In addition, we explored a subgroup analysis for potential heterogeneity and publication bias among the included literature.

Results

Twenty-four articles (3,044 participants, 3,044 samples) which met the eligibility criteria were included in this study. The pooled sensitivity and specificity of ADA for abdominal TB detection were 93% [95% confidence interval (CI): 0.89-0.95] and 95% (95% CI: 0.93-0.96), respectively. PLR and NLR were 18.6 (95% CI: 14.0-24.6) and 0.08 (95% CI: 0.05-0.12), respectively. DOR and AUROC were 236 (95% CI: 134-415) and 0.98 (95% CI: 0.96-0.99), respectively. Furthermore, no heterogeneity or publication bias was found.

Conclusions

Our meta-analysis found ADA to be of excellent diagnostic value for abdominal TB and could be used as an auxiliary diagnostic tool.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier: CRD42022297931.

Accuracy of Xpert Ultra for the diagnosis of paediatric tuberculosis in a low TB burden country: a prospective multicentre study

Introduction

Childhood pulmonary tuberculosis (TB) remains a diagnostic challenge. This study aimed to evaluate the performance of Xpert Ultra for the diagnosis of pulmonary TB in children in a low TB prevalence setting.

Methods

Prospective, multicentre, diagnostic accuracy study. Children with clinical or radiological suspicion of pulmonary TB were recruited at 11 paediatric units in Spain. Up to three gastric or sputum specimens were taken on 3 consecutive days, and analysed by Xpert MTB/RIF, Xpert Ultra and culture in parallel.

Results

86 children were included (median age 4.9 years, IQR 2.0–10.0; 51.2% male). The final diagnosis was pulmonary TB in 75 patients (87.2%); 33 (44.0%) were microbiologically confirmed. A total of 219 specimens, comprising gastric aspirates (n=194; 88.6%) and sputum specimens (n=25; 11.4%), were analysed. Using culture as reference standard and comparing individual specimens, the sensitivity was 37.8% (14/37) for Xpert MTB/RIF and 81.1% (30/37) for Xpert Ultra (p<0.001); specificity was 98.4% (179/182) and 93.4% (170/182), respectively (p=0.02). In the per-patient analysis, considering positive results on any specimen, the sensitivity was 42.9% (9/21) for Xpert MTB/RIF and 81.0% for Xpert Ultra (17/21, p=0.01); specificity was 96.9% (63/65) and 87.7% (57/65, p=0.07), respectively.

Conclusions

In children with pulmonary TB in a low burden setting, Xpert Ultra has significantly higher sensitivity than the previous generation of Xpert assay and only marginally lower specificity. Therefore, in children undergoing evaluation for suspected pulmonary TB, Xpert Ultra should be used in preference to Xpert MTB/RIF whenever possible.

The Practical Value of Xpert MTB/RIF Ultra for Diagnosis of Pulmonary Tuberculosis in a High Tuberculosis Burden Setting: a Prospective Multicenter Diagnostic Accuracy Study

Due to the probability of decreased specificity, the practical value of performing the Xpert MTB/RIF Ultra (Xpert Ultra) assay over the Xpert assay for diagnosing pulmonary tuberculosis (TB) and rifampicin (RIF) resistance in a high TB burden setting was evaluated. Participants were recruited consecutively in three tertiary hospitals in China and allocated to the TB case detection and/or rifampicin (RIF) resistance detection group. Each sputum specimen was subjected to smear, MGIT960 liquid culture, and Xpert, and Xpert Ultra assay in parallel. Drug susceptibility testing was conducted for all recovered isolates in the RIF resistance detection group. In total, 1,079 patients were recruited to the case detection group and 450 to the RIF resistance detection group. Xpert Ultra had higher sensitivity than Xpert (92.26%, 322/349 versus 89.40%, 312/349; P = 0.006), whereas the most prominent increase was identified in the smear-negative patients (83.70% versus 78.52%; P = 0.039). The specificity of Xpert Ultra was slightly lower than that of Xpert (96.30%, 495/514 versus 98.25%, 505/514; P = 0.055). Reclassifying trace results as negative resulted in a 4.01% loss of sensitivity (from 92.26% to 88.25%) accompanied by a 1.37% gain in specificity (from 96.30% to 97.67%). Both the sensitivity (97.64% versus 99.21%, P = 0.313) and specificity (96.90% versus 97.21%, P = 0.816) of Xpert Ultra and Xpert for detection RIF resistance were comparable. In conclusion, Xpert Ultra could improve the diagnosis of smear-negative pulmonary TB in contrast to the Xpert assay. A high percentage of TB history did not significantly decrease the specificity of the test, which supports the potential role of Xpert Ultra as an initial diagnostic tool for TB. IMPORTANCE Xpert Ultra is more sensitive than Xpert, especially in smear-negative TB. A high percentage of TB history in the non-TB population did not significantly affect the reliability of the assay, which supports the potential role of Xpert Ultra as an initial diagnostic tool for TB.

Global trends of research on tuberculous pleurisy over the past 15 years: A bibliometric analysis

Tuberculous pleurisy (TP) is a common type of extrapulmonary tuberculosis (EPTB). With the development of research and changes in TP patient characteristics, an increasing number of studies have revealed the prevalence, risk factors, and novel diagnosis techniques. Thus, this bibliometric analysis was performed to identify global scientific output characteristics and research hotspots and frontiers for TP over the past 15 years. We searched the Web of Science Core Collection (WoSCC) Science Citation Index Expanded (SCI-expanded) for literature published between 2007 and 2021 and recorded their information. The Bibliometrix software package was used for bibliometric indicator analysis, and VOSviewer was used to visualize the trends of and hotspots in TP research. A total of 1,464 original articles were reviewed, and the results indicated that the annual number of publications (Np) focusing on TP has increased over the past 15 years. China had the largest number of papers and the highest H-index, and the United States ranked first for number of citations (Nc). EGYPTIAN KNOWLEDGE BANK and PLOS ONE were the most prolific unit and journal, respectively. The use of the Xpert assay and immune-related biomarker detection to diagnose TP appears to be a recent research hotspot. This bibliometric study demonstrated that the number of publications related to TP have tended to increase. China is a major producer, and the United States is an influential country in this field. Research in the past 15 years has been predominantly clinical research. The diagnosis of TP was the focus of research, and the exploration of novel diagnostic techniques, verification of diagnostic markers, and combination of diagnostic methods have been recent research hotspots. Immune-related biomarkers should be given more attention in the field of TP diagnosis.

Evaluation of trace calls by Xpert MTB/RIF ultra for clinical management in low TB burden settings

Background

Clinical interpretation of trace results by Xpert MTB/RIF Ultra assay (Ultra) used as an initial diagnostic test for tuberculosis (TB) may be challenging. The aim of the study was to evaluate the frequency and epidemiology of trace readouts in routine clinical practice in a low TB prevalence setting and to propose guidance on how to manage patients with trace calls considering the data available (clinical, radiological, bacteriological etc.).

Materials and methods

A retrospective, observational, monocentric study was conducted at IRCCS Azienda Ospedaliero-Universitaria of Bologna, Italy between November 2017—December 2020. Presumptive TB patients with at least one Ultra trace result during diagnostic workup before treatment were included in the study. Patients with ongoing anti-TB treatment at the time of the trace call result or with no clinical data available were excluded from the study.

Results

Fifty-nine presumptive TB patients with Ultra trace readouts were included in the study (mean age 37.0 years, 61% males). Four patients had a history of TB in the last 2 years. Twenty-five (42.4%) of the 59 samples with trace results were respiratory material. 57/59 (96.6%) patients started anti-TB treatment soon after obtaining trace results, based on clinical, radiological or other information available, while for two patients with a recent history of TB the trace result did not lead to anti-TB treatment. Culture was positive for M. tuberculosis for 31/59 (52.5%) samples with trace calls: 13/25 (52.0%) were respiratory samples and 18/33 (54.5%) non-respiratory samples. The clinical and/or radiological findings of 47/57 (82.4%) patients given anti-TB therapy improved during treatment.

Conclusion

In low TB incidence settings, Ultra trace calls in presumptive TB patients should be considered as true-positive and treatment should be started promptly, except in cases of recent history of TB, where careful evaluation of other diagnostic criteria is necessary before starting anti-TB treatment. A decisional algorithm for clinical management is proposed.

Xpert MTB/RIF Assay for the Diagnosis of Lymph Node Tuberculosis in Children: A Systematic Review and Meta-Analysis

Background: Lymph node tuberculosis (LNTB) is the leading type of extrapulmonary tuberculosis (EPTB) causing death in children. The Xpert MTB/RIF assay is a novel rapid test for the diagnosis of LNTB. Although previous evidence suggests that Xpert is reliably accurate in diagnosing EPTB in children, information is lacking for the specific type of LNTB in children. The aim of this study was to systematically assess the accuracy and reliability of Xpert for the diagnosis of LNTB in children. Methods: We systematically searched four databases, Embase, Cochrane Library, PubMed, and Web of Science, which extracted relevant data according to predefined inclusion and exclusion criteria. The data were analyzed by meta-Disc 1.4 and Stata 12.0 software to determine sensitivity, specificity, diagnostic odds ratio (DOR), etc. Results: A total of 646 samples from 8 studies were included in the analysis. The pooled sensitivity, specificity, negative likelihood ratio (NLR), positive likelihood ratio (PLR,) and combined diagnostic odds ratio (DOR) of Xpert for all samples were 0.79 (95% CI 0.70, 0.87), 0.90 (95% CI 0.86, 0.92), 0.29 (95% CI 0.19, 0.43), 7.20 (95% CI 3.32, 15.60), and 37.56 (95% CI 13.04, 108.15), respectively. The area under the curve (AUC) of the summary receiver operating characteristic (sROC) curve was 0.9050. Conclusion: Overall, Xpert showed moderate sensitivity and high specificity compared with culture in the diagnosis of LNTB in children. In addition, after analyzing the combined diagnostic odds ratio and positive LR, our study showed that Xpert has excellent diagnostic accuracy.

Differential Impact of the rpoB Mutant on Rifampin and Rifabutin Resistance Signatures of Mycobacterium tuberculosis Is Revealed Using a Whole-Genome Sequencing Assay

Drug resistance in Mycobacterium tuberculosis (MTB) has long been a serious health issue worldwide. Most drug-resistant MTB isolates were identified due to treatment failure or in clinical examinations 3~6 months postinfection. In this study, we propose a whole-genome sequencing (WGS) pipeline via the Nanopore MinION platform to facilitate the efficacy of phenotypic identification of clinical isolates. We used the Nanopore MinION platform to perform WGS of clinical MTB isolates, including susceptible (n = 30) and rifampin- (RIF) or rifabutin (RFB)-resistant isolates (n = 20) according to results of a susceptibility test. Nonsynonymous variants within the rpoB gene associated with RIF resistance were identified using the WGS analytical pipeline. In total, 131 variants within the rpoB gene in RIF-resistant isolates were identified. The presence of the emergent Asp531Gly or His445Gln was first identified to be associated with the rifampin and rifabutin resistance signatures of clinical isolates. The results of the minimum inhibitory concentration (MIC) test further indicated that the Ser450Leu or the mutant within the rifampin resistance-determining region (RRDR)-associated rifabutin-resistant signature was diminished in the presence of novel mutants, including Phe669Val, Leu206Ile, or Met148Leu, identified in this study.

IMPORTANCE Current approaches to diagnose drug-resistant MTB are time-consuming, consequently leading to inefficient intervention or further disease transmission. In this study, we curated lists of coding variants associated with differential rifampin and rifabutin resistant signatures using a single molecule real-time (SMRT) sequencing platform with a shorter hands-on time. Accordingly, the emerging WGS pipeline constitutes a potential platform for efficacious and accurate diagnosis of drug-resistant MTB isolates.

Bridging the Gap in End Tuberculosis Targets in the Elderly Population in Eastern China: Observational Study From 2015 to 2020

BACKGROUND

With a progressive increase in the aging process, the challenges posed by pulmonary tuberculosis (PTB) are also increasing for the elderly population.

OBJECTIVE

This study aimed to identify the epidemiological distribution of PTB among the elderly, forecast the achievement of the World Health Organization's 2025 goal in this specific group, and predict further advancement of PTB in the eastern area of China.

METHODS

All notified active PTB cases aged ≥65 years from Zhejiang Province were screened and analyzed. The general epidemiological characteristics were depicted and presented using the ArcGIS software. Further prediction of PTB was performed using R and SPSS software programs.

RESULTS

Altogether 41,431 cases aged ≥65 years were identified by the surveillance system from 2015 to 2020. After excluding extrapulmonary TB cases, we identified 39,832 PTB cases, including laboratory-confirmed (23,664, 59.41%) and clinically diagnosed (16,168, 40.59%) PTB. The notified PTB incidence indicated an evident downward trend with a reduction of 30%; however, the incidence of bacteriologically positive cases was steady at approximately 60/100,000. Based on the geographical distribution, Quzhou and Jinhua Cities had a higher PTB incidence among the elderly. The delay in PTB diagnosis was identified, and a significantly prolonged treatment course was observed in the elderly. Moreover, a 50% reduction of PTB incidence by the middle of 2024 was predicted using a linear regression model. It was found that using the exponential smoothing model would be better to predict the PTB trend in the elderly than a seasonal autoregressive integrated moving average model.

CONCLUSIONS

More comprehensive and effective interventions such as active PTB screening combined with physical checkup and succinct health education should be implemented and strengthened in the elderly. A more systematic assessment of the PTB epidemic trend in the elderly population should be considered to incorporate more predictive factors.

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.

Diagnostic Performance of Xpert MTB/RIF Ultra Compared with Predecessor Test, Xpert MTB/RIF, in a Low TB Incidence Setting: a Retrospective Service Evaluation

The aim of this study was to evaluate the performance of Xpert MTB/RIF Ultra (Ultra) compared with its predecessor, Xpert MTB/RIF (Xpert), in the diagnosis of tuberculosis (TB) in a low TB incidence country. Retrospective analysis was performed on 689 clinical samples received between 2015 and 2018, on which Xpert was performed, and on 715 samples, received between 2018 and 2020, on which Ultra was performed. Samples were pulmonary (n = 830) and extrapulmonary (n = 574) in nature, and a total of 264 were culture positive for Mycobacterium tuberculosis complex (MTBC). The diagnostic performance of both assays was analyzed using culture as the reference standard. The sensitivity of Ultra for culture positive (smear positive and smear negative) MTBC samples, was 93.2% (110/118) compared with 82.2% (120/146) for Xpert (P = 0.0078). In smear negative-culture positive samples, Ultra had a sensitivity of 74.2% (23/31) versus 36.11% (13/36) for Xpert (P = 0.0018). Specificity of both assays was comparable at 94.8% (566/597) for Ultra and 95.8% (520/543) for Xpert (P = 0.4475). The sensitivity of Ultra and Xpert assays among exclusively pulmonary samples was 95.3% (82/86) and 90.3% (84/93), respectively (P = 0.1955), and 87.5% (28/32) and 67.9% (36/53), respectively, among extrapulmonary samples (P = 0.0426). Ultra showed improved performance compared with Xpert in a low TB incidence setting, particularly in smear negative and extrapulmonary MTBC disease. The specificity of Ultra was lower than Xpert, however, this was not statistically significant. IMPORTANCE The study demonstrates the improved sensitivity of the Ultra compared with the Xpert, particularly in smear negative TB disease, for both pulmonary and extrapulmonary samples in a low TB incidence setting. Cycle threshold (Ct) value for both assays was found to positively correlate with time to TB culture positivity, suggesting that Ct and semiquantitative results could be used as indicators of sample MTBC bacillary burden, and thus, perhaps, of transmission potential. This may have implications for the designation of patient isolation precautions.

Diagnostic accuracy of nanopore sequencing using respiratory specimens in the diagnosis of pulmonary tuberculosis

OBJECTIVES

The aim of this study was to assess the role of nanopore sequencing using respiratory specimens in the early diagnosis of pulmonary tuberculosis (PTB) and simultaneously compare it head-to-head with Mycobacterium tuberculosis (MTB) culture, and Xpert MTB/rifampin (RIF).

METHODS

The clinical data of 164 patients with suspected PTB were retrospectively reviewed to determine the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) of the acid-fast bacilli (AFB) smear, MTB culture, Xpert MTB/RIF, and nanopore sequencing and assess their diagnostic accuracy compared with culture combined with clinical diagnosis.

RESULTS

The overall sensitivity, specificity, PPV, NPV, and AUC of the AFB smear were 27.6%, 87.5%, 84.2%, 33.3%, and 0.58, respectively; for MTB culture, these values were 57.8%, 100.0%, 100.0%, 49.5%, and 0.79, respectively; for Xpert MTB/RIF, these values were 62.9%, 97.9%, 98.7%, 52.2%, and 0.80, respectively; and for nanopore sequencing, these values were 94.8%, 97.9%, 99.1%, 88.7%, and 0.96, respectively.

CONCLUSION

The diagnostic accuracy of nanopore sequencing was excellent in terms of PTB diagnosis and was considerably better than that of the Xpert MTB/RIF and MTB culture. Nanopore sequencing could be an effective alternative to Xpert MTB/RIF for the initial detection of PTB to improve the accuracy of PTB diagnosis.

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.

Head-to-head comparison of the efficacy of Xpert MTB/RIF Ultra and Xpert MTB/RIF for the diagnosis of tuberculous pleurisy: A systematic review and meta-analysis

BACKGROUND

The aim of this study was to evaluate the diagnostic accuracy of Xpert MTB/RIF Ultra (Xpert Ultra) and Xpert MTB/RIF (Xpert) for the diagnosis of tuberculous pleurisy (TBP) head-to-head using meta-analysis method.

METHODS

On May 12, 2021, we searched multiple databases for reports that used Xpert Ultra and Xpert for TBP diagnosis head-to-head and screened eligible studies for inclusion. Accuracy of Xpert Ultra and Xpert were compared to that of the composite reference standard (CRS) and culture. When heterogeneity was evident, sources of heterogeneity were explored using subgroup analyses, sensitivity analysis, and meta-regression analyses.

RESULTS

Five articles met the inclusion criteria for meta-analysis. When results from different specimens or different reference standards were reported in the same article, we analyzed them as separate studies. Thus, 6 studies compared Xpert Ultra and Xpert with CRS, 5 studies compared Xpert Ultra and Xpert with culture. Pooled sensitivity and specificity of Xpert Ultra were 52% and 98% compared to CRS, and 82% and 77% compared to culture. Pooled sensitivity and specificity of Xpert were 22% and 99% compared to CRS, and 48% and 94% compared to culture. Significant heterogeneity in sensitivity was observed compared to CRS.

CONCLUSION

The sensitivity of Xpert Ultra was moderate but better than that of the Xpert; however, its specificity was lower. The role of Xpert Ultra and Xpert in the early and rapid diagnosis of TBP was limited.

Application of Metagenomic Next-Generation Sequencing in Mycobacterium tuberculosis Infection

The fight against Mycobacterium tuberculosis (MTB) has been going on for thousands of years, while it still poses a threat to human health. In addition to routine detections, metagenomic next-generation sequencing (mNGS) has begun to show presence as a comprehensive and hypothesis-free test. It can not only detect MTB without isolating specific pathogens but also suggest the co-infection pathogens or underlying tumor simultaneously, which is of benefit to assist in comprehensive clinical diagnosis. It also shows the potential to detect multiple drug resistance sites for precise treatment. However, considering the cost performance compared with conventional assays (especially Xpert MTB/RIF), mNGS seems to be overqualified for patients with mild and typical symptoms. Technology optimization of sequencing and analyzing should be conducted to improve the positive rate and broaden the applicable fields.