Clinical Characteristics and Radiologic Features of Immunocompromised Patients With Pauci-Bacillary Pulmonary Tuberculosis Receiving Delayed Diagnosis and Treatment

Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures

BACKGROUND

Blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease. However, an unresolved issue is whether gene set enrichment analysis of the signature transcripts alone is sufficient for prediction and differentiation or whether it is necessary to use the original model created when the signature was derived. Intra-method comparison is complicated by the unavailability of original training data and missing details about the original trained model. To facilitate the utilization of these signatures in TB research, comparisons between gene set scoring methods cross-data validation of original model implementations are needed.

METHODS

We compared the performance of 19 TB gene signatures across 24 transcriptomic datasets using both rrebuilt original models and gene set scoring methods. Existing gene set scoring methods, including ssGSEA, GSVA, PLAGE, Singscore, and Zscore, were used as alternative approaches to obtain the profile scores. The area under the ROC curve (AUC) value was computed to measure performance. Correlation analysis and Wilcoxon paired tests were used to compare the performance of enrichment methods with the original models.

RESULTS

For many signatures, the predictions from gene set scoring methods were highly correlated and statistically equivalent to the results given by the original models. In some cases, PLAGE outperformed the original models when considering signatures' weighted mean AUC values and the AUC results within individual studies.

CONCLUSION

Gene set enrichment scoring of existing gene sets can distinguish patients with active TB disease from other clinical conditions with equivalent or improved accuracy compared to the original methods and models. These data justify using gene set scoring methods of published TB gene signatures for predicting TB risk and treatment outcomes, especially when original models are difficult to apply or implement.

State-of-the-art detection of Mycobacterium tuberculosis in blood during tuberculosis infection using phage technology

Tuberculosis (TB), an aerosol-transmitted infection caused by Mycobacterium tuberculosis (Mtb), remains the commonest cause of death globally, from an infectious bacterial disease. Nine years on from the launch of the World Health Organization (WHO)'s END-TB strategy, disease incidence rates are stubbornly unchanged [1]. While this represents, in part, a reversal of improving trends caused by the COVID-19 pandemic, it also reflects the fragility and inadequacy of healthcare systems to sustain TB control [2]. Although multifactorial, a key reason for this is the ineffectiveness of existing clinical tools to meet the two key objectives of the END-TB strategy-(i) early diagnosis and treatment of TB disease (to limit onward transmission); and (ii) disease prevention through screening for asymptomatic TB infection (TBI). Meeting both objectives will rely on the development of new biomarkers with high accuracy, but the global nature of the TB problem also requires that new tests are rapid, low cost and can be measured in patients by sampling from universally accessible sites. In this review, we will present the accumulating evidence for circulating Mtb in both TB disease and asymptomatic TBI and discuss the potential utility of novel bacteriophage-based technology for blood-based detection of Mtb.

BALF metagenomic next-generation sequencing analysis in hematological malignancy patients with suspected pulmonary infection: clinical significance of negative results

Purpose

Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) is gradually being used in hematological malignancy (HM) patients with suspected pulmonary infections. However, negative results are common and the clinical value and interpretation of such results in this patient population require further analysis.

Methods

Retrospective analysis of 112 HM patients with suspected pulmonary infection who underwent BALF mNGS and conventional microbiological tests. The final diagnosis, imaging findings, laboratory results and treatment regimen of 29 mNGS-negative patients were mainly analyzed.

Results

A total of 83 mNGS positive and 29 negative patients (15 true-negatives and 14 false-negatives) were included in the study. Compared to false-negative patients, true-negative patients showed more thickening of interlobular septa on imaging (p < 0.05); fewer true-negative patients had acute respiratory symptoms such as coughing or sputum production (p < 0.05) clinically; On the aspect of etiology, drug-related interstitial pneumonia (6/15, 40%) was the most common type of lung lesion in true-negative patients; on the aspect of pathogenesis, false-negative patients mainly missed atypical pathogens such as fungi and tuberculosis (8/14, 57.1%). Regarding treatment, delayed anti-infection treatment occurred after pathogen missing in mNGS false-negative patients, with the longest median time delay observed for anti-tuberculosis therapy (13 days), followed by antifungal therapy (7 days), and antibacterial therapy (1.5 days); the delay in anti-tuberculosis therapy was significantly longer than that in antibacterial therapy (p < 0.05).

Conclusion

For HMs patients with imaging showing thickening of interlobular septa and no obvious acute respiratory symptoms, lung lesions are more likely caused by drug treatment or the underlying disease, so caution should be exercised when performing BALF mNGS. If BALF mNGS is negative but infection is still suspected, atypical pathogenic infections should be considered.

Comparison of gene set scoring methods for reproducible evaluation of multiple tuberculosis gene signatures

Rationale

Many blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease, predict risk of progression from infection to disease, and monitor TB treatment outcomes. However, an unresolved issue is whether gene set enrichment analysis (GSEA) of the signature transcripts alone is sufficient for prediction and differentiation, or whether it is necessary to use the original statistical model created when the signature was derived. Intra-method comparison is complicated by the unavailability of original training data, missing details about the original trained model, and inadequate publicly-available software tools or source code implementing models. To facilitate these signatures' replicability and appropriate utilization in TB research, comprehensive comparisons between gene set scoring methods with cross-data validation of original model implementations are needed.

Objectives

We compared the performance of 19 TB gene signatures across 24 transcriptomic datasets using both re-rebuilt original models and gene set scoring methods to evaluate whether gene set scoring is a reasonable proxy to the performance of the original trained model. We have provided an open-access software implementation of the original models for all 19 signatures for future use.

Methods

We considered existing gene set scoring and machine learning methods, including ssGSEA, GSVA, PLAGE, Singscore, and Zscore, as alternative approaches to profile gene signature performance. The sample-size-weighted mean area under the curve (AUC) value was computed to measure each signature's performance across datasets. Correlation analysis and Wilcoxon paired tests were used to analyze the performance of enrichment methods with the original models.

Measurement and Main Results

For many signatures, the predictions from gene set scoring methods were highly correlated and statistically equivalent to the results given by the original diagnostic models. PLAGE outperformed all other gene scoring methods. In some cases, PLAGE outperformed the original models when considering signatures' weighted mean AUC values and the AUC results within individual studies.

Conclusion

Gene set enrichment scoring of existing blood-based biomarker gene sets can distinguish patients with active TB disease from latent TB infection and other clinical conditions with equivalent or improved accuracy compared to the original methods and models. These data justify using gene set scoring methods of published TB gene signatures for predicting TB risk and treatment outcomes, especially when original models are difficult to apply or implement.

Stabilization of Tuberculosis Reporter Enzyme Fluorescence (REFtb) Diagnostic Reagents for Use at the Point of Care

Tuberculosis is one of the most frequent causes of death in humans worldwide. One of the primary reasons tuberculosis remains a public health threat is that diagnosis can take weeks to months, is often not very sensitive and cannot be accomplished in many remote environments. A rapid, sensitive and inexpensive point-of-care (POC) diagnostic would have a major impact on tuberculosis eradication efforts. The tuberculosis diagnostic system REFtb is based on specific detection of the constitutively expressed β-lactamase (BlaC) in Mycobacterium tuberculosis using a custom fluorogenic substrate designated as CDG-3. REFtb has potential as a diagnostic for tuberculosis that could be very inexpensive (<USD 2.00/test), used at the POC and could provide definitive diagnosis within 10 min. However, the reagents for REFtb are currently in liquid form, making them more susceptible to degradation and difficult to transport. We evaluated the improvement in the stability of REFtb reagents by lyophilization under a variety of conditions through their effects on the performance of REFtb. We found that lyophilization of REFtb components produces an easily reconstituted powder that displays similar performance to the liquid system and that lactose represents one of the most promising excipients for use in a final POC REFtb diagnostic system. These studies provide the foundation for the production of a stable POC REFtb system that could be easily distributed worldwide with minimal or no requirement for refrigeration.

Diagnostic yield of post-bronchoscopy sputum for diagnosing pauci-bacillary pulmonary tuberculosis

BACKGROUND

A few studies have mentioned that post-bronchoscopy sputum (PBS) could improve the diagnostic yield in pauci-bacillary pulmonary tuberculosis (PTB). Therefore, we evaluated the diagnostic yield of PBS for diagnosing pauci-bacillaryPTB.

METHODS

Clinical data of immunocompromised adult patients with pauci-bacillary PTB were retrospectively retrieved at a tertiary hospital in Seoul, South Korea over a 5-year period. We analyzed patients who underwent bronchoscopy examinations for diagnosing pauci-bacillary PTB.

RESULTS

Ninety patients were finally analyzed. Of these patients, 76 patients were tested with PBS. Six (8%) of these patients had positive results on AFB smear of PBS alone. Additionally, 52 patients (68%) had positive results on mycobacterial culture and 12 (16%) had positive results on mycobacterial culture of PBS exclusively. Therefore, in this study population, a total of 18 patients (20%) were finally diagnosed as having PTB with PBS results only, even though AFB smear microscopy and culture of other specimens had negative results.

CONCLUSIONS

PBS could improve the diagnostic yield by 20% when diagnosing pauci-bacillary PTB. In addition, about 8% of the patients could be diagnosed rapidly because of AFB smear microscopy positivity for PBS. Therefore, PBS use should be considered as a complementary diagnostic approach in patients with suspected pauci-bacillary PTB.

Mycobacterium tuberculosis in solid organ transplant donors and recipients

PURPOSE OF REVIEW

Due to impaired immune response, solid organ transplant (SOT) recipients are susceptible to tuberculosis (TB) and its subsequent morbidity and mortality. Current prevention strategies, diagnostic and treatment approach to TB infection in donors and recipients were reviewed in this article.

RECENT FINDINGS

Screening of latent tuberculosis infection (LTBI) in donors and recipients is the cornerstone of TB-preventive strategy in recipients and requires an assessment of TB risk factors, TB-specific immunity testing, and radiographic evaluation. Interferon-gamma release assay has superseded the tuberculin skin test in LTBI evaluation despite its recognized limitations. LTBI treatment should be offered to transplant candidates and living donors before transplantation and donation, respectively. Diagnosis of TB disease can be challenging because of nonspecific clinical presentation in the recipient and is limited by the sensitivity of current diagnostics. The approach to LTBI and TB disease treatment is similar to the general population, but can be challenging because of potential drug interactions and toxicities.

SUMMARY

The appropriate evaluation of donors and recipients for TB can mitigate posttransplant TB disease. Current approaches to diagnosis and treatment parallels that of immunocompetent hosts. Future research evaluating existing and novel diagnostics and treatment in transplant recipients is needed.

Mycobactericidal Effects of Different Regimens Measured by Molecular Bacterial Load Assay among People Treated for Multidrug-Resistant Tuberculosis in Tanzania

Rifampin or multidrug-resistant tuberculosis (RR/MDR-TB) treatment has largely transitioned to regimens free of the injectable aminoglycoside component, despite the drug class’ purported bactericidal activity early in treatment. We tested whether Mycobacterium tuberculosis

Rifampin or multidrug-resistant tuberculosis (RR/MDR-TB) treatment has largely transitioned to regimens free of the injectable aminoglycoside component, despite the drug class’ purported bactericidal activity early in treatment. We tested whether Mycobacterium tuberculosis killing rates measured by tuberculosis molecular bacterial load assay (TB-MBLA) in sputa correlate with composition of the RR/MDR-TB regimen. Serial sputa were collected from patients with RR/MDR- and drug-sensitive TB at days 0, 3, 7, and 14, and then monthly for 4 months of anti-TB treatment. TB-MBLA was used to quantify viable M. tuberculosis 16S rRNA in sputum for estimation of colony forming units per ml (eCFU/ml). M. tuberculosis killing rates were compared among regimens using nonlinear-mixed-effects modeling of repeated measures. Thirty-seven patients produced 296 serial sputa and received treatment as follows: 13 patients received an injectable bedaquiline-free reference regimen, 9 received an injectable bedaquiline-containing regimen, 8 received an all-oral bedaquiline-based regimen, and 7 patients were treated for drug-sensitive TB with conventional rifampin/isoniazid/pyrazinamide/ethambutol (RHZE). Compared to the adjusted M. tuberculosis killing of −0.17 (95% confidence interval [CI] −0.23 to −0.12) for the injectable bedaquiline-free reference regimen, the killing rates were −0.62 (95% CI −1.05 to −0.20) log₁₀ eCFU/ml for the injectable bedaquiline-containing regimen (P = 0.019), −0.35 (95% CI −0.65 to −0.13) log₁₀ eCFU/ml for the all-oral bedaquiline-based regimen (P = 0.054), and −0.29 (95% CI −0.78 to +0.22) log₁₀ eCFU/ml for the RHZE regimen (P = 0.332). Thus, M. tuberculosis killing rates from sputa were higher among patients who received bedaquiline but were further improved with the addition of an injectable aminoglycoside.

Clinical and radiologic characteristics of radiologically missed miliary tuberculosis

While chest CT provides important clue for diagnosis of miliary tuberculosis (TB), patients are occasionally missed on initial CT, which might delay the diagnosis. This study was to evaluate the clinical and radiological characteristics of radiologically missed miliary TB.Total 117 adult patients with microbiologically confirmed miliary TB in an intermediate TB-burden country were included. 'Missed miliary TB' were defined as the case in which miliary TB was not mentioned as a differential diagnosis in the initial CT reading. Clinical characteristics and radiologic findings including the predominant nodule size, demarcation of miliary nodules and disease extent on CT were retrospectively evaluated. Findings were compared between the missed and non-missed miliary TB groups. Multivariable analyses were performed to determine independent risk factors of missed miliary TB.Of 117 patients with miliary TB, 13 (11.1%) were classified as missed miliary TB; these patients were significantly older than those with non-missed miliary TB (median age, 71 vs 57 years, P = .024). There was a significant diagnostic delay in the missed miliary TB group (P < .001). On chest CT, patients with missed miliary TB had a higher prevalence of ill-defined nodules (84.6% vs 14.4%; P < .001), miliary nodule less than 2 mm showing granular appearance (69.2% vs 12.5%; P < .001), and subtle disease extent (less than 25% of whole lung field, 46.2% vs 8.7%; P < .001). Multivariable analysis revealed that only CT findings including ill-defined nodule (Odd ratios [OR], 15.64; P = .002) and miliary nodule less than 2 mm (OR, 10.08; P = .007) were independently associated with missed miliary TB.Approximately 10% of miliary TB could be missed on initial chest CT, resulting in a delayed diagnosis and treatment. Caution is required in patients with less typical CT findings showing ill-defined miliary nodules less than 2 mm showing granular appearance and follow-up CT might have a benefit.

Tuberculosis diagnostics: overcoming ancient challenges with modern solutions

Rapid, sensitive, accurate and portable diagnostics are a mainstay of modern medicine. Tuberculosis is a disease that has been with us since time immemorial and, despite the fact that it can be treated and cured, it still remains the world's biggest infectious killer, taking the lives of millions annually. There have been important developments in the diagnostic devices for tuberculosis however, these are often prone to error, expensive, lack the necessary sensitivity or accuracy and, crucially, not sufficiently portable and thus not applicable in the remote, rural areas, where they are most needed. Modern solutions have been emerging in the past decade, seeking to overcome many of the inhibiting issues in this field by utilising recent advances in molecular biology, genetics and sequencing or even completely ‘reinventing the wheel’, by developing novel and unprecedented diagnostic techniques. In this mini review, the issues and challenges arising from the historical methods of diagnosing tuberculosis are discussed, followed by outlaying their particular lack of appropriateness for regions of the world where tuberculosis still remains endemic. Subsequently, more recent developments of new methods and technological advancements as ‘modern weapons’ in the battle to defeat this disease and associated challenges are reviewed, and finally an outlook is presented, highlighting the future of the modern solutions under development, which are envisioned to lay the platform for improvements in delivering timely intervention, reduce immense expense and burden on healthcare systems worldwide, while saving millions of lives and eventually, may enable the eradication of this ancient disease.

Delays in diagnosing pulmonary tuberculosis within a context of medium incidence, Medellín, Colombia, 2017: an operational research

BACKGROUND

Delay in tuberculosis (TB) diagnosis is one of the first obstacles for controlling the disease. Delays generate greater deterioration of the health of the patients and increase the possibilities of transmission and infection at home and in the community. The aim of the study was to identify profiles and individual variables associated with patient delays and health care system delays in patients with pulmonary tuberculosis (PTB) in Medellín, Colombia, a city that notifies 1400 new cases per year.

METHODS

A retrospective cohort study in adults with PTB was conducted from May to September of 2017. Sociodemographic, health care-seeking behaviour, and clinical variables were measured. The outcomes were patient delay and health care system delay. The data were obtained from records of the local TB program, and a questionnaire was applied by the health care team that performs routine field visits. Simple correspondence analysis was used to identify groups (profiles), and their characteristics. Cox's proportional hazards model was carried out to identify the variables associated with the delays.

RESULTS

The study included 183 patients. The total delay median was 101 days (IQR: 64-163). Patient delay was of 35 days (IQR: 14-84), the profile with greater delay belonged to consumers of psychoactive substances. The health care system delay was of 27 days (IQR: 7-89), the attributes of the profile with greater delay were being a female, having more than two consultations before the diagnosis, and having prescribed antibiotics. Basic-medium educational level [HR_a = 0.69; 95% CI (0.49-0.97)] and having a TB home contact [HR_a = 0.68; 95% CI (0.48-0.96)] were associated with greater patient delay. Having negative acid-fast bacilli (AFB) smear [HR_a = 0.64; 95% CI (0.45-0.92)] and more than two consultations before the diagnosis [HR_a = 0.33; 95% CI (0.22-0.49)] was associated with greater health care system delay.

CONCLUSIONS

Data from epidemiological surveillance allowed locating risk groups with delays in TB diagnosis which requires the prioritisation of the local TB control program to promote early detection and prevention of adverse outcomes.

Rapid Tuberculosis Diagnosis Using Reporter Enzyme Fluorescence

Tuberculosis is the most frequent cause of death in humans from a single infectious agent. Due to low numbers of bacteria present in sputum during early infection, diagnosis does not usually occur until >3 to 4 months after symptoms develop. We created a new more sensitive diagnostic that can be carried out in 10 min with no processing or technical expertise.

Tuberculosis is the most frequent cause of death in humans from a single infectious agent. Due to low numbers of bacteria present in sputum during early infection, diagnosis does not usually occur until >3 to 4 months after symptoms develop. We created a new more sensitive diagnostic that can be carried out in 10 min with no processing or technical expertise. This assay utilizes the Mycobacterium tuberculosis-specific biomarker BlaC in reporter enzyme fluorescence (REF) that has been optimized for clinical samples, designated REFtb, along with a more specific fluorogenic substrate, CDG-3. We report the first evaluation of clinical specimens with REFtb assays in comparison to the gold standards for tuberculosis diagnosis, culture and smear microscopy. REFtb assays allowed diagnosis of 160 patients from 16 different countries with a sensitivity of 89% for smear-positive, culture-positive samples and 88% for smear-negative, culture-positive samples with a specificity of 82%. The negative predictive value of REFtb for tuberculosis infection is 93%, and the positive predictive value is 79%. Overall, these data point toward the need for larger accuracy studies by third parties using a commercially available REFtb kit to determine whether incorporation of REFtb into the clinical toolbox for suspected tuberculosis patients would improve case identification. If results similar to our own can be obtained by all diagnostic laboratories, REFtb would allow proper treatment of more than 85% of patients that would be missed during their initial visit to a clinic using current diagnostic strategies, reducing the potential for further spread of disease.