Implementation Research to Inform the Use of Xpert MTB/RIF in Primary Health Care Facilities in High TB and HIV Settings in Resource Constrained Settings

Impact of molecular diagnostic tests on diagnostic and treatment delays in tuberculosis: a systematic review and meta-analysis

BACKGROUND

Countries with high TB burden have expanded access to molecular diagnostic tests. However, their impact on reducing delays in TB diagnosis and treatment has not been assessed. Our primary aim was to summarize the quantitative evidence on the impact of nucleic acid amplification tests (NAAT) on diagnostic and treatment delays compared to that of the standard of care for drug-sensitive and drug-resistant tuberculosis (DS-TB and DR-TB).

METHODS

We searched MEDLINE, EMBASE, Web of Science, and the Global Health databases (from their inception to October 12, 2020) and extracted time delay data for each test. We then analysed the diagnostic and treatment initiation delay separately for DS-TB and DR-TB by comparing smear vs Xpert for DS-TB and culture drug sensitivity testing (DST) vs line probe assay (LPA) for DR-TB. We conducted random effects meta-analyses of differences of the medians to quantify the difference in diagnostic and treatment initiation delay, and we investigated heterogeneity in effect estimates based on the period the test was used in, empiric treatment rate, HIV prevalence, healthcare level, and study design. We also evaluated methodological differences in assessing time delays.

RESULTS

A total of 45 studies were included in this review (DS = 26; DR = 20). We found considerable heterogeneity in the definition and reporting of time delays across the studies. For DS-TB, the use of Xpert reduced diagnostic delay by 1.79 days (95% CI - 0.27 to 3.85) and treatment initiation delay by 2.55 days (95% CI 0.54-4.56) in comparison to sputum microscopy. For DR-TB, use of LPAs reduced diagnostic delay by 40.09 days (95% CI 26.82-53.37) and treatment initiation delay by 45.32 days (95% CI 30.27-60.37) in comparison to any culture DST methods.

CONCLUSIONS

Our findings indicate that the use of World Health Organization recommended diagnostics for TB reduced delays in diagnosing and initiating TB treatment. Future studies evaluating performance and impact of diagnostics should consider reporting time delay estimates based on the standardized reporting framework.

The Performance of Computer-Aided Detection Digital Chest X-ray Reading Technologies for Triage of Active Tuberculosis Among Persons With a History of Previous Tuberculosis

BACKGROUND

Digital chest X-ray (dCXR) computer-aided detection (CAD) technology uses lung shape and texture analysis to determine the probability of tuberculosis (TB). However, many patients with previously treated TB have sequelae, which also distort lung shape and texture. We evaluated the diagnostic performance of 2 CAD systems for triage of active TB in patients with previously treated TB.

METHODS

We conducted a retrospective analysis of data from a cross-sectional active TB case finding study. Participants ≥15 years, with ≥1 current TB symptom and complete data on history of previous TB, dCXR, and TB microbiological reference (Xpert MTB/RIF) were included. dCXRs were evaluated using CAD4TB (v.7.0) and qXR (v.3.0). We determined the diagnostic accuracy of both systems, overall and stratified by history of TB, using a single threshold for each system that achieved 90% sensitivity and maximized specificity in the overall population.

RESULTS

Of 1884 participants, 452 (24.0%) had a history of previous TB. Prevalence of microbiologically confirmed TB among those with and without history of previous TB was 12.4% and 16.9%, respectively. Using CAD4TB, sensitivity and specificity were 89.3% (95% CI: 78.1-96.0%) and 24.0% (19.9-28.5%) and 90.5% (86.1-93.3%) and 60.3% (57.4-63.0%) among those with and without previous TB, respectively. Using qXR, sensitivity and specificity were 94.6% (95% CI: 85.1-98.9%) and 22.2% (18.2-26.6%) and 89.7% (85.1-93.2%) and 61.8% (58.9-64.5%) among those with and without previous TB, respectively.

CONCLUSIONS

The performance of CAD systems as a TB triage tool is decreased among persons previously treated for TB.

Cost and affordability of scaling up tuberculosis diagnosis using Xpert MTB/RIF testing in West Java, Indonesia

In Indonesia, a significant number of tuberculosis (TB) cases may be missed, due to the low sensitivity and specificity of the currently used diagnostic algorithm. In this regard, the rapid molecular test using Xpert MTB/RIF, which has recently been introduced in Indonesia, can improve case detection. Thus, this study determined the cost and affordability of incorporating Xpert MTB/RIF testing for TB diagnosis. For this purpose, we estimated the costs (from the health system and societal perspectives) of reaching the TB detection target in Depok municipality, and applied the findings to the West Java province of Indonesia. The resources available for the health and TB program were also analyzed to support the decision to scale up the TB diagnosis using Xpert MTB/RIF testing. According to the results, the unit cost for TB diagnosis per person was USD 27.22 and USD 70.16 from the health system and societal perspectives, respectively. To reach the target of 109,843 TB cases for the 2020–2024 time period, Depok municipality would need USD 2,989,927 and USD 2,549,455 from the health system viewpoint, assuming the machine’s lifespan of five and 10 years, respectively. Extrapolating these results to the West Java province, USD 56,353,833 would be necessary to test 2,076,413 cases from 2019 to 2024. However, in order to accelerate the case detection target up to 2024, West Java requires additional funds. The implication of the findings is that the central government must consider local capacity to accelerate TB case detection and ensure that the installation of Xpert MTB/RIF machines is included in the overall costs.

Rifampicin-Resistant Multidrug-Resistant Tuberculosis Cases in Selected Hospitals in Western Oromia, Ethiopia: Cross-Sectional Retrospective Study

Purpose

With the recommendation of World Health Organization (WHO) and as per the Ethiopian National Implementation Guideline, GeneXpert is used for rapid diagnosis of rifampicin (RIF)-resistant multidrug-resistant tuberculosis (MDR-TB) from the suspected TB patients; however, there were limited findings in Ethiopia particularly in the study area showing the magnitude of RIF-resistant MDR-TB and related factors among suspected TB cases. Hence, we aimed to assess resistance to RIF as a biomarker for the detection of MDR-TB cases from the suspected TB patients in selected hospitals, Western Oromia, Ethiopia.

Patients and Methods

We have conducted a cross-sectional review on 2300 registered GeneXpert data as clinically suspected TB cases in three governmental hospitals, Western Oromia, Ethiopia, between October 2015 and April 2016 to assess resistance to RIF as a biomarker for the detection of MDR-TB cases. Trained data collectors enumerated the data using pre-tested semi-structured questionnaires from the Gene Xpert records found in the registration logbook available at each hospital laboratories. Following checking the data for completeness, we have cleaned and entered our data into SPSS version 20 to compute different analyses. P-value of ≤0.05 was taken as statistically significant.

Results

A total of 2300 TB suspected cases were included in the study. The overall prevalence of TB diagnosed by the GeneXpert assay was 21.3% (491/2300). In all TB confirmed cases, RIF-resistant TB accounted for 25.9% (127/491) which expressed rpoB gene mutations. Sex (being male), age (within 16-30 age group), patient category (relapse, loss to follow-up, treatment failure and had MDR-TB contact) were significantly associated with rifampicin-resistant TB. Relapse patient was 20 times more likely to develop MDR-TB when compared to the new patient (P-value= 0.01, COR = 20.0, 95%C.I = 17.5-42.5).

Conclusion

The rifampicin-resistant TB is prevalent in all age groups. The strong association and high prevalence of RIF-resistant TB to failure after treatment in this study require more attention towards improving the treatment to minimize evolving of the MDR-TB cases.

Preliminary Results on Pulmonary Tuberculosis Detection in Chest X-Ray Using Convolutional Neural Networks

Tuberculosis (TB), is an ancient disease that probably affects humans since pre-hominids. This disease is caused by bacteria belonging to the mycobacterium tuberculosis complex and usually affects the lungs in up to 67% of cases. In 2019, there were estimated to be over 10 million tuberculosis cases in the world, in the same year TB was between the ten leading causes of death, and the deadliest from a single infectious agent. Chest X-ray (CXR) has recently been promoted by the WHO as a tool possibly placed early in screening and triaging algorithms for TB detection. Numerous TB prevalence surveys have demonstrated that CXR is the most sensitive screening tool for pulmonary TB and that a significant proportion of people with TB are asymptomatic in the early stages of the disease. This study presents experimentation of classic convolutional neural network architectures on public CRX databases in order to create a tool applied to the diagnostic aid of TB in chest X-ray images. As result the study has an AUC ranging from 0.78 to 0.84, sensitivity from 0.76 to 0.86 and specificity from 0.58 to 0.74 depending on the network architecture. The observed performance by these metrics alone are within the range of metrics found in the literature, although there is much room for metrics improvement and bias avoiding. Also, the usage of the model in a triage use-case could be used to validate the efficiency of the model in the future.

Tuberculosis: evaluation of the time between identification of symptoms and beginning of treatment

ABSTRACT Objective: To analyze the time elapsed between the identification of respiratory symptoms and the beginning of tuberculosis treatment, considering the sputum smear microscopy and the RMT. Method: Descriptive, retrospective epidemiological study, carried out in two Health Units, which were the only units that performed diagnosis by sputum smear microscopy and Rapid Molecular Test in the city. Data on respiratory symptoms with a positive result for tuberculosis were used. Analysis of data distribution and variance was performed, with a significance level of 5%. Results: The longest time interval found was “result/beginning of treatment”, for both tests, with a median of 3 days. It was found that the patient takes longer to receive the result when performing the Rapid Molecular Test. Conclusion: Patients who had the Rapid Molecular Test waited longer for results when compared to sputum smear microscopy, leading to a reflection on the need for further studies on the operation of health services.

A systematic review of the diagnostic accuracy of artificial intelligence-based computer programs to analyze chest x-rays for pulmonary tuberculosis

We undertook a systematic review of the diagnostic accuracy of artificial intelligence-based software for identification of radiologic abnormalities (computer-aided detection, or CAD) compatible with pulmonary tuberculosis on chest x-rays (CXRs). We searched four databases for articles published between January 2005-February 2019. We summarized data on CAD type, study design, and diagnostic accuracy. We assessed risk of bias with QUADAS-2. We included 53 of the 4712 articles reviewed: 40 focused on CAD design methods (“Development” studies) and 13 focused on evaluation of CAD (“Clinical” studies). Meta-analyses were not performed due to methodological differences. Development studies were more likely to use CXR databases with greater potential for bias as compared to Clinical studies. Areas under the receiver operating characteristic curve (median AUC [IQR]) were significantly higher: in Development studies AUC: 0.88 [0.82–0.90]) versus Clinical studies (0.75 [0.66–0.87]; p-value 0.004); and with deep-learning (0.91 [0.88–0.99]) versus machine-learning (0.82 [0.75–0.89]; p = 0.001). We conclude that CAD programs are promising, but the majority of work thus far has been on development rather than clinical evaluation. We provide concrete suggestions on what study design elements should be improved.

Diagnosis of rifampicin-resistant tuberculosis: Discordant results by diagnostic methods

The performance of the Xpert© MTB/RIF and MTBDRplus assays for the detection of rifampicin resistant Mycobacterium tuberculosis was compared to culture-based drug susceptibility testing in 30 specimens with rifampicin-resistant and rifampicin-indeterminate Xpert MTB/RIF results collected between March 2012 and March 2014. Xpert MTB/RIF and MTBDRplus were 100% sensitive and 100% concordant for rifampicin resistance detection, but 3 of 13 samples (23%) positive for rifampicin resistance on Xpert MTB/RIF and MTBDRplus were negative for rifampicin resistance on mycobacteria growth indicator tube drug susceptibility testing. Specificity was 72% for Xpert MTB/RIF and 80% for MTBDRplus. Positive predictive value for Xpert MTB/RIF for multidrug resistant tuberculosis was 47.8% for new patients and 77.8% for previously treated patients; negative predictive value was 100% for both new and previously treated patients. The discordant rifampicin resistance test results indicate a need to fully characterise circulating rifampicin resistant Mycobacterium tuberculosis strains in Zambia and to inform the development of guidelines for decision-making in relation to diagnosis of drug-resistant tuberculosis.

High HIV and active tuberculosis prevalence and increased mortality risk in adults with symptoms of TB: a systematic review and meta-analyses

INTRODUCTION

HIV and tuberculosis (TB) remain leading causes of preventable death in low- and middle-income countries (LMICs). The World Health Organization (WHO) recommends HIV testing for all individuals with TB symptoms, but implementation has been suboptimal. We conducted a systematic literature review and meta-analyses to estimate HIV and TB prevalence, and short-term (two to six months) mortality, among adults with TB symptoms at community- and facility level.

METHODS

We searched Embase, Global Health and MEDLINE databases, and reviewed conference abstracts for studies reporting simultaneous HIV and TB screening of adults in LMICs published between January 2003 and December 2017. Meta-analyses were performed to estimate prevalence of HIV, undiagnosed TB and mortality risk at different health system levels.

RESULTS

Sixty-two studies including 260,792 symptomatic adults were identified, mostly from Africa and Asia. Median HIV prevalence was 19.2% (IQR: 8.3% to 40.4%) at community level, 55.7% (IQR: 20.9% to 71.2%) at primary care level and 80.7% (IQR: 73.8% to 84.6%) at hospital level. Median TB prevalence was 6.9% (IQR: 3.3% to 8.4%) at community, 20.5% (IQR: 11.7% to 46.4%) at primary care and 36.4% (IQR: 22.9% to 40.9%) at hospital level. Median short-term mortality was 22.6% (IQR: 15.6% to 27.7%) among inpatients, 3.1% (IQR: 1.2% to 4.2%) at primary care and 1.6% (95% CI: 0.45 to 4.13, n = 1 study) at community level.

CONCLUSIONS

Adults with TB symptoms have extremely high prevalence of HIV infection, even when identified through community surveys. TB prevalence and mortality increased substantially at primary care and inpatient level respectively. Strategies to expand symptom-based TB screening combined with HIV and TB testing for all symptomatic individuals should be of the highest priority for both disease programmes in LMICs with generalized HIV epidemics. Interventions to reduce short-term mortality are urgently needed.

Empiric tuberculosis treatment in South African primary health care facilities - for whom, where, when and why: Implications for the development of tuberculosis diagnostic tests

Background

The extent and circumstances under which empiric tuberculosis (TB) treatment (treatment without microbiological confirmation at treatment initiation) is administered in primary health care settings in South Africa are not well described.

Methods

We used data from a pragmatic evaluation of Xpert MTB/RIF in which persons undergoing TB investigations by PHC nurses were followed for six months. Following Xpert or smear-microscopy at enrolment, investigations for tuberculosis were undertaken at the discretion of health care workers. We identified persons whose TB treatment was initiated empirically (no microbiological confirmation at time of treatment initiation at a primary health care facility) and describe pathways to treatment initiation.

Results

Of 4665 evaluable participants, 541 persons were initiated on treatment of whom 167 (31%) had negative sputum tests at enrolment. Amongst these 167, the median number of participant visits to health care providers prior to treatment initiation was 3 (interquartile range [IQR] 2–4). Chest radiography, sputum culture or hospital referral was done in 106/167 (63%). Reasons for TB treatment start were: 1) empiric (n = 82, 49%); 2) a positive laboratory test (n = 49, 29%); 3) referral and treatment start at a higher level of care (n = 28, 17%); and 4) indeterminable (n = 8, 5%). Empiric treatment accounted for 15% (82/541) of all TB treatment initiations and 1.7% (82/4665) of all persons undergoing TB investigations. Chest radiography findings compatible with TB (63/82 [77%]) were the basis for treatment initiation amongst the majority of empirically treated participants. Microbiological confirmation of TB was subsequently obtained for 11/82 (13%) empirically-treated participants. Median time to empiric treatment start was 3.9 weeks (IQR 1.4–11 weeks) after enrolment.

Conclusion

Uncommon prescription of empiric TB treatment with reliance on chest radiography in a nurse-managed programme underscores the need for highly sensitive TB diagnostics suitable for point-of-care, and strong health systems to support TB diagnosis in this setting.

Impact of Point-of-Care Xpert MTB/RIF on Tuberculosis Treatment Initiation. A Cluster-randomized Trial

RATIONALE

Point-of-care (POC) diagnostics have the potential to reduce pretreatment loss to follow-up and delays to initiation of appropriate tuberculosis (TB) treatment.

OBJECTIVES

To evaluate the effect of a POC diagnostic strategy on initiation of appropriate TB treatment.

METHODS

We conducted a cluster-randomized trial of adults with cough who were HIV positive and/or at high risk of drug-resistant TB. Two-week time blocks were randomized to two strategies: (1) Xpert MTB/RIF test (Cepheid, Sunnyvale, CA) performed at a district hospital laboratory or (2) POC Xpert MTB/RIF test performed at a primary health care clinic. All participants provided two sputum specimens: one for the Xpert test and the other for culture as a reference standard. The primary outcome was the proportion of participants with culture-positive pulmonary tuberculosis (PTB) initiated on appropriate TB treatment within 30 days.

MEASUREMENTS AND MAIN RESULTS

Between August 22, 2011, and March 1, 2013, 36 two-week blocks were randomized, and 1,297 individuals were enrolled (646 in the laboratory arm, 651 in the POC arm), 159 (12.4%) of whom had culture-positive PTB. The proportions of participants with culture-positive PTB initiated on appropriate TB treatment within 30 days were 76.5% in the laboratory arm and 79.5% in the POC arm (odds ratio, 1.13; 95% confidence interval, 0.51-2.53; P = 0.76; risk difference, 3.1%; 95% confidence interval, -16.2 to 10.1). The median time to initiation of appropriate treatment was 7 days (laboratory) versus 1 day (POC).

CONCLUSIONS

POC positioning of the Xpert test led to more rapid initiation of appropriate TB treatment. Achieving one-stop diagnosis and treatment for all people with TB will require simpler, more sensitive diagnostics and broader strengthening of health systems. Clinical trial registered with www.isrctn.com (ISRCTN 18642314) and www.sanctr.gov.za (DOH-27-0711-3568).

Digital CXR with computer aided diagnosis versus symptom screen to define presumptive tuberculosis among household contacts and impact on tuberculosis diagnosis

BACKGROUND

Household (HH) contact tracing is a strategy that targets high risk groups for TB. Symptom based screening is the standard used to identify HH contacts at risk for TB during HH contact tracing for TB. However, this strategy may be limited due to poor performance in predicting TB. The objective of this study was to compare CXR with Computer Aided Diagnosis (CAD) against symptom screen for defining presumptive TB and how TB detection changes with each method.

METHODS

Household contacts of consecutive index bacteriologically confirmed TB cases were visited by study teams and given TB/HIV education to raise awareness of the risk of TB following close contact with a TB patient. Contacts were encouraged to visit the health facility for screening; where symptoms history was obtained and opt out HIV testing was provided as part of the screening process. CXR was offered to all regardless of symptoms, followed by definitive sputum test with either Xpert MTB RIF or smear microscopy.

RESULTS

Among 919 HH contacts that presented for screening, 865 were screened with CXR and 464 (53.6%) had an abnormal CXR and the rest had a normal CXR. Among 444 HH contacts with valid sputum results, 274 (61.7%) were symptom screen positive and 255 (57.4%) had an abnormal CXR. Overall, TB was diagnosed in 32/444 (7.2%); 13 bacteriologically unconfirmed and 19 bacteriologically confirmed. Of 19 bacteriologically confirmed TB 8 (42.1%) were symptom screen negative contacts with an abnormal CXR and these 6/8 (75.0%) were HIV positive. Among the 13 bacteriologically unconfirmed TB cases, 7 (53.8%) were HIV positive and all had an abnormal CXR.

CONCLUSION

Symptom screen if used alone with follow on definitive TB testing only for symptom screen positive individuals would have missed eight of the 19 confirmed TB cases detected in this study. There is need to consider use of other screening strategies apart from symptom screen alone for optimal rule out of TB especially in HIV positive individuals that are at greatest risk of TB and present atypically.

Rolling Out Xpert® MTB/RIF for TB Detection in HIV-Infected Populations:An Opportunity for Systems Strengthening

Background

To eliminate preventable deaths, disease and suffering due to tuberculosis, improved diagnostic capacity is critical. The Cepheid Xpert MTB/RIF^® assay is recommended by the World Health Organization as the initial diagnostic test for people with suspected HIV-associated tuberculosis. However, despite high expectations, its scale-up in real-world settings has faced challenges, often due to the systems that support it.

Opportunities for System Strengthening

In this commentary, we discuss needs and opportunities for systems strengthening to support widespread scale-up of Xpert MTB/RIF as they relate to each step within the tuberculosis diagnostic cascade, from finding presumptive patients, to collecting, transporting and testing sputum specimens, to reporting and receiving results, to initiating and monitoring treatment and, ultimately, to ensuring successful and timely treatment and cure. Investments in evidence-based interventions at each step along the cascade and within the system as a whole will augment not only the utility of Xpert MTB/RIF, but also the successful implementation of future diagnostic tests.

Conclusion

Xpert MTB/RIF will only improve patient outcomes if optimally implemented within the context of strong tuberculosis programmes and systems. Roll-out of this technology to people living with HIV and others in resource-limited settings offers the opportunity to leverage current tuberculosis and HIV laboratory, diagnostic and programmatic investments, while also addressing challenges and strengthening coordination between laboratory systems, laboratory-programme interfaces, and tuberculosis-HIV programme interfaces. If successful, the benefits of this tool could extend beyond progress toward global End TB Strategy goals, to improve system-wide capacity for global disease detection and control.

The development, evaluation and performance of molecular diagnostics for detection of Mycobacterium tuberculosis

The unique pathogenesis of tuberculosis (TB) poses several barriers to the development of accurate diagnostics: a) the establishment of life-long latency by Mycobacterium tuberculosis (M.tb) after primary infection confounds the development of classical antibody or antigen based assays; b) our poor understanding of the molecular pathways that influence progression from latent to active disease; c) the intracellular nature of M.tb infection in tissues means that M.tb and/or its components, are not readily detectable in peripheral specimens; and d) the variable presence of M.tb bacilli in specimens from patients with extrapulmonary TB or children. The literature on the current portfolio of molecular diagnostics tests for TB is reviewed here and the developmental pipeline is summarized. Also reviewed are data from recently published operational research on the GeneXpert MTB/RIF assay and discussed are the lessons that can be taken forward for the design of studies to evaluate the impact of TB diagnostics.

Automatic detection of pleural effusion in chest radiographs

Automated detection of Tuberculosis (TB) using chest radiographs (CXRs) is gaining popularity due to the lack of trained human readers in resource limited countries with a high TB burden. The majority of the computer-aided detection (CAD) systems for TB focus on detection of parenchymal abnormalities and ignore other important manifestations such as pleural effusion (PE). The costophrenic angle is a commonly used measure for detecting PE, but has limitations. In this work, an automatic method to detect PE in the left and right hemithoraces is proposed and evaluated on a database of 638 CXRs. We introduce a robust way to localize the costophrenic region using the chest wall contour as a landmark structure, in addition to the lung segmentation. Region descriptors are proposed based on intensity and morphology information in the region around the costophrenic recess. Random forest classifiers are trained to classify left and right hemithoraces. Performance of the PE detection system is evaluated in terms of recess localization accuracy and area under the receiver operating characteristic curve (AUC). The proposed method shows significant improvement in the AUC values as compared to systems which use lung segmentation and the costophrenic angle measurement alone.