Implications of Failure to Routinely Diagnose Resistance to Second-Line Drugs in Patients With Rifampicin-Resistant Tuberculosis on Xpert MTB/RIF: A Multisite Observational Study

Drug-resistant tuberculosis: a persistent global health concern

Drug-resistant tuberculosis (TB) is estimated to cause 13% of all antimicrobial resistance-attributable deaths worldwide and is driven by both ongoing resistance acquisition and person-to-person transmission. Poor outcomes are exacerbated by late diagnosis and inadequate access to effective treatment. Advances in rapid molecular testing have recently improved the diagnosis of TB and drug resistance. Next-generation sequencing of Mycobacterium tuberculosis has increased our understanding of genetic resistance mechanisms and can now detect mutations associated with resistance phenotypes. All-oral, shorter drug regimens that can achieve high cure rates of drug-resistant TB within 6-9 months are now available and recommended but have yet to be scaled to global clinical use. Promising regimens for the prevention of drug-resistant TB among high-risk contacts are supported by early clinical trial data but final results are pending. A person-centred approach is crucial in managing drug-resistant TB to reduce the risk of poor treatment outcomes, side effects, stigma and mental health burden associated with the diagnosis. In this Review, we describe current surveillance of drug-resistant TB and the causes, risk factors and determinants of drug resistance as well as the stigma and mental health considerations associated with it. We discuss recent advances in diagnostics and drug-susceptibility testing and outline the progress in developing better treatment and preventive therapies.

Reflex Xpert MTB/XDR Testing of Residual Rifampicin-Resistant Specimens: A Clinical Laboratory-Based Diagnostic Accuracy and Feasibility Study in South Africa

Background

The World Health Organization-approved Xpert MTB/XDR test detects Mycobacterium tuberculosis and resistance to isoniazid, fluoroquinolones, ethionamide, and injectable drugs directly in specimens. This pragmatic, laboratory-based study assessed the diagnostic accuracy and feasibility of a reflex testing approach, where Xpert MTB/XDR was performed on residual specimens previously processed for Xpert MTB/RIF Ultra.

Methods

Routine respiratory specimens, processed for Xpert MTB/RIF Ultra, were stored in sample reagent buffer at 2°C-8°C. If rifampicin resistant, the residual specimen was assessed for adequate volume (≥2 mL) and tested with Xpert MTB/XDR, with storage time recorded. A second specimen was used for routine and reference standard testing (culture and sequencing).

Results

Specimens (99% sputum) from 763 participants submitted to 2 large routine laboratories were included. Xpert MTB/XDR yielded valid resistance detection results in 639 (84%), compared with 507 (66%) for routine testing (difference [95% CI], 18% [13%-22%]). The median turnaround time for results was 23 hours for Xpert MTB/XDR and 15 days for routine testing. While 748 specimens (98%) were ≥2 mL, only 102 (13%) were stored for ≤4 hours. By the reference standard, 284 of 394 (72%) were isoniazid resistant, and 57 of 380 (15%) were fluroquinolone resistant. The sensitivities of Xpert MTB/XDR were 94% (95% CI, 91%-97%) for isoniazid and 91% (81%-97%) for fluoroquinolone resistance detection. The specificities were 98% (94%-100%) and 100% (98%-100%), respectively.

Conclusions

Xpert MTB/XDR performed favorably compared with the reference, and the reflex testing approach increased results availability over routine testing, while dramatically decreasing turnaround time from weeks to hours. Laboratory workflow precluded testing within the manufacturer-recommended 4-hour storage time, but longer storage did not appear detrimental.

Integration Challenges and Opportunity of Implementing Non-Communicable Disease Screening Intervention with Tuberculosis Patient Care: A Mixed Implementation Study

Background

Despite the comorbidity, early detection and treatment of the two diseases are highly recommended; however, a few pilot studies were conducted, which are mainly focused on diabetes mellitus screening and the integration opportunity and challenges were not known. The study aimed to identify integrated implementation challenges and opportunities of non-communicable disease and risk factors screening intervention with tuberculosis patient care.

Methods

A mixed implementation study design was used. Data were collected from a sample of 443 tuberculosis patients, 21 key informants and facility observations. For quantitative data, descriptive statistics for proportion were summarized in tables and figures. Four distinct implementation frame was adapted for thematic analysis of audio recordings, daily verbatim transcription, and descriptive field notes.

Results

The prevalence of hypertension and diabetes mellitus among tuberculosis patients were 6.55% and 5.64%, respectively. Totally 9 subthemes and 21 new codes were developed, of which 13 and 8 new codes were developed for integrated implementation challenges and opportunities, respectively. The absence of medical equipment, skill and knowledge training, record and report system, cooperative integration, feedback, referral system, shortage of supporting agencies, and services not free were external challenges, whereas lack of trained health workers, focal persons, and increased workload and absence of awareness creation were internal challenges. Despite the challenges, the presence of health extension programs, non-governmental organizations, community health care insurance and associations for diabetes mellitus were external opportunities. Availability of assigned focal persons, trained stakeholders, guidelines, information systems and compatible tuberculosis program structure were internal opportunities.

Conclusion

The majority of TB patients were not comorbid with NCDs. We build a favourable system for integrated implementation developing an integration platform and structural authority at a different organization by addressing identified challenges and applying facilitators is crucial.

Standardization of a stool concentration method for Mycobacterium tuberculosis detection in the pediatric population

Background

The inability of young children to expectorate sputum and paucibacillary status of Mycobacterium tuberculosis (MTB) increases its diagnostic complexity. In this study, we aimed to standardize a stool concentration method for the detection of MTB and its drug resistance by line probe assay (LPA).

Methods

The stool from 10 healthy children spiked with H37Rv in five different dilutions (1:1, 1:10, 1:100, 1:1000, and 1:10,000), and stool from 10 confirmed TB and 54 clinically diagnosed TB children were subjected to an in-house stool concentration protocol. All the processed filtrates were subjected to smear microscopy, solid culture, Xpert ultra testing, and LPA.

Results

Of 10 control samples, growth was seen in four samples (neat 1:1). In smear microscopy, bacilli could be seen in eight samples (1:1 and 1:10). Xpert ultra testing could detect MTB in eight samples in all dilutions with different loads. LPA could detect MTB in all samples and dilutions. In microbiologically confirmed children, seven out of 10 stool samples tested were positive. Out of 54 children with clinically diagnosed TB, 4 (7.4%) could be confirmed by microbiological diagnosis.

Conclusion

The protocol standardized in this study proves to be better working in the molecular detection of MTB.

Predicting resistance to fluoroquinolones among patients with rifampicin-resistant tuberculosis using machine learning methods

Background

Limited access to drug-susceptibility tests (DSTs) and delays in receiving DST results are challenges for timely and appropriate treatment of multi-drug resistant tuberculosis (TB) in many low-resource settings. We investigated whether data collected as part of routine, national TB surveillance could be used to develop predictive models to identify additional resistance to fluoroquinolones (FLQs), a critical second-line class of anti-TB agents, at the time of diagnosis with rifampin-resistant TB.

Methods and findings

We assessed three machine learning-based models (logistic regression, neural network, and random forest) using information from 540 patients with rifampicin-resistant TB, diagnosed using Xpert MTB/RIF and notified in the Republic of Moldova between January 2018 and December 2019. The models were trained to predict the resistance to FLQs based on demographic and TB clinical information of patients and the estimated district-level prevalence of resistance to FLQs. We compared these models based on the optimism-corrected area under the receiver operating characteristic curve (OC-AUC-ROC). The OC-AUC-ROC of all models were statistically greater than 0.5. The neural network model, which utilizes twelve features, performed best and had an estimated OC-AUC-ROC of 0.87 (0.83,0.91), which suggests reasonable discriminatory power. A limitation of our study is that our models are based only on data from the Republic of Moldova and since not externally validated, the generalizability of these models to other populations remains unknown.

Conclusions

Models trained on data from phenotypic surveillance of drug-resistant TB can predict resistance to FLQs based on patient characteristics at the time of diagnosis with rifampin-resistant TB using Xpert MTB/RIF, and information about the local prevalence of resistance to FLQs. These models may be useful for informing the selection of antibiotics while awaiting results of DSTs.

The Role of GeneXpert MTB/RIF in Reducing Treatment Delay Among Multidrug Resistance Tuberculosis Patients: A Propensity Score Matched Analysis

Background

Methods

Results

Conclusion

Characteristics of rifampicin-resistant tuberculosis detection in China, 2015-2019

Background

The very high burden of rifampicin resistance tuberculosis (RR-TB) and the very low detection of RR-TB cases are a major challenge that China has been facing. This study analyzed the characteristics of RR-TB detection in China after the change of RR-TB detection strategy since 2015, aiming to provide reference and evidence for the development of more precise national drug resistance tuberculosis prevention and control policy.

Methods

We extracted data related to rifampicin resistance screening from the national Tuberculosis Information Management System (TBIMS) from 2015 to 2019, and used descriptive research methods to analyze the screening rate of presumptive RR-TB, the number and duration of RR-TB patients detected and drug resistance testing methods in each year. Chi-square test was used to compare the differences in component ratio or rate between years, and Kruskal Wallis test was used to compare the differences in median days for detection of RR-TB patients in each year.

Results

A total of 68,200 RR-TB cases were detected during 2015–2019, of which 48.1% were new cases. The number and detection rate of RR-TB cases increased year by year, from 10 019 and 14.3% in 2015 to 18 623 and 28.7% in 2019, respectively. Of the bacteriologically confirmed TB cases, 81.9% were tested for RR in 2019, a considerable increase from 29.5% in 2015. In 2019, only 41.0% of RR-TB cases had fluoroquinolones (FQs) susceptibility testing performed, and this proportion has been declining year by year since 2016. The proportion of application of rapid molecular tools increased from 24.0% in 2015 to 67.1% in 2019, and the median days to obtain RR results was significantly shortened. In 2019, 76.0% of RR-TB cases were diagnosed as presumptive RR-TB in county-level hospitals.

Conclusions

After China modified the RR-TB detection strategy, the screening rate of RR and the number of RR-TB cases increased significantly. The RR testing methods now predominantly utilize rapid molecular tools. However, comprehensive measures should be implemented to close the gap in the detection of RR-TB cases. It is imperative to take FQs susceptibility testing seriously and effectively strengthen the laboratory capacity of county-level hospitals.

Graphical Abstract

Ease and equity of access to free DR-TB services in Nigeria- a qualitative analysis of policies, structures and processes

Introduction

Persistent low rates of case notification and treatment coverage reflect that accessing diagnosis and treatment for drug-resistant tuberculosis (DR-TB) in Nigeria remains a challenge, even though it is provided free of charge to patients. Equity in health access requires availability of comparable, appropriate services to all, based on needs, and irrespective of socio-demographic characteristics. Our study aimed to identify the reasons for Nigeria’s low rates of case-finding and treatment for DR-TB. To achieve this, we analyzed elements that facilitate or hinder equitable access for different groups of patients within the current health system to support DR-TB management in Nigeria.

Methods

We conducted documentary review of guidelines and workers manuals, as well as 57 qualitative interviews, including 10 focus group discussions, with a total of 127 participants, in Nigeria. Between August and November 2017, we interviewed patients who were on treatment, their treatment supporter, and providers in Ogun and Plateau States, as well as program managers in Benue and Abuja. We adapted and used Levesque’s patient-centered access to care framework to analyze DR-TB policy documents and interview data.

Results

Thematic analysis revealed inequitable access to DR-TB care for some patient socio-demographic groups. While patients were mostly treated equally at the facility level, some patients experienced more difficulty accessing care based on their gender, age, occupation, educational level and religion. Health system factors including positive provider attitudes and financial support provided to the patients facilitated equity and ease of access. However, limited coverage and the absence of patients’ access rights protection and considerations in the treatment guidelines and workers manuals likely hampered access.

Conclusion

In the context of Nigeria’s low case-finding and treatment coverage, applying an equity of access framework was necessary to highlight gaps in care. Differing social contexts of patients adversely affected their access to DR-TB care. We identified several strengths in DR-TB care delivery, including the current financial support that should be sustained. Our findings highlight the need for government’s commitment and continued interventions.

Factors influencing diagnosis and treatment initiation for multidrug-resistant/rifampicin-resistant tuberculosis in six sub-Saharan African countries: a mixed-methods systematic review

BACKGROUND

Drug-resistant tuberculosis burdens fragile health systems in sub-Saharan Africa (SSA), complicated by high prevalence of HIV. Several African countries reported large gaps between estimated incidence and diagnosed or treated cases. Our review aimed to identify barriers and facilitators influencing diagnosis and treatment for drug-resistant tuberculosis (DR-TB) in SSA, which is necessary to develop effective strategies to find the missing incident cases and improve quality of care.

METHODS

Using an integrative design, we reviewed and narratively synthesised qualitative, quantitative and mixed-methods studies from nine electronic databases: Medline, Global Health, CINAHL, EMBASE, Scopus, Web of Science, International Journal of Tuberculosis and Lung Disease, PubMed and Google Scholar (January 2006 to June 2019).

RESULTS

Of 3181 original studies identified, 55 full texts were screened, and 29 retained. The studies included were from 6 countries, mostly South Africa. Barriers and facilitators to DR-TB care were identified at the health system and patient levels. Predominant health system barriers were laboratory operational issues, provider knowledge and attitudes and information management. Facilitators included GeneXpert MTB/RIF (Xpert) diagnosis and decentralisation of services. At the patient level, predominant barriers were patients being lost to follow-up or dying due to lengthy diagnostic and treatment delays, negative public sector care perceptions, family, work or school commitments and using private sector care. Some patient-level facilitators were HIV positivity and having more symptoms.

CONCLUSION

Case detection and treatment for DR -TB in SSA currently relies on individual patients presenting voluntarily to the hospital for care. Specific interventions targeting identified barriers may improve rates and timeliness of detection and treatment.

Treatment as prevention and other interventions to reduce transmission of multidrug-resistant tuberculosis

Drug-resistant tuberculosis (DR-TB) represents a major programmatic challenge at the national and global levels. Only ∼30% of patients with multidrug-resistant TB (MDR-TB) were diagnosed, and ∼25% were initiated on treatment for MDR-TB in 2016. Increasing evidence now points towards primary transmission of DR-TB, rather than inadequate treatment, as the main driver of the DR-TB epidemic. The cornerstone of DR-TB transmission prevention should be earlier diagnosis and prompt initiation of effective treatment for all patients with DR-TB. Despite the extensive scale-up of Xpert^® MTB/RIF testing, major implementation barriers continue to limit its impact. Although there is longstanding evidence in support of the rapid impact of treatment on patient infectiousness, delays in the initiation of effective DR-TB treatment persist, resulting in ongoing transmission. However, it is also imperative to address the burden of latent drug-resistant tuberculous infection because it is estimated that many DR-TB patients will become infectious before seeking care and encounter various diagnostic delays before treatment. Addressing latent DR-TB primarily consists of identifying, treating and following the contacts of patients with MDR-TB, typically through household contact evaluation. Adjunctive measures, such as improved ventilation and use of germicidal ultraviolet technology can further reduce TB transmission in high-risk congregate settings. Although many gaps remain in our biological understanding of TB transmission, implementation barriers to early diagnosis and rapid initiation of effective DR-TB treatment can and must be overcome if we are to impact DR-TB incidence in the short and long term.

Rifampicin Resistant Tuberculosis in Lesotho: Diagnosis, Treatment Initiation and Outcomes

The Lesotho guidelines for the management of drug-resistant tuberculosis (TB) recommend initiation of patients diagnosed with rifampicin resistant (RR)-TB on a standardized drug resistant regimen while awaiting confirmation of rifampicin resistant TB (RR-TB) and complete drug susceptibility test results. Review of diagnostic records between 2014 and 2016 identified 518 patients with RR-TB. Only 314 (60.6%) patients could be linked to treatment records at the Lesotho MDR hospital. The median delay in treatment initiation from the availability of Xpert MTB/RIF assay result was 12 days (IQR 7–19). Only 32% (101) of patients had a documented first-line drug resistant test. MDR-TB was detected in 56.4% of patients while 33.7% of patients had rifampicin mono-resistance. Only 7.4% of patients assessed for second-line resistance had a positive result (resistance to fluoroquinolone). Treatment success was 69.8%, death rate was 28.8%, loss to follow up was 1.0%, and 0.4% failed treatment. Death was associated with positive or unavailable sputum smear at the end of first month of treatment (Fisher exact p < 0.001) and older age (p = 0.007). Urgent attention needs to be given to link patients with RR-TB to care worldwide. The association of death rate with positive sputum smear at the end of the first month of treatment should trigger early individualization of treatment.

Access to second-line drug susceptibility testing results among patients with Rifampicin resistant tuberculosis after introduction of the Hain® Line Probe Assay in Southern provinces, Zimbabwe

OBJECTIVES

To determine the proportion of rifampicin-resistant tuberculosis (RR-TB) patients who accessed second-line drug susceptibility testing (SL-DST) results following introduction of the Hain technology in southern provinces, Zimbabwe.

DESIGN

Cohort study using secondary data.

RESULTS

Xpert MTB/RIF results were used to identify 133 RR-TB patients for this study. Their mean age (SD) was 37.9 (11.1) years, 83 (62%) were males and 106 (80%) were HIV-infected. There were 6 (5%) participants who had pre-treatment attrition. Of the 133 pulmonary TB (PTB) patients, 117 (80%) had additional sputum specimens collected; 96 (72%) specimens reached the National TB Reference Laboratory (NTBRL); 95 (71%) were processed; 68 (51%) had SL-DST results. Only 53 (40%) SL-DST results reached the peripheral facilities. Median time from specimen reception at the NTBRL to SL-DSTs was 40 days, interquartile range (IQR: 28-67). Median time from presumptive diagnosis of RR-TB by health care worker to SL-DST results was 50days (IQR: 39-80), and increased to 79days (IQR: 39-101) in facilities >250km from the NTBRL. The proportion with any fluoroquinolone resistance was 9 (13.2%).

CONCLUSION

Although RR-TB patients with PTB were initiated timely on treatment, access to SL-DSTs by facilities needs improvement. Health inequities exist as remote areas are less likely to get SL-DST results in time.

Impact of Xpert MTB/RIF and decentralized care on linkage to care and drug-resistant tuberculosis treatment outcomes in Johannesburg, South Africa

Background

In 2011, South Africa improved its ability to test for rifampicin-resistant TB (RR-TB) by introducing GeneXpert MTB/RIF. At the same time, the South African National TB program adopted a policy decentralized, outpatient treatment for drug resistant (DR-) TB. We aim to analyze the impact of these changes on linkage to care and DR-TB treatment outcomes.

Methods

We retrospectively matched adult patients diagnosed with laboratory-confirmed RR-TB in Johannesburg from 07/2011–06/2012 (early cohort) and 07/2013–06/2014 (late cohort) with records of patients initiating DR-TB treatment at one of the city’s four public sector treatment sites. We determine the proportion of persons diagnosed with RR-TB who initiated DR-TB treatment and report time to treatment initiation (TTI) before and after the implementation of Xpert MTB/RIF roll-out in Johannesburg, South Africa. We conducted a sub-analysis among those who initiated DR-TB treatment at the decentralized outpatient DR-TB centers to determine if delays in treatment initiation have a subsequent impact on treatment outcomes.

Results

Five hundred ninety four patients were enrolled in the early cohort versus 713 in the late cohort. 53.8 and 36.8% of patients were diagnosed with multi-drug resistant TB in the early and late cohorts, respectively. The proportion of RR-TB confirmed cases diagnosed by Xpert MTB/RIF increased from 43.4 to 60.5% between the early and late cohorts, respectively. The proportion who initiated treatment increased from 43.1% (n = 256) to 60.3% (n = 430) in the late cohort. Pre-treatment mortality during the early and the late cohort reduced significantly from 17.5 to 5.8% while lost to follow-up remained high.

Although TTI reduced by a median of 19 days, from 33 days (IQR 12–52) in the early cohort to 14 days (IQR 7–31) in the late cohort, this did not translate to improved treatment outcomes and we found no difference in terms of treatment success or on-treatment mortality for those that initiated without delay vs. those that deferred initiation.

Conclusion

Pre-treatment mortality reduced significantly during late Xpert MTB/RIF coverage but there was no significant difference after treatment was initiated. Despite improvements there is still a significant diagnosis and treatment gap for patients diagnosed with RR-TB and improving treatment outcomes remains critical.

Electronic supplementary material

The online version of this article (10.1186/s12913-018-3762-x) contains supplementary material, which is available to authorized users.

Stool Culture for Diagnosis of Pulmonary Tuberculosis in Children

Bacteriological confirmation of Mycobacterium tuberculosis is achieved in the minority of young children with tuberculosis (TB), since specimen collection is resource intensive and respiratory secretions are mostly paucibacillary, leading to limited sensitivity of available diagnostic tests. Although molecular tests are increasingly available globally, mycobacterial culture remains the gold standard for diagnosis and determination of drug susceptibility and is more sensitive than molecular methods for paucibacillary TB. We evaluated stool culture as an alternative to respiratory specimens for the diagnosis of suspected intrathoracic TB in a subgroup of 188 children (median age, 14.4 months; 15.4% HIV infected) enrolled in a TB diagnostic study at two local hospitals in Cape Town, South Africa. One stool culture was compared to overall bacteriological confirmation by stool Xpert and by Xpert and culture of multiple respiratory specimens. After decontamination/digestion with NALC (N-acetyl-l-cysteine)-NaOH (1.25%), concentrated fluorescent smear microscopy, Xpert MTB/RIF, and liquid culture were completed for all specimens. Culture contamination of stool specimens was high at 41.5%. Seven of 90 (7.8%) children initiating TB treatment were stool culture positive for M. tuberculosis. Excluding contaminated cultures, the sensitivity of stool culture versus confirmed TB was 6/25 (24.0%; 95% confidence interval [CI] = 9.4 to 45.1%). In addition, stool culture detected TB in 1/93 (1.1%) children with “unconfirmed TB.” Testing the same stool by Xpert increased sensitivity to 33.3% (95% CI = 18.0 to 51.8%). In conclusion, stool culture had low sensitivity for M. tuberculosis detection in children with intrathoracic TB. Reducing culture contamination through improved laboratory protocols may enable more reliable estimates of its diagnostic utility.