Multidrug-resistant tuberculosis surveillance and cascade of care in Madagascar: a five-year (2012-2017) retrospective study

A tuberculosis elimination-focused geospatial approach to optimising access to diagnostic GeneXpert machines in Fiji

OBJECTIVES

Fiji could be the first country to eliminate tuberculosis. To inform this strategy, we aimed to identify how many GeneXpert® machines are required to enable over 90% of Fijians to be within one-hour easy access.

METHODS

We used Geographic Information System (Quantum GIS; QGIS), OpenStreetMap and population data (Kontur) to map possible facilities in relation to QGIS generated 60-min drive-time isochrones, with correction for missing road data. For outer islands, we calculated a distance to nearest hub operation.

RESULTS

The solution comprised 24 GeneXpert® machines, allocating 7 GeneXpert® to Viti Levu, 6 GeneXpert® to Vanua Levu and 11 to other islands. This resulted in 827,810 people, 93.6% of Fiji's population, being within 1 h of a machine. Twenty-one thousand four hundred seventy-nine people on outer islands were an average of 43 km by water from the nearest facility.

CONCLUSIONS

We conclude that over 90% of Fijians could be within an hour of a GeneXpert® machine with placement of 24 machines.

Concordance of targeted and whole genome sequencing for Mycobacterium tuberculosis genotypic drug susceptibility testing

Targeted Next Generation Sequencing (tNGS) and Whole Genome Sequencing (WGS) are increasingly used for genotypic drug susceptibility testing (gDST) of Mycobacterium tuberculosis. Thirty-two multi-drugs resistant and 40 drug susceptible isolates from Madagascar were tested with Deeplex® Myc-TB and WGS using the Mykrobe analysis pipeline. Sixty-four of 72 (89 %) yielded concordant categorical gDST results for drugs tested by both assays. Mykrobe didn't detect pncA K96T, pncA Q141P, pncA H51P, pncA H82R, rrs C517T and rpsL K43R mutations, which were identified as minority variants in corresponding isolates by tNGS. One discrepancy (rrs C517T) was associated with insufficient sequencing depth on WGS. Deeplex® Myc-TB didn't detect inhA G-154A which isn't covered by the assay's amplification targets. Despite those targets being included in the Deeplex® Myc-TB assay, a pncA T47A and a deletion in gid were not identified in one isolate respectively. The evaluated WGS and tNGS gDST assays show high but imperfect concordance.

Barriers to engagement in the care cascade for tuberculosis disease in India: A systematic review of quantitative studies

BACKGROUND

India accounts for about one-quarter of people contracting tuberculosis (TB) disease annually and nearly one-third of TB deaths globally. Many Indians do not navigate all care cascade stages to receive TB treatment and achieve recurrence-free survival. Guided by a population/exposure/comparison/outcomes (PECO) framework, we report findings of a systematic review to identify factors contributing to unfavorable outcomes across each care cascade gap for TB disease in India.

METHODS AND FINDINGS

We defined care cascade gaps as comprising people with confirmed or presumptive TB who did not: start the TB diagnostic workup (Gap 1), complete the workup (Gap 2), start treatment (Gap 3), achieve treatment success (Gap 4), or achieve TB recurrence-free survival (Gap 5). Three systematic searches of PubMed, Embase, and Web of Science from January 1, 2000 to August 14, 2023 were conducted. We identified articles evaluating factors associated with unfavorable outcomes for each gap (reported as adjusted odds, relative risk, or hazard ratios) and, among people experiencing unfavorable outcomes, reasons for these outcomes (reported as proportions), with specific quality or risk of bias criteria for each gap. Findings were organized into person-, family-, and society-, or health system-related factors, using a social-ecological framework. Factors associated with unfavorable outcomes across multiple cascade stages included: male sex, older age, poverty-related factors, lower symptom severity or duration, undernutrition, alcohol use, smoking, and distrust of (or dissatisfaction with) health services. People previously treated for TB were more likely to seek care and engage in the diagnostic workup (Gaps 1 and 2) but more likely to suffer pretreatment loss to follow-up (Gap 3) and unfavorable treatment outcomes (Gap 4), especially those who were lost to follow-up during their prior treatment. For individual care cascade gaps, multiple studies highlighted lack of TB knowledge and structural barriers (e.g., transportation challenges) as contributing to lack of care-seeking for TB symptoms (Gap 1, 14 studies); lack of access to diagnostics (e.g., X-ray), non-identification of eligible people for testing, and failure of providers to communicate concern for TB as contributing to non-completion of the diagnostic workup (Gap 2, 17 studies); stigma, poor recording of patient contact information by providers, and early death from diagnostic delays as contributing to pretreatment loss to follow-up (Gap 3, 15 studies); and lack of TB knowledge, stigma, depression, and medication adverse effects as contributing to unfavorable treatment outcomes (Gap 4, 86 studies). Medication nonadherence contributed to unfavorable treatment outcomes (Gap 4) and TB recurrence (Gap 5, 14 studies). Limitations include lack of meta-analyses due to the heterogeneity of findings and limited generalizability to some Indian regions, given the country's diverse population.

CONCLUSIONS

This systematic review illuminates common patterns of risk that shape outcomes for Indians with TB, while highlighting knowledge gaps-particularly regarding TB care for children or in the private sector-to guide future research. Findings may inform targeting of support services to people with TB who have higher risk of poor outcomes and inform multicomponent interventions to close gaps in the care cascade.

Global inequalities in mental health problems: understanding the predictors of lifetime prevalence, treatment utilisation and perceived helpfulness across 111 countries

Socio-economic inequalities in mental health problems are found in measures covering prevalence, treatment utilisation, and treatment helpfulness. However, whether these inequalities exist globally and what factors explain between-country variation is unclear. We use a nationally representative individual-level survey dataset (Wellcome Global Monitor, 2020) in 111 countries (N = 117,088) to test if socio-economic factors (household income, education), psycho-social factors (stigma perception, trust in health professionals) and country-level factors (GDP, Gini, health expenditure) predict (1) self-reported lifetime prevalence of anxiety and depression symptomology, (2) treatment utilisation and (3) perceived treatment helpfulness talking to a mental health professional and taking prescribed medication. Multi-level logistic regression models were used. Across both HICs and LMICs, being in the richest income quintile within each country is associated with a lower probability of experiencing symptoms of anxiety and depression compared to the poorest quintile (OR = 0.67 CI[0.64-0.70]), as well as a higher probability of talking to a mental health professional (OR = 1.25[1.14-1.36]), and of perceiving this treatment as very helpful (OR = 1.23[1.07-1.40]). However, being among the richest income quintile is not associated with taking prescribed medication (OR = 0.97[0.89-1.06]) and its perceived helpfulness (OR = 1.06[0.94-1.21]) across all countries. Trust in health practitioners is associated with higher mental health professional utilisation (OR = 1.10[1.06-1.14]) and helpfulness (OR = 1.32[1.25-1.40]). This analysis reveals a global 'triple inequality in mental health', whereby disadvantages of lower SES individuals persist in three outcomes (lifetime prevalence, treatment utilisation and helpfulness). Treatment utilisation and helpfulness also vary by trust in healthcare professionals and treatment type. Policymakers must address all three inequalities and their fundamental causes.

Improving measurement of tuberculosis care cascades to enhance people-centred care

Care cascades represent the proportion of people reaching milestones in care for a disease and are widely used to track progress towards global targets for HIV and other diseases. Despite recent progress in estimating care cascades for tuberculosis (TB) disease, they have not been routinely applied at national and subnational levels, representing a lost opportunity for public health impact. As researchers who have estimated TB care cascades in high-incidence countries (India, Madagascar, Nigeria, Peru, South Africa, and Zambia), we describe the utility of care cascades and identify measurement challenges, including the lack of population-based disease burden data and electronic data capture, the under-reporting of people with TB navigating fragmented and privatised health systems, the heterogeneity of TB tests, and the lack of post-treatment follow-up. We outline an agenda for rectifying these gaps and argue that improving care cascade measurement is crucial to enhancing people-centred care and achieving the End TB goals.

A social network analysis model approach to understand tuberculosis transmission in remote rural Madagascar

BACKGROUND

Quality surveillance data used to build tuberculosis (TB) transmission models are frequently unavailable and may overlook community intrinsic dynamics that impact TB transmission. Social network analysis (SNA) generates data on hyperlocal social-demographic structures that contribute to disease transmission.

METHODS

We collected social contact data in five villages and built SNA-informed village-specific stochastic TB transmission models in remote Madagascar. A name-generator approach was used to elicit individual contact networks. Recruitment included confirmed TB patients, followed by snowball sampling of named contacts. Egocentric network data were aggregated into village-level networks. Network- and individual-level characteristics determining contact formation and structure were identified by fitting an exponential random graph model (ERGM), which formed the basis of the contact structure and model dynamics. Models were calibrated and used to evaluate WHO-recommended interventions and community resiliency to foreign TB introduction.

RESULTS

Inter- and intra-village SNA showed variable degrees of interconnectivity, with transitivity (individual clustering) values of 0.16, 0.29, and 0.43. Active case finding and treatment yielded 67%-79% reduction in active TB disease prevalence and a 75% reduction in TB mortality in all village networks. Following hypothetical TB elimination and without specific interventions, networks A and B showed resilience to both active and latent TB reintroduction, while Network C, the village network with the highest transitivity, lacked resiliency to reintroduction and generated a TB prevalence of 2% and a TB mortality rate of 7.3% after introduction of one new contagious infection post hypothetical elimination.

CONCLUSION

In remote Madagascar, SNA-informed models suggest that WHO-recommended interventions reduce TB disease (active TB) prevalence and mortality while TB infection (latent TB) burden remains high. Communities' resiliency to TB introduction decreases as their interconnectivity increases. "Top down" population level TB models would most likely miss this difference between small communities. SNA bridges large-scale population-based and hyper focused community-level TB modeling.

Treatment cascade for patients with multidrug- or rifampicin-resistant tuberculosis and associated factors with patient attrition in southeastern China: a retrospective cohort study

OBJECTIVES

To address gaps in health services for multidrug- or rifampicin-resistant tuberculosis (MDR/RR-TB), a treatment cascade model was used to evaluate patient retention and attrition at each successive step required to achieve a successful treatment outcome.

METHODS

From 2015-2018, a four-step treatment cascade model was established in patients with confirmed MDR/RR-TB in southeast China. Step 1: diagnosis of MDR/RR-TB, step 2: Initiation of treatment, step 3: still under treatment at 6 month and step 4: cure or completion of MDR/RR-TB treatment, with each successive step including a gap that shows attrition of patients between steps. The retention and attrition of each step were graphed. Multi-variate logistic regression was carried out to further identify potential factors associated with the attrition.

RESULTS

In the treatment cascade consisting of 1752 MDR/RR-TB patients, the overall patient attrition rate was 55.8% (978/1752), with 28.0% (491/1752), 19.9% (251/1261), and 23.4% (236/1010) of patients attrition in the first, second, and third gap. Factors associated with MDR/RR-TB patients not initiating treatment included age ≥60 years (OR:2.875), and time for diagnosis ≥30 days (OR: 2.653). Patients who were diagnosed with MDR/RR-TB through rapid molecular test (OR: 0.517) and non-migrant residents of Zhejiang Province (OR: 0.273) both exhibited a lower likelihood of attrition during the treatment initiation phase. Meanwhile, old age (OR: 2.190) and non-resident migrants to the province were factors associated with not completing ≥ 6 months of treatment. Old age (OR: 3.883), retreatment (OR: 1.440), and time to diagnosis ≥30 days (OR: 1.626) were factors contributing to poor treatment outcomes.

CONCLUSION

Several programmatic gaps were identified in the MDR/RR-TB treatment cascade. Future policies should provide more comprehensive support for vulnerable populations to improve the care quality at each step.

SARS-CoV-2 Testing Strategies in the Diagnosis and Management of COVID-19 Patients in Low-Income Countries: A Scoping Review

The accuracy of diagnostic laboratory tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can impact downstream clinical procedures in managing and controlling the outbreak of coronavirus disease 2019 (COVID-19). To assess the effectiveness of laboratory tools for managing COVID-19 patients in low-income countries (LICs), we systematically searched the PubMed, Embase, Scopus and CINHAL databases for reports published between January 2020 and June 2022. We found that 22 of 1303 articles reported the performance of various SARS-CoV-2 detection tools across 10 LICs. These tools were (1) real-time reverse transcriptase polymerase chain reaction (RT-PCR); (2) reverse transcription loop-mediated isothermal amplification (RT-LAMP); (3) rapid diagnostic tests (RDTs); (4) enzyme-linked immunosorbent assay (ELISA); and (5) dot-blot immunoassay. The detection of COVID-19 is largely divided into two main streams-direct virus (antigen) detection and serology (immunoglobulin)-based detection. Point-of-care testing using antigen-based RDTs is preferred in LICs because of cost effectiveness and simplicity in the test procedures. The nucleic acid amplification technology (RT-PCR and RT-LAMP) has the highest diagnostic performance among the available tests, but it is not broadly used in this context due to costs and shortage of facilities/trained staff. The serology-based test method is affected by antibody interferences and varying amounts of SARS-CoV-2 immunoglobulins expressed at different stages of disease onset. We further discuss the effectiveness and shortcomings of each of these tools in the diagnosis and management of COVID-19. Using the LICs as the study model, our findings highlight ways to improve the quality and turnaround time of COVID-19 testing in resource-constrained settings, notably through local/international collaborative efforts to refine the molecular-based or immunoassay-based testing technologies.

Complexities and benefits of adopting next-generation sequencing-based tuberculosis diagnostics: a qualitative study among stakeholders in low and high-income countries

OBJECTIVES

To clarify perceived benefits, barriers and facilitators of Mycobacterium tuberculosis next-generation sequencing implementation in Madagascar and Canada, towards informing implementation of this diagnostic technology in public health agencies and clinical settings in and beyond these settings.

DESIGN

This qualitative study involved conducting semistructured interviews with key stakeholders engaged with next-generation sequencing implementation in Madagascar and Canada. Team-based descriptive analysis supported by Nvivo V.12.0 was used to identify key themes.

SETTING

The study was conducted with participants involved at the clinical, diagnostic and surveillance levels of tuberculosis (TB) management from Madagascar and Canada.

PARTICIPANTS

Eighteen participants were interviewed (nine Madagascar and nine Canada) and included individuals purposively sampled based on involvement with TB surveillance, laboratory diagnosis and clinical management.

RESULTS

The following five themes emerged in the analysis of Malagasy and Canadian interviews: (1) heterogeneity in experience with established TB diagnostics, (2) variable understanding of new sequencing-based diagnostics potential; (3) further evidence as being key to expand adoption; (4) ethical arguments and concerns; (5) operational and system-level considerations.

CONCLUSION

There persists important lack of familiarity with TB next-generation sequencing (TB NGS) applications among stakeholders in Canada and Madagascar. This translates into skepticism on the evidence underlying its use and its true potential value added within global public health systems. If deployed, TB NGS testing should be integrated with clinical and surveillance programmes. Although this is perceived as a priority, leadership and funding responsibilities for this integration to happen remains unclear to clinical, laboratory and public health stakeholders.

Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis

BACKGROUND

Mycobacterium tuberculosis whole-genome sequencing (WGS) has been widely used for genotypic drug susceptibility testing (DST) and outbreak investigation. For both applications, Illumina technology is used by most public health laboratories; however, Nanopore technology developed by Oxford Nanopore Technologies has not been thoroughly evaluated. The aim of this study was to determine whether Nanopore sequencing data can provide equivalent information to Illumina for transmission clustering and genotypic DST for M tuberculosis.

METHODS

In this genomic analysis, we analysed 151 M tuberculosis isolates from Madagascar, South Africa, and England, which were collected between 2011 and 2018, using phenotypic DST and matched Illumina and Nanopore data. Illumina sequencing was done with the MiSeq, HiSeq 2500, or NextSeq500 platforms and Nanopore sequencing was done on the MinION or GridION platforms. Using highly reliable PacBio sequencing assemblies and pairwise distance correlation between Nanopore and Illumina data, we optimise Nanopore variant filters for detecting single-nucleotide polymorphisms (SNPs; using BCFtools software). We then used those SNPs to compare transmission clusters identified by Nanopore with the currently used UK Health Security Agency Illumina pipeline (COMPASS). We compared Illumina and Nanopore WGS-based DST predictions using the Mykrobe software and mutation catalogue.

FINDINGS

The Nanopore BCFtools pipeline identified SNPs with a median precision of 99·3% (IQR 99·1-99·6) and recall of 90·2% (88·1-94·2) compared with a precision of 99·6% (99·4-99·7) and recall of 91·9% (87·6-98·6) using the Illumina COMPASS pipeline. Using a threshold of 12 SNPs for putative transmission clusters, Illumina identified 98 isolates as unrelated and 53 as belonging to 19 distinct clusters (size range 2-7). Nanopore reproduced 15 out of 19 clusters perfectly; two clusters were merged into one cluster, one cluster had a single sample missing, and one cluster had an additional sample adjoined. Illumina-based clusters were also closely replicated using a five SNP threshold and clustering accuracy was maintained using mixed Illumina and Nanopore datasets. Genotyping resistance variants with Nanopore was highly concordant with Illumina, having zero discordant SNPs across more than 3000 SNPs and four insertions or deletions (indels), across 60 000 indels.

INTERPRETATION

Illumina and Nanopore technologies can be used independently or together by public health laboratories performing M tuberculosis genotypic DST and outbreak investigations. As a result, clinical and public health institutions making decisions on which sequencing technology to adopt for tuberculosis can base the choice on cost (which varies by country), batching, and turnaround time.

FUNDING

Academy for Medical Sciences, Oxford Wellcome Institutional Strategic Support Fund, and the Swiss South Africa Joint Research Award (Swiss National Science Foundation and South African National Research Foundation).

Epidemiology of tuberculosis and susceptibility to antituberculosis drugs in Reunion Island

BACKGROUND

Tuberculosis is the first fatal infectious agent in the world with 1.2 million annual deaths for 10 million cases. Little is known about the epidemiology of tuberculosis and its resistance in Reunion Island, which is at the heart of migratory flows from highly endemic Indian Ocean territories.

METHODS

We carried out a retrospective observational study of cases of tuberculosis disease in Reunion Island between 2014 and 2018. The epidemiological, demographic, microbiological, clinical and social characteristics were analyzed from mandatory declarations, microbiology database and medical files.

RESULTS

265 cases of tuberculosis disease were recorded over the period, ie an incidence of 6.2 / 100,000 inhabitants. 114 patients (43%) were born or resided > 6 months in the rest of the Indian Ocean area. The risk of infection was increased if birth in Madagascar (OR 23.5), Comoros (OR 8.9) or Mayotte (OR 6.8). The prevalence of HIV co-infection was low (2.5%). There were 31 cases (14.4%) of resistance to antituberculosis including 3 (1.4%) of multidrug-resistant tuberculosis and 0 case of extensively drug-resistant tuberculosis. The female gender (61.3% of resistant) was associated with resistance. The resistance rate was not significantly different depending on the geographic origin.

CONCLUSION

This is the first exhaustive epidemiological study of tuberculosis in Reunion Island. The incidence there is relatively low but increased for people with links to neighboring islands, particularly Madagascar. The prevalence of multidrug resistance is low, with no associated increased risk for patients from the Indian Ocean area.

Tuberculosis care cascade in Zambia - identifying the gaps in order to improve outcomes: a population-based analysis

OBJECTIVE

Tuberculosis (TB) remains a leading cause of morbidity and mortality in Zambia, especially for people living with HIV (PLHIV). We undertook a care cascade analysis to quantify gaps in care and align programme improvement measures with areas of need.

DESIGN

Retrospective, population-based analysis.

SETTING

We derived national-level estimates for each step of the TB care cascade in Zambia. Estimates were informed by WHO incidence estimates, nationally aggregated laboratory and notification registers, and individual-level programme data from four provinces.

PARTICIPANTS

Participants included all individuals with active TB disease in Zambia in 2018. We characterised the overall TB cascade and disaggregated by drug susceptibility results and HIV status.

RESULTS

In 2018, the total burden of TB in Zambia was estimated to be 72 495 (range, 40 495-111 495) cases. Of these, 43 387 (59.8%) accessed TB testing, 40 176 (55.4%) were diagnosed with TB, 36 431 (50.3%) were started on treatment and 32 700 (45.1%) completed treatment. Among all persons with TB lost at any step along the care cascade (n=39 795), 29 108 (73.1%) were lost prior to accessing diagnostic services, 3211 (8.1%) prior to diagnosis, 3745 (9.4%) prior to initiating treatment and 3731 (9.4%) prior to treatment completion. PLHIV were less likely than HIV-negative individuals to successfully complete the care cascade (42.8% vs 50.2%, p<0.001). Among those with rifampicin-resistant TB, there was substantial attrition at each step of the cascade and only 22.8% were estimated to have successfully completed treatment.

CONCLUSIONS

Losses throughout the care cascade resulted in a large proportion of individuals with TB not completing treatment. Ongoing health systems strengthening and patient-centred engagement strategies are needed at every step of the care cascade; however, scale-up of active case finding strategies is particularly critical to ensure individuals with TB in the population reach initial stages of care. Additionally, a renewed focus on PLHIV and individuals with drug-resistant TB is urgently needed to improve TB-related outcomes in Zambia.

Understanding the gaps in DR-TB care cascade in Nigeria: A sequential mixed-method study

Background

Despite the availability of free drug-resistant tuberculosis (DR-TB) care in Nigeria since 2011, the country continues to tackle low case notification and treatment rates. In 2018, 11% of an estimated 21,000 cases were diagnosed and 9% placed on treatment. These low rates are nevertheless a marked improvement from 2015 when only 3.4% were diagnosed and 2.3% placed on treatment of an estimated 29,000 cases. This study describes the Nigerian DR-TB care cascade from 2013 to 2017 and considers factors influencing gaps in care.

Methods

Our study utilized a mixed-method design. For the quantitative component, we utilized the national diagnosis and treatment databases, as well as the World Health Organization’s estimates for prevalence to construct a 5-year care cascade: numbers of patients at each level of DR-TB care, including incident cases, individuals who accessed testing, were diagnosed, initiated treated and completed treatment in Nigeria between 2013 and 2017. Using retrospective data for patients diagnosed in 2015, we performed the Fisher’s exact test to determine the association between patient (age and gender) and provider/patient (region- north or south) variables, permitting a closer look at the gaps in care revealed across the 5 years. Barriers to care were explored using framework thematic analysis of 57 qualitative interviews and focus group discussions with patients, including 5 cases not initiated on treatment from the 2015 cohort, treatment supporters, community members, healthcare workers and program managers in 2017.

Results

A 5-year analysis of cascade of care data shows significant, but inadequate, increases in overall numbers of cases accessing care. On average, between 2013 and 2017, 80% of estimated cases did not access testing; 75% of those who tested were not diagnosed; 36% of those diagnosed were not initiated on treatment and 23% of these did not finish treatment. In 2015, children and patients in Northern Nigeria had odds of 0.3 [95% CI 0.1–0.7] and 0.4 [0.3–0.5] of completing treatment once diagnosed; while males were shown to have a 1.34 [95% CI 1.0–1.7] times greater chance of completing treatment after diagnosis. The main themes from qualitative data identified barriers to care along the care cascade at individual, family and community, as well as health systems levels. At the individual level, a lack of awareness of the true cause of disease and the availability of ‘free’ care was a recurring theme. Family interference was found to be a particular challenge for children and women. At the health system level, low index of suspicion, lack of rapid diagnostic tools and human resource shortages appeared to limit patients’ access.

Conclusions

Any gains in diagnostic technology and shorter regimens are lost with inadequate access to DR-TB services. The biggest losses in the Nigerian cascade happen before treatment initiation. There is a need for urgent action on identified gaps in the DR-TB cascade in order to improve care continuity at multiple stages, improve health service delivery and facilitate TB control in Nigeria.