Operationalising targeted next-generation sequencing for routine diagnosis of drug-resistant TB

BACKGROUND

Phenotypic drug susceptibility testing (pDST) for Mycobacterium tuberculosis can take up to 8 weeks, while conventional molecular tests identify a limited set of resistance mutations. Targeted next-generation sequencing (tNGS) offers rapid results for predicting comprehensive drug resistance, and this study sought to explore its operational feasibility within a public health laboratory in Mumbai, India.

METHODS

Pulmonary samples from consenting patients testing Xpert MTB-positive were tested for drug resistance by conventional methods and using tNGS. Laboratory operational and logistical implementation experiences from study team members are shared below.

RESULTS

Of the total number of patients tested, 70% (113/161) had no history of previous TB or treatment; however, 88.2% (n = 142) had rifampicin-resistant/multidrug-resistant TB (RR/MDR-TB). There was a high concordance between resistance predictions of tNGS and pDST for most drugs, with tNGS more accurately identifying resistance overall. tNGS was integrated and adapted into the laboratory workflow; however, batching samples caused significantly longer result turnaround time, fastest at 24 days. Manual DNA extraction caused inefficiencies; thus protocol optimisations were performed. Technical expertise was required for analysis of uncharacterised mutations and interpretation of report templates. tNGS cost per sample was US$230, while for pDST this was US$119.

CONCLUSIONS

Implementation of tNGS is feasible in reference laboratories. It can rapidly identify drug resistance and should be considered as a potential alternative to pDST.

Clinical utility of target-based next-generation sequencing for drug-resistant TB

BACKGROUND: In high TB burden countries, access to drug susceptibility testing is a major bottleneck. Targeted next-generation sequencing (tNGS) is a promising technology for rapid resistance detection. This study assessed the role of tNGS for the diagnosis of drug-resistant TB (DR-TB).METHODS: A total of 161 samples from bacteriologically confirmed TB cases were subjected to tNGS using the Deeplex^® Myc-TB kit and sequenced using the MiSeq platform. These samples were also processed for conventional phenotypic DST (pDST) using 13 drugs on Mycobacteria Growth Indicator Tube and line-probe assays (MTBDRplus and MTBDRsl).RESULTS: There were 146 DR-TB and 15 drug-susceptible TB (DS-TB) samples. About 70% of patients with DR-TB had no previous TB treatment history. Overall, 88.2% had rifampicin-resistant/multidrug-resistant TB (RR/MDR-TB), 58.5% pre-extensively drug-resistant TB (pre-XDR-TB) and 9.2% had XDR-TB as defined by the WHO (2020). Around 8% (n = 13) of samples were non-culturable; however, identified 8 were resistant to first and second-line drugs using tNGS. Resistance frequency was similar across methods, with discordance in drugs less reliable using pDST or with limited mutational representation within databases. Sensitivities were aligned with literature reports for most drugs. We observed 10% heteroresistance, while 75% of strains were of Lineages 2 and 3.CONCLUSIONS: Programme data supported tNGS in the diagnosis of DR-TB for early treatment using individualised regimens.

How physical activity behavior affected well-being, anxiety and sleep quality during COVID-19 restrictions in Iran

OBJECTIVE

The Islamic Republic of Iran has displayed one of the highest rates of COVID-19 infection in the world and the highest rate of mortality in the Middle East. Iran has used a stringent package of preventive health measures to mitigate the spread of infection, which however has negatively affected individuals' physical and psychological health. This study aimed at examining whether physical-activity (PA) behavior, anxiety, well-being, and sleep-quality changed in response to the COVID-19-related public health restrictions enforced in Iran.

PATIENTS AND METHODS

An online questionnaire was disseminated to adults residing in Iran from November 17, 2020, to February 13, 2021 (~88 days), during Iran's strictest public health restrictions. Main outcome measures included Godin-Shephard Leisure-Time Exercise Questionnaire, General Anxiety Disorder-7, Mental Health Continuum-Short Form, and Pittsburgh Sleep Quality Index.

RESULTS

A total of 3,323 adults (mean age 30±11 years, 54.3% female) participated in the survey. Firstly, the restrictions generally reduced PA behavior: (a) among inactive participants (IPs), 60.6% became less active vs. 5.1% who became more active; and (b) among active participants (APs), 49.9% became less active vs. 22.8% who became more active. Secondly, PA behavior was associated with higher well-being and sleep quality during the restrictions: (a) APs reported higher (or lower) levels of well-being and sleep quality (or anxiety) than did IPs; and (b) among IPs as well as among APs, the more active the participants, the greater (or lower) the levels of well-being and sleep quality (or anxiety).

CONCLUSIONS

This study showed the beneficial role of PA behavior for well-being, anxiety, and sleep quality during the COVID-19 restrictions, whereas such restrictions appeared to decrease PA participation. Active lifestyle should be then encouraged during the COVID-19 outbreak while taking precautions.

New TB drugs for the treatment of children and adolescents with rifampicin-resistant TB in Mumbai, India

SETTING: Médecins Sans Frontières (MSF) clinic in Mumbai, India.OBJECTIVE: To determine the final treatment outcomes, culture conversion and adverse events (AEs) during treatment among children and adolescents (0-19 years) with rifampicin-resistant tuberculosis (RR-TB) who received ambulatory injectable-free treatment, including bedaquiline (BDQ) and/or delamanid (DLM) during September 2014-January 2020.DESIGN: This was a retrospective cohort study based on review of routinely collected programme data.RESULTS: Twenty-four patients were included; the median age was 15.5 years (min-max 3-19) and 15 (63%) were females. None were HIV-coinfected. All had fluoroquinolone resistance. Twelve received treatment, including BDQ and DLM, 11 received DLM and one BDQ. The median exposure to BDQ (n = 13) and DLM (n = 23) was 82 (IQR 80-93) and 82 (IQR 77-96) weeks, respectively. Seventeen (94%) patients with positive culture at baseline (n = 18) had negative culture during treatment; median time for culture-conversion was 7 weeks (IQR 5-11). Twenty-three (96%) had successful treatment outcomes: cured (n = 16) or completed treatment (n = 7); one died. Eleven (46%) had 17 episodes of AEs. Two of 12 serious AEs were associated with new drugs (QTcF >500 ms).CONCLUSION: Based on one of the largest global cohorts of children and adolescents to receive new TB drugs, this study has shown that injectable-free regimens containing BDQ and/or DLM on ambulatory basis were effective and well-tolerated among children and adolescents and should be made routinely accessible to these vulnerable groups.

Surgical interventions for pulmonary tuberculosis in Mumbai, India: surgical outcomes and programmatic challenges

Setting: While surgery for pulmonary tuberculosis (PTB) is considered an important adjunct for specific cases, including drug-resistant tuberculosis, operational evidence on its feasibility and effectiveness is limited. Objective: To describe surgical outcomes and programmatic challenges of providing surgery for PTB in Mumbai, India. Design: A descriptive study of routinely collected data of surgical interventions for PTB from 2010 to 2014 in two Mumbai hospitals, one public, one private. Results: Of 85 patients, 5 (6%) died and 17 (20%) had complications, with wound infection being the most frequent. Repeat operation was required in 12 (14%) patients. Most procedures were performed on an emergency basis, and eligibility was established late in the course of treatment. Median time from admission to surgery was 51 days. Drug susceptibility test (DST) patterns and final treatment outcomes were not systematically collected. Conclusion: In a high-burden setting such as Mumbai, important data on surgery for PTB were surprisingly limited in both the private and public sectors. Eligibility for surgery was established late, culture and DST were not systematically offered, the interval between admission and surgery was long and TB outcomes were not known. Systematic data collection would allow for proper evaluation of surgery as adjunctive therapy for all forms of TB under programmatic conditions.

Double trouble: tuberculosis and substance abuse in Nagaland, India

The diagnosis and treatment of tuberculosis (TB) in people who use and/or inject illicit drugs (PWUIDs) remains a barrier to achieving universal coverage for TB in India and globally. This report describes treatment outcomes in PWUIDs who received treatment for drug-susceptible TB at the Mon District Hospital in Nagaland, India, during 2012-2013. The median age of the patients was 39 years, and most (92%) were male. Two thirds (33/49) of the patients had a successful TB treatment outcome. A previous TB episode and residence in a semi-urban area were associated with unsuccessful treatment outcomes. Separate diagnostic and treatment algorithms, including regular adherence counselling and opioid substitution therapies, should be considered for PWUIDs.

Yield and economic benefits of common bean (Phaseolus vulgaris) and soybean (Glycine max) inoculation in northern Tanzania

On-farm experiments were conducted in farmers’ fields at 12 different sites in the 2 districts of Moshi and Rombo in northern Tanzania during the 2000–01 cropping season to study the effects of (brady)rhizobial inoculation in combination with P supply on growth and grain yields of soybean and common bean, and to assess the economic returns of these different technologies to farmers. A low level of N was included as an indicator of endogenous soil N status. The treatments included (brady)rhizobial inoculation, N fertilisation (30 kg N/ha as urea), P application [26 kg P/ha as triple super phosphate (TSP)], (brady)rhizobial inoculation + P fertilisation (26 kg/ha as TSP) and unfertilised uninoculated control. The study was conducted as a randomised complete block design with each of the 12 farmers’ fields as a replicate. At harvest, plant growth of soybean and common bean was significantly (P≤0.05) greater with (brady)rhizobial inoculation compared with N and P supply or uninoculated control in the 2 districts. Relative to uninoculated unfertilised plots, grain yields of common bean were markedly (P≤0.05) increased by 60–78% from inoculation alone, and 82–95% from inoculation + 26 kg P/ha; with soybean there was 127–139% increase in grain yield from inoculation alone, and 207–231% from inoculation + P. Thus, the combined application of bacterial inoculants and P fertiliser to field plants of soybean and common bean significantly (P≤0.05) increased biomass production and grain yield compared with the single use of N and P or (brady)rhizobial strains. From economic analysis, the increase in grain yield with inoculation translated into a significantly (P≤0.05) higher marginal rate of return and dollar profit for soybean and common bean farmers in northern Tanzania. With common bean, there was a 66 and 92% increase, respectively, in dollar profit with inoculation at Moshi and Rombo districts respectively relative to control; these profit margins rose to 84 and 102% with provision of supplemental P (26 kg P/ha). With soybean, however, the increase in profit with inoculation was much larger, about 140 and 153% at Rombo and Moshi, respectively, and these rose to 224 and 250% with P supply.