Precision medicine and public health interventions: tuberculosis as a model?

Implementation of targeted next-generation sequencing for the diagnosis of drug-resistant tuberculosis in low-resource settings: a programmatic model, challenges, and initial outcomes

Targeted next-generation sequencing (tNGS) from clinical specimens has the potential to become a comprehensive tool for routine drug-resistance (DR) prediction of Mycobacterium tuberculosis complex strains (MTBC), the causative agent of tuberculosis (TB). However, TB mainly affects low- and middle-income countries, in which the implementation of new technologies have specific needs and challenges. We propose a model for programmatic implementation of tNGS in settings with no or low previous sequencing capacity/experience. We highlight the major challenges and considerations for a successful implementation. This model has been applied to build NGS capacity in Namibia, an upper middle-income country located in Southern Africa and suffering from a high-burden of TB and TB-HIV, and we describe herein the outcomes of this process.

Understanding why at-risk population segments do not seek care for tuberculosis: a precision public health approach in South India

INTRODUCTION

Delaying care-seeking for tuberculosis (TB) symptoms is a major contributor to mortality, leading to worse outcomes and spread. To reduce delays, it is essential to identify barriers to care-seeking and target populations most at risk of delaying. Previous work identifies barriers only in people within the health system, often long after initial care-seeking.

METHODS

We conducted a community-based survey of 84 625 households in Chennai, India, to identify 1667 people with TB-indicative symptoms in 2018-2019. Cases were followed prospectively to observe care-seeking behaviour. We used a comprehensive survey to identify care-seeking drivers, then performed multivariate analyses to identify care-seeking predictors. To identify profiles of individuals most at risk to delay care-seeking, we segmented the sample using unsupervised clustering. We then estimated the per cent of the TB-diagnosed population in Chennai in each segment.

RESULTS

Delayed care-seeking characteristics include smoking, drinking, being employed, preferring different facilities than the community, believing to be at lower risk of TB and believing TB is common. Respondents who reported fever or unintended weight loss were more likely to seek care. Clustering analysis revealed seven population segments differing in care-seeking, from a retired/unemployed/disabled cluster, where 70% promptly sought care, to a cluster of employed men who problem-drink and smoke, where only 42% did so. Modelling showed 54% of TB-diagnosed people who delay care-seeking might belong to the latter segment, which is most likely to acquire TB and least likely to promptly seek care.

CONCLUSION

Interventions to increase care-seeking should move from building general awareness to addressing treatment barriers such as lack of time and low-risk perception. Care-seeking interventions should address specific beliefs through a mix of educational, risk perception-targeting and social norms-based campaigns. Employed men who problem-drink and smoke are a prime target for interventions. Reducing delays in this group could dramatically reduce TB spread.

Tuberkulose - Wann daran denken, wie diagnostizieren?

Obwohl die Tuberkulose mithilfe von Antibiotika gut heilbar ist und die Zahlen in Deutschland wieder stetig rückläufig sind, stirbt rechnerisch alle 22 Sekunden auf der Welt ein Mensch an Tuberkulose, 95% davon in Entwicklungs- und Schwellenländern. Die WHO hat in ihrer End-Tuberkulose-Strategie das Ziel formuliert, im Vergleich zu 2015 die Zahl der Tuberkuloseerkrankungen pro 100.000 Einwohner bis 2035 weltweit um 90% und die Zahl der Todesfälle um 95% zu senken. Die Coronakrise hat hier zu großen Rückschritten geführt, fast zwei Drittel der Tuberkuloseprogramme weltweit sind unterbrochen worden. Damit ist in vielen Teilen der Welt die Erreichung dieser Ziele gefährdet und es wird sogar mit zunehmenden Fallzahlen in den nächsten Jahren gerechnet. Aber gerade die Tatsache, dass die Erkrankung bei uns seltener wird führt zu einer Zunahme der Dauer vom ersten Symptom bis zur Tuberkulosediagnose. Der vorliegende Artikel soll Ihnen eine Hilfestellung geben, wann die Tuberkulose in die Differenzialdiagnostik einzubeziehen ist und wie das Krankheitsbild diagnostiziert werden kann. Die Therapie, ihre häufigsten Nebenwirkungen und die Problematik resistenter Tuberkuloseformen werden ebenfalls kurz dargestellt.

Tuberculosis treatment outcomes in a rural area of Senegal: a decade of experience from 2010 to 2019 by StopTB Italia

Background: Tuberculosis (TB) unevenly affects individuals across the globe, especially in rural areas of low-income countries. Aim of the study was to assess the impact of social protection to increase TB awareness on treatment outcomes among TB patients in a rural area of Senegal. Materials & methods: The study, conducted in Fimela district (Senegal) from 1 January 2010 to 31 December 2019 and the intervention started from 31 January 2013, includes activities to increase awareness, active case finding, active follow-up and social protection. Results: Overall, 435 subjects - mainly male and young - were included in the analysis. Among TB cases, 94% had pulmonary involvement, 87% had no previous TB history, and 6% resulted positive HIV. Improved outcome was observed once intervention began (from 71 to 91%, p < 0.001); whereas mortality decreased (from 15 to 5%; p < 0.001), especially for those HIV co-infected for whom TB mortality rate dropped from 70 to 29%. Conclusion: After beginning the cooperation program, TB treatment success increased as a result of the decline of mortality, especially in people living with HIV.

Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples

Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The goal of this study was to evaluate the use of the tNGS-based DST solution Genoscreen Deeplex Myc-TB, for use on the compact, low-cost Oxford Nanopore Technologies MinION sequencer. One hundred four DNA samples extracted from smear-positive sputum sediments, previously sequenced using the Deeplex assay on an Illumina MiniSeq, were resequenced on MinION after applying a custom library preparation. MinION read quality, mapping statistics, and variant calling were computed using an in-house pipeline and compared to the reference MiniSeq data. The average percentage of MinION reads mapped to an H37RV reference genome was 90.8%, versus 99.5% on MiniSeq. The mean depths of coverage were 4,151× and 4,177× on MinION and MiniSeq, respectively, with heterogeneous distribution across targeted genes. Composite reference coverage breadth was >99% for both platforms. We observed full concordance between technologies in reporting the clinically relevant drug-resistant markers, including full gene deletions. In conclusion, we demonstrated that the workflow and sequencing data obtained from Deeplex on MinION are comparable to those for the MiniSeq, despite the higher raw error rates on MinION, with the added advantage of MinION's portability, versatility, and low capital costs. Targeted NGS on MinION is a promising DST solution for rapidly providing clinically relevant data to manage complex DR-TB cases.

Precision, Equity, and Public Health and Epidemiology Informatics - A Scoping Review

OBJECTIVES

This scoping review synthesizes the recent literature on precision public health and the influence of predictive models on health equity with the intent to highlight central concepts for each topic and identify research opportunities for the biomedical informatics community.

METHODS

Searches were conducted using PubMed for publications between 2017-01-01 and 2019-12-31.

RESULTS

Precision public health is defined as the use of data and evidence to tailor interventions to the characteristics of a single population. It differs from precision medicine in terms of its focus on populations and the limited role of human genomics. High-resolution spatial analysis in a global health context and application of genomics to infectious organisms are areas of progress. Opportunities for informatics research include (i) the development of frameworks for measuring non-clinical concepts, such as social position, (ii) the development of methods for learning from similar populations, and (iii) the evaluation of precision public health implementations. Just as the effects of interventions can differ across populations, predictive models can perform systematically differently across subpopulations due to information bias, sampling bias, random error, and the choice of the output. Algorithm developers, professional societies, and governments can take steps to prevent and mitigate these biases. However, even if the steps to avoid bias are clear in theory, they can be very challenging to accomplish in practice.

CONCLUSIONS

Both precision public health and predictive modelling require careful consideration in how subpopulations are defined and access to data on subpopulations can be challenging. While the theory for both topics has advanced considerably, there is much work to be done in understanding how to implement and evaluate these approaches in practice.

Celebrating World Tuberculosis Day at the time of COVID-19

March 24th, the tuberculosis (TB) day, is the global call to raise awareness, celebrate successes and remind the world that TB is still the N°1 killer among the infectious causes of death [1]. TB is preventable and curable disease, and its control is a highly cost-effective health intervention. However, diagnostic delay and inadequate treatment contribute to the severity and mortality of the disease as well as the risk of transmission and development of drug resistance. Despite the fact that TB disproportionately impacts low- and middle- income countries, it does not spare any country in the world including those in the European Union/European Economic Area where more than 4000 of people still die for the disease every year [2]. Moreover, the high number of multidrug-resistant (MDR)-TB cases in some countries of the World Health Organization (WHO) European Region poses a growing public health threat. Despite the sheer numbers, TB has for too long been overshadowed by HIV and malaria, and currently by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the coronavirus disease 2019 (COVID-19) epidemic.

Isoniazid-resistant tuberculosis: A problem we can no longer ignore

Giorgia Sulis and Madhukar Pai discuss the global distribution, and approaches to diagnosis and treatment, of isoniazid-resistant tuberculosis.