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Implementing molecular tuberculosis diagnostic methods in limited-resource and high-burden countries

Anca Vasiliu, Antonia Morita Iswari Saktiawati, Raquel Duarte, Christoph Lange, Daniela Maria Cirillo on behalf of the UNITE4TB Consortium
Breathe 2022 18: 220226; DOI: 10.1183/20734735.0226-2022
Anca Vasiliu
1Baylor College of Medicine, Department of Pediatrics, Global TB Program, Houston, TX, USA
14Contributed equally as first authors
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Antonia Morita Iswari Saktiawati
2Universitas Gadjah Mada, Faculty of Medicine, Public Health and Nursing, Department of Internal Medicine, and Center for Tropical Medicine, Yogyakarta, Indonesia
14Contributed equally as first authors
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Raquel Duarte
3EPI Unit, Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal
4Unidade de Investigação Clínica da Administração Regional de Saúde do Norte, Porto, Portugal
5Departamento de Ciências de Saúde Pública, Ciências Forenses e Educação Médica, Universidade do Porto, Porto, Portugal
6Serviço de Pneumologia, Centro Hospitalar de Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
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  • For correspondence: raquelafduarte@gmail.com
Christoph Lange
7Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
8German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
9Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
10Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
11Department of Medicine, Karolinska Institute, Stockholm, Sweden
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Daniela Maria Cirillo
12IRCCS San Raffaele Scientific Institute, Milan, Italy
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Abstract

Tuberculosis (TB) is one of the deadliest infectious diseases in the world with more than a million people dying of TB each year. Accurate and timely TB diagnosis has the potential to alleviate the global TB burden; therefore, one of the pillars of the End TB Strategy developed by the World Health Organization (WHO) is the early diagnosis of TB, including universal drug-susceptibility testing (DST). The WHO emphasises the importance of DST before treatment initiation, using molecular WHO-recommended rapid diagnostic tests (mWRDs). Currently available mWRDs are nucleic acid amplification tests, line probe assays, whole genome sequencing, and targeted next-generation sequencing. However, implementing the sequencing mWRDs in routine laboratories in low-income countries is constrained by the existing infrastructure, high cost, the specialised skills needed, data storage, and the current delay in results compared with other routine methods. These limitations are pronounced in resource-limited settings, which often have a high TB burden and need for innovative TB diagnostic technologies. In this article we propose several possible solutions, like adapting infrastructure capacity to needs, advocating for lowering costs, building bioinformatics and laboratory capacity, and increasing the use of open-access resources for software and publications.

Abstract

Next-generation sequencing has the potential to drastically change the landscape of tuberculosis diagnosis worldwide. Considerate implementation in low-resource settings should ensure access and sustainability, especially through new portable platforms. https://bit.ly/3iiWFyo

Introduction

Tuberculosis (TB) represents an enormous burden on global health, with 9.9 million new people developing TB, and 1.3 million dying from TB in 2020 [1]. In the first high-level meeting on TB, the United Nations released commitments to four global targets, one of which is diagnosing and treating 40 million people with TB in 2018–2022 [2, 3]. An important barrier to reaching these targets is the availability of innovative methods for TB diagnosis. Moreover, one of the key components of the End TB Strategy issued by the World Health Organization (WHO) is the early diagnosis of TB, including universal drug-susceptibility testing (DST) [4]. The WHO guidelines stress the importance of DST before treatment by molecular WHO-recommended rapid diagnostic tests (mWRDs) [2]. However, DST coverage for first-line drugs only ranges from 41% to 93%, and there is suboptimal DST coverage for second-line drugs [2]. Notably, there are no WHO-recommended rapid methods for DST of newer and repurposed drugs, which is worrisome as the use of these drugs is increasing.

This viewpoint discusses the currently available mWRDs and the challenges of their implementation, especially in resource-limited settings, providing possible solutions.

Currently available mWRDs

Table 1 shows the current mWRDs with their methods, advantages, and limitations.

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TABLE 1

Molecular tuberculosis (TB) diagnostic methods

To facilitate the application of these mWRDs, the WHO issued the first catalogue of drug-resistance mutations in Mycobacterium tuberculosis (MTB) [5]. It was built from high-quality phenotypic DST data, standardised whole genome sequencing (WGS) for generation of unbiased, raw sequence data, a standardised bioinformatics pipeline for variant detection and annotation, and a standardised and validated methodological approach for associating genotype with phenotype. This catalogue contains 1200 variants associated with resistance and 246 variants not associated with resistance [5]. However, this catalogue has difficulty classifying rare mutations, probably does not classify the mutations conferring modest minimum inhibitory concentration (MIC), and does not consider the lineage effects, resistance levels and co-occurrence of mutations. An updated version of the catalogue will be issued in the following months, addressing most of these shortcomings.

Challenges in implementing sequencing mWRDs in resource-limited settings

The implementation of sequencing mWRDs in routine laboratories in low-income countries (LICs) is hampered by the currently available technology, its high cost, the very specialised skill set needed to process and analyse the outputs, data storage, and the current delay in results availability compared with other current routine methods. These limitations are more pronounced and consequential in resource-limited settings, which often have a high TB burden and a crucial need for innovative TB diagnostic technologies.

Existing infrastructure

A major challenge in sequencing methods is that they generate vast amounts of data that require strong expertise and powerful machines to extract and analyse. The required infrastructure to effectively obtain results using WGS is not available in many laboratories in LICs. The data obtained from sequencing methods need to be properly stored in data warehouses that are yet to be developed in most LICs. Cloud storage represents another storage solution; however, the existing internet capacity needs to be improved before this option can be realistically accessible in LICs.

Cost of the machines and reagents

The cost of WGS varies by the type of assays, equipment, and software used. The commercial cost of sequencing an MTB genome is between USD 150 and USD 300 [6]. This cost includes the process of resequencing, where the MTB genome sequence is compared to a reference genome.

The costs are increased when establishing a sequencing facility in low-income settings due to the costs of shipments, customs, and the eventual profit margin for local companies. Lessons learnt from implementing WGS in Kyrgyzstan show that the main cost drivers were not using library preparation and sequencing kits to their full capacity during initial training, and partly by prices charged by the regional distributor exceeding those charged to laboratories in Europe and North America [7]. In addition to hardware costs, data manipulation and analysis are done using software licensed and commercialised by companies, representing an additional cost to institutions in LICs.

Training and capacity building

Local capacity needs to be built in both the laboratory and bioinformatics aspects of MTB WGS as many institutions continue to suffer from an insufficient number of experienced personnel that can perform, supervise, and train others in bioinformatics and sequencing research [8]. The fields of sequencing and novel TB diagnostic methods are interdisciplinary, requiring knowledge and training in biology, chemistry, and bioinformatics. In addition to training laboratory staff, there is a need to build capacity for clinicians to interpret the results of sequencing and adequately incorporate them into their routine clinical practice.

Possible solutions

Adapting infrastructure capacity to needs

Decision makers at the country level need to be aware of and adapt the sequencing capacity to the country's needs. National programmes should avoid obtaining the sequencing infrastructure and not using it, because when not in use the maintenance of the machines is even higher, with implicit cost consequences. Therefore, LICs could opt for a national referral hub where all samples would be processed and then returned to health centres. Moreover, several countries could share a regional referral hub for sequencing TB strains, with shared infrastructure and human resources. Another effective strategy would be to mutualise resources with other pathologies (e.g. coronavirus disease 2019 (COVID-19), malaria, or even cancer) for surveillance, antimicrobial resistance control and research [9–11]. The lessons learnt from the COVID-19 pandemic response could inform TB sequencing technologies and inform local and regional stakeholders on the best strategies to implement [9, 12, 13].

Advocating for lowering costs

When sequencing methods are widespread and used at a large scale, there are compelling arguments to advocate with companies to lower the cost of machines and reagents. Using next-generation sequencing (NGS) (USD 50–100) instead of WGS (USD 150–300) as a diagnostic tool would help reduce costs without reducing the advantages of these innovative tools [6]. Mutualising costs with other countries for third-generation sequencing techniques like nanopore might address some of the existing challenges regarding infrastructure or cost, and could be a competitor for current sequencing companies in low-income and high-burden countries [14].

Building bioinformatics and laboratory capacity

An increasing number of universities are offering training in bioinformatics in low-resource settings. Bioinformatics education in Africa is currently being shaped through initiatives such as H3ABioNet, a project funded through the US National Institutes of Health [15]. One of the network's main remits is to build human capacity in bioinformatics in Africa. Proposed solutions include continuous mentorship and support, train-the-trainer programmes, internships, knowledge transfer programmes and e-learning platforms [16]. While being a much-needed initiative in the current landscape, the long-term sustainability of this kind of project remains of concern, with countries needing to take ownership of bioinformatics training and capacity building. In the future, most of the technology could be automated, leaving less of the processing burden to laboratory staff.

Data interpretation and sharing

Data analysis and visualisations should be available in real-time, and be simplified and easy to interpret by laboratory staff and clinicians to facilitate clinical decisions. Access to knowledge and results sharing should be available to researchers and decision-makers in resource-limited settings through open access publications and open license software.

Conclusion

The landscape of genome sequencing for TB diagnosis and DST is rapidly evolving, with promising technologies being developed. Nevertheless, access to these innovative diagnostic methods should be granted in all types of settings, with an emphasis on high-burden countries.

Footnotes

  • Disclaimer: This communication reflects the authors’ view and neither IMI nor the European Union, EFPIA, or any Associated Partners are responsible for any use that may be made of the information contained therein.

  • Conflict of interest: None of the authors has any potential financial conflict of interest related to this manuscript.

  • Support statement: The present paper is submitted on behalf of the UNITE4TB Consortium. This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement number 101007873. The JU receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA, Deutsches Zentrum für Infektionsforschung e.V. (DZIF), and LudwigMaximilians-Universität München (LMU). EFPIA/AP contribute to 50% of funding, whereas the contribution of DZIF and the LMU University Hospital Munich has been granted by the German Federal Ministry of Education and Research.

  • Received September 27, 2022.
  • Accepted December 5, 2022.
  • Copyright ©ERS 2023
http://creativecommons.org/licenses/by-nc/4.0/

Breathe articles are open access and distributed under the terms of the Creative Commons Attribution Non-Commercial Licence 4.0.

References

  1. ↵
    1. World Health Organization
    . Global Tuberculosis Report. Geneva, World Health Organization, 2021. https://www.who.int/publications/i/item/9789240037021
  2. ↵
    1. World Health Organization
    . WHO consolidated guidelines on tuberculosis – module 3: rapid diagnostics for tuberculosis detection. Geneva, World Health Organization, 2021. https://www.who.int/publications/i/item/9789240029415
  3. ↵
    1. Sakamoto H,
    2. Lee S,
    3. Ishizuka A, et al.
    Challenges and opportunities for eliminating tuberculosis – leveraging political momentum of the UN high-level meeting on tuberculosis. BMC Public Health 2019; 19: 76. doi:10.1186/s12889-019-6399-8
    OpenUrlPubMed
  4. ↵
    1. Lönnroth K,
    2. Raviglione M
    . The WHO's new end TB strategy in the post-2015 era of the sustainable development goals. Trans R Soc Trop Med Hyg 2016; 110: 148–150. doi:10.1093/trstmh/trv108
    OpenUrlCrossRefPubMed
  5. ↵
    1. Walker TM,
    2. Miotto P,
    3. Köser CU, et al.
    The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis. Lancet Microbe 2022; 3: e265–e273. doi:10.1016/S2666-5247(21)00301-3
    OpenUrl
  6. ↵
    1. Dlamini MT,
    2. Lessells R,
    3. Iketleng T, et al.
    Whole genome sequencing for drug-resistant tuberculosis management in South Africa: what gaps would this address and what are the challenges to implementation? J Clin Tuberc Mycobact Dis 2019; 16: 100115. doi:10.1016/j.jctube.2019.100115
    OpenUrl
  7. ↵
    1. Vogel M,
    2. Utpatel C,
    3. Corbett C, et al.
    Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country. Sci Rep 2021; 11: 15333. doi:10.1038/s41598-021-94297-z
    OpenUrl
  8. ↵
    1. Rivière E,
    2. Heupink TH,
    3. Ismail N, et al.
    Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries. Brief Bioinform 2021; 22: bbaa246. doi:10.1093/bib/bbaa246
    OpenUrl
  9. ↵
    1. Leite JA,
    2. Vicari A,
    3. Perez E, et al.
    Implementation of a COVID-19 genomic surveillance regional network for Latin America and Caribbean region. PLoS One 2022; 17: e0252526. doi:10.1371/journal.pone.0252526
    OpenUrlPubMed
    1. Akoniyon OP,
    2. Adewumi TS,
    3. Maharaj L, et al.
    Whole genome sequencing contributions and challenges in disease reduction focused on malaria. Biology (Basel) 2022; 11: 587. doi:10.3390/biology11040587
    OpenUrl
  10. ↵
    1. Argimón S,
    2. Masim MAL,
    3. Gayeta JM, et al.
    Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines. Nat Commun 2020; 11: 2719. doi:10.1038/s41467-020-16322-5
    OpenUrl
  11. ↵
    1. Meredith LW,
    2. Hamilton WL,
    3. Warne B, et al.
    Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect Dis 2020; 20: 1263–1271. doi:10.1016/S1473-3099(20)30562-4
    OpenUrlPubMed
  12. ↵
    1. Mboowa G,
    2. Mwesigwa S,
    3. Kateete D, et al.
    Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings. F1000Res 2021; 10: 598. doi:10.12688/f1000research.53567.1
    OpenUrl
  13. ↵
    1. Wang Y,
    2. Zhao Y,
    3. Bollas A, et al.
    Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39: 1348–1365. doi:10.1038/s41587-021-01108-x
    OpenUrlCrossRef
  14. ↵
    1. Mulder NJ,
    2. Adebiyi E,
    3. Alami R, et al.
    H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa. Genome Res 2016; 26: 271–277. doi:10.1101/gr.196295.115
    OpenUrlAbstract/FREE Full Text
  15. ↵
    1. Tastan Bishop Ö,
    2. Adebiyi EF,
    3. Alzohairy AM, et al.
    Bioinformatics education – perspectives and challenges out of Africa. Brief Bioinform 2015; 16: 355–364. doi:10.1093/bib/bbu022
    OpenUrlCrossRefPubMed
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Implementing molecular tuberculosis diagnostic methods in limited-resource and high-burden countries
Anca Vasiliu, Antonia Morita Iswari Saktiawati, Raquel Duarte, Christoph Lange, Daniela Maria Cirillo
Breathe Dec 2022, 18 (4) 220226; DOI: 10.1183/20734735.0226-2022

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Implementing molecular tuberculosis diagnostic methods in limited-resource and high-burden countries
Anca Vasiliu, Antonia Morita Iswari Saktiawati, Raquel Duarte, Christoph Lange, Daniela Maria Cirillo
Breathe Dec 2022, 18 (4) 220226; DOI: 10.1183/20734735.0226-2022
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