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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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  • ORCID record for Anca Vasiliu
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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Tables

  • TABLE 1

    Molecular tuberculosis (TB) diagnostic methods

    Nucleic acid amplification tests (NAATs)Line probe assays (LPAs)Whole genome sequencing (WGS)Targeted next-generation sequencing (tNGS)
    MechanismAmplify the DNA using PCR, and detect a particular nucleic acid sequencePCR-based tests that use LPA as detection (detect the binding pattern of DNA amplification products to probes that target specific parts of the Mycobacterium tuberculosis genome, resistance-associated mutations to anti-TB drugs, or the wild-type DNA sequence)Analyse the entire genomic DNA sequence at a single timeFocus on amplicons (DNA amplification products) or targets known to have strong associations with mutations
    AdvantagesDetect specific mutations associated with resistance to selected anti-TB drugsDetect resistance to a wide range of first-line and second-line agents and provide mutation-specific data for common variantsCan identify low frequency variantsCan identify low frequency variants in targeted regions with high confidence
    Can be used directly on clinical specimensCan be used directly on clinical specimensImprove detection of various types of mutationsCan be used directly on clinical specimens
    Short turn-around timeShort turn-around time (5 h)Assess a broader range of drugs compared with phenotypic DSTShorten turn-around time if performed from clinical specimens
    Provide unbiased detection of mutations mediating low
    or moderate MIC
    Can also be used for surveillance and source investigation
    LimitationsCannot identify low frequency variantsLow availability of supply chain
    Sometimes follow-up actions (e.g. sequencing) are needed to guide appropriate TB treatmentNeed high technical and analytical skills Need high storage size and security
    High cost (capital investment costs, running costs, data storage costs)
    Need for culture
    High cost, but less than WGS; tNGS requires adding the PCR step; the decrease in cost could be linked to the running of many samples in the same flow cell
    Longer turn-around time than other mWRDs methods
    Difficulty interpreting whole-genome variation data in the context of the high number of rare variants
    Example of platformsXpert MTB/RIF and Xpert MTB/RIF Ultra (Cepheid); Truenat (Molbio); Abbott RealTime MTB and Abbott RealTime MTB RIF/INH (Abbott); BD MAX MDR-TB (Becton Dickinson); cobas MTB and cobas
    MTB-RIF/INH (Roche); FluoroType MTBDR and FluoroType MTB (Hain Lifescience/Bruker)
    GenoType MTBDRplus v1 and v2, and GenoType MTBDRsl (Hain Lifescience/Bruker); Genoscholar NTM+MDRTB II, and Genoscholar PZA-TB II (Nipro)Miseq, MiniSeq, NextSeq, HiSeq (Illumina); Personal Genome Machine (Ion Torrent); PacBio RS II (Pacific Biosciences); MinION (Oxford Nanopore Technologies)

    DST: drug-susceptibility testing; MIC: minimum inhibitory concentration; mWRD: molecular WHO-recommended rapid diagnostic tests.

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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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    • Article
      • Abstract
      • Abstract
      • Introduction
      • Currently available mWRDs
      • Challenges in implementing sequencing mWRDs in resource-limited settings
      • Possible solutions
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    • Respiratory infections and tuberculosis
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