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) Mechanism Amplify the DNA using PCR, and detect a particular nucleic acid sequence PCR-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 time Focus on amplicons (DNA amplification products) or targets known to have strong associations with mutations Advantages Detect specific mutations associated with resistance to selected anti-TB drugs Detect resistance to a wide range of first-line and second-line agents and provide mutation-specific data for common variants Can identify low frequency variants Can identify low frequency variants in targeted regions with high confidence Can be used directly on clinical specimens Can be used directly on clinical specimens Improve detection of various types of mutations Can be used directly on clinical specimens Short turn-around time Short turn-around time (5 h) Assess a broader range of drugs compared with phenotypic DST Shorten turn-around time if performed from clinical specimens Provide unbiased detection of mutations mediating low
or moderate MICCan also be used for surveillance and source investigation Limitations Cannot identify low frequency variants Low availability of supply chain Sometimes follow-up actions (e.g. sequencing) are needed to guide appropriate TB treatment Need high technical and analytical skills Need high storage size and security High cost (capital investment costs, running costs, data storage costs)
Need for cultureHigh 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 platforms Xpert 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.