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

doi:10.1183/20734735.0226-2022

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 MIC
			Can 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 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 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)