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

Abstract

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.

Keywords: Genomic diagnostic; Genomic surveillance; Mycobacterium tuberculosis complex (MTBC); NGS clinical use; NGS programmatic implementation; Next generation sequencing (NGS); high TB burden countries; low- and middle-income countries.

Figure 1

Proposed tNGS implementation roadmap, diagnostic flowchart and tested drugs for the detection of drug-resistance TB cases including NGS technologies for enhanced genotypic resistance prediction of M. tuberculosis complex (MTBC) strains. (A) Roadmap for building tNGS capacity in low- and middle-income countries (from left to right). (B) Flowchart including the GeneXpert MTB/RIF Ultra and MTB/XDR (or any other endorsed test with similar application) as screening tests for selection of samples to downstream targeted next-generation sequencing (tNGS). Hands-on time refers specifically to the theoretical amount of time needed to perform the test, excluding the time needed to collect the clinical specimen. Turn-around time (TAT) refers to the theoretical amount of time needed to perform the test added to the theoretical time to have available clinical specimens (specially affected when additional samples have to be collected). The TAT for tNGS in routine settings is expected to be around 6–8 days from the entry test result. Dashed boxes indicate the panel of drug-resistances investigated by each test, green, yellow and red colors indicate the relative hands-on time, reference: (12). (C) Venn diagram depicting the panel of drug-resistances investigated by each test, worth mentioning that the number of amplified targets is different between the molecular DST tests. pDST, phenotypic drug sensitivity testing; INH, isoniazid; RIF, rifampicin; FQN, Fluoroquinolones; CPM, capreomycin; AMK, amikacin; S, streptomycin; EMB, ethambutol; KAN, kanamycin; ETH, ethionamide; BDQ, bedaquiline; CFZ, clofazimine; LIN, linezolid; PZA, pyrazinamide.