The use of next-generation sequencing for the surveillance of drug-resistant tuberculosis: an implementation manual

Overview

This document provides practical guidance on planning and implementing next-generation sequencing (NGS) technology for characterization of Mycobacterium tuberculosis complex (MTBC) bacteria. The aim is to detect mutations associated with drug resistance in the context of a surveillance system for tuberculosis (TB). It complements two other publications on TB:

• The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guide, which provides an overview of NGS methods and workflows, and a comprehensive review of the scientific evidence on characterization of the genetic basis of phenotypic drug resistance to major anti-TB drugs; and
• Guidance for the surveillance of drug resistance in tuberculosis, which provides guidance for establishing continuous surveillance systems for drug-resistant TB (DR-TB) or, in settings where this is not yet possible, for conducting periodic surveys. This includes the incorporation of NGS into laboratory testing algorithms for DR-TB surveillance.