The World Health Organization (WHO) recently published The use of next-generation sequencing for the surveillance of drug-resistant tuberculosis: an implementation manual (1) which provides practical guidance on planning and implementing next-generation sequencing (NGS) technology for characterization of Mycobacterium tuberculosis complex (MTBC) bacteria. In this manual, the focus is on the detection of mutations associated with drug resistance for the surveillance of drug resistance in tuberculosis (TB). The implementation guidance is also appropriate for the implementation of targeted NGS tests to detect mutations associated with drug resistance, to guide clinical decision-making for treatment of drug-resistant TB (DR-TB).
This implementation manual 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 (2), 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 medicines; and
- The catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance (3).
The technical guide (2) offers a framework for making decisions about NGS-based drug susceptibility testing (DST), a roadmap for implementation, and practical guidance for country planning and implementation of NGS-based DST. The main steps for implementing targeted NGS for the detection of mutations associated with drug resistance in TB are the same as the ones described in Section 3.5 of the main text, with an emphasis on the nuances of the NGS technologies (e.g. NGS equipment, bioinformatics needs and reporting forms). The main steps are as follows:
- Define the intended immediate and future use of NGS tests in the country, in line with the objectives of the country’s national strategic plan (NSP) for TB. This will have important implications for the choice of technologies and equipment to use, the selection of a site or sites for conducting testing, specimen referral systems and target turnaround times for results.
- Establish a technical working group to lead planning, including performing a readiness assessment, developing a costed operational plan with timelines and milestones, and overseeing compliance with relevant regulatory processes and procedures.
- Based on the intended use of NGS in the country, select, procure and set up equipment in a safe, secure and functional testing site or sites.
- Establish forecasting, ordering and distribution procedures to ensure a reliable and timely supply of quality-assured reagents and consumables.
- Develop and deploy a well-defined, comprehensive set of standard operating procedures (SOPs) to address all aspects of the laboratory testing process, from sample collection to reporting of results. Provide clear decision-making guidance for the selection of people for NGS-based DST.
- Secure adequate storage capacity and processes for backup and retrieval of the large amounts of data generated by NGS; select and implement relevant bioinformatic tools to analyse and interpret NGS data; and develop SOPs for data security, sharing and ensuring confidentiality.
- Implement a comprehensive quality assurance (QA) programme that includes quality control (QC), performance indicator monitoring, proficiency testing, re-checking or interlaboratory comparisons, regular onsite supportive supervision with timely feedback, corrective actions and follow-up for each step of the process.
- Update surveillance forms and registers to capture the relevant data on the person being treated and NGS, ideally through an electronic case-based recording and reporting system. Standardize the recording of NGS results in an easy-to-read format, to facilitate their interpretation.
- Develop and implement training, mentoring and competency assessment programmes to ensure that the workforce is well-trained and has the knowledge, skills and abilities to implement NGS.
- Establish and monitor a set of indicators or milestones to assess the implementation process. Implement a framework for monitoring and evaluation (M&E) to assess the impact of NGS.
The manual also has 17 annexes to help inform the implementation process:
Annex 1: Template of a Gantt chart for an implementation roadmap
Annex 2: NGS implementation high level checklist
Annex 3: Checklists for situational analysis
Annex 4: Example of an NGS situational analysis – the South African experience
Annex 5: Budgetary considerations for NGS implementation
Annex 6: List of commercially available NGS instruments
Annex 7: Installation checklist and resources
Annex 8: List of essential equipment and reagents required for NGS
Annex 9: Estimated data storage needs based on anticipated NGS workload
Annex 10: Key quality indicators and quality control considerations for NGS workflows
Annex 11: ERLTB-NET Proficiency testing programme for TB NGS
Annex 12: Data and quality indicators for NGS-based DST
Annex 13: Examples of NGS-based DST reporting forms
Annex 14: Example TOR for senior NGS scientist, molecular biologist and bioinformatics officer
Annex 15: Suggested agenda for NGS training programmes
Annex 16: Competency assessment
Annex 17: Impact measures
References for Annex 3
- The use of next-generation sequencing for the surveillance of drug-resistant tuberculosis: an implementation manual. Geneva: World Health Organization; 2023. (https://www.who.int/publications/i/item/9789240078079).
- The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guide. (WHO/CDS/TB/2018.19). Geneva: World Health Organization; 2018 (https://apps.who.int/iris/handle/10665/274443).
- Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance, second edition. Geneva: World Health Organization; 2023 (https://www.who.int/publications/i/item/9789240082410).