Challenges for Validating Targeted-NGS for Culture-free Drug Resistance Detection in Tuberculosis

Tuberculosis (TB) has continued to be a global epidemic despite efforts being focused on advances in treatment strategies, disease diagnostics, within the context of the Stop TB Strategy. Currently, TB is the leading... [ view full abstract ]

Tuberculosis (TB) has continued to be a global epidemic despite efforts being focused on advances in treatment strategies, disease diagnostics, within the context of the Stop TB Strategy. Currently, TB is the leading infectious disease killer with an estimated 1.5 million days per year and 10.4 million new TB cases in 2016 alone. A major hurdle in controlling and impacting TB is the development of drug resistance. In 2016 an estimated 580,000 people were infected with resistance strains of Mycobacterium tuberculosis complex (MTBC). Dependent upon the location there is a strong probability that for these patients the drugs will fail. The use of NGS for the identification of resistance associated mutations in MTBC is currently available and appears to be promising solution for low and middle income countries to (i) hasten the diagnosis of drug resistance and (ii) provide guidance in providing in the appropriate therapy for the affected patient. The current gold standard in TB drug resistance detection is phenotypic testing that can take weeks for a results due to the slow growth nature of MTBC and also exposes technical personnel to unwarranted safety risks of exposure and infection. Targeted-NGS approaches have been developed that allow detection of resistance associated mutations directly from patient primary samples (i.e. sputum), eliminating the costly and time consuming need for culture. While NGS has been rapidly evolving and has great potential to be used in the clinical setting for infectious disease and antibiotic resistance detection, the development of reference material for use in the validation of NGS assays has lagged behind. Over the past year we have been exploring the different types of materials (i.e. culture, synthetic controls, patient samples) that will be needed during validation of a tuberculosis NGS assay.  Combining a rapid targeted NGS approach allowing drug resistance detection directly from patient samples, with the development of reference material we can compare and contrast different assays and work toward clinical validation of a tuberculosis NGS assay.