Whole Genome Sequencing of Drug Resistant Tuberculosis in India: Genotype-Phenotype Correlation, Clinical Impact of Resistance, and Sequencing Directly from Sputum

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Project Summary / Abstract Tuberculosis (TB) is the primary infectious disease killer worldwide, with 25% of global cases in India and 12% of India's multidrug-resistant TB (MDR-TB, resistant to rifampin and isoniazid) in Mumbai. Reliance on standardized treatment regimens means drug susceptibility testing (DST) is not performed for most Indian TB patients at diagnosis, resulting in delayed use of effective drugs, and poor outcomes for 45% of MDR-TB patients. In a prospective cohort of MDR-TB patients cared for at the specialty referral center where this K23 will be conducted, the average patient reports 6 months between symptom onset and MDR-TB treatment. Four of these are after diagnosis, but before comprehensive resistance testing is completed. This is time during which disease progression and transmission continue, while patients receive drugs that don't help and many suffer significant side effects. MDR-TB treatment programs need rapid, comprehensive DST, which can be achieved in India through whole genome sequencing (WGS). This K23 Mentored Patient-Oriented Career Development Award will allow the recipient to develop a research career pursuing more comprehensive, rapid diagnosis through the combination of WGS and minimum inhibitory concentration (MIC) testing of patient samples in a clinical cohort. This scientific plan will evaluate DST for MDR-TB through an assessment of WGS of cultured TB specimens as a method of second-line DST in comparison to MIC-based DST and standard DST methods; an assessment of the impact of low-level resistance identified by MIC, hetero-resistance identified by WGS, and pharmacokinetic parameters on longitudinal outcomes in a cohort of MDR-TB patients; and an assessment WGS of Mycobacterium tuberculosis DNA directly from sputum as an alternative to culture-based WGS for DST. These aims are nested in an IRB-approved longitudinal cohort of 200 adult and adolescent patients initiating treatment for MDR-TB at a private multispecialty referral hospital in Mumbai. This mentored research will train the applicant to generate and analyze data optimizing DST for TB and shortening time to individualized therapy for MDR-TB. The applicant is an Infectious Diseases-trained physician at Johns Hopkins University with a longstanding commitment to patient-oriented research in resource-limited settings. He has spent 2 years developing a clinical cohort of MDR-TB patients in Mumbai, where he has lived through an NIH Fogarty Global Health Fellowship. His long-term goals are to develop expertise in the interpretation and clinical application of WGS data to MDRTB with the ultimate goal of translating WGS into a useful clinical diagnostic tool. This K23 will facilitate skill development in the generation, analysis, and interpretation of WGS, MIC, and pharmacokinetic data. Training will include formal coursework, supervised data analysis, laboratory work, and mentorship by a team with expertise in cohort studies, bioinformatics, WGS, mycobacteriology, clinical pharmacology, and MDR-TB treatment. Collectively, the activities of this K23 will provide a pathway to an independent career as a clinical investigator able to design, test, and disseminate novel personalized approaches to the therapy of MDR-TB.