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Simplified Sequencing for TB Drug Resistance Testing


041 Simplified Sequencing for TB Drug Resistance Testing

Direct to Phase II will be accepted

Fast Track will be accepted

Number of anticipated awards: 1-2

Budget (total costs):

Phase I: up to $600,000 per year for up to two years;

Phase II: up to $3,000,000 for up to 3 years


People living with HIV/AIDS have increased mortality when infected with MDR and XDR TB, worsened by delays starting an appropriate treatment regimen due to poor access to drug sensitivity testing (DST). While the WHO recommends routine DST at each new presentation of TB, only 12% of newly infected individuals globally had access to a resistance test in 2014. Poor laboratory infrastructure and high cost have been cited as primary factors blocking access to TB resistance testing. Current WHO-approved testing approaches, such as GeneXpert and line probe assays at present detect only a limited set of resistance mutations relevant for up to two TB drugs. Additionally, current molecular tests have been shown to have lower sensitivity in populations with a high HIV burden, due to the lower bacillary load among HIV/TB co-infected patients and higher prevalence of smear negative disease.

Sequencing-based diagnostics hold great promise for the establishment of low-cost, simplified TB drug resistance testing, capable of determining resistance to a broad range of drugs and in diverse TB strains. Crucially, the data generated from sequencing-based diagnostics can concurrently be used for individualizing therapy as well as allow surveillance of the prevalence and emergence of resistance, and accurately determining TB transmission patterns in a population.

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In order to improve the quality of patient care through accurate testing, while concurrently enabling global surveillance of resistance patterns, a simplified sequencing device integrated with an accurate sequencing analysis software platform, is needed.

Project goal:

The goal of this project is to develop a low-cost, easy-to-use platform for TB drug resistance testing and surveillance for settings with high HIV prevalence and limited information technology and laboratory resources. The resulting platform must rapidly and accurately generate sequence data from smear negative sputum to enable the prediction of resistance to all first and second line anti-TB drugs while performing highly accurate analysis of the sequence data to produce clinically actionable resistance reports.

Phase I activities:

• Develop a technique allowing simultaneous sequencing from a single sputum sample (patient sample or spiked) of at least 40 key genes and genetic regions associated with resistance to at least the following tuberculosis drugs: isoniazid, rifampin, ethambutol, pyrazinamide, kanamycin, amikacin, capreomycin, streptomycin, moxifloxacin, ofloxacin, para-amino salicylic acid, cycloserine ethionamide/protionamide, terizidone.

• Refine technique to generate accurate sequencing data on first and second line drugs from single smear negative culture positive sputum sample.

Phase II activities:

• Develop a self-contained device for settings with limited laboratory resources incorporating the following :

• Simple operation requiring few steps, and minimal operator training

• No need for external electricity (battery power can be proposed)

• Short per-sample running time with high sample throughput

• Sufficient accuracy to allow clinically relevant results

• Operate with no significant biosafety concerns,

• Software to interpret data to provide immediate clear results for susceptibility to TB drugs listed above with no need for clinician interpretation, aligning with global efforts to standardize reporting language,

• Ability to upload sequencing data to central data repository

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