The overarching objectives of Project 4 are to develop and verify the performance of a sample-in answer-out system for detecting MDR-TB in low-resource operating environments, translate innovative and verified molecular signatures into field deployable diagnostic tests, and transfer systems to Lima Peru for joint, preclinical testing and evaluation ahead of commercial production. We will meet these objectives by taking advantage of patented Akonni manufacturing, sample preparation, amplification, microfluidic, and micorarray technologies through three inter-related specific Aims: 1) Develop and verify methods, consumables, and equipment for automated nucleic acid extraction from decontaminated sputum.
This Aim also includes fundamental science for purifying nucleic acids from large-volumen, non-invasive clinical specimens such as urine, and supporting Harvard Project 2 and collaborators in Peru to determine whether or not MTB signatures can be reliably detected in children and in clinical samples other than sputum, 2) Develop and verify low-cost, sample preparation and amplification microarray consumables. Consumables are designed for long-term storage at room temperature, and will maintain an entirely closed-amplicon work flow that is required for molecular diagnostics in low-resource settings.
This Aim also includes translating new, innovative MDR- and XDR-TB signatures from Harvard Projects 1 and 3 into a next-generation, field-deployable diagnostic test. 3) Develop sample-in, answer-out integrated system (hardware, software, and consumables from Aims 1 and 2) for pre-clinical testing with Harvard collaborators in Lima, Peru. The resulting sample preparation methods, consumables, and instrument will be generally extensible to other Category A-C panel tests for use in low-resource environments.
Project 4 advances the overall objectives ofthe Center by translating fundamental science, knowledge, and innovative molecular markers into robust, low-cost diagnostics and systems, and transferring those consumables and systems to clinical users for pre-clinical testing and evaluation in the field.
|Farhat, Maha R; Jacobson, Karen R; Franke, Molly F et al. (2016) Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis. J Clin Microbiol 54:727-33|
|Farhat, Maha R; Sultana, Razvan; Iartchouk, Oleg et al. (2016) Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med 194:621-30|
|Rock, Jeremy M; Lang, Ulla F; Chase, Michael R et al. (2015) DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader. Nat Genet 47:677-81|
|Farhat, M R; Mitnick, C D; Franke, M F et al. (2015) Concordance of Mycobacterium tuberculosis fluoroquinolone resistance testing: implications for treatment. Int J Tuberc Lung Dis 19:339-41|
|Farhat, Maha R; Shapiro, B Jesse; Sheppard, Samuel K et al. (2014) A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens. Genome Med 6:101|