Rapid Research in Diagnostics Development (R2D2) for TB Network
In high burden countries, many patients with tuberculosis (TB) are never diagnosed or treated with effective drug regimens, leading to ongoing transmission and increased mortality. A primary reason is that current TB diagnostics are inadequate with key issues including inadequate sensitivity, high costs, inability to be used at lower levels of the health system and/or failure to identify drug resistance. No single test is likely to address all these limitations and therefore the World Health Organization (WHO) has described optimal test characteristics for different use-cases in the form of target product profiles (TPPs). To advance novel solutions for high priority TPPs, identifying promising technologies and linking their developers to experienced clinical study sites to facilitate evaluation and performance feedback is essential. The overall goal of the Rapid Research in Diagnostics Development for TB Network (R2D2 TB Network) is to address the critical unmet need for better TB diagnostics in order to close the “diagnostic gap” and thereby improve patient and public health outcomes. To achieve this goal, the R2D2 TB Network will solicit, review and prioritize the most relevant novel TB diagnostics across different phases of development and across different use cases for evaluation during the award period (Objective 1). We will leverage our partnership with a biotech incubator to bring in technology innovators not already working in the TB field and with a key NGO that has been a leader in developing the current TB diagnostics pipeline. Clinical studies to assess accuracy and usability of tests in earlier phases of development will allow for iterative test optimization (Objective 2). These studies will be nested, where possible, within large-scale, multi-center assessments of the accuracy and usability of design-locked diagnostics to facilitate WHO policy review (Objective 3). The clinical studies will rigorously follow WHO guidance for specific use-cases as well as general guidelines for high- quality diagnostic evaluations. For design-locked diagnostics, we will complement the clinical studies with assessments of incremental value through empirical costing, health economic and transmission modeling studies (Objective 4) to further support WHO- and country-level policy reviews. To accomplish these objectives, the R2D2 TB Network brings together investigators with a broad range of relevant expertise related to TB diagnostic research and 12 experienced clinical study sites in 10 high-burden countries that provide access to relevant populations for evaluating TB diagnostics. The PIs overseeing the network have deep expertise in coordination of multi-center studies, a demonstrated history of working with a broad range of product developers, experience in the review and endorsement practices of the WHO and regulatory authorities, and more than a decade of collaborative leadership experience. By fostering and supporting a strong, collaborative network of investigators, product developers and stakeholders across diverse geographic sites, the R2D2 TB Network will advance the next-generation of TB diagnostics.
Sponsor: NIH, NIAID
PI: Adithya Cattamanchi, MD and Payam Nahid, MD
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Host Proteomic Biosignatures for a Urine-based Diagnosis of Pulmonary Tuberculosis in Children
Difficulty in obtaining sputum and a low sputum bacillary load are major barriers to diagnosis, and necessitate the development of a non-sputum, biomarker-based assay for childhood intrathoracic TB disease. We will identify a host proteomic biosignature in urine that can achieve the goal accuracy for a triage and/or diagnostic test for pulmonary TB in children.
Source: National Hearth, Lung, and Blood Institute
PI: Devan Jaganath
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Improving The Molecular Diagnosis Of Drug Resistant Tuberculosis
The overall goal of this proposal is to fundamentally advance molecular diagnostics for pre-XDR and XDR TB. Targeted next-generation deep sequencing of all known genes and gene regions associated with Mycobacterium tuberculosis drug resistance will be performed on stored culture isolates from all patients diagnosed with pre-XDR and XDR TB and a random sample of patients diagnosed with MDR TB through the Philippines Programmatic Management of Drug-resistant Tuberculosis (PMDT) Program. Results will be used to assess the characterize the frequency of hetero-resistance for different anti-TB drugs, determine the ability of current molecular assays to identify resistance in the presence of mixed bacillary populations, and assess the impact of hetero-resistance on treatment outcomes. In addition, whole genome next-generation sequencing will be performed in cases (FQ- and SLI-resistant isolates without a known mutation) and controls (FQ- and SLI-susceptible isolates) to identify novel genetic markers of FQ and SLI resistance. Prediction models will be developed to quantify improvements in diagnostic accuracy for FQ and SLI resistance when adding the novel genetic markers and experiments will be performed to identify which novel mutations directly cause FQ or SLI resistance. The analyses will result in a comprehensive description of reasons for discordance between phenotypic and genotypic tests for resistance to FQ and SLI, evidence on the impact of hetero-resistance on treatment outcomes, and a list of novel mutations that improve prediction of and direclty cause FQ and SLI resistance.
Sponsor: NIH, NIAID
PI: Midori Kato-Maeda, MD and Adithya Cattamanchi, MD
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Handheld and population-based sequencing for rapid detection of new and repurposed drug resistance in M. tuberculosis
Rifampin-resistant tuberculosis (RR-TB) remains a global public health crisis. Molecular TB assays such as Xpert have led to dramatic increases in RR-TB case detection and ongoing expansion of the global estimated need for newer treatments. Longstanding critical barriers of routine phenotypic drug susceptibility testing include prolonged turnaround time and infrastructure requirements that preclude efficient scale-up, contributing significantly to the DR-TB diagnostic gap. Our goal in proposing this work is to improve patient outcomes through strategic and evidence-based use of genomics tools in high burden settings. We will leverage collaborations with international non-profit organizations, a South African MRC- funded cohort, and commercial partners to translate our established targeted deep sequencing assay onto a cost-efficient, handheld nanopore-based sequencing platform (Aim 1, near-clinic solution); and prospectively sequence patient samples early in the course of their treatment in two diverse geographic regions with differing RR-TB and HIV epidemics (Aim 2, centralized solution). These efforts will translate modern-day pathogen genomics into population benefits and contribute to extending the effective lifespan of hard fought new and repurposed anti-TB drugs.
Sponsor: NIH, NIAD
PI: John Metcalfe, MD, PhD, MPH
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Novel Methods Of Pharmacologic Monitoring For Multidrug Resistant Tuberculosis Treatment In The Setting Of HIV Infection
A major barrier to routine pharmacologic monitoring within clinical trials and among high-risk patients (such as persons with concomitant MDR-TB and HIV) is that current methods to monitor medication exposure (i.e., plasma levels) require phlebotomy, a cold chain, and are generally not repeated frequently enough to characterize drug exposure over time. Moreover, high post-dose exposure in plasma after a directly-observed dose cannot confirm long-term adherence. Our goal in proposing this study is to determine whether an assessment of a panel of second-line TB drug concentrations in small hair samples, an easily accessible biomatrix, determined via liquid-chromatography /tandem mass-spectrometry will improve our ability to predict the risk of treatment failure, acquired drug resistance, or death in patients with MDR-TB, with a particular emphasis on those with HIV co-infection, in ongoing clinical trials of MDR-TB evaluating bedaquiline and delamanid - the first new drug classes created specifically to treat TB in over 50 years - and a South African Medical Research Council-supported phase III pragmatic randomized controlled trial examining the effectiveness of a novel 6-month, injectable-free MDR-TB regimen.
Sponsor: NIH, NIAID
PI: John Metcalfe, MD, PhD, MPH and Monica Gandhi, MD, MPH
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Childhood ‘Omics’ and Mycobacterium tuberculosis-derived BiOsignatures (COMBO) for TB diagnosis in high HIV prevalence settings
The overall objective is to identify biomarker signatures that meet recommended accuracy thresholds for a non-sputum, biomarker-based TB triage and/or diagnostic test among young children with HIV infection. In Aim 1, we will use an ultra-sensitive electrochemoluminescence (ECL)-based immunoassay to assess the presence of Mtb proteins ESAT- 6, CFP-10, MPT64, MPT32, and Ag85B in a discovery set of banked blood and urine samples from 100 children under 5 years old with confirmed TB and 200 with unlikely TB per NIH consensus definitions (50% HIV prevalence in both groups). In Aim 2, we will use the same discovery set to perform targeted and untargeted mass spectrometry with functional assessment through pathway analysis, in vitro models and in vivo mouse models to identify host proteins, post-translational modifications and metabolites that distinguish children with confirmed versus unlikely TB. In Aim 3, we will use the candidate Mtb and host biomarkers identified in Aims 1 and 2 to derive biosignatures with up to 10 analytes consisting of Mtb proteins only, host biomarkers only, and both Mtb- and host-derived biomarkers. Biosignatures that meet WHO TPP criteria in the discovery set will be evaluated. Completion of these aims will result in identification of promising biosignatures that can be further validated in large-scale field studies and translated into point-of-care triage and/or diagnostic tests for childhood TB.
Sponsor: NIH, NIAD
PI: Adithya Cattamanchi, MD and Joel Ernst, MD
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Sputum Transcriptomic Expression Profiling in Study 31: Express 31
The objective of the NIAID-funded Express 31 Study, a multi-center, international collaboration led by faculty at UCSF, Stanford University, Yale University and University of Colorado Denver, is to evaluate sputum Mtb transcriptional profiling as a novel biomarker for predicting relapse and as a surrogate endpoint for clinical trials. Our central hypothesis is that TB treatment outcomes are driven by Mtb physiologic changes measurable via pathogen-targeted transcriptional profiling. Our long- term objective is to develop novel surrogate markers and provide new biologic insights into drug tolerance through direct, in vivo molecular monitoring of Mtb populations during treatment. Our scientific approach will be to perform sputum Mtb transcriptional profiling in culture-confirmed, drug-susceptible pulmonary TB patients co-enrolled in a large, Phase 3, open-label, randomized clinical trial led by the CDC TB Trials Consortium (TBTC) and the NIAID/DAIDS AIDS Clinical Trials Group (ACTG), Study 31/ACTG 5349. In this program, we will perform genome-wide Mtb transcriptional profiling in participants in each treatment arm to provide a comprehensive roadmap of physiologic and pharmacodynamic effects of TB treatment on the Mtb transcriptome, with biological interpretations of key drug-tolerance pathways. We will also build advanced pharmacokinetic models to select Mtb transcripts that can predict relapse and serve as surrogate endpoints for clinical trials. This unique research program has the potential to inaugurate a new era in which drug-development is based not on culture- based surrogates but on precise, in vivo molecular markers of pathogen physiologic state during TB treatment.
Sponsor: NIH, NIAID
PIs: Payam Nahid, MD, MPH, Luke Davis, MD, Gary Schoolnik, MD, and Nicholas Walter, MD
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Redefining Tuberculosis Meningitis with Metagenomics and Host Transciptomics
Mycobacterium tuberculosis (TB) affects >10 million people worldwide and carries devastating consequences with ~1.3 million deaths in 2016. Meningitis is the most feared complication of TB with 50-60% mortality in HIV+ persons. Unfortunately, current diagnostic assays are insensitive, and the ability to rapidly characterize the antimicrobial resistance (AMR) profile is severely limited, resulting in only 1 in 5 of the 480,000 multi-drug resistant TB patients receiving appropriate therapy in 2015. To address this critical gap, we will engage a novel combination of metagenomic next generation sequencing (mNGS) coupled with a CRISPR/Cas9- based targeted enrichment method to detect TB and AMR genes and longitudinal host transcriptional profiling to better understand TB meningitis pathogenesis. We have pioneered cerebrospinal fluid (CSF) mNGS at the University of California San Francisco which is an unbiased tool that, in a single assay, can detect the whole range of neurologic infections. Furthermore, we incorporate a novel CRISPR/Cas9-based gene targeting strategy called FLASH (Finding Low Abundance Sequences by Hybridization) to enhance detection of low abundance TB and AMR gene targets by over 104-fold. Thus, we are well positioned to critically test this proposal's central hypotheses which are that CSF mNGS coupled with FLASH is 1) more sensitive and specific than conventional CSF TB diagnostics, 2) enables simultaneous and comprehensive detection of TB AMR genes, and 3) can be used to identify host gene expression biomarkers that discriminate between patients with variable responses to TB meningitis therapy. . We will enroll a prospective cohort of over ~1,300 adults presenting with suspected CNS infection in Kampala and Mbarara, Uganda and test >600 subjects with suspected TBM. The deep clinical phenotyping of this cohort will critically inform the hypotheses being tested herein. These experiments will generate the most comprehensive molecular assessment of TB meningitis in sub- Saharan Africa to date and specifically inform 1) revisions of the TB meningitis uniform case definition, 2) detection of non-TB neurologic infections masquerading as suspected TB meningitis, 3) empiric antibiotic recommendations based on AMR patterns, 4) targets for the next-generation point-of-care diagnostic assays for TB meningitis, and 5) candidate prognostic CSF transcriptional biomarkers for treatment response.
Sponsor: NIH, National Institute of Allergy and Infectious Diseases
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Host Pathogen Mapping Initiative (HPMI)
Although much attention has been devoted to developing therapeutic approaches that specifically target pathogenic organisms, work must also be done to uncover host-directed therapies. To accomplish this, it is critical to understand the many interactions between the pathogenic genes and proteins hijack and re-wire the host machinery during infection. The Host Pathogen Map Initiative will apply systematic approaches to comprehensively map the molecular networks that underlie pathogenesis and will use these maps as a key resource for novel therapies.
Sponsor: NIH, National Institute of Allergy and Infectious Diseases
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Evaluation of a novel breath sensor for rapid, low-cost diagnosis of tuberculosis in children
Tuberculosis (TB) remains a leading cause of morbidity and mortality among children worldwide. This study will result in validation of two promising candidate biomarkers and of a novel low-cost, reagent-free, handheld technology for detecting them in exhaled breath. If successful, we anticipate the breath sensor technology will move toward commercialization and be scaled-up rapidly given its simplicity and low manufacturing costs (<1 USD at scale), thereby improving the health of children worldwide.
Sponsor: NIH, National Heart, Lung, and Blood Institute
PI: Adithya Cattamanchi, MD and Swomitra Mohanty, PhD
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Host Proteomic Biosignatures for a Urine-based Diagnosis of Pulmonary Tuberculosis in Children
Difficulty in obtaining sputum and a low sputum bacillary load are major barriers to diagnosis, and necessitate the development of a non-sputum, biomarker-based assay for childhood intrathoracic TB disease. We will identify a host proteomic biosignature in urine that can achieve the goal accuracy for a triage and/or diagnostic test for pulmonary TB in children.
Source: NIH, National Heart, Lung, and Blood Institute
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Novel next-generation sequencing assay for monitoring multidrug resistant tuberculosis treatment in the setting of HIV infection
This study will help us understand how M. tuberculosis drug resistance evolves under therapy while simultaneously developing a new comprehensive, time- and cost-efficient drug susceptibility test in order to optimize treatment and greatly improve how we diagnose and monitor patients.
Sponsor: NIH, National Institute of Allergy and Infectious Diseases
PI: John Metcalfe, MD, PhD, MPH and David Engelthaler, PhD
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New radiotracer development to study immune cell mobilization of granzyme proteolytic activity
The overall goal of this project is to develop first in class radiotracers to study in vivo how immune cells mobilize granzymes to combat deadly pathogens. This project will span new probe development and application to clinically relevant animal models of viral or bacterial infections and conclude with late stage preclinical studies to establish the long term feasibility of human imaging for this novel probe class. If successful, this project will confer new translational tools to begin probing the emerging non-cytotoxic functions in host defense for this enigmatic enzyme class.
Sponsor: NIH, National Institute of Allergy and Infectious Diseases
PI: Michael Evans, PhD and Charles Craik, PhD and David Wilson, MD, PhD
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