New approach for rapidly predicting drug-resistant TB using the first Confidence Graded Mutations List to support diagnostic development published by a global TB consortium and ReSeqTB partners

• First confidence graded list of mutations associated with predicting drug resistance in Mycobacterium tuberculosis complex
• Revolutionary step towards the establishment of standardized, internationally recognized rules to predict phenotypic resistance to anti-tuberculosis drugs

Milan, Italy & Geneva, Switzerland – 08 January 2018 – A global TB consortium announced today the publication of the first graded list of mutations associated with predicting drug resistance in Mycobacterium tuberculosis complex (MTBC), based on systematic and comprehensive analyses of over 1,700 published datasets. The paper was published in the European Respiratory Journal by the consortium comprising 30 organizations, including IRCCS Ospedale San Raffaele, Milan, Italy; Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland; Critical Path Institute (C-Path), Tucson, AZ, USA; and other ReSeqTB partners.

Tuberculosis (TB) is the world’s deadliest infectious disease. In 2016 alone, 10.4 million people fell ill with TB and 1.7 million died from their disease. Drug-resistant TB (DR-TB) accounts for a quarter of the TB deaths annually and, in 2016, 75% of the 490,000 new DR-TB cases went undiagnosed. The spread of DR-TB is a major global health challenge, exacerbated by the limited availability of representative DR-TB surveillance data and the lack of rapid, accurate diagnostic tests for comprehensive drug resistance testing.

The study published uses a standardized, analytical approach for interpreting MTBC genetic mutations associated with drug resistance. The consensus-driven method includes a comprehensive review of MTBC phenotypic and genotypic drug resistance data to quantify the most common mutations as predictors of DR-TB. The results of this study will support the clinical interpretation of existing molecular diagnostics and next generation sequencing approaches, as well as promoting development of new rapid diagnostics and enabling effective targeted antibiotic therapy for patients with DR-TB.

“Tackling drug resistance is critical to ending the TB epidemic,” said Paolo Miotto, researcher at the Emerging Bacterial Pathogens Unit at IRCCS Ospedale San Raffaele (which is recognized by WHO as a collaborating centre), and first author on the paper. “There is an urgent need for internationally recognized rules for the unambiguous clinical interpretation of genetic changes that can predict phenotypic resistance to anti-TB drugs. The Global Mutations List moves us closer to achieving that goal, as it will enable developers to build new diagnostic tests that will give prescribers the information they need to optimize treatment according to their patients’ individual genetic profiles.”

“In Europe, it is crucial that we can rely on molecular tools for quicker diagnoses. Compared with traditional microbiology, new diagnostic methods using genomics could optimize diagnosis, decrease time to treatment and reduce waste of funds,” says Daniela Cirillo, Head of the Emerging Bacterial Pathogens Unit at IRCCS Ospedale San Raffaele.

The novel mutation scoring system developed for this study will facilitate significantly improved clinical interpretation of resistance-associated mutations in patients with TB. This innovative approach has also been incorporated into the Relational Sequencing for TB (ReSeqTB) platform. ReSeqTB (https://platform.reseqtb.org/) is a global knowledge base to support TB drug resistance surveillance, research and clinical decision making through the curation, analysis, interpretation and reporting of mutations associated with TB drug resistance.

“The confidence graded mutation approach addresses a major bottleneck for implementing sequencing technologies and molecular diagnostics in high TB burden settings,” said Debra Hanna, Executive Director for the Critical Path to TB Drug Regimens (CPTR) at C-Path. Marco Schito, Scientific Director for CPTR added, “We will use this approach in ReSeqTB to build confidence in suspected resistance-associated mutations and to help us identify additional mutations associated with resistance to new and repurposed drugs. This will help us identify patients who could benefit from the WHO ‘short’ MDR-TB treatment regimen as well as future optimized regimens.”

The ReSeqTB team also released the companion ReSeqTB Confidence Graded Mutations List, a tool for diagnostic developers creating new, rapid diagnostics for drug resistance. Publicly available on the ReSeqTB website, the Mutations List will allow for the prioritization of specific mutations for target-based assays, and provide interpretation guidelines for mutations identified in sequencing-based assays. These solutions will enable improved diagnosis and effective treatment regimens to better manage patients with drug-resistant TB.

The findings from the review suggest that using confidence graded mutations only to predict phenotypic resistance reduces ambiguity in interpretation of genotypic tests. This is especially true for the prediction of resistance to antibiotics that often have discordant phenotypic test results in liquid or solid media (e.g. the ‘disputed’ rpoB mutations). Additionally, the use of only confidence graded mutations as markers of resistance results in improved specificity with only a slight decrease in sensitivity for prediction of phenotypic resistance when compared with the use of all mutations found in resistance genes.

Catharina Boehme, CEO of FIND, added, “The global TB consortium and the partners involved in this study are helping to solve one of the greatest challenges in TB diagnostics. This collaboration, and the expanding resources provided by the ReSeqTB knowledge base, will help stakeholders such as healthcare professionals, researchers, and diagnostic developers to identify and categorize MTBC mutations associated with drug resistance.”

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About the study
This study provides a standardised and comprehensive approach for the interpretation of mutations as predictors of M. tuberculosis drug resistant phenotypes. Raw genotype-phenotype correlation data were extracted as part of a systematic review to develop a standardised analytical approach for interpreting resistance-associated mutations. These data have implications for the clinical interpretation of molecular diagnostics and next generation sequencing, as well as efficient individualised therapy for patients with drug-resistant TB. The study was supported by the Bill & Melinda Gates Foundation under grant agreement to address how to score mutations in the ReSeqTB data sharing platform initiative. K. Dheda is supported by the South African MRC and EDCTP. I. Comas is supported by the Ministerio de Economía y Competitividad (Spanish Government) research grant and the European Research Council (ERC). L. Chindelevitch is supported by a Sloan Fellowship. FIND’s participation in this study was supported by the Bill & Melinda Gates Foundation, UK aid from the UK Government and the Australian government.

Study partners and co-authors: IRCCS Ospedale San Raffaele, Milano, Italy; University of Gondar, Gondar, Ethiopia; Simon Fraser University, Burnaby, BC, Canada; Centers for Disease Control and Prevention, GA, USA; McMaster University, Hamilton, Ontario, Canada; Critical Path Institute, Tucson, AZ, USA; National Institutes of Health, Rockville, MD, USA; World Health Organization, Geneva, Switzerland; Research Center Borstel, Borstel, Germany; Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland; Chinese Academy of Sciences, Beijing, China; Stellenbosch University, South Africa; University of Oxford, Oxford, United Kingdom; Public Health England, London, United Kingdom; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Karolinska institute, Stockholm and the Public Health Agency of Sweden, Solna, Sweden; Hinduja Hospital, Mumbai, India; Biomedicine Institute of Valencia (IBV-CSIC), Valencia, Spain; Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain; CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Madrid, Spain; Translational Genomics Research Institute, Flagstaff, AZ, USA; Harvard School of Public Health, Boston, Massachusetts, United States; Rutgers-New Jersey Medical School, Newark, NJ, USA; Institute of Tropical Medicine, Antwerp, Belgium; University of Cape Town, Cape Town, South Africa; Aga Khan University, Stadium Road, Karachi, Pakistan; National institute for research in Tuberculosis (ICMR), Chennai, India; University of Cambridge, Cambridge, UK; University of California, San Diego, CA, USA.

About ReSeq TB
The Relational Sequencing TB Data Platform (ReSeqTB) is a joint initiative of the Critical Path Institute (C-Path) – Critical Path to TB Drug Regimens (CPTR) initiative, FIND, the World Health Organization, the Stop TB Partnership’s New Diagnostics Working Group, and the US Centers for Disease Control and Prevention, with contributions from several partner organizations and funding from the Bill & Melinda Gates Foundation. As a data-sharing platform and analytic visualization tool, ReSeqTB can be used to discover, grade, and track key bacterial drug resistance mutations. The resource facilitates the development of new diagnostics capable of rapidly testing drug susceptibility, which could be used to identify effective treatment regimens for better managing patients with drug-resistant TB.

About IRCCS Ospedale San Raffaele
Ospedale San Raffaele is a university and research hospital established in 1971 to provide international-level specialised care for the most complex and difficult health conditions. Since 2012, it is part of Gruppo ospedaliero San Donato, the leading hospital group in Italy. San Raffaele is a multi-speciality center with over 50 clinical specialties and over 1,300 beds. Research focuses on integrating basic, translational and clinical activities to provide the most advanced care to its patients. For further information, visit www.hsr.it.

About FIND
FIND was established in 2003 as a global non-profit dedicated to accelerating the development, evaluation and delivery of high-quality, affordable diagnostic tests for poverty-related diseases, now including malaria, tuberculosis, HIV/AIDS, sleeping sickness, hepatitis C, leishmaniasis, Chagas disease, Buruli ulcer, non-malarial fever and diseases with outbreak potential, such as Ebola. FIND has partnered in the delivery of 20 new diagnostic tools and created an enabling environment for numerous others through the provision of specimen banks, reagent development and better market visibility. FIND also supports better access to new diagnostics through implementation, quality assurance and lab strengthening work. FIND has nearly 200 partners globally, including research institutes and laboratories, health ministries and national disease control programmes, commercial partners, bilateral and multilateral organizations, especially WHO, and clinical trial sites.

[1] Miotto P, et al. A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. Eur Resp J 2017;50:1701354. DOI: 10.1183/13993003.01354-2017
[2] WHO Global Tuberculosis Report 2017. Available at: http://apps.who.int/iris/bitstream/10665/259366/1/9789241565516-eng.pdf?ua=1