Real Time, Portable DNA Sequencing Fights Drug-Resistant TB
International scientific team including Stony Brook researchers are training scientists in Madagascar how to use the technology to combat disease
Medical researchers in Madagascar are trained by the global consortium on how to load DNA on the portable sequencer.
Credit: Institut Pasteur de Madagascar
Stony Brook, NY, June 1, 2018 — Scientists in Madagascar have for the first time performed DNA sequencing in-country using novel, portable technology to rapidly identify the bacteria responsible for tuberculosis (TB) and its drug resistance profile. The project, led by a global team of doctors and scientists from Madagascar’s National TB Program, Stony Brook University, the Institut Pasteur Madagascar (IPM), University of Oxford and the European Bioinformatics Institute (EMBL-EBI) is seeking to transform the surveillance, diagnosis and treatment of TB and other infectious diseases in Madagascar.
This is the first time DNA sequencing has been performed in Madagascar – enabled through deployment of the portable, affordable MinON sequencing device.
Beyond performing DNA sequencing on samples submitted to the nation reference laboratory for TB, the team partnered with TB clinics in the country to evaluate the ability to perform these analyses outside the labs or “in the field”. To achieve public health impact, their objective is to bring TB DNA sequencing closer to the patients for rapid diagnosis.
“This exercise has provided evidence that we can identify TB and its drug resistance properties using real time DNA sequencing technology,” said Niaina Rakotosamimanana, head of the mycobacterium unit at IPM. “We have done this in the lab and are doing more development towards providing this in a rural setting without traditional lab facilities and very limited resources. This is exactly where technology is needed – close to where the TB outbreaks are actually taking place.”
“We have trained 22 scientists to perform DNA sequencing using the MinION platform. This will allow better characterization and understanding of a variety of infectious diseases which represent public health threats in Madagascar,” said Simon Grandjean Lapierre, Research Coordinator from Stony Brook University, a member of the global consortium and of Stony Brook’s Global Health Institute. “Our long term goal, as part of our broader TB strategy, is to increase capacity and work on methods development so that DNA sequencing can become part of routine TB diagnosis and surveillance in Madagascar.”
DNA sequencing as a tool to fight TB: now accessible to developing countries, where it is needed most
In high-income countries, DNA sequencing of TB samples is increasingly being deployed for diagnosis and surveillance of the disease. It delivers rich information about potential drug resistant bacteria, and can identify transmission between patients, with a level of precision and speed unachievable by the traditional methods. However, due to the cost and complexity of DNA sequencing systems, these insights have so far remained out of reach of low- and middle-income countries, where TB has the greatest health impact. The MinION increases DNA sequencing technology accessibility, due to its portability and cost.
Genomic surveillance provides opportunities to gain rich information about the pathogens that are affecting a population. The impact of access to DNA sequencing in Madagascar will not be limited to tackling TB. The scientists from Institut Pasteur de Madagascar have also now sequenced a range of viruses and bacteria that are endemic to the country. Complete genomes of pathogens including Coronavirus (a variant of SARS and MERS-CoV), Respiratory Syncytial Virus (the common cold virus), carbapenemase-producing strains of Klebsiella pneumonia (a bacteria highly resistant to antibiotics) and Yersinia pestis (the bacteria responsible for plague) have been sequenced. Insights from these studies could help to bring future outbreaks of these diseases under control more quickly.
The training led by Stony Brook University, the Institut Pasteur Madagascar, Oxford University and EMBL-EBI, will be extended to healthcare facilities of the National TB Program of Madagascar.
As part of a larger study funded by the Wellcome Trust, the Academy of Medical Sciences and NIHR Oxford Biomedical Research Centre the team of researchers aim to develop more capacity for DNA sequencing and use this tool prospectively to identify TB drug resistance, better understand the dynamics of TB transmission in Madagascar and evaluate impact on public health.
The research and use of the portable DNA sequencing technology is also supported by Stop TB Partnership’s TB REACH.
TB in Madagascar
TB is a devastating disease which affected 59,000 Malagasy patients and killed about 13,000 of them in 2016 (WHO, 2017). Drug resistant strains circulate in the country and the National TB Program along with its partners have been driving new methods to rapidly identify and interrupt the spread of the disease in Madagascar.
Drug resistant TB
Multidrug resistance or MDR-TB – defined by resistance to two of the major anti-TB drugs – isoniazid and rifampicin – is one of the major challenges in the fight against TB worldwide. The most at risk patients are those who are immunodeficient or are in contact with other patients infected with MDR-TB and those who previously received anti-TB drugs, such as patients who failed therapy, who have relapsed after completing treatment or who did not complete their full treatment course. This emphasizes the need for robust and comprehensive drug susceptibility testing methods, patient to patient transmission early recognition and treatment adherence support.
As part of the End TB strategy, the TB community, led by the World Health Organization (WHO), established ambitious targets for TB control. These include the reduction of TB infections by 90% and of TB-related deaths by 95% in 2035.
The TB challenge in Madagascar
Madagascar has a population of approximately 25 million people of which a vast majority resides in rural and sometimes enclaved areas with poor access to healthcare. In 2016, the reported incidence of TB was 237 cases per 100,000 inhabitants according to the WHO.
It is a priority to diagnose cases of MDR-TB at an early stage of disease to avoid further transmission in this context of poor access to care and high proximity of patients in enclaved communities. Genomic information – from DNA sequencing of the TB samples – can help scientists understand where the drug resistant strains are and how they are spreading within a population. This epidemiological information promises to provide important insights for forming public health strategies.
Stony Brook University – Global Health Institute
The Stony Brook University Global Health Institute works with ministries of health and research institutions across the world to achieve public health impact through better use of data and innovative technologies. In Madagascar, the institute has implemented a bi-directional drone-assisted delivery program to enhance TB care in enclaved communities. This initiative serves as a model for other countries such as Nepal where drones are also newly used for TB care. In partnership with the National TB Program, the Global Health Institute has also initiated the use of digital adherence monitoring technologies and produced a Malagasy video-based TB training curriculum for patients and community healthcare workers. More recently, Stony Brook integrated this research consortium to support capacity building around TB DNA sequencing in Madagascar. This new diagnostic tool aligns perfectly with the Institute’s previous work which already focuses on every aspects of the TB cascade of care.
Institut Pasteur de Madagascar
The Institut Pasteur de Madagascar (IPM) created in 1898, is a non-profit private foundation under the Ministry of Public Health from Madagascar and recognized of public utility by the Government of the Malagasy Republic. This status gives IPM four main tasks: research activities directly applied to Malagasy national health priorities; Public health activities with its National Reference Centers bringing expertise to the Malagasy Ministry of Public health; Training and learning activities essential in the Malagasy context and service activities (Medical laboratory, Hygiene and food laboratory, international vaccine center). The IPM is member of the Institut Pasteur International Network that regroups 33 research institutes from 5 continents around the world.
The IPM research projects are aligned with national priorities and meet the challenges of international health. The focus of IPM’s fight against ID includes researching new ways of preventing and treating of chronic disease. As a direct result of these projects, the public health sector, in close partnership with the Ministry of Public Health in Madagascar, designed and developed ID surveillance which ensures quality diagnostics (IPM hosts 10 national or international (WHO) reference laboratories) or to intervene in the epidemic response.
University of Oxford – Modernising Medical Microbiology
Modernising Medical Microbiology (MMM) is a research group within University of Oxford, a world-leading centre of learning, teaching and research and the oldest University in the English-speaking world. MMM aims to transform the way we investigate infectious diseases, bringing cutting-edge scientific techniques to clinical care. The group has spearheaded the use of pathogen whole genome sequencing (WGS) for enhancing clinical microbiology which has the potential, in one step, to comprehensively identify micro-organism species, drug-resistance and genetic relatedness. Research over the last 5 years has been at the forefront demonstrating the ability of WGS to accurately predict phenotypic resistance in Mycobacterium tuberculosis, Staphylococcus aureus, Escherichia coli and Klebsiella spp and produced the first WGS solution for clinical use which was implemented for mycobacteria in the UK by Public Health England.
In parallel, MMM is leading a multidisciplinary collaboration including M. tuberculosis (TB) experts from five continents to uncover all, or nearly all, genomic variation causing resistance to anti-tuberculosis drugs. This work on TB together with translating whole genome sequencing solutions for other pathogens aims to deliver diagnostic solutions to high, medium and low income countries. Successfully doing so will have a profound effect on the management of infectious diseases in many underserved communities around the world.
European Bioinformatics Institute (EMBL-EBI)
The European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. We help scientists realise the potential of ‘big data’ by enhancing their ability to exploit complex information to make discoveries that benefit humankind. We are at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease.We are part of EMBL and are located on the Wellcome Genome Campus, one of the world’s largest concentrations of scientific and technical expertise in genomics.
Oxford Nanopore Technologies
Oxford Nanopore has developed the world’s first and only nanopore DNA sequencer, the MinION. The MinION is a portable, real-time, long-read, low-cost device that has been designed to bring easy biological analyses to anyone, whether in scientific research, education or a range of real-world applications such as disease/pathogen surveillance, environmental monitoring, food-chain surveillance, self-quantification or even microgravity biology. Commercially available since 2015, the MinION is in use by a thriving community of scientists in more than 70 countries, where it is enabling myriad applications within the traditional laboratory environment and in the field. Nanopore sensing technology is fully scalable. The GridION X5 is a desktop device that includes compute module and the ability to run up to five MinION Flow Cells. The high-throughput, high-sample number PromethION is currently being released in the PromethION Early Access Programme (PEAP). Oxford Nanopore is focused on making DNA-based analyses easy enough for any user and so we are working to simplify the sample preparation and data-analysis processes. For sample preparation, this includes a 5–10 minute sample prep kit and VolTRAX , a rapid, programmable, automated USB sample preparation device designed to prepare DNA for addition to a nanopore sequencing device.
Contact: Gregory Filiano,