Centre for Genomic Pathogen Surveillance

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Centre for Genomic Pathogen Resistance
Oxfordshire UK location map.svg
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Location within Oxfordshire
General information
TypeGenomic Epidemiology Research Centre
AddressBig Data Institute, Old Road Campus, University of Oxford, Headington, OX3 7LF
Coordinates 51°45′10″N1°13′02″W / 51.7528154°N 1.2170949°W / 51.7528154; -1.2170949
Elevation15 m (49 ft)
Completed2015
OwnerOxford University

The Centre for Genomic Pathogen Surveillance is a computational genomics research institute in Oxfordshire.

Contents

History

The Centre for Genomic Pathogen Surveillance opened in 2015 as a joint project between Imperial College London and Wellcome Sanger Institute. In 2017 it was announced that the centre would house a new Global Health Research Unit funded by the National Institute for Health Research (NIHR) to look at antibiotic resistance. [1] [2] This has seen the centre becoming involved with surveillance of antibiotic resistance in a number of countries, for example, the Philippines. [3]

From 2018 to 2021 the Wellcome Sanger Institute and University of Oxford co-hosted the CGPS. From September 2021 the CGPS has been based at the University of Oxford.

During the COVID-19 pandemic, the centre received funding as part of the COG-UK consortium. [4]

On 22 September 2022 it was announced that the Centre for Genomic Pathogen Surveillance, part of the Big Data Institute at the University of Oxford, was awarded funding worth £7m for their work as an NIHR Global Health Research Unit (GHRU) for the next five years. The Centre’s research and capacity building work focuses on delivering genomics and enabling data for the surveillance of antimicrobial resistance (AMR). [5]

Structure

The centre's director is David Aanensen. [6] [7]

The centre is principally funded, and directed, by the Department of Health and Social Care. [8] In 2019, it was agreed that there would be collaboration between the Centre for Genomic Pathogen Surveillance, the European Centre for Disease Prevention and Control, and the Wellcome Sanger Institute, towards improving the monitoring and tracking of infectious diseases across Europe. [9]

Applications created at the centre

Under the auspices of the centre, the Epicollect5 (used for data entry from distributed observers, e.g. by 'citizen science' programs), Microreact, [10] [11] and Pathogenwatch applications have been generated and shared. [6] Microreact [12] has seen extensive use during the COVID-19 pandemic, and is a component of the Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin) software tool. [7] [13] [14]

Location

The centre is located at the Big Data Institute, Nuffield Department of Medicine, University of Oxford.

See also

Related Research Articles

<span class="mw-page-title-main">Antimicrobial resistance</span> Resistance of microbes to drugs directed against them

Antimicrobial resistance (AMR) occurs when microbes evolve mechanisms that protect them from the effects of antimicrobials. All classes of microbes can evolve resistance to the point that one or more drugs used to fight them are no longer effective. Fungi evolve antifungal resistance, viruses evolve antiviral resistance, protozoa evolve antiprotozoal resistance, and bacteria evolve antibiotic resistance. Together all of these come under the umbrella of antimicrobial resistance.

<span class="mw-page-title-main">Wellcome Trust</span> British healthcare research charity established in 1936

The Wellcome Trust is a charitable foundation focused on health research based in London, United Kingdom. It was established in 1936 with legacies from the pharmaceutical magnate Henry Wellcome to fund research to improve human and animal health. The aim of the Trust is to "support science to solve the urgent health challenges facing everyone." It had a financial endowment of £29.1 billion in 2020, making it the fourth wealthiest charitable foundation in the world. In 2012, the Wellcome Trust was described by the Financial Times as the United Kingdom's largest provider of non-governmental funding for scientific research, and one of the largest providers in the world. According to their annual report, the Wellcome Trust spent GBP £1.1 billion on charitable activities across their 2019/2020 financial year. According to the OECD, the Wellcome Trust's financing for 2019 development increased by 22% to US$327 million.

<span class="mw-page-title-main">Wellcome Sanger Institute</span> British genomics research institute

The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.

<span class="mw-page-title-main">Global health</span> Health of populations in a global context

Global health is the health of the populations in the worldwide context; it has been defined as "the area of study, research, and practice that places a priority on improving health and achieving equity in health for all people worldwide". Problems that transcend national borders or have a global political and economic impact are often emphasized. Thus, global health is about worldwide health improvement, reduction of disparities, and protection against global threats that disregard national borders, including the most common causes of human death and years of life lost from a global perspective.

<span class="mw-page-title-main">Sainsbury Laboratory</span> Plant research laboratory in Norwich, Norfolk, England

The Sainsbury Laboratory (TSL) is a research institute located at the Norwich Research Park in Norwich, Norfolk, England, that carries out fundamental biological research and technology development on aspects of plant disease, plant disease resistance and microbial symbiosis in plants.

<span class="mw-page-title-main">Wellcome Genome Campus</span> Scientific research campus in Hinxton, Cambridgeshire, England

The Wellcome Genome Campus is a scientific research campus built in the grounds of Hinxton Hall, Hinxton in Cambridgeshire, England.

The National Institute for Health and Care Research (NIHR) is the British government's major funder of clinical, public health, social care and translational research. With a budget of over £1.2 billion in 2020–21, its mission is to "improve the health and wealth of the nation through research". The NIHR was established in 2006 under the government's Best Research for Best Health strategy, and is funded by the Department of Health and Social Care. As a research funder and research partner of the NHS, public health and social care, the NIHR complements the work of the Medical Research Council. NIHR focuses on translational research, clinical research and applied health and social care research.

<span class="mw-page-title-main">One Health Trust</span>

One Health Trust, formerly the Center for Disease Dynamics, Economics & Policy, is a public health research organization with offices in Washington, D.C., New Delhi, and Bangalore, India.

<span class="mw-page-title-main">Wellcome Centre for Human Genetics</span> Research Institute at the University of Oxford

The Wellcome Centre for Human Genetics is a human genetics research centre of the Nuffield Department of Medicine in the Medical Sciences Division, University of Oxford, funded by the Wellcome Trust among others.

<span class="mw-page-title-main">Jeremy Farrar</span> British medical researcher

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<span class="mw-page-title-main">Antibiotic use in livestock</span> Use of antibiotics for any purpose in the husbandry of livestock

Antibiotic use in livestock is the use of antibiotics for any purpose in the husbandry of livestock, which includes treatment when ill (therapeutic), treatment of a group of animals when at least one is diagnosed with clinical infection (metaphylaxis), and preventative treatment (prophylaxis). Antibiotics are an important tool to treat animal as well as human disease, safeguard animal health and welfare, and support food safety. However, used irresponsibly, this may lead to antibiotic resistance which may impact human, animal and environmental health.

Combating Antibiotic Resistant Bacteria Biopharmaceutical Accelerator (CARB-X) is a global nonprofit partnership focused on supporting the development of new antibacterial products. Its mission is to strengthen the pipeline of vaccines, rapid diagnostics, antibiotics and non-traditional products to prevent, diagnose and treat life-threatening bacterial infections.

Kevin Outterson is a lawyer, a professor of law and the Austin B. Fletcher Professor Boston University School of Law (2023-present). He is also the executive director of Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator, a global non-profit partnership that supports companies developing new antibiotics, diagnostics, vaccines and other products to address drug-resistant bacterial infections.

Sharon Jayne Peacock is a British microbiologist who is Professor of Public Health and Microbiology in the Department of Medicine at the University of Cambridge. Peacock also sits on Cambridge University Council.

<span class="mw-page-title-main">Nicole Soranzo</span> Italian British geneticist

Nicole Soranzo is an Italian-British senior group leader in human genetics at the Wellcome Sanger Institute, Professor of Human Genetics at the University of Cambridge. She is an internationally recognised Human Geneticist who has focused on the application of cutting edge genomic technologies to study the spectrum of human genetic variation associated with cardio-metabolic and immune diseases. She has led many large-scale discovery efforts including more than 1,000 novel genetic variants associated with cardio-metabolic diseases and their risk factors as well as establishing the HaemGen consortium, which is a worldwide effort to discover genetic determinants of blood cell formation and also interpretation of the downstream consequences of sequence variation through a host of integrative analyses and functional approaches.

EARS-Net otherwise known as European Antimicrobial Resistance Surveillance Network is a central and comprehensive database for the European Union that focuses on eight different bacterial pathogens.

Alison Helen Holmes is a British infectious diseases specialist, who is a professor at Imperial College London and the University of Liverpool. Holmes serves as Director of the National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance and Consultant at Hammersmith Hospital. Holmes is on the Executive Committee of the International Society of Infectious Diseases, and she serves on a variety of World Health Organization (WHO) expert groups related to antimicrobial use, Antimicrobial Resistance (AMR), infection prevention and sepsis. Her research considers how to mitigate antimicrobial resistance.

The MRC Centre for Global Infectious Disease Analysis is a Medical Research Council funded research centre at Imperial College London and a WHO collaborating centre. It is part of the Department of Infectious Disease Epidemiology at School of Public Health within the Imperial College Faculty of Medicine. Neil Ferguson is the director of the centre, along with four associate directors: Christl Donnelly, Azra Ghani, Nicholas Grassly, and Timothy Hallett. The centre also collaborates UK Health Protection Agency, and the US Centre for Disease Control. The centre's main research areas are disease outbreak analysis and modelling, vaccines, global health analytics, antimicrobial resistance, and developing methods and tools for studying these areas. The centre was previously called the MRC Centre for Outbreak Analysis and Modelling.

<span class="mw-page-title-main">Ilina Singh</span> British academic

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<span class="mw-page-title-main">COVID-19 Genomics UK Consortium</span> British genomics research consortium

The COVID-19 Genomics UK (COG-UK) consortium was a group of academic institutions and public health agencies in the United Kingdom created in April 2020 to collect, sequence and analyse genomes of SARS-CoV-2 at scale, as part of COVID-19 pandemic response.

References

  1. "Funding and Awards". fundingawards.nihr.ac.uk. Retrieved 2 March 2021.
  2. "The Centre for Genomic Pathogen Surveillance to house the Global Health Research Unit to monitor antibiotic resistant bacteria around the globe". www.sanger.ac.uk. 21 July 2017. Retrieved 7 March 2021.
  3. Argimón, Silvia; Masim, Melissa A. L.; Gayeta, June M.; Lagrada, Marietta L.; MacAranas, Polle K. V.; Cohen, Victoria; Limas, Marilyn T.; Espiritu, Holly O.; Palarca, Janziel C.; Chilam, Jeremiah; Jamoralin, Manuel C.; Villamin, Alfred S.; Borlasa, Janice B.; Olorosa, Agnettah M.; Hernandez, Lara F. T.; Boehme, Karis D.; Jeffrey, Benjamin; Abudahab, Khalil; Hufano, Charmian M.; Sia, Sonia B.; Stelling, John; Holden, Matthew T. G.; Aanensen, David M.; Carlos, Celia C. (1 June 2020). "Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines". Nature Communications. 11 (1): 2719. Bibcode:2020NatCo..11.2719A. doi:10.1038/s41467-020-16322-5. PMC   7264328 . PMID   32483195. S2CID   219156667.
  4. Paul Brackley (20 November 2020). "£12.2m funding will help Cambridge-led COG-UK expand Covid-19 genomic surveillance". www.cambridgeindependent.co.uk. Retrieved 8 March 2021.
  5. "Major new NIHR Global Health Research Unit to focus on data science and genomic surveillance of antimicrobial resistance — Oxford Big Data Institute". www.bdi.ox.ac.uk. Retrieved 4 November 2022.
  6. 1 2 Professor David Aanensen, Director of the Centre for Genomic Pathogen Surveillance and Group Leader www.sanger.ac.uk, accessed 7 March 2021
  7. 1 2 David Aanensen Director of The Centre for Genomic Pathogen Surveillance 2021 www.ndm.ox.ac.uk, accessed 7 March 2021
  8. NIHR Home page www.nihr.ac.uk, accessed 2 March 2021
  9. Commitment to collaborate on using genomics for pathogen surveillance across Europe 14 March 2019 www.sanger.ac.uk, accessed 7 March 2021
  10. Hospitals in Europe are contributing to the spread of extremely drug-resistant bacteria 30 July 2019, www.zmescience.com, accessed 8 March 2021
  11. Superbug infections tracked across Europe 5 May 2016 www.sciencedaily.com, accessed 8 March 2021
  12. "Microreact has been developed by the Centre for Genomic Pathogen Surveillance at Imperial College London and the Wellcome Genome Campus" microreact.org, accessed 8 March 2021
  13. "Pangolin web application release". virological.org. May 2020. Retrieved 18 February 2021.
  14. How the Covid-19 Genomics UK Consortium sequenced Sars-Cov-2 12 April 2021 www.computerweekly.com, accessed 26 May 2021