2019 Chief Medical Officer’s Report published

Sanger Institute researchers contribute to Professor Dame Sally Davies' eleventh annual report

In Professor Dame Sally Davies’ eleventh and final annual report as England’s Chief Medical Officer and UK Chief Medical Advisor, she outlines the UK’s leading role in global health and highlights the need to share international knowledge and experience.

The report makes clear that by focusing purely on domestic health, we risk failing to control the shifting tide of global threats. Diseases and their determinants do not respect international borders. Ebola, antimicrobial resistance and widening health inequalities are already presenting significant challenges.

Accompanied by a collection of letters from key world health leaders to the Chief Medical Officer, Professor Davies’ report makes a series of recommendations to secure a prospering health system and population both at home and across the world.

Professor Nicholas Thomson, Wellcome Sanger Institute and London School of Hygiene and Tropical Medicine

Professor Nick Thomson, group leader at the Sanger Institute and Professor of Bacterial Genomics and Evolution at the London School of Hygiene and Tropical Medicine contributed to this year’s report. Professor Thomson works as part of an international partnership that responds to cholera outbreaks around the globe. In 2017 the team employed genomic surveillance to trace the source of the cholera outbreak in Yemen.

In his postcard he highlights the importance of international collaboration and working across borders to undertake vital genomic surveillance of this deadly pathogen:

Genomics in a conflict zone

by Professor Nicholas Thomson

Cholera is a killer in waiting. It can move rapidly when conditions allow; poor sanitation, no clean drinking water and a lack of public health systems caused by natural disasters or civil unrest help fuel it’s spread. In Yemen, as a result of the brutal civil war, cholera took hold. 16 million people out of the population of 28 million do not have access to clean drinking water[1] meaning the majority of the population are part of a humanitarian disaster. Yemeni people have experienced two outbreaks of cholera; the first in 2016 and the second in 2017, which combined, are the worst in recorded history. By 2018, the disease had affected over 1 million people and caused almost 2,500 deaths.[2]

To understand the spread and transmission of microorganisms, I, with colleagues from the Sanger Institute, am part of an international partnership which responds to cholera outbreaks around the globe. With colleagues from Institut Pasteur, Médecins Sans Frontières (MSF) / Doctors Without Borders, the Ministeries of Health for Sana’a and Saudi Arabia along with other National public health and research institutes, we use genomics to trace the source and routes of transmission of microbes. For Vibrio cholerae, the bacterium that causes cholera, we monitor how it emerges, evolves and transmits – within and between households, towns, regions and countries. Genomics can identify optimum treatment options, influence policy and monitor the risk of future outbreaks.

V. cholerae isolates were collected from stool samples across the Yemeni population and a temporary refugee centre on the Saudi Arabia–Yemen border. The bacterial genomes were sequenced at the Institut Pasteur, and in collaboration we analysed the data at the Sanger Institute. We compared the sequences to a collection of over 1,000 cholera samples from the current, ongoing global pandemic, caused by a single lineage of V. cholerae, 7PET. By combining our data and efforts we were able to show that the Yemen outbreak was also caused by the pandemic 7PET lineage, and is likely to have entered the region with the movement of people from Eastern Africa, where it was circulating prior to 2016. Originally, the outbreaks in Yemen were thought to be caused by non-7PET strains. We also found that unlike the majority of 7PET bacterial isolates those responsible for the Yemen outbreak are missing four genes responsible for resistance to commonly used antibiotics, making the bacterium more suceptilble to antibiotic treatment, and the Yemeni population more vulnerable without it.

It has taken a huge collaborative effort across continents to shed important new light on this bacterium, to enable us to answer the question of what caused the cholera in Yemen. We couldn’t do it without local and international partnerships. Building capacity and providing training are a vital part of our work. Our approach is repeated across the globe to understand the root causes of other outbreaks including in Latin America and Asia.

Many may think of cholera as a disease of the past, but it’s still deadly today. We are showing that international monitoring, specifically using genomics, provides vital evidence to help inform control strategies. UK science, with its connections to international collaborations, is a powerful force against some of the most deadly diseases on the planet.

“In addition to helping understand the outbreak better, our work helped improve sample collection, surveillance efforts and patient management. We were able to hand out hygiene kits to everyone we evaluated as part of the study in the community, and helped people understand how to stop the spread. We have also developed methodologies for working in resource limited settings. We worked with local scientists and were able to contribute to people’s professional development. It is important there is an exchange of ideas and methods between everyone involved.”

Ankur Rakesh is a volunteer doctor with Médecins Sans Frontières (MSF) / Doctors Without Borders Who travelled to Yemen in July 2017.

As an epidemiologist with MSF Ankur works on outbreak response, control, surveillance and operational research. He collected the samples for genome sequencing, working together with local doctors in Sana’a, often in dangerous situations as the war continued around them.

“The UK is a global leader in health research and genome-based science at the Sanger Institute is at the forefront. The Sanger Institute fully endorses Dame Sally’s recommendations and reiterates that the UK Government must ensure that UK research organisations are able to attract and retain global talent through funding and an appropriate immigration system.”

Sarion Bowers Head of Policy at the Wellcome Sanger Institute

More information

The text for the postcard was kindly supplied by Professor Nicholas Thomson, Wellcome Sanger Institute and the London School of Hygiene & Tropical Medicine.


[1] https://www.unicef.org/yemen/reallives_12757.html

[2] World Health Organization Outbreak update – Cholera in Yemen, 19 July 2018 http://www.emro.who.int/pandemic-epidemic-diseases/cholera/outbreak-update-cholera-in-yemen-19-july-2018.html

Read the full report

Health, our global asset – partnering for progresshttps://www.gov.uk/government/collections/chief-medical-officer-annual-reports

Selected websites

  • England’s Chief Medical Officer and UK Chief Medical Advisor's Annual Reports

    Professor Dame Sally Davies’ eleventh and final annual report as England’s Chief Medical Officer and UK Chief Medical Advisor – Health, our global asset – partnering for progress – outlines the UK’s leading role in global health and highlights the need to share international knowledge and experience.

    Find the report here: https://www.gov.uk/government/collections/chief-medical-officer-annual-reports

  • LSHTM: London School of Hygiene and Tropical Medicine

  • Médecins Sans Frontières UK

  • Wellcome Sanger Institute

    The Wellcome Sanger Institute is a world leading genomics research centre. We undertake large-scale research that forms the foundations of knowledge in biology and medicine. We are open and collaborative; our data, results, tools and technologies are shared across the globe to advance science. Our ambition is vast – we take on projects that are not possible anywhere else. We use the power of genome sequencing to understand and harness the information in DNA. Funded by Wellcome, we have the freedom and support to push the boundaries of genomics. Our findings are used to improve health and to understand life on Earth. Find out more at www.sanger.ac.uk or follow us on Twitter, Facebook, LinkedIn and on our Blog.

  • Wellcome

    Wellcome exists to improve health by helping great ideas to thrive. We support researchers, we take on big health challenges, we campaign for better science, and we help everyone get involved with science and health research. We are a politically and financially independent foundation.