Cholera pandemic's source discovered

Researchers have tracked the spread of antibiotic-resistant strains back to the Bay of Bengal

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Dr Nick Thomson
Children swimming in the sewage infected Bay of Bengal, the source of the latest cholera pandemic

Researchers have used next-generation sequencing to trace the source and explain the spread of the latest (seventh) cholera pandemic. They have also highlighted the impact of the acquisition of resistance to antibiotics on shaping outbreaks and show resistance was first acquired around 1982.

Whole-genome sequencing reveals that the particular cholera type responsible for the current pandemic can be traced back to an ancestor that first appeared 40 years ago in the Bay of Bengal. From this ancestor, cholera has spread repeatedly to different parts of the world in multiple waves.

These findings offer much better understanding of the mechanisms behind the spread of cholera – a diarrhoeal infection which is usually linked to unhygienic conditions and poor sanitation systems often found in disaster areas, such as the Haitian earthquake in October 2010. It is estimated that cholera affects 3 million to 5 million people each year, with 100,000-120,000 deaths.

The team tracked the spread of the organism by analysing the genomes of the causative bacterium Vibrio cholerae taken from 154 patients across the world over the last 40 years. Using the ability to track single DNA changes in the genome of this strain, they were able to map the transmission routes of the bacteria, aiding future health planning and enabling ‘backtracking’ of the disease to its origin.

They discovered that the current strain of the bacterium – known as the El Tor strain – first became resistant to antibiotics in 1982 by acquiring the genetic region SXT, which entered the bacterium’s genome at that time, triggering renewed global transmission from the original source.

“Through comparing the genomes of 154 cases of cholera, we have made important discoveries as to how the pandemic has developed. Our research shows the importance of global transmission events in the spread of cholera. This goes against previous beliefs that cholera always arises from local strains, and provides useful information in understanding cholera outbreaks.”

Dr Julian Parkhill A senior group leader at the Wellcome Trust Sanger Institute and a senior author of the study

The study crucially identified the origins of the pandemic strain to its roots 40 years ago in the Bay of Bengal. From this base, it has since infected people around the world, including Africa, South Asia and South America.

“Looking at the past 40 years of transmissions from continent to continent, we found that the Bay of Bengal acts as a reservoir for cholera, where it can thrive and spread. By tracking how the disease is spread, our maps of transmission could influence future decisions on how to tackle this disease.”

Dr Nicholas Thomson from the Sanger Institute and one of the first authors of the study

The analysis shows that there was not a simple single spread of a strain of V. cholerae out from the Bay of Bengal. The evidence suggests that there have been at least three independent overlapping waves of intercontinental spread with a common ancestor in the 1950s Representing the original El Tor strain. These movements are strongly correlated with human activity, suggesting that the strain has been carried by human travel.

“These findings are opening up new pathways for researchers studying all fields of bacterial infection: from investigating how genetic changes enable strains to build up resistance to antibiotics, to being able to track a disease’s transmission and trace it back to its roots. These first initial discoveries could be the key to unlocking many other bacterial pandemics.”

Ankur Mutreja, first author from the Sanger Institute

“This is among the first study that merges evolutionary information with emergence of contemporary new variants of Vibrio cholerae and then uses the phylogenetic signatures to track the intercontinental spread of cholera. These findings in due course will lead us to understand why cholera pandemics begin in Asia and then spread as a wave across the world.”

Professor G Balakrish Nair Director of the National Institute of Cholera and Enteric Diseases in Beliaghata, India

More information


This work was supported by The Wellcome Trust and The International Vaccine Institute is supported by the Governments of Korea, Sweden, and Kuwait.

Participating Centres

  • Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
  • International Vaccine Institute, Kwanak, Seoul, Korea
  • Department of Pharmacy, Hanyang University, Kyeonggi-do, Korea
  • Seoul National University, Gwanak-gu, Seoul, Korea
  • Centre for Microbiology Research, KEMRI at Kenyatta Hospital Compound, Kenya
  • Department of Microbiology and Immunology and University of Gothenburg Vaccine Research Institute, University of Gothenburg, Göteborg, Sweden
  • National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
  • University of Cambridge, Department of Veterinary Medicine, Cambridge, UK


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Selected websites

  • The Wellcome Trust Sanger Institute

    The Wellcome Trust Sanger Institute, which receives the majority of its funding from the Wellcome Trust, was founded in 1992. The Institute is responsible for the completion of the sequence of approximately one-third of the human genome as well as genomes of model organisms and more than 90 pathogen genomes. In October 2006, new funding was awarded by the Wellcome Trust to exploit the wealth of genome data now available to answer important questions about health and disease.

  • The Wellcome Trust

    The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests.