A team of researchers has found that the strain of bacteria causing the largest known cholera epidemic in recent history, in Yemen, has origins in South Asia and East Africa.
The researchers identified the exact genetic make-up of the bacteria and compared it to other known strains to understand how the Yemeni strain evolved. The study, published in the journal Nature, could help in controlling outbreaks in the future by providing guidance on which antibiotics to use.
Since 2016, cholera has afflicted 1.1 million people and killed 2,300 people in Yemen, according to a 2018 estimate cited in the medical journal The Lancet. A Unicef statement issued in late March found that in 2019, health-care workers have seen an additional 109,000 suspected cases of cholera and 109 deaths, with a third of the cases being children under five.
In the new study, published in January, scientists from the United Kingdom’s Wellcome Sanger Institute, France’s Pasteur Institute, Yemen’s National Centre of Public Health Laboratories, in Sana’a, and other institutions examined the genetic make-up of the bacteria causing the Yemeni epidemic and were able to make conclusions about its origins.
“It was a real surprise, as it revealed the true source of the epidemic and identified the type of antibiotics that could be used to treat cholera,” said Samar Saeed Nasher, a scientist at the National Centre of Public Health Laboratories who worked on the study.
The researchers used 42 samples of cholera in Yemen taken during 2016 and 2017. Thirty-nine samples were from the three main governorates in Yemen and three from a refugee camp on the Saudi border. An additional 74 samples, for comparison’s sake, came from “reference countries” where cholera has occurred—France, Iraq, South Sudan, Kenya, Saudi Arabia and India. Those samples were studied in the context of an international genetic database of 1,087 samples of the cholera bacteria.
The cholera strain causing Yemen’s epidemic is related to a strain that first appeared in 2006 in India and later spread to West Africa, East Africa and Haiti, according to the researchers. However, the Yemeni strain did not come directly from South Asia or the Middle East, Nasher said, but came to Yemen from East Africa where cholera outbreaks spread between 2013 and 2014.
“The analysis of the genetics of this species shows it is very different from the cholera strain that spread in the Middle East during the war in Iraq, but the strain was compatible with the strain that caused the recent outbreaks in East Africa’s Kenya, Tanzania and Uganda between 2015 and 2016,” she said.
Nasher said the cholera strain in Yemen showed resistance to three types of antibiotics, with 17 antibiotics succeeding in eradicating the bacteria, most notably a low-cost and highly effective antibiotic, Polymyxin B.
“Genomics has enabled the research team to discover the cause of the devastating and ongoing epidemic in Yemen, giving researchers the opportunity to prepare for future outbreaks,” Nick Thompson, a professor at the Wellcome Sanger Institute and the London School of Hygiene & Tropical Medicine, who supervised the study, wrote in an e-mail. “This information helps guide coping strategies to reduce the impact of future epidemics.”