Science in a conflict zone: tracking cholera in Yemen
Categories: Sanger Science2 January 20198.6 min read

Science in a conflict zone: Investigating cholera in Yemen

By: Alison Cranage, Science Writer at the Wellcome Sanger Institute

A mother holding her child in MSF supported cholera treatment centre in Al-Sadaqa hospital. The child had cholera and was suffering from acute watery diarrhoea. Image credit: Malak Shaher, MSF
Image credit: Malak Shaher / MSF

The brutal conflict in Yemen is taking a devastating toll. Almost four years of fighting has forced 3 million people to flee their homes. UN agencies have warned that more than 10,000 have been killed, while an estimated three-quarters of the Yemeni population needs humanitarian support and it is thought that up to 13 million people are on the brink of starvation.

In addition to the civil war, Yemen is experiencing the worst epidemic of cholera in recent history, according to a paper published in Nature. The fighting has destroyed infrastructure, leaving 16 of the 29 million Yemeni population without access to clean water and basic sanitation. Vibrio cholerae, the bacteria which causes the disease, thrives in such conditions, spreading rapidly through vulnerable populations. If it is caught in time, patients can be treated with rehydration therapy. But, in Yemen, the public health system is under intense pressure. Only half of the country’s hospitals are operational, and aid is struggling to get in because ports have been bombed. In such a situation, cholera is deadly.

Ahmed of Al-Habelayn, Lahj governorate was hospitalized to MSF supported cholera treatment center in Al-Sadaqa hospital in Yemen. He is responsible for a family of four children, his wife and his mother. Ahmed is a daily worker. He was concerned of who is going to provide food for his family while he is in the hospital. Cholera has been affecting a large number of Yemenis especially the vulnerable ones. Image credit: Malak Shaher, MSF
Image Credit: Malak Shaher / MSF

Recent estimates report that 1 million people have been affected and over 2,500 have died from the disease since reports of cholera were first confirmed in September 2016, most of them children. Researchers, doctors, public health specialists have been working tirelessly to understand the outbreak, treat patients and control the spread.

We spoke to Ankur Rakesh, a volunteer doctor with Médecins Sans Frontières (MSF) / Doctors Without Borders, who travelled to Yemen in July 2017. Ankur completed his post graduate medical education with National Centre for Disease Control, India and is now based in his family home near Delhi. As an epidemiologist with MSF, Ankur works on outbreak response, control, surveillance and operational research.

MSF nurse while receiving a suspected cholera patient at MSF cholera treatment centre in Al-Kuwait hospital in Sana’a. Image credit: Malak Shaher, MSF
Image Credit: Malak Shaher / MSF

He was collaborating with researchers from around the world, including the Institute Pasteur, Paris and here at the Wellcome Sanger Institute.

His strongest recollections are of the people he met. “What they are going through is so hard to define. There is no public electricity, no public supply of clean drinking water and the price of food is skyrocketing. Due to the ongoing conflict, many of the civil servants, including doctors, have not received regular salaries for months. But they carry on working and serving their communities. Their dedication and their determination is inspiring.”

Working under pressure in Sana’a

Ankur was based in a hospital in Sana’a city with a team of 10 local doctors; most of them recently qualified graduates. They worked closely with other local experts to collect samples of cholera, which would be analysed using genomic techniques, nearly 7,000 km away in Paris, France.

An MSF medical team is working together with MoH staff in the cholera treatment centre in Al-Sadaqa hospital in Aden. Image credit: Malak Shaher, MSF
Image Credit: Malak Shaher / MSF

The team and local colleagues would keep in touch via WhatsApp. In addition to coordinating the study, they shared information about conditions in Sana’a each day – to see if it was safe to leave their base to go to a particular area. Some days they had to stop working completely due to political demonstrations or increased bombings.

“One day we could not carry out any field activities, because there was a demonstration - a huge crowd was in front of the Al Sabeen Hospital where we had to go and recruit patients to help understand the factors related to the spread of cholera. On many of the days, you could hear shootings, though we did not know if they were for celebratory reasons or due to a conflict. On one of these days, I carried on working at my computer in my office until a colleague ran in shouting at me ‘Are you crazy? Get away from the window, there is active shooting out there!’ On some of the days there would be heightened surveillance by the fighter planes, bombings and increased armed weapon noise. It was difficult!”

A Yemeni nurse working with the Ministry of Health with a patient in MSF supported cholera treatment center in Al-Sadaqa hospital in Yemen.  Image credit: Malak Shaher, MSF
Image Credit: Malak Shaher / MSF

When bombing was nearby, the advice was to open the windows. “If they were shut, the pressure from a blast could blow shards of glass into the room that would kill you. My national team members would do this at their homes and advised me to do the same. People were learning to live with the conflict.”

“There were a couple of nights when we had to run to the basement of our house because the bombing was dangerously close. The whole building shook and the plaster dust was coming down from the ceiling. But we were lucky – many of my national colleagues didn’t have a basement to go to. They just carried on with whatever way they could protect themselves and their families.”

Ankur asked his colleagues how they coped. He said they always replied, “I am doing it for my people. I am doing it for Yemen.

Collecting cholera samples - kindness in the middle of conflict

MSF nurse giving IV fluid to a patient inside the MSF supported cholera treatment center in Al-Sadaqa hospital. Image credit: Malak Shaher, MSF
Image Credit: Malak Shaher / MSF

Ankur was working in the cholera treatment centres supported by MSF. His team would explain the study to the patients and ask permission to take stool samples for diagnosis and analysis. Then, when conditions allowed, they would travel to patients’ homes.

“When we visited the homes of patients, to collect drinking water samples, we were always invited to sit in a ‘Mafrash’. It’s a welcoming room with a really big sofa - where we were treated with absolute kindness. The hospitality of the people even in the midst of conflict and onslaught of outbreaks was humbling."

The situation on the streets was unpredictable, with fighter planes often overhead. Ankur recalls one of his Yemeni colleagues would cover her ears and duck every time a jet flew past. He said it was heart wrenching to see her reaction. “In India, when a jet flies over, children run outside to see the spectacle. But not in Yemen."

Creating laboratory conditions with limited supplies

At the cholera treatment centre, the team would diagnose samples using rapid diagnosis kits. The test is not 100 per cent accurate, but is quick and can be used after only minimal training.

“Catching cholera early means that people can be effectively treated with rehydration, so rapid diagnosis is vital. We were able to help organize that.” Ankur then took samples to the central laboratory in Sana’a. There, they were grown (cultured) – a standard microbiology technique used to confirm the presence of the Vibrio cholerae bacteria

Running a laboratory in a conflict zone wasn’t easy. The central lab in Sana’a didn’t always have power, so they had to support the lab with fuel on many occasions. Getting supplies (plasticware, glassware, growth media for the bacteria) was also an issue.

Ankur said the airport at Sana’a has been virtually destroyed. “When our small plane took off, one could see broken down aircraft lying on the ground in pieces. The main building had also borne the onslaught of the bombings. At that time, there were only UN, Red Cross and MSF flights allowed on some of the days of the week and getting supplies onto those flights wasn’t always possible.”

The team had to source products locally, then get them validated with technical advisors based at the headquarters, or wait. Before the team arrived, the lab was not getting many positive cultures of the bacteria. Ankur and his team helped train other staff in sample collection and transportation techniques for culture – leaving them with improved skills in diagnosing cholera.

Importing research samples of a highly infectious, deadly disease into France

Transporting the bacteria to France for genome sequencing was the biggest challenge the team faced. Getting permissions to get them across borders was, in Ankur’s words, ‘a nightmare’.

No one wants to import a highly infectious, deadly disease into their country and so regulations are understandably tight. But they made it eventually. “Everyone took a very big sigh of relief as we had risked a lot to collect those samples and they helped us gain insight into the whole outbreak.”

Surveillance helps care on the ground and seeks to stop the next epidemic

Ankur said that in addition to helping understand the outbreak better, their work has already 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 also helped people understand how to stop the spread. The people caught there in the conflict are just like us. We need to do everything we can to support them."

Daryl Domman is one of Ankur’s collaborators at the Sanger Institute. He analysed genome sequences of the cholera bacterium from the Yemeni samples.

“From the genomic analysis we were able to tell that the ongoing cholera outbreak in the Yemen is part of the 7th global pandemic. Most likely it came into the country with the movement of people from East Africa.

“Cholera is a killer in waiting. Where there is poor sanitation, no clean water and public health systems are struggling, if cholera is there, it can easily take hold. It’s an awful situation whenever it happens."

The key to stopping the cholera outbreak in Yemen is ending the war and restoring the country’s infrastructure. But genomics has a role too - in tracking the spread of the bacteria and identifying treatment options to help manage future outbreaks

Ankur left with some sense of hope, “Years of war and crisis haven’t dampened the spirit and hope for peace in the people I met. They are working tirelessly, all risking themselves for the larger benefit.”
“With more humanitarian aid and support from the international community, there could be more hope.”

About the author

Alison Cranage is the Science Writer at the Wellcome Sanger Institute.

Further information

Research News: Mystery of Yemen cholera epidemic solved
Research News: Cholera tracked at household level
Research News: Risk of cholera epidemics estimated with new rule book