Cholera, an old foe, is becoming a new kind of problem for Kenya

But Kenya is gunning for elimination. KC Cheng surveys the state of play.

  • 17 April 2024
  • 7 min read
  • by Kang-Chun Cheng
A child collects water from a borehole tap in Manyatta Secondary of Laisamis town in northern Kenya's Marsabit County. Credit: Kang-Chun Cheng
A child collects water from a borehole tap in Manyatta Secondary of Laisamis town in northern Kenya's Marsabit County. Credit: Kang-Chun Cheng


Before 2014, cholera outbreaks in Kenya were fairly predictably associated with heavy rainfall and flooding. But the risk factors and transmission dynamics have evolved during the current wave of outbreaks, says Dr Samuel Kariuki, a chief research scientist and director at the Centre for Microbiology Research at the Kenya Medical Research Institute (KEMRI). He describes the current spate of outbreaks as "numerous and constant", occurring even during dry seasons.

Oral cholera vaccines (OCVs) save many lives each year worldwide, but making populations safe from the waterborne bacterium's brutal onslaught is finally a matter of access to clean water and sanitation. "It's all about resources," Kariuki continues. "HIV, tuberculosis and malaria already have established systems for surveillance and secured funding. At MoH (Kenya's Ministry of Health), we have programmes for these big diseases. But it's lacking for cholera."

"In terms of immediate or short-term management or control, vaccines are very effective. But for the long-term, you must invest in improving water supply and sanitation"

– Dr Emmanuel Okunga, head of the Health Ministry's Disease Surveillance and Response Unit

However, Dr Emmanuel Okunga, the head of the Health Ministry’s Disease Surveillance and Response Unit, points out that cholera management is an energetically evolving picture. “Things have changed a lot in the past two years.” There’s “greater awareness” as Kenya realises cholera is quite a serious disease, he says.

Grappling with cholera

Cholera is an acute, highly contagious bacterial infection transmitted when food or water, or food contaminated by Vibrio cholerae, are ingested. Defeated in wealthy countries many decades ago, cholera remains a large-scale threat to public health in many poorer countries. Left untreated, people with cholera can dehydrate and die within hours of their first symptom.

In Kenya, rolling humanitarian crises – mainly due to climate change and political insecurity in Somalia, Kenya's northern neighbour – are a source of heightened vulnerability. As communities are displaced into inadequately provisioned, crowded camps in some places, the risks of cholera transmission increase. According to the World Health Organization (WHO), Kenya has been experiencing large-scale outbreaks of cholera since 2014: 10,568 reported cases in 2015, 5,208 in 2019. In the year to October 2023, Kenya had reported 12,120 cases, with a case fatality rate of 1.7%.

A young man collecting water for household use from Lake Baringo in Kenya's former Rift Valley Province.
A young man collecting water for household use from Lake Baringo in Kenya's former Rift Valley Province.
Credit: Kang-Chun Cheng

That amounts to more deaths than any country wants to see in an outbreak. Ideally, with treatment, cholera fatality rates can remain as low as 1%. Care is straightforward, relying mainly on the inexpensive oral rehydration solutions that are estimated to have saved tens of millions of lives since the 1980s. But rapid access to care needs to be available.

The Global Task Force for Cholera Control (GTFCC) by WHO developed a Global Roadmap for Ending Cholera by 2030, emphasising the need for multi-sectoral interventions – from identifying disease transmission and reporting that essential information to government agencies, to sensitising afflicted or vulnerable communities with hygiene reminders and providing sanitation facilities, and facilitating OCV campaigns – in hotspot areas.

Spiking scourge

In 2022, Kenya's Ministry of Health (MoH) and Ministry of Water, Sanitation and Irrigation launched the National Multi-Sectoral Cholera Elimination Plan, which envisions a 90% reduction in cholera deaths by 2030. The successful implementation of this multi-sectoral plan depends on coordination between both the national and county governments, as well as political goodwill.

While specific hotspots account for a bulk of cases, the disease is widespread geographically. Sixty-eight percent of Kenya's counties reported cholera cases between the years of 2015 and 2022, for a total of 30,431 "suspected" cases (according to WHO, cases are considered "confirmed" when a sample is obtained from a patient and tested positive in a laboratory; cases are considered "suspected" when observed by health care workers and treated for cholera based on symptoms).

Meanwhile, research published in May 2023, in the journal PLOS Neglected Tropical Diseases, identified Garissa, Tana River and Wajir as three especially high-risk counties. By the MoH's definition, that means that the average annual incidence surpassed 70 cases per 100,000 people. Those three counties are home to nearly 3 million people – 6% of the population. Droughts from 2020–2023 severely depleted water supplies, likely exacerbating the rate of outbreaks since limited and difficult access to water compromises hygiene.

In 2023, there were a total of 8,926 reported cases of cholera in Kenya . Those nearly 9,000 cases resulted in 145 deaths, according to WHO.

Shoring up immunity

In response, the MoH launched an OCV campaign. A first successful round kicked off in February 2023, with 2.2 million people above the age of one year vaccinated in Nairobi, Garissa, Tana River and Wajir County, leading to a sizable reduction of cases in those areas. The International Coordinating Group (ICG), which administers the Gavi-supported global OCV stockpile, sent another 1.5 million doses of OCV for a vaccine campaign that began on 3 August 32023. "MoH has a really strong relationship with ICG," says Kariuki.

Kariuki says 2023 marked "the first time the [cholera] vaccine was used in large numbers for the public".

Vaccine centres operated at churches, mosques, settlements and public water taps – even sometimes taking the form of home visits. "Before the vaccination drive, there was a lot of community engagement, spreading messages about risk. Communities are able to take ownership of some of these activities and come out strongly to take up the vaccine," Kariuki explains.

Now, the country is aiming to acquire vaccines for a preventive rather than reactive campaign. "In fact," the Ministry's Okunga says, "our target – the current plan – is elimination."

That'll take vaccines – and more. "For any disease – in terms of immediate or short-term management or control – vaccines are very effective," Okunga continues. "But for the long term, you must invest in improving water supply and sanitation. That's the link that's missing."

Increased public awareness of the best modes of defence against cholera – including behavioural interventions like hand-washing, recognising symptoms and understanding risk factors – has been propelled by communities witnessing the havoc cholera can wreak. The outbreaks themselves have shocked people into action, spurring large-scale demand for immunisation.

The pressure is on

"In a devolved governance [structure] like in Kenya [with its regional county governments], we need to have coordination structures at all levels of government," says Okunga. Thorough follow-ups of cholera cases – ensuring that those who were treated are fully recovered, and patients are no longer at risk of transmission – will help to effectively eliminate the spread of the disease.

Kariuki says that since 2012, strains of cholera have been developing drug resistance, which is unprecedented and very "scary on the health care side". Using genomic analysis, he and his research team traced the origins of resistant strains to outbreaks in Yemen in 2008. Two years later, those strains were in Kenya.

Dr Riro Mwita is a doctor of internal medicine at Kiambu Hospital in Kiambu, just north of the capital city of Nairobi, an epicentre of outbreaks that sprang up in October 2022. Dr Mwita estimates that a quarter of his patients last year sought cholera treatment.

"It's mainly because of rising populations and migrations," Mwita says. "There are challenges with water provision in peri-urban areas, where populations are growing very fast." People with few livelihood options are selling water on the road in hand carts – you cannot be sure if that's clean, he continues. "They may even be collecting water from pools. That's not something you want. Ideally, you have piped water."

Infrastructure expansion to improve water and sewage systems is on the Kenyan government's radar: in 2022, it partnered with the Danish government to improve water systems for more than 300,000 people as part of a US$ 150 million project.

Meanwhile, climate change is taking a toll on water sources. In the highland areas that provide most of the nation's water, people are encroaching into once-wild spaces, and there's a lot of pressure on the land from cultivation. "This is a bigger, long-term issue," says Mwita. "For me, [cholera] is about hygiene. Vaccine campaigns shouldn't be the primary focus, there should be priorities on urban planning, sanitation and proper sewage systems."

But in the meantime, the vaccines are doing what they do: buying time and saving lives.