During the rainy season of last year (Autumn 2024), cholera broke out , alongside a cluster of other epidemics, in eastern Sudan, specifically in the states of Kassala and Al-Gadarif. The outbreak was driven by extreme weather patterns and torrential rainfall that triggered widespread flooding. These floods devastated infrastructure and public facilities, particularly sanitation systems, leading to negative public health practices such as open defecation. Consequently, drinking water sources became contaminated with wastewater and raw sewage. This public health emergency coincided with the presence of hundreds of thousands of internally displaced persons living in camps, exacerbating the conditions that fostered such practices.
What struck the capital, Khartoum, in May this year, however, a sudden and widespread cholera outbreak during the dry season (Summer 2025), may at first appear perplexing. After all, in the Sudanese collective memory, cholera has long been associated with the flood season. Yet the truth is that the bacteria responsible for cholera, Vibrio cholerae, follows a biological rhythm that is not confined to flood periods. In fact, the summer months offer the most fertile ground for its proliferation. The cholera bacterium thrives in aquatic environments, including rivers. It moves fluidly, swimming in a straight line with oscillations to the left and right, much like the movement of fish, an adaptation that aligns with the currents of the Nile River.
Under certain environmental conditions, the bacterium can survive for extended periods in water by forming symbiotic relationships with microscopic organisms, including both phytoplankton and zooplankton.
A scanning electron microscope image of the vibrio cholerae bacterium. Image courtesy of the Electron Microscope Facility
Hydroclimatology, the study of the intersection between climate systems and water bodies, explains the environmental factors that fuel cholera’s reproduction in summer, by examining the interplay between climate variables and the hydrodynamics of the Nile River, particularly its two tributaries: the Blue Nile and the White Nile.
One key factor is the speed of the river’s flow. Rapid water flow helps keep the Nile clean by flushing out sediments, organic matter, and saline soils deposited through agricultural activity along its banks. Any reduction in flow speed, however, can create an ecosystem rich in nutrients, especially when coupled with high temperatures, which promote the growth of microscopic organisms in freshwater systems.
The river’s hydrodynamics also play a critical role in the spatial distribution of cholera outbreaks in cities along its banks. While the flow of the Blue Nile varies sharply between flood and dry seasons, the White Nile maintains a relatively stable flow. Before reaching Sudan, the waters of the White Nile pass through the Sudd wetlands in South Sudan, an area teeming with biological material, aquatic vegetation, and shrubs. In this region, nearly half of the White Nile’s volume is lost through branching and evaporation. The terrain of the White Nile Basin also lacks significant gradient, which further slows its flow.
Since Khartoum lies at the confluence of these two rivers, it is important to note that during the summer months (April–May), the Blue Nile’s flow is at its lowest. At this point, the White Nile contributes approximately 80 per cent of the Nile’s total water volume, until the rainy season returns and the Blue Nile surges once again.
The same ecosystem that nurtures aquatic life becomes a hotbed for what has been termed ‘the blue death.
However, due to the complex interplay of environmental factors, slow river flow alone is not sufficient to trigger a cholera outbreak. Temperature levels and hours of sunlight also play pivotal roles, creating optimal conditions for the proliferation of plankton, the microscopic hosts that shelter vibrio cholerae. The bacterium lives symbiotically with zooplankton, particularly copepods, which serve as incubators for its growth. Higher temperatures shorten the bacterium’s reproductive cycle, enabling it to multiply rapidly.
Meanwhile, rising salinity levels, caused by agricultural runoff and reduced water flow, contribute to a homogenous aquatic environment rich in nutrients. While this creates a perfect breeding ground for microorganisms, it is disastrous for human populations. The same ecosystem that nurtures aquatic life becomes a hotbed for what has been termed “the blue death,” named after the bluish-grey pallor that overtakes cholera victims due to acute dehydration.
A close-up of copepods, which serve as biological hosts for vibrio cholerae in aquatic environments
For 13 days this May, maximum temperatures in Khartoum State ranged between 47°C and 48°C.
Such intense heat significantly affects the physical characteristics of the Nile River, especially during its slow flow, where nutrient levels increase and dissolved oxygen decreases, creating ideal conditions for anaerobic bacteria to flourish. These bacteria break down organic matter and produce foul odors. This may explain what some residents told Atar: that the Nile appears nearly stagnant, its waters noticeably murky and malodorous.
Cholera bacteria cannot be eradicated, as they are endemic to aquatic environments.
In fact, their presence in the Nile is not necessarily harmful unless the aforementioned environmental conditions are present. For instance, cholera would likely not have spread so aggressively in Khartoum State had the outages of electricity and water coincided with the rainy season (July–October), when the Nile’s strong current would have swept away many cholera-hosting particles.
Similarly, the outbreak may not have been as severe if residents had depended on Nile water during the winter months (December–January), when lower temperatures and reduced sunlight inhibit the proliferation of phytoplankton and their associated fauna.
On the other hand, it remains impossible to determine the primary source of the cholera strain.
Was it recently introduced through open defecation into the river, or has it been present in the Nile for some time?
These questions keep the hypothesis alive that cholera bacteria may have traveled via the Jabal Awlia Reservoir, a continuation of the contaminated White Nile waters that triggered the outbreak in Kosti back in March. Notably, Atar’s coverage shows recorded cases in Omdurman, specifically in the areas of Al-Jamoiya and Al-Salha.
It is also worth noting that South Sudan continues to suffer from cholera outbreaks, recording the highest global infection rates in March.
Swamps around the country’s Sudd wetlands retain stagnant water and provide ideal breeding grounds for pathogens. Since the White Nile sustains all the conditions favourable for cholera bacteria to persist, the hypothesis of southward contamination remains plausible, especially in the absence of on-site sampling from Nile waters south of Jabal Awlia Dam.
Global cholera incidence map, showing infection rates in gradients from light to dark, with South Sudan having the highest rates
Studying aquatic ecosystems and the dynamic interactions that govern bacterial equilibrium with their biotic environment, alongside understanding how these ecosystems impact public health amid armed conflict, poverty, and climate change, is essential for shaping effective environmental management policies.
Although the Grand Ethiopian Renaissance Dam might stabilize Blue Nile flow, the greater environmental concern remains the White Nile.
In Sudan, cholera outbreaks typically peak twice: once in the summer, when high temperatures slow the flow of both Nile tributaries; and again, during the rainy season, amid heavy downpours.
Although the initial operation of the Grand Ethiopian Renaissance Dam, expected this September, might stabilize Blue Nile flow throughout the year, mitigating outbreak risks tied to stagnant water, the greater environmental concern remains the White Nile. Without state-level action to limit public exposure to its waters during the summer, this health hazard will persist.
Research papers should, therefore, place greater focus on developing predictive models for the environmental factors that fuel cholera’s spread, especially by monitoring the rise of phytoplankton in the White Nile during periods of extreme heat.
Such models would empower public health officials to take proactive steps, like rolling out preventive vaccinations in advance.
Investing in meteorological monitoring and forecasting centres is no longer a luxury.
These tools have become early warning systems that communities rely on to brace for potential environmental disasters. The ability to anticipate cholera and other seasonal epidemics forms a first line of defense and could save substantial effort and resources.
While the cholera outbreak is expected to decline in the coming weeks with the end of summer, a new challenge is looming.
According to a report published this May by the IGAD Climate Prediction and Applications Centre, rainfall during the upcoming rainy season across central Sudan is expected to increase by 55 per cent. The spike in precipitation will also affect northern, southern, and western Ethiopia, including the Blue Nile’s headwaters. This suggests a rainy season that may prove disastrous for Sudan’s vulnerable communities, now forced to endure the nightmare of cholera in both summer and fall.
