Seated on his desk clad in a black trouser with a matching tie and a light green shirt, Jean Bosco Mbonigaba stares keenly at the lines of code on his screen. Just months before, nearly three years after starting his PhD in Public Health at the University of Rwanda, Mbonigaba became a fellow at the African Modelling Network for Neglected Tropical Diseases (AM2NTD), an opportunity that introduced him into disease modelling, giving his soil-transmitted helminths (STH) research project the kick-start it needed to scale.
Now, the graphics on his screen were not just heatmaps of Rwanda, but maps that told a story of how his STH modelling project has advanced in the last few months, with potential to be part of the country’s roadmap for STH control, and eventual elimination.
Mbonigaba’s journey into the NTD world
Mbonigaba's journey into the NTD world began in 2008, right after high school, when he joined a project by the Ministry of Health to map Neglected Tropical Diseases (NTDs) in Rwanda. Having received training in medical laboratory science during high school, he worked at the project part-time, conducting field laboratory testing, an experience that sparked his lasting interest in NTDs.
Over the years, as he worked, alongside pursuing his bachelors and masters degree, he progressed professionally and rose through the ranks to be part of Rwanda’s NTD program leadership. At his role, as the director for Rwanda NTD program, he oversaw the development of the first fully approved, comprehensive NTD master plan, which included elimination targets and milestones for multiple NTDs, including soil-transmitted helminths (STH), schistosomiasis, trachoma, lymphatic filariasis, and leprosy. Mbonigaba told AM2NTD that the NTD master plan went on to become a reference document, with the World Health Organisation (WHO) using it as a model for other countries.
It was no brainer that when he made the decision to go back to school to pursue his PhD, he chose the NTDs path.
For his PhD, Mbonigaba is focusing on STH (intestinal worms) control and elimination, informed by persistent high prevalence of this NTD in some districts in Rwanda, even after multiple treatment rounds.
The scale of STH problem in Rwanda
In Rwanda, STH remains a significant yet often invisible public health problem. In some regions, prevalence can reach extremely high levels, up to 90%, according to Mbonigaba. This means that a large share of children and adults in Rwanda are living with chronic infections.
The infections are silent, and most cases do not present as dramatic emergencies, but they quietly undermine health. For instance, children may suffer anemia, stunting, mental retardation, and poor school performance, while adults experience fatigue and reduced productivity. Occasionally, the burden becomes very visible and severe, as in the hospital stories Mbonigaba recounts, for instance, children whose intestines are so damaged by worms that surgeons must remove segments, or a pregnant woman whose intestines were literally filled with worms discovered during echography, and underwent the surgery. These are extreme cases, but they reveal the scale and seriousness of the underlying problem.
Mbonigaba explained that what makes STH particularly persistent in Rwanda is the interaction between environmental conditions and human behavior. He pointed out that Rwanda’s soil is likely favorable for the survival of worm eggs such that when the soil is contaminated, eggs can remain viable for years, so the environment remains a source of infective eggs long after the original contamination. The fragile or rocky soil in some parts of the country also makes it difficult to dig deep to secure improved latrines, and as a result, many toilets are shallow and more exposed to flies and the surrounding environment. Climate change effects such as flooding, heavy rains and resulting landslides spread human faeces in the environment. This means faeces remains close to the surface, making it easier for infective worm eggs to spread to farming soil, crops, households, food, and water. This creates a puzzle. Rwanda is known for its cleanliness and it is true even in rural areas, people and environment are clean, and sanitation coverage looks good, yet STH prevalence remains high. The explanation lies in these less visible interactions between soil type, improved latrine construction difficulties, and the ability of eggs to survive and circulate, as well as climate change effects.
Behavioral factors complete this picture. STH is classically spread via the fecal - oral route, so even small gaps in hygiene can sustain transmission, eating without hand washing during farming activities, children playing in contaminated soil and then putting their hands in their mouths, inconsistent handwashing with soap after defecation, or raw food such as sugar cane, carrots or food prepared without adequate attention to contamination risks. Latrines, even when they exist, may be poorly constructed, poorly maintained, or overused, and in some instances, a number of households may still practice open defecation in or near fields, especially during farming activities or some may be using human excreta as fertilizers for their crops. All of this allows human feces, and thus worm eggs, to reach the soil and stay there. At the same time, because most infections are chronic and not immediately dramatic, communities and decision-makers can underestimate how serious the problem is, prioritizing other, more visible conditions while STH continues to sap health and potential in the background.
There is also a system dimension. Rwanda already generates a vast amount of routine health data through digital platforms like DHIS2, public health facilities database. Every month, hundreds of health centers and dozens of hospitals contribute data that could be used to map hotspots, track seasonal patterns, and evaluate the impact of interventions. However, as Mbonigaba explains, these data are rarely used to their full potential. They are not regularly analyzed to answer basic program questions, such as where STH is most concentrated, how patterns shift over the year, or whether interventions are truly changing the situation in specific districts. Instead, programs often wait for large national surveys to update their understanding, which means slow feedback loops and missed opportunities to adapt strategies quickly. In practice, this underuse of data becomes another behavioral factor at the institutional level: the system keeps generating numbers but does not routinely transform them into insights and actions.
Together, these environmental, behavioral, and systemic factors explain why STH remains such a challenge in Rwanda.
However, Mbonigaba hopes to take lessons learned from AM2NTD program and the larger Center for Epidemiological Modelling and Analysis (CEMA) especially on ensuring national programs use data to guide strategies - which can only happen when capacity is built.
“By training interns and young professionals to improve data quality, perform regular analyses, and identify hotspots in real time, the program can start to turn its own routine data into a tool for changing behavior and targeting interventions,” he said.
What has happened so far?
“Rwanda has been constant in implementing Mass Drug Administration (MDA), but the rate of decrease of STH prevalence is quite moderate, actually, it is very low in some areas, and even some districts have no decrease at all. So, I want to explore what went wrong or what is going wrong at this rate,” said Mbonigaba.
He added that he also wants to explore what can be done differently in terms of how interventions are implemented. And, among different interventions, which is best and can be scaled up to other high-prevalence areas.
On this, Mbonigaba is looking into several strategies and first among them is using different drug regimens, more frequent treatment (up to three times per year) and combination of therapies like albendazole with other drugs, to see impact on prevalence and intensity.
He is also looking into the effectiveness of community-led Water Sanitation, and Hygiene (WASH) mobilization that encourages a collective approach. This is where people adopt a community-led total sanitation approach but without shaming, focusing instead on community-driven improvements in water, sanitation, and hygiene.
Mbonigaba is also conducting context-sensitive analysis of local transmission foci like schools, markets, churches, and how infection patterns differ even within the same administrative unit.
He says, while elimination of STH as a public health problem in Rwanda is not out of reach, only if appropriate drug regimens (treatment therapies, and frequencies) alongside community and individual-level healthy behavior are used in the right way and supported by strong, context-specific implementation.
Still, drugs alone are insufficient, he says, policy changes and behavior change are as crucial. For instance, he says, in areas where human feces had been used as fertilizers; once this practice was prohibited by local policy makers, and that they availed sufficient industrial fertilizers, infection indicators improved, suggesting that regulatory and behavioral measures can significantly reinforce drug-based control.
Within the AM2NTD, Mbonigaba is analyzing one-year data following Rwanda interventions to identify what is working and what is not, estimate the likely impact and cost of scaling successful approaches, and project how long it might take to reach elimination under different scenarios.
“We have to produce some clear message of what can be done and how to do it, so that we can now reverse the situation sustainably. I think it's critical. The lives of people on the ground depend on the findings, as well as the country's uptake of these findings to inform policy, planning, and practice. The current investment needs also depend on the findings from this study, for us to achieve our national goals,” said Mbonigaba.
“I think this is the critical contribution of AM2NTD to the Rwanda national plan.”
