[ABUJA, SciDevNet] In the dry, isolated area of Karamoja in northeastern Uganda – the country’s poorest sub-region – children have long suffered from malnutrition and water shortages.

Now a study has shown that nearly half the food and water consumed by under-fives in the region is contaminated with drug-resistant Salmonella, further limiting their chances of survival.

The peer-reviewed study, published in BioMed Central, found contamination in samples of both raw and cooked foods, as well as in community and household water.

More than 90 per cent of the Salmonella enterica strains identified by researchers were resistant to azithromycin, one of the most common antibiotics, while more than a third were resistant to multiple drugs.

Ronald Mpagi, the study’s lead author and a microbiology researcher at Uganda’s Gulu University, told SciDev.Net he was driven to investigate persistent malnutrition in Karamoja after years of government and donor programmes showed little progress.

A semi-arid area, Karamoja suffers chronic water scarcity, leaving families without reliable safe drinking water. Most households are nomadic pastoralists living in manyattas, enclosed homesteads where cattle are kept close to people.

Color-enhanced scanning electron micrograph showing Salmonella Typhimurium (red) invading cultured human cells. In north-eastern Uganda, a study has shown that nearly half the food and water in the region is contaminated with drug-resistant Salmonella. Rocky Mountain Laboratories, NIAID, (Public domain)

Over 60 per cent of the population practices open defecation, overwhelming limited sanitation systems.

“The available toilets cannot really accommodate the growing population of the Karamoja people,” Mpagi told SciDev.Net.

“Most of the toilets are built in designated places, but because many families are nomadic, they move with their animals and cannot return to use these facilities before continuing their journey.”

These conditions create a cycle where human waste, livestock, food and water intersect, spilling contamination into children’s meals. Diarrhoea, a common outcome, is among the five leading causes of under-five mortality.

Repeated diarrhoeal illness prevents children from absorbing nutrients, leaving them weak and vulnerable.

Bwambale Benard, a Ugandan public health nutritionist and food systems specialist, says that once first-line antibiotics fail, children stay sick longer, malnutrition worsens, and mortality rises.

But Benard points out that children are not the only ones at risk. Infections also affect pregnant women, the elderly, and whole households, leaving families unproductive and draining limited incomes.

“So we are going to have a community that is ill, sickly, that cannot be productive, and so they are not contributing productively to the GDP of a country, or even they are not able to sustain their families,” he told SciDev.Net.

A USAID-funded project in 2017 projected malnutrition will cost Uganda an estimated 19 trillion Ugandan Shillings (US$7.7 billion) in lost productivity by 2025.

Benard believes that if left unchecked, drug-resistant Salmonella could also undermine Uganda’s development targets.

He stressed the need for safer food handling to prevent recontamination, adding that ending open defecation requires tackling both cultural and practical barriers.

Andrew Kambugu, executive director of the Infectious Diseases Institute at Makerere University, Uganda, says the country has developed systems to detect antimicrobial resistance before it escalates.

In partnership with Uganda’s Ministry of Health, his team runs a surveillance network supported by the UK Aid–funded Fleming Fund.

Operating in seven referral hospitals across the country, the system monitors resistance patterns and provides early warnings.

“With the surveillance system, it means that if we see what we call clusters of patients that present diarrhoea due to Salmonella, we will be able to see that because we are collecting the data – and it will act as an early warning system to tell us that in that hospital there is a problem,” Kambugu told SciDev.Net.

He says hospitals are tracked closely and while clusters do not always confirm diarrhoea outbreaks, they prompt further investigation and guide the Ministry of Health’s response.

Kambugu said the recent findings from Karamoja were striking.

“In the regions that have been [by his institute], we do not have this high rate. I think it is unusual,” he said, adding that the cultural practices and access to water issues in Karamoja could be responsible for the situation.

Daniel Kyabayinze, director of public health at Uganda’s Ministry of Health, told SciDev.Net the government was reinforcing hygiene education in Karamoja and training farmers on safer post-harvest handling.

He linked these measures to Uganda’s National Action Plan on Antimicrobial Resistance, now in its fifth year and aligned with the WHO Global Action Plan.

Under the plan, referral hospitals feed lab data into antibiograms – laboratory reports that show which antibiotics are effective against different bacteria – which shape procurement and treatment decisions.

Kyabayinze said the study revealed an important opportunity to improve outcomes. While widely used drugs like azithromycin and ciprofloxacin showed high resistance, older and cheaper medicines such as co-trimoxazole still had very low resistance.

“So we can roll out the cheaper and more friendly drugs, especially in regions like Karamoja,” he said.

This piece was produced by SciDev.Net’s Sub-Saharan Africa English desk.