WHO warns of drug-resistant diseases in Kenyan children

The rise of drug-resistant infections is becoming a threat to Kenya’s goal of reducing the number of children dying before their fifth birthday to 25 deaths per 1,000 live births by 2030—a target set by the World Health Organization (WHO), a new study has found.

A post-mortem analysis of children under five who died in Kisumu and Siaya counties between 2021 and 2023, conducted by the Child Health and Mortality Prevention Surveillance, revealed alarmingly high rates of E. coli and Klebsiella pneumoniae –two bacteria commonly associated with serious infections.

These pathogens were resistant to key antibiotics such as ampicillin, sulfamethoxazole-trimethoprim and ceftriaxone, which are among the most accessible and affordable treatments available in Kenyan health facilities.

The study found that out of the total cases, 23.7 percent had blood culture isolates, with E. coli accounting for 32 percent and Klebsiella pneumoniae for 27.5 percent. Among the 34 cerebrospinal fluid cultures, 47.1 percent were E. coli, while 29.4 percent were Klebsiella pneumoniae. The resistance patterns were consistent across different age groups within the under-five bracket.

Antimicrobial resistance occurs when bacteria, viruses, fungi and parasites evolve and become unresponsive to drugs, making infections harder to treat. It increases the risk of disease spreading, serious illness and death. For children under five, whose immune systems are still developing, the consequences could often be fatal.

“This study highlights a critical gap in our understanding of antimicrobial resistance in young children in Kenya,” said the researchers.

“If left unchecked, drug resistance will continue to limit treatment options and contribute significantly to preventable child mortality.”

Antimicrobial resistance is a growing global threat, contributing to an estimated 4.9 million deaths annually. Projections indicate that the number could rise to 10 million deaths per year by 2050 if urgent action is not taken.

Children in low- and middle-income countries, such as Kenya, are particularly vulnerable.

This microbial threat comes at a time when Kenya’s overall child health landscape is already under pressure. More than half of all under-five deaths in Kenya occur during the neonatal period, specifically within the first 28 days of life.

The 2022 Kenya Demographic and Health Survey reported that 51 percent of child deaths occur during this vulnerable window, often due to complications of childbirth, birth asphyxia, infection or preterm birth.

Read: Concern as nations cut on health spending globally

Although Kenya has made efforts to expand maternal and neonatal services, significant gaps remain. Many rural health facilities lack essential equipment such as incubators and oxygen, and some mothers still give birth at home without the help of skilled birth attendants.

Charles Momanyi, a paediatrician in Nairobi, attributes many infant deaths to delays in care by caregivers.

"Many mothers don't know the warning signs of serious illness in children," he explains.

"They often wait too long to go to hospital, sometimes until it's too late." He stressed that promoting maternal education can help reduce under-five mortality. "Educated mothers are more likely to follow immunisation schedules, maintain hygiene and seek timely medical care."

Immunisation, one of the most effective tools for reducing under-five deaths, has also suffered significant setbacks.

According to the WHO, global immunisation coverage was stagnating before the H1N1 pandemic and worsened in 2020 and 2021 due to pandemic-related disruptions.

In 2023, there was widespread shortages of vaccines for diseases such as measles, polio and pneumonia, putting countless children at risk. Missed vaccinations weaken herd immunity and reintroduce once-controlled diseases into vulnerable populations.

A USAid report on Preventing Child and Maternal Deaths 2024 warns that Kenya is off track to meet the Sustainable Development Goal on child survival.

While Kenya has made progress over the past two decades, reducing its under-five mortality rate from 115 deaths per 1,000 live births in 2003 to 34.8 in 2022, it's still above the WHO threshold.

The report attributes the slower progress to preventable infections, continued neonatal deaths and a high prevalence of malaria among children.

"Since 2000, we have seen a 55 percent reduction in under-five mortality and a 42 percent reduction in maternal mortality in USAid's 25 priority countries. USAid's programmes have driven these reductions, saving the lives of more than 7.4 million women and children over the past decade. This success has been made possible by USAID's stewardship, the generosity of the American people, and bipartisan support from Congress," the report said.

Meanwhile, Kenya's health financing remains inadequate. In the proposed national budget for 2025/2026, the treasury allocated Sh132.4 billion to the Ministry of Health, about 3.1 percent of total budget, which still falls below the 15 percent threshold set by the Abuja Declaration.

These budgetary constraints have led to chronic underfunding of reproductive, maternal, newborn, child and adolescent health (RMNCAH) programmes and an over-reliance on donor-funded initiatives, the future of which is uncertain following recently announced cuts in health aid from the United States.

In addition, the decentralisation of health services has complicated the implementation of child health programmes. While counties are now responsible for primary health care, disparities in resource allocation have led to inequities between regions.

"Some counties lack skilled staff, essential medicines and basic infrastructure, while others struggle with data collection, making it difficult to plan for or respond to health emergencies," said Dr Momamyi.

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