Drug-Resistant Bacteria Found in Post-Mortem Tests of Kenyan Children Under Five

 A recent study conducted under the Child Health and Mortality Prevention Surveillance (CHAMPS) programme has revealed a worrying rise in antimicrobial-resistant (AMR) bacteria among children under five who died in Kenya between 2021 and 2023, signalling a looming public health crisis.

The study, which focused on mortality cases in rural Siaya and urban Kisumu counties, examined blood and cerebrospinal fluid samples from 634 deceased children.

Results from the study showed that Escherichia coli and Klebsiella pneumoniae—two common and potentially deadly bacteria—were not only prevalent but also resistant to several first-line antibiotics, including ampicillin, sulfamethoxazole-trimethoprim, and ceftriaxone.

Findings of this study were presented by a team of researchers led by Jim Katieno at the just concluded 2025 CHAMPS Network Meeting in Nairobi attended by 160 delegates from CHAMPS study sites including KEMRI who also commemorated 10 years since the establishment of the network. It was also attended by key partners and stakeholders.

Out of the total cases, 23.7 percent (150) had blood culture isolates, with E. coli accounting for 32 percent and Klebsiella pneumoniae for 27.5 percent. Among the 34 (5.4 percent) 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 is a growing global threat, contributing to an estimated 4.9 million deaths annually, with projections indicating that 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 study highlights a critical gap in our understanding of antimicrobial resistance in young children in Kenya,” the researchers noted. “If left unchecked, drug resistance will continue to limit treatment options and contribute significantly to preventable child mortality.”

The study calls for continuous nationwide monitoring of antimicrobial resistance trends and the development of robust antimicrobial stewardship programs. Additionally, it recommends further research on bacterial resistance in morbidity cases to support evidence-based policy formulation.

As Kenya and other developing nations grapple with the dual burden of infectious diseases and rising drug resistance, the findings serve as a wake-up call to prioritize investment in diagnostic capacity, surveillance, and regulation of antibiotic use in both clinical and community settings.

CHAMPS Kenya is based at the KEMRI’s Centre for Global Health Research (CGHR) in Kisumu County under the leadership of Dr. Victor Akello.