Abstract Description

Undernutrition is a critical health concern with profound impacts on several United Nations Sustainable Development Goals (SDGs), particularly SDG 2. The World Health Organization (WHO) estimates that over 100 million children under the age of five are stunted. Evidence has shown that stunting is more prevalent among children living in informal settlements, where unsanitary conditions are common. These conditions have been shown to favour the spread of antimicrobial resistance genes (ARGs). Given the intersection of informal settlements, stunting, pathogens and ARGs, this study aimed to investigate these associations using the gut microbiome as a proxy for health. To address this, we used 16S rRNA gene sequencing and SmartChip quantitative PCR targeting ARGs and pathogen markers. We found differences in microbial composition, with children living in informal housing exhibiting reduced microbial diversity. Such reductions are associated with poor gut health and decreased protection against disease. A statistically significant difference (p=0.034) was found between microbiomes of stunted and non-stunted children, indicating that nutritional deficiencies can reshape microbial communities in ways that directly affect growth. Notably, pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Legionella were detected in high abundances in informal settlements. ARGs potentially carried by these pathogens, including blaTem, blaCTX-M_5 and intl1-1, were detected in stunted children. These genes confer resistance to antibiotics commonly prescribed to children with severe malnutrition and are involved in mobile genetic elements. These findings highlight the role of informal housing in exacerbating stunting and highlight the urgent need for targeted interventions to curb prevalence in marginalised communities.