Stunting is associated with a gut microbiome enriched in mobile antibiotic resistance genes and opportunistic pathogens in children from urban informal settlements
1
Microbiology, Stellenbosch university, Stellenbosch, South Africa
2
Department of Economics,, Stellenbosch University, Stellenbosch, South Africa
Popul. Med. 2026;8(Supplement Supplement 1):A470
ABSTRACT
ABSTRACT:
Undernutrition remains a major global health challenge and presents multiple impediments to the attainment of several United Nations Sustainable Development Goals. Estimates by the World Health Organization suggest that over 100 million children, under five, are stunted, with the burden disproportionately concentrated in the global South. There is some evidence suggesting that overcrowding, inadequate sanitation, and relatively high exposure to enteric pathogens may explain this increased burden. Such environments are conducive to the dissemination of antimicrobial resistance genes (ARGs), posing increased health risks to undernourished children. However, few studies have investigated these dynamics across diverse settings in the African continent. Here, we investigated stunting, informal housing, pathogens, and ARGs using the gut microbiome as a proxy for child health. Stool samples (n=153), collected from children living in informal settlements, were analysed using 16S rRNA gene sequencing to characterise microbial community structure and high-throughput quantitative PCR to quantify ARGs and pathogen-associated markers. Children characterized as stunted exhibited higher within-sample microbial diversity (Shannon index) compared with those from non-stunted children, alongside a significant difference in overall community composition between groups (PERMANOVA p = 0.034). This result suggests that distinct gut microbial assemblages may be linked to impaired growth. Indicator species analysis revealed Prevotella 9 with a stronger association (p=0.002) to stunted children's gut microbiomes, while Bifidobacterium associated (p =0.004) more with non-stunted children, highlighting contrasting microbial signatures linked to nutritional status. Opportunistic pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Legionella spp., were frequently detected in children’s microbiomes. Notably, mobile resistance genes bla-TEM, bla-CTX–M and the class 1 integron intI1 were significantly more prevalent in stunted children and were often associated with these opportunistic pathogens. 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
Undernutrition remains a major global health challenge and presents multiple impediments to the attainment of several United Nations Sustainable Development Goals. Estimates by the World Health Organization suggest that over 100 million children, under five, are stunted, with the burden disproportionately concentrated in the global South. There is some evidence suggesting that overcrowding, inadequate sanitation, and relatively high exposure to enteric pathogens may explain this increased burden. Such environments are conducive to the dissemination of antimicrobial resistance genes (ARGs), posing increased health risks to undernourished children. However, few studies have investigated these dynamics across diverse settings in the African continent. Here, we investigated stunting, informal housing, pathogens, and ARGs using the gut microbiome as a proxy for child health. Stool samples (n=153), collected from children living in informal settlements, were analysed using 16S rRNA gene sequencing to characterise microbial community structure and high-throughput quantitative PCR to quantify ARGs and pathogen-associated markers. Children characterized as stunted exhibited higher within-sample microbial diversity (Shannon index) compared with those from non-stunted children, alongside a significant difference in overall community composition between groups (PERMANOVA p = 0.034). This result suggests that distinct gut microbial assemblages may be linked to impaired growth. Indicator species analysis revealed Prevotella 9 with a stronger association (p=0.002) to stunted children's gut microbiomes, while Bifidobacterium associated (p =0.004) more with non-stunted children, highlighting contrasting microbial signatures linked to nutritional status. Opportunistic pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Legionella spp., were frequently detected in children’s microbiomes. Notably, mobile resistance genes bla-TEM, bla-CTX–M and the class 1 integron intI1 were significantly more prevalent in stunted children and were often associated with these opportunistic pathogens. 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
| eISSN: | 2654-1459 |
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