Evidence on linking diarrheagenic E. coli with stunted childhood growth and overgrowth of small intestinal bacterial taxa impacting vulnerable child gut health

Stunted growth is an emerging global challenge affecting more than 30% population of children under 5 years of age in low- and middle-income countries. Despite such high global prevalence of stunting the mechanism of pathogenesis and the role of associated gut microbiota is poorly understood. The present study was designed to investigate the association of pathogenic strains of E. coli with the residential gut microbiota of stunted growth children. A total of 64 stool sample were collected from children aged =5 years and were processed for isolation and molecular characterization of diarrheagenic E. coli. Selected stool samples (n=39) were then analysed for microbiome analysis using 16S ribosomal RNA (rRNA) gene sequencing to determine correlation between change in microbiota with the presence of different E. coli strains. Pathotyping of the isolated E. coli (n=64) showed that 39.68% belonged to one of the five pathotypes of E. coli whereas the remaining were non-typeable. Among the different pathotypes EPEC was found to be most prevalent (52%; n=13), followed by EAEC (20%; n=5), EIEC (12%; n=3), EHEC (8%; n=2) and ETEC 2 (8%; n=2). Phylogrouping analysis showed that Majority of the strains belonged to B2 (28.12%). Microbiome analysis showed that microbial diversity was significantly decreased in stunted children samples in associated with different phylogroup. Moreover, the colonization of these strains were found to be significantly associated with energy utilization pathways such as Denovoprine-2 and glyoxylate-by. Relative abundance analysis showed that the genera Escherichia-Shigella and Enterococcus were found to be associated with stunted growth in children. The study suggests that environmentally transmitted E. coli phylogroups entering into the gut of the vulnerable child influencing the overall microbial community which affect the performance of gut leading to stunted growth.