Fecal microbiome profiling of children with <i>Shigella</i> diarrhea from low- and middle-income countries

<i>Shigella</i> is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing <i>Shigella</i> infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without <i>Shigella</i> identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with <i>Shigella</i> diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of <i>Shigella</i>. Our results showed that <i>Shigella</i> qPCR positive cases were characterized by a significantly higher abundance of <i>Shigella</i> and other <i>Proteobacteria</i>, alongside a lower abundance of the probiotic genus <i>Bifidobacterium</i>. This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to <i>Shigella</i> infection. While no significant difference in <i>Shigella</i> abundance was found between the <i>Shigella</i> culture positive and culture negative groups, genera <i>Bifidobacterium</i> and <i>Ligilactobacillus</i> were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with <i>Shigella</i> infection and a possible correlation between increased pathogenicity and the <i>Shigella</i> culturability. These findings might contribute to a more comprehensive understanding of <i>Shigella</i> pathogenicity and improving diagnostic methods for <i>Shigella</i>.IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with <i>Shigella</i> representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with <i>Shigella</i> and to investigate the factors affecting <i>Shigella</i> culturability. We identified a distinct intestinal microbial profile associated with <i>Shigella</i>-infected diarrheal children, observed a correlation between increased pathogenicity and the <i>Shigella</i> culturability, and also proposed some potential factors that might promote the <i>in vitro</i> growth of <i>Shigella</i> strains. These findings might provide evidence for improving diagnostic methods for <i>Shigella</i>.