Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services

Hospital-onset diarrhea was associated with distinct microbiome features, including differences in phage-bacteria dynamics involving key diarrhea-associated taxa, as well as a higher abundance of virulence factors and antimicrobial resistance markers. These findings underscore the potential value of shotgun metagenomics as a complementary approach for infection surveillance and the development of precision diagnostic strategies in hospital settings.