BioProject

Background: Hospital environments contain several factors that can alter the intestinal microbiome of patients. Among the most critical risk factors to patient health in these settings are the circulation of virulence factors (VFs) and antibiotic resistance markers (ARMs) from potentially pathogenic organisms. Shotgun metagenomics aids in describing the microbiome composition throughout microbial communities profiling while also providing functional profiling targeting crucial molecular markers associated with the risk of diseases, mainly at the hospital level. Thus, we characterized the intestinal microbiome of patients with diarrhea admitted to hospitalization (Hosp, n=24) and emergency departments (ER, n=17) at the Hospital Universitario Mayor Méderi in Bogotá, Colombia. The collected fecal samples were subjected to shotgun metagenomics for subsequent taxonomical profiling of bacterial and viral communities and identification of VFs and ARMs. Results: Our results showed a high abundance of species belonging to the Enterobacteriaceae family in the study groups, such as Klebsiella pneumoniae and Escherichia coli. Additionally, viral families such as Myoviridae, Siphoviridae, and Podoviridae displayed high abundance in both groups, being crAss-like viruses particularly notable. Interestingly, the differentially abundant members between the study groups were Escherichia-specific and Klebsiella-specific phages (p<0.05). Additionally, we identified virulence factors associated with Klebsiella pneumoniae capsule and secretion systems. Also, we highlighted the presence of different toxins of Clostridioides difficile and Clostridium perfringens in the study groups. Finally, Hosp patients exhibited many genomic and plasmid ARMs, with those conferring resistance to glycopeptides showing a differential abundance between groups. Conclusions: This study provides microbiome profiling performed in hospitalization and emergency patients in Colombia. Thus, this information can contribute to optimizing treatments and practices for managing patients in these facilities.