The objectives of this study are to dissect the main microbial, clinical, and antimicrobial resistance determinants that impact colonization and infection by vancomycin-resistant enterococci (VRE), extended-spectrum beta-lactamase producing Enterobacterales (ESBL-E), carbapenem-resistant Enterobacterales (CRE), and Clostridium difficile; to evaluate the role of commensal microbiota in VRE, ESBL-E/CRE, and C. difficile colonization, and to define the functional aspects of keystone microbiota and mechanisms of protection against colonization/infection.
Patients will be recruited from both intensive care units (n=500) and stem cell transplant units (n=500) and will be followed until discharge from these units, or for a maximum of four weeks. In addition to stool, blood, and oral samples, enrolled patients will have clinical data collected by chart review to evaluate colonization/infection-related clinical status, microbiological laboratory information, exposure to antibiotics, and clinical outcomes. Positive clinical cultures taken during the course of hospitalization will also be collected for analysis.
