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BACKGROUND: Residents of long-term care facilities (LTCFs) are at increased risk for colonization and development of infections with multidrug-resistant organisms. This study was undertaken to determine prevalence of asymptomatic rectal colonization with Clostridium difficile (and proportion of 027/NAP1/BI ribotype) or carbapenem-resistant Enterobacteriaceae (CRE) in an LTCF population. METHODS: Active surveillance was performed for C difficile and CRE rectal colonization of 301 residents in a 320-bed (80-bed ventilator unit), hospital-affiliated LTCF with retrospective chart review for patient demographics and potential risk factors. RESULTS: Over 40% of patients had airway ventilation and received enteral feeding. One-third of these patients had prior C difficile-associated infection (CDI). Asymptomatic rectal colonization with C difficile occurred in 58 patients (19.3%, one-half with NAP1+), CRE occurred in 57 patients (18.9%), and both occurred in 17 patients (5.7%). Recent CDI was significantly associated with increased risk of C difficile +/- CRE colonization. Multivariate logistic regression analysis revealed presence of tracheostomy collar to be significant for C difficile colonization, mechanical ventilation to be significant for CRE colonization, and prior CDI to be significant for both C difficile and CRE colonization. CONCLUSIONS: The strong association of C difficile or CRE colonization with disruption of normal flora by mechanical ventilation, enteral feeds, and prior CDI carries important implications for infection control intervention in this population.