Diversity and persistence of MRSA and VRE in skilled nursing facilities: environmental screening, whole-genome sequencing and development of a dispersion index

Abstract

Environmental contamination with methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) in skilled nursing facilities (SNFs) may contribute to patient acquisition. We assessed diversity and association of MRSA and VRE isolates in a SNF wing and developed a mathematical index to define each strain's tendency to persist in rooms and spread horizontally. Longitudinal study of MRSA and VRE colonization and contamination among successive patient occupancies in a cluster of nine SNF private rooms during eight months characterized by microbiological testing and whole genome isolate typing. 'Dispersion index" of a strain is defined as the number of rooms it was found in (including the patient), divided by the average of times it was found consecutively in the same room. MRSA (ten strain types) and VRE (seven types) were recovered from room or patient in 16.4% and 35.6% of the occupancies, respectively. MRSA showed moderate horizontal spread and several episodes of same-room persistence (three distinct strain types) (overall dispersion index: 1.08). VRE showed high tendency towards horizontal spread /new introductions (overall dispersion index: 3.25), and only one confirmed persistence episode. The emerging picture of high diversity among contaminating strains and high likelihood of room persistence despite terminal cleaning (MRSA) and horizontal spread between rooms (VRE) in this setting calls for improved cleaning practices, heightened contact precautions, and most of all to establish individually tailored facility screening programs to enable informed choices based on local, measurable and actionable epidemiologic parameters. University of Michigan OAIC REC Scholarship to M.C. National Institutes of Health K24 AG050685 to L.M.