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Hospital acquired infections (HAIs) impact 650,000 patients annually, with estimated costs in the billions of dollars. The hospital environment is a reservoir for bacteria that can cause such infections. We have performed two large-scale genomic analyses of bacteria associated with hospital plumbing and infrastructure, in order to better characterize this environment. In the first study, we identified hospital plumbing as the reservoir for a cluster of multi-drug resistant Sphingomonas koreensis isolates collected from patients over a decade. In a second study, sink drains, housekeeping equipment and high-touch surfaces were surveyed for carbapenemase-producing organisms (CPOs). We compared culture and whole genome sequencing data from this survey with previously collected information from five years of patient isolates. These studies further our understanding of gene-flow between clinically relevant microorganisms and the importance of bacterial reservoirs within the hospital environment.