This was a retrospective cohort study of all pediatric and adult in- and outpatients in whom a 16-plex rtPCR assay for respiratory viruses was performed for upper and lower RTI, from either the Kantonsspital St. Gallen or Children’s hospital of Eastern Switzerland. Both hospitals are tertiary-care Swiss teaching hospitals with active infectious diseases consult services and easily accessible web-based local guidelines (www.guidelines.ch) for the treatment of community-acquired or hospital-acquired pneumonia. The guidelines are strongly recommended for use but not strictly reinforced, and include use of rtPCR as optional diagnostic in hospitalized patients, particularly with immune suppression. The study period was from September 2012 (when this assay was introduced) to November 2014. The documented application dates of anti-infective medication were matched with the date of rtPCR analysis in order to determine whether treatment was changed in response to rtPCR results. The main outcome of interest was whether antibiotic therapy was modified according to results of multiplex rtPCR. Secondary outcomes were prevalence and distribution of positive results of rtPCR, complications, length of stay (LOS), and antibiotic therapy depending on identified pathogens.