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Reduced gastrointestinal tract bacterial community diversity has been associated with increased risk for healthcare-associated infections, including Clostridium difficile infection. We sought to develop a model for concomitant change in bacterial community diversity at gastrointestinal and respiratory tract sites, drawing upon a recently completed cohort study of 92 subjects recruited from a long-term acute care hospital (LTACH) for dense longitudinal oral, endotracheal aspirate (ET), and stool specimen collection.

We evaluated the first 30 subjects enrolled from the LTACH cohort, for whom complete antibiotic administration data and 16S rRNA gene (V1–V2 amplicon) sequencing data were available. Sequencing was performed via the Illumina HiSeq platform; operational taxonomic units (OTUs) were formed and taxonomy assigned (GreenGenes 13.8) via …