Microbiota disruption and colonization by carbapenem-resistant Pseudomonas aeruginosa in ICU patients

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) can colonize the gastrointestinal (GI) tract of intensive care unit (ICU) patients. CRPA colonization puts patients at increased risk for CRPA infection. We examined relationships between the microbiota, medications, and CRPA colonization acquisition. Data and peri-rectal swabs were obtained from a cohort of ICU patients at the University of Maryland Medical Center in Baltimore Maryland. We classified 109 patients into three groups by CRPA colonization-acquisition status and antimicrobial exposure. Data from 16S rRNA gene sequencing of an ICU admission swab and = one additional swab was used to evaluate associations between patient characteristics, medications, the GI microbiota, and CRPA colonization acquisition. Results indicated that ICU patients had low levels of diversity and high relative abundances of pathobionts. Piperacillin-tazobactam was prescribed more frequently to patients with CRPA colonization acquisition than those without. Piperacillin-tazobactam was associated with low abundance of potentially protective taxa (e.g., Lactobacillus and Clostridiales) and increased risk of Enterococcus domination. A subset of correlated taxa, which were identified at ICU admission, were associated with lower risk of CRPA colonization-acquisition. We concluded that antibiotics differed in their impact on the microbiota. Certain bacterial taxa (e.g., Clostridiales) were negatively associated with CRPA colonization acquisition. These taxa may be markers of risk for CRPA colonization-acquisition and/or serve a protective role in the gut of ICU patients.