Investigating the fecal microbiota in patients colonized with Klebsiella pneumoniae and/or vancomycin-resistant Enterococcus. Homo sapiens fecal microbiota

Klebsiella pneumoniae and Vancomycin-resistant Enterococci (VRE) colonization in the gut has been associated with subsequent infection in ICU populations. While some healthcare systems routinely screen for VRE colonization, screening is not necessarily done for K. pneumoniae. This project aimed to identify factors involved in co-colonization with both of these organisms. ICU patients were screened for VRE and K. pneumoniae by rectal swab culture over two time periods: July-October 2014 (n=1,209) and January-May, 2016 (n=1,243). Patient demographics, baseline laboratory data, comorbidities, and outcomes were analyzed. 16S rRNA gene-based analysis was performed on a subset of patients (n=248) to identify microbiota characteristics associated with VRE and K. pneumoniae colonization. In multivariable analysis, VRE colonization was significantly associated with K. pneumoniae colonization in the 2016 cohort (P=0.03) and approached significance in the 2014 cohort (P=0.08). VRE colonization was associated with poor underlying health whereas K. pneumoniae colonization was associated with advanced age. The most prevalent operational taxonomic units (OTUs) in the gut included E. coli/Shigella spp., Klebsiella and Enterococcus, consistent with high rates of detectable K. pneumoniae and VRE by culture. Patients who were colonized with K. pneumoniae had a lower abundance of an E. coli/Shigella spp. OTU, and Klebsiella and Enterococcus themselves were the main drivers of differences in community structure based on colonization status. In conclusions, K. pneumoniae colonized patients without significant comorbidities or broad disruption of the microbiome. Screening ICU patients for K. pneumoniae and VRE simultaneously could be an efficient approach for novel infection prevention strategies.