Low microbial diversity characterizes the fecal microbiota of patients colonized with multidrug-resistant microorganisms.
Background: The emergence and dissemination of multidrug-resistant organisms (MDRO) is a global threat. Timely identification of MDRO-colonized patients is critical in order to limit the spread of MDROs in the hospital setting. The goal of this study was to characterize fecal microbiome signatures predictive of MDRO colonization.
Methods: Two rectal swabs were obtained from patients within 48 hours of hospitalization to a tertiary care center in Boston, MA. Swabs were processed for the presence of MDRO using conventional cultures and for microbial community analyses (V4 region, 16S rRNA sequencing, Illumina MiSeq sequencer). Patients were grouped according to the presence of MDRO (MDRO+) or absence of MDRO (MDRO-). Clinical and demographic data, as well as structural and compositional characteristics of the fecal microbiome were compared between groups. Diagnostic performance of microbial diversity metrics was also assessed.
Results: Forty-four patients were included, of which 11 (25%) were MDRO+. MDRO+ patients had more comorbidities (median Charlson index =7 vs. 4, P =0.05) and were more frequently exposed to antimicrobials within 3 months prior to admission (90.9% vs 48.8%, P =0.02). Microbial diversity was significantly reduced among MDRO+ patients, compared to MDRO- patients (figure 1A, B, and C). After adjusting for prior antimicrobial exposure, prior stay in a health-care associated institution and comorbidities, the Shannon index was inversely associated with MDRO-colonization at admission (OR 0.26; 95% CI =0.07 – 0.92). Among microbial diversity metrics, the Shannon index showed the best diagnostic performance for detecting MDRO- patients (ROC =0.79 [figure 1D]). Using a Shannon index cut-off point of ³3.6, the sensitivity and specificity to rule out MDRO colonization was 94% and 64%, respectively. Analyses of weighted UniFrac distances showed separate clustering of samples according to MDRO colonization status. MDRO+ patients had higher abundance of Enterococcus spp. (LDA =4.9, P =0.03) and Stenotrophomonas spp. (LDA =4.4, P = 0.01).
Conclusion: A low microbial diversity of the fecal microbiome was a signature of MDRO+ patients. Microbial community assessment may become a useful tool to guide infection control policies.
J. Ugalde, None
E. M. D'Agata, None