Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention

• Type of Material: Article
• Authors: AL Halpin, Centers for Disease Control and Prevention; TJB de Man, Centers for Disease Control and Prevention; Colleen Kraft, Emory University; KA Perry, Centers for Disease Control and Prevention; AW Chan, Duke University; S Lieu, Emory University; Jeffrey Mikell, Emory University; BM Limbago, Centers for Disease Control and Prevention; LC McDonald, Centers for Disease Control and Prevention
• Language: English
• Date: 2016-07-01
• Publisher: Elsevier: 12 months
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2016
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1016/j.ajic.2016.01.003
• Title of Journal or Parent Work: American Journal of Infection Control
• ISSN: 0196-6553
• Volume: 44
• Issue: 7
• Start Page: 830
• End Page: 836
• Grant/Funding Information: This work was supported in part by the Center for AIDS Research (P30 AI050409 awarded to C.K.)
• Keywords: Infectious Diseases; Public, Environmental & Occupational Health; Science & Technology; long-term acute care; carbapenem-resistant Enterobacteriaceae; DISEASE; intestinal microbiome; antibiotic use; HEALTH; STEM-CELL TRANSPLANTATION; Infection control; CLOSTRIDIUM-DIFFICILE INFECTION; GUT MICROBIOTA; vancomycin-resistant enterococci; RISK; Life Sciences & Biomedicine; COLONIZATION; Clostridium difficile
• Research Categories: Biology, Virology; Health Sciences, Public Health

Abstract

Background Composition and diversity of intestinal microbial communities (microbiota) are generally accepted as a risk factor for poor outcomes; however, we cannot yet use this information to prevent adverse outcomes. Methods Stool was collected from 8 long-term acute care hospital patients experiencing diarrhea and 2 fecal microbiota transplant donors; 16S rDNA V1-V2 hypervariable regions were sequenced. Composition and diversity of each sample were described. Stool was also tested for Clostridium difficile, vancomycin-resistant enterococci (VRE), and carbapenem-resistant Enterobacteriaceae. Associations between microbiota diversity and demographic and clinical characteristics, including antibiotic use, were analyzed. Results Antibiotic exposure and Charlson Comorbidity Index were inversely correlated with diversity (Spearman = -0.7). Two patients were positive for VRE; both had microbiomes dominated by Enterococcus faecium, accounting for 67%-84% of their microbiome. Conclusions Antibiotic exposure correlated with diversity; however, other environmental and host factors not easily obtainable in a clinical setting are also known to impact the microbiota. Therefore, direct measurement of microbiome disruption by sequencing, rather than reliance on surrogate markers, might be most predictive of adverse outcomes. If and when microbiome characterization becomes a standard diagnostic test, improving our understanding of microbiome dynamics will allow for interpretation of results to improve patient outcomes.