title: Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA. Electronic address: ALaufer@cdc.gov.
authors.forename: Alison Laufer
authors.initials: AL
authors.lastname: Halpin
authors.affiliation: Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA.
authors.forename: Tom J B
authors.initials: TJ
authors.lastname: de Man
authors.affiliation: Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA.
authors.forename: Colleen S
authors.initials: CS
authors.lastname: Kraft
authors.affiliation: Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA.
authors.forename: K Allison
authors.initials: KA
authors.lastname: Perry
authors.affiliation: Division of Infectious Diseases, Duke University, Durham, NC.
authors.forename: Austin W
authors.initials: AW
authors.lastname: Chan
authors.affiliation: Department of Medicine, Emory University, Atlanta, GA.
authors.forename: Sung
authors.initials: S
authors.lastname: Lieu
authors.affiliation: Department of Medicine, Emory University, Atlanta, GA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Mikell
authors.affiliation: Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA.
authors.forename: Brandi M
authors.initials: BM
authors.lastname: Limbago
authors.affiliation: Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA.
authors.forename: L Clifford
authors.initials: LC
authors.lastname: McDonald
mesh_terms: D000328:Adult; D000368:Aged; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D016000:Cluster Analysis; D003430:Cross-Sectional Studies; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D003967:Diarrhea / Q000382:microbiology; D000069467:Fecal Microbiota Transplantation; D005243:Feces / Q000382:microbiology*; D005260:Female; D000069196:Gastrointestinal Microbiome; D006761:Hospitals; D006801:Humans; D008134:Long-Term Care; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D010802:Phylogeny; D010865:Pilot Projects; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: Clostridium difficile; Infection control; antibiotic use; carbapenem-resistant Enterobacteriaceae; intestinal microbiome; long-term acute care; vancomycin-resistant enterococci