Alison Laufer Halpin1, Tom J B de Man2, Colleen S Kraft3, K Allison Perry2, Austin W Chan4, Sung Lieu5, Jeffrey Mikell5, Brandi M Limbago2, L Clifford McDonald2. 1. Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA. Electronic address: ALaufer@cdc.gov. 2. Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA. 3. Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA. 4. Division of Infectious Diseases, Duke University, Durham, NC. 5. Department of Medicine, Emory University, Atlanta, GA.
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. Published by Elsevier Inc.
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. Published by Elsevier Inc.
Authors: T Z DeSantis; P Hugenholtz; N Larsen; M Rojas; E L Brodie; K Keller; T Huber; D Dalevi; P Hu; G L Andersen Journal: Appl Environ Microbiol Date: 2006-07 Impact factor: 4.792
Authors: J I Arango; A Restrepo; D L Schneider; N S Callander; J L Ochoa-Bayona; M I Restrepo; P Bradshaw; J Patterson; C O Freytes Journal: Bone Marrow Transplant Date: 2006-03 Impact factor: 5.483
Authors: Johan Dicksved; Jonas Halfvarson; Magnus Rosenquist; Gunnar Järnerot; Curt Tysk; Juha Apajalahti; Lars Engstrand; Janet K Jansson Journal: ISME J Date: 2008-04-10 Impact factor: 10.302
Authors: Erik R Dubberke; Kimberly A Reske; Yan Yan; Margaret A Olsen; L Clifford McDonald; Victoria J Fraser Journal: Clin Infect Dis Date: 2007-12-15 Impact factor: 9.079
Authors: Rafael Araos; Veronica Montgomery; Juan A Ugalde; Graham M Snyder; Erika M C D'Agata Journal: Infect Control Hosp Epidemiol Date: 2017-09-13 Impact factor: 3.254
Authors: Teppei Shimasaki; Anna Seekatz; Christine Bassis; Yoona Rhee; Rachel D Yelin; Louis Fogg; Thelma Dangana; Enrique Cornejo Cisneros; Robert A Weinstein; Koh Okamoto; Karen Lolans; Michael Schoeny; Michael Y Lin; Nicholas M Moore; Vincent B Young; Mary K Hayden Journal: Clin Infect Dis Date: 2019-05-30 Impact factor: 9.079
Authors: C F Kelley; C S Kraft; T Jb de Man; C Duphare; H-W Lee; J Yang; K A Easley; G K Tharp; M J Mulligan; P S Sullivan; S E Bosinger; R R Amara Journal: Mucosal Immunol Date: 2016-11-16 Impact factor: 7.313