title: Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study.
abstract: The gut microbiota composition of elderly hospitalized patients with Clostridium difficile infection (CDI) exposed to previous antibiotic treatment is still poorly investigated. The aim of this study was to compare the microbiota composition by means of 16S rRNA microbial profiling among three groups of hospitalized elderly patients (age ≥ 65) under standard diet including 25 CDI-positive (CDI group), 29 CDI-negative exposed to antibiotic treatment (AB+ group) and 30 CDI-negative subjects not on antibiotic treatment (AB- group). The functional properties of the gut microbiomes of CDI-positive vs CDI-negative subjects were also assessed by shotgun metagenomics. A significantly lower microbial diversity was detected in CDI samples, whose microbiomes clustered separately from CDI-negative specimens. CDI was associated with a significant under-representation of gut commensals with putative protective functionalities, including Bacteroides, Alistipes, Lachnospira and Barnesiella, and over-representation of opportunistic pathogens. These findings were confirmed by functional shotgun metagenomics analyses, including an in-depth profiling of the Peptostreptococcaceae family. In CDI-negative patients, antibiotic treatment was associated with significant depletion of few commensals like Alistipes, but not with a reduction in species richness. A better understanding of the correlations between CDI and the microbiota in high-risk elderly subjects may contribute to identify therapeutic targets for CDI.
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.|Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Ticinesi
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.
authors.forename: Jacoline
authors.initials: J
authors.lastname: Gerritsen
authors.affiliation: Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.|Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Nouvenne
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mancabelli
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Duranti
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Marta
authors.initials: M
authors.lastname: Mangifesta
authors.affiliation: GenProbio srl, Parma, Italy.
authors.forename: Alice
authors.initials: A
authors.lastname: Viappiani
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Ferrario
authors.affiliation: Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy.|Geriatric Unit, Parma University Hospital, Parma, Italy.
authors.forename: Marcello
authors.initials: M
authors.lastname: Maggio
authors.affiliation: Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.
authors.forename: Fulvio
authors.initials: F
authors.lastname: Lauretani
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.
authors.forename: Willem
authors.initials: W
authors.lastname: De Vos
authors.affiliation: APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
authors.affiliation: Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.|Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy.
authors.forename: Tiziana
authors.initials: T
authors.lastname: Meschi
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D044822:Biodiversity; D003015:Clostridium Infections / Q000188:drug therapy* / Q000382:microbiology*; D003428:Cross Infection / Q000188:drug therapy* / Q000382:microbiology*; D003430:Cross-Sectional Studies; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005260:Female; D000069196:Gastrointestinal Microbiome; D006760:Hospitalization; D006801:Humans; D008297:Male; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S