title: Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa.
abstract: Cystic fibrosis (CF) lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp) and 52 P. aeruginosa-negative (Pn) pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA) from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.
authors.affiliation: Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.|Laboratoire de Bactériologie, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon (HCL), Bron, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Pages-Monteiro
authors.affiliation: Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Marti
authors.affiliation: Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.
authors.forename: Carine
authors.initials: C
authors.lastname: Commun
authors.affiliation: Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.
authors.forename: Nolwenn
authors.initials: N
authors.lastname: Alliot
authors.affiliation: Equipe de recherche, UMR CNRS 5558, INRA, INRIA, Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1 & ISPB, Lyon, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Bardel
authors.affiliation: CIRI, International Center for Infectiology Research, INSERM U1111, CNRS UMR5308, Université de Lyon, Ecole Normale Supérieure de Lyon, France.
authors.forename: Helene
authors.initials: H
authors.lastname: Meugnier
authors.affiliation: Laboratoire de Bactériologie, Centre hospitalier Lyon Sud, Hospices Civils de Lyon, Saint-Genis-Laval, France.|Centre de Ressources et de Compétences (CRCM) adulte, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite France, France.
authors.forename: Michele
authors.initials: M
authors.lastname: Perouse-de-Montclos
authors.affiliation: Centre de ressources et Compétences (CRCM) enfant, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Lyon, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Reix
authors.affiliation: Centre de Ressources et de Compétences (CRCM) adulte, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite France, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Durieu
authors.affiliation: Centre de Ressources et de Compétences (CRCM) adulte, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite France, France.
authors.forename: Stephane
authors.initials: S
authors.lastname: Durupt
authors.affiliation: Laboratoire de Bactériologie, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon (HCL), Bron, France.|Equipe de recherche Pathogénie des Staphylocoques, INSERM U851, Bron, France.
authors.forename: Francois
authors.initials: F
authors.lastname: Vandenesch
authors.affiliation: Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.|Laboratoire de Bactériologie, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon (HCL), Bron, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Freney
authors.affiliation: Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.
authors.forename: Benoit
authors.initials: B
authors.lastname: Cournoyer
authors.affiliation: Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.|Laboratoire de Bactériologie, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon (HCL), Bron, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Doleans-Jordheim
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001419:Bacteria / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D016000:Cluster Analysis; D003550:Cystic Fibrosis / Q000150:complications* / Q000175:diagnosis; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D016521:Electrophoresis, Gel, Pulsed-Field; D014644:Genetic Variation; D006801:Humans; D015994:Incidence; D056186:Metagenomics; D008826:Microbial Sensitivity Tests; D064307:Microbiota; D016133:Polymerase Chain Reaction; D011552:Pseudomonas Infections / Q000150:complications* / Q000453:epidemiology / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D012335:RNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism; D013183:Sputum / Q000382:microbiology*
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S