title: Molecular detection of multiple emerging pathogens in sputa from cystic fibrosis patients.
abstract: BACKGROUND
  There is strong evidence that culture-based methods detect only a small proportion of bacteria present in the respiratory tracts of cystic fibrosis (CF) patients.
  
  
  RESULTS
  Standard microbiological culture and phenotypic identification of bacteria in sputa from CF patients have been compared to molecular methods by the use of 16S rDNA amplification, cloning and sequencing. Twenty-five sputa from CF patients were cultured that yield 33 isolates (13 species) known to be pathogens during CF. For molecular cloning, 760 clones were sequenced (7.2+/-3.9 species/sputum), and 53 different bacterial species were identified including 16 species of anaerobes (30%). Discrepancies between culture and molecular data were numerous and demonstrate that accurate identification remains challenging. New or emerging bacteria not or rarely reported in CF patients were detected including Dolosigranulum pigrum, Dialister pneumosintes, and Inquilinus limosus.
  
  
  CONCLUSIONS
  Our results demonstrate the complex microbial community in sputa from CF patients, especially anaerobic bacteria that are probably an underestimated cause of CF lung pathology. Metagenomic analysis is urgently needed to better understand those complex communities in CF pulmonary infections.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France.
authors.forename: Fadi
authors.initials: F
authors.lastname: Bittar
authors.forename: Hervé
authors.initials: H
authors.lastname: Richet
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Dubus
authors.forename: Martine
authors.initials: M
authors.lastname: Reynaud-Gaubert
authors.forename: Nathalie
authors.initials: N
authors.lastname: Stremler
authors.forename: Jacques
authors.initials: J
authors.lastname: Sarles
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Rolain
mesh_terms: D000328:Adult; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification*; D001421:Bacteria, Anaerobic / Q000235:genetics* / Q000302:isolation & purification*; D002648:Child; D003550:Cystic Fibrosis / Q000382:microbiology*; D017931:DNA Primers; D005784:Gene Amplification; D006801:Humans; D008168:Lung / Q000382:microbiology / Q000473:pathology; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013183:Sputum / Q000382:microbiology*
chemical_list: D017931:DNA Primers; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S