title: Methods to classify bacterial pathogens in cystic fibrosis.
abstract: Many bacteria can be detected in CF sputum, pathogenic and commensal. Modified Koch's criteria for identification of established and emerging CF pathogens are therefore described. Methods are described to isolate bacteria and to detect bacterial biofilms in sputum or lung tissue from CF patients by means of conventional culturing and staining techniques and by the PNA FISH technique. Additionally, the confocal scanning laser microscopy technique is described for studying biofilms in vitro in a flow cell system. The recA-gene PCR and the RFLP-based identification methods are described for identification of isolates from the Burkholderia complex to the species level. DNA typing by PFGE, which can be used for any bacterial pathogen, is described as it is employed for Pseudomonas aeruginosa. A commercially available ELISA method is described for measuring IgG antibodies against P. aeruginosa in CF patients.
authors.affiliation: Department of Clinical Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark. tbjarnsholt@sund.ku.dk
authors.forename: Thomas
authors.initials: T
authors.lastname: Bjarnsholt
authors.forename: Xiaohui Chen
authors.initials: XC
authors.lastname: Nielsen
authors.forename: Ulla
authors.initials: U
authors.lastname: Johansen
authors.forename: Lena
authors.initials: L
authors.lastname: Nørgaard
authors.forename: Niels
authors.initials: N
authors.lastname: Høiby
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D018441:Biofilms; D019117:Burkholderia / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D019121:Burkholderia Infections / Q000235:genetics / Q000382:microbiology*; D003550:Cystic Fibrosis / Q000235:genetics / Q000382:microbiology*; D004269:DNA, Bacterial / Q000032:analysis; D016521:Electrophoresis, Gel, Pulsed-Field; D004797:Enzyme-Linked Immunosorbent Assay; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D018613:Microscopy, Confocal; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D011552:Pseudomonas Infections / Q000235:genetics / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D011938:Rec A Recombinases / Q000032:analysis; D013183:Sputum / Q000737:chemistry / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D011938:Rec A Recombinases