title: Direct amplification of rRNA genes in diagnosis of bacterial infections.
abstract: A broad-range bacterial PCR targeting rRNA genes (rDNAs) was used to directly analyze 536 clinical samples obtained from 459 hospitalized patients during a 4-year study period. The molecular diagnosis based on DNA sequencing of the PCR product was compared to that obtained by bacterial culture. The bacteriological diagnosis was concordant for 447 (83%) specimens. Broad-range rDNA PCR was the only method that yielded an etiologic diagnosis for 11 (2.4%) of 459 patients. Compared to culture and clinical assessment, the sensitivity of the PCR method combined with sequencing was 74.2%, and the specificity was between 98.7 and 99.6%. At present, the described molecular approach proved superior to bacterial culture in two clinical situations: infections caused by bacteria with unusual growth requirements and specimens taken during antimicrobial treatment of the patient.
authors.affiliation: Department of Medical Microbiology, University of Turku, Turku, Finland. kaisu.rantakokko@utu.fi
authors.forename: K
authors.initials: K
authors.lastname: Rantakokko-Jalava
authors.forename: S
authors.initials: S
authors.lastname: Nikkari
authors.forename: J
authors.initials: J
authors.lastname: Jalava
authors.forename: E
authors.initials: E
authors.lastname: Eerola
authors.forename: M
authors.initials: M
authors.lastname: Skurnik
authors.forename: O
authors.initials: O
authors.lastname: Meurman
authors.forename: O
authors.initials: O
authors.lastname: Ruuskanen
authors.forename: A
authors.initials: A
authors.lastname: Alanen
authors.forename: E
authors.initials: E
authors.lastname: Kotilainen
authors.forename: P
authors.initials: P
authors.lastname: Toivanen
authors.forename: P
authors.initials: P
authors.lastname: Kotilainen
mesh_terms: D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D001419:Bacteria / Q000302:isolation & purification; D001424:Bacterial Infections / Q000175:diagnosis* / Q000188:drug therapy; D001431:Bacteriological Techniques; D016208:Databases, Factual; D005387:Finland; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D012335:RNA, Ribosomal / Q000235:genetics / Q000302:isolation & purification*; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000302:isolation & purification; D012338:RNA, Ribosomal, 23S / Q000235:genetics / Q000302:isolation & purification; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D000900:Anti-Bacterial Agents; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S