title: Etiology of community-acquired pneumonia: increased microbiological yield with new diagnostic methods.
abstract: BACKGROUND
  The microbial etiology of community-acquired pneumonia (CAP) is still not well characterized. During the past few years, polymerase chain reaction (PCR)-based methods have been developed for many pathogens causing respiratory tract infections. The aim of this study was to determine the etiology of CAP among adults-especially the occurrence of mixed infections among patients with CAP-by implementing a new diagnostic PCR platform combined with conventional methods.
  
  
  METHODS
  Adults admitted to Karolinska University Hospital were studied prospectively during a 12-month period. Microbiological testing methods included culture from blood, sputum, and nasopharyngeal secretion samples; sputum samples analyzed by real-time quantitative PCR for Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis; nasopharyngeal specimens analyzed by use of PCR; serological testing for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and viruses common in the respiratory tract; and urine antigen assays for detection of pneumococcal and Legionella pneumophila antigens.
  
  
  RESULTS
  A microbial etiology could be identified for 67% of the patients (n = 124). For patients with complete sampling, a microbiological agent was identified for 89% of the cases. The most frequently detected pathogens were S. pneumoniae (70 patients [38%]) and respiratory virus (53 patients [29%]). Two or more pathogens were present in 43 (35%) of 124 cases with a determined etiology.
  
  
  CONCLUSIONS
  By supplementing traditional diagnostic methods with new PCR-based methods, a high microbial yield was achieved. This was especially evident for patients with complete sampling. Mixed infections were frequent (most commonly S. pneumoniae together with a respiratory virus).
authors.affiliation: Department of Medicine, Karolinska Institutet, Stockholm, Sweden. sniclas.johansson@karolinska.se
authors.forename: Niclas
authors.initials: N
authors.lastname: Johansson
authors.forename: Mats
authors.initials: M
authors.lastname: Kalin
authors.forename: Annika
authors.initials: A
authors.lastname: Tiveljung-Lindell
authors.forename: Christian G
authors.initials: CG
authors.lastname: Giske
authors.forename: Jonas
authors.initials: J
authors.lastname: Hedlund
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D017714:Community-Acquired Infections / Q000175:diagnosis / Q000382:microbiology; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D011014:Pneumonia / Q000175:diagnosis* / Q000382:microbiology* / Q000821:virology; D011446:Prospective Studies; D014777:Virus Diseases / Q000175:diagnosis*; D055815:Young Adult