title: The Use of Polymerase Chain Reaction Amplification for the Detection of Viruses and Bacteria in Severe Community-Acquired Pneumonia.
abstract: BACKGROUND
  Pathogens are often not identified in severe community-acquired pneumonia (CAP), and the few studies using polymerase chain reaction (PCR) techniques for virus detection are from temperate countries.
  
  
  OBJECTIVE
  This study assesses if PCR amplification improves virus and bacteria detection, and if viral infection contributes to mortality in severe CAP in a tropical setting, where respiratory pathogens have less well-defined seasonality.
  
  
  METHODS
  In this cohort study of patients with severe CAP in an intensive care unit, endotracheal aspirates for intubated patients and nasopharyngeal swabs for non-intubated patients were sent for PCR amplification for respiratory viruses. Blood, endotracheal aspirates for intubated patients, and sputum for non-intubated patients were analysed using a multiplex PCR system for bacteria.
  
  
  RESULTS
  Out of 100 patients, using predominantly cultures, bacteria were identified in 42 patients; PCR amplification increased this number to 55 patients. PCR amplification identified viruses in 32 patients. In total, only bacteria, only viruses, and both bacteria and viruses were found in 37, 14, and 18 patients, respectively. The commonest viruses were influenza A H1N1/2009 and rhinovirus; the commonest bacterium was Streptococcus pneumoniae. Hospital mortality rates for patients with no pathogens, bacterial infection, viral infection, and bacterial-viral co-infection were 16.1, 24.3, 0, and 5.6%, respectively (p = 0.10). On multivariable analysis, virus detection was associated with lower mortality (adjusted odds ratio 0.12, 95% confidence interval 0.2-0.99; p = 0.049).
  
  
  CONCLUSIONS
  Viruses and bacteria were detected in 7 of 10 patients with severe CAP with the aid of PCR amplification. Viral infection appears to be independently associated with lower mortality.
authors.affiliation: Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
authors.forename: Wen Ting
authors.initials: WT
authors.lastname: Siow
authors.forename: Evelyn Siew-Chuan
authors.initials: ES
authors.lastname: Koay
authors.forename: Chun Kiat
authors.initials: CK
authors.lastname: Lee
authors.forename: Hong Kai
authors.initials: HK
authors.lastname: Lee
authors.forename: Venetia
authors.initials: V
authors.lastname: Ong
authors.forename: Wang Jee
authors.initials: WJ
authors.lastname: Ngerng
authors.forename: Hui Fang
authors.initials: HF
authors.lastname: Lim
authors.forename: Adeline
authors.initials: A
authors.lastname: Tan
authors.forename: Julian Wei-Tze
authors.initials: JW
authors.lastname: Tang
authors.forename: Jason
authors.initials: J
authors.lastname: Phua
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D015331:Cohort Studies; D017714:Community-Acquired Infections / Q000175:diagnosis / Q000382:microbiology / Q000401:mortality / Q000821:virology; D005260:Female; D017052:Hospital Mortality; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics; D007251:Influenza, Human / Q000175:diagnosis* / Q000401:mortality / Q000821:virology; D007362:Intensive Care Units; D008297:Male; D008875:Middle Aged; D060885:Multiplex Polymerase Chain Reaction; D015999:Multivariate Analysis; D010850:Picornaviridae Infections / Q000175:diagnosis* / Q000401:mortality / Q000821:virology; D018410:Pneumonia, Bacterial / Q000175:diagnosis* / Q000382:microbiology / Q000401:mortality; D011018:Pneumonia, Pneumococcal / Q000175:diagnosis* / Q000382:microbiology / Q000401:mortality; D011024:Pneumonia, Viral / Q000175:diagnosis* / Q000401:mortality / Q000821:virology; D011446:Prospective Studies; D012229:Rhinovirus / Q000235:genetics; D013296:Streptococcus pneumoniae / Q000235:genetics