Enhanced identification of viral and atypical bacterial pathogens in lower respiratory tract samples with nucleic acid amplification tests

J Med Virol. 2006 May;78(5):702-10. doi: 10.1002/jmv.20595.


The advantages of nucleic acid amplification tests (NAT) over conventional methods for the detection of pathogens in lower respiratory tract samples have not been established. NAT for respiratory pathogens were performed on 439 endotracheal tube (ETT) and bronchoalveolar lavage (BAL) samples. A potential pathogen was detected in 87 samples. Of 22 samples that tested positive by conventional methods, 15 tested positive for the same pathogen by NAT, 1 tested positive for a different pathogen, 2 had co-infections identified only by NAT, and 4 tested negative by NAT. An additional 73 pathogens were detected by NAT in 65 samples including 30 pathogens that were missed by conventional methods (19 adenovirus, 6 respiratory syncytial virus, 3 parainfluenza virus 1-4, 2 influenza A), 41 pathogens not routinely identified by conventional methods in most laboratories (23 rhinovirus, 8 human coronavirus OC43, 5 human metapneumovirus (hMPV), 2 human coronavirus 229E, 2 human coronavirus NL63, 1 Chlamydophila pneumoniae) and 2 pathogens from samples where no respiratory virus testing was requested (1 influenza A, 1 parainfluenza virus). Four of 52 patients who had multiple BAL samples submitted on the same day had negative and positive results by NAT on different samples. NAT improves detection of potential pathogens from ETT and BAL samples.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged, 80 and over
  • Bronchi / microbiology*
  • Bronchoalveolar Lavage
  • Child
  • Child, Preschool
  • Chlamydia Infections / diagnosis
  • Chlamydophila pneumoniae / genetics
  • Chlamydophila pneumoniae / isolation & purification
  • DNA Viruses / genetics
  • DNA, Bacterial / genetics
  • Humans
  • Infant
  • Intubation, Intratracheal
  • Middle Aged
  • Nucleic Acid Amplification Techniques
  • RNA Viruses / genetics
  • Respiratory Tract Infections / diagnosis*
  • Sensitivity and Specificity
  • Trachea / microbiology*
  • Virus Diseases / diagnosis*


  • DNA, Bacterial