Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Clin Infect Dis. 2016 Apr 1;62(7):817-823. doi: 10.1093/cid/civ1214. Epub 2016 Jan 7.

Abstract

Background: The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP.

Methods: Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns.

Results: Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients.

Conclusions: Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy.

Keywords: PCR; bacterial load; community-acquired pneumonia; molecular testing; viral.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Anti-Bacterial Agents / pharmacology
  • Bacterial Load
  • Community-Acquired Infections* / diagnosis
  • Community-Acquired Infections* / microbiology
  • Community-Acquired Infections* / virology
  • Female
  • Haemophilus influenzae / drug effects
  • Haemophilus influenzae / genetics
  • Humans
  • Male
  • Microbial Sensitivity Tests
  • Middle Aged
  • Molecular Diagnostic Techniques / methods*
  • Pneumonia, Bacterial* / diagnosis
  • Pneumonia, Bacterial* / microbiology
  • Pneumonia, Bacterial* / virology
  • Pneumonia, Viral* / diagnosis
  • Pneumonia, Viral* / microbiology
  • Pneumonia, Viral* / virology
  • Polymerase Chain Reaction
  • Retrospective Studies
  • Streptococcus pneumoniae / drug effects
  • Streptococcus pneumoniae / genetics
  • Viral Load

Substances

  • Anti-Bacterial Agents