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

Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Naomi J Gadsby  1 , Clark D Russell  1   2 , Martin P McHugh  1 , Harriet Mark  1 , Andrew Conway Morris  3 , Ian F Laurenson  1 , Adam T Hill  4 , Kate E Templeton  1
Affiliations

Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Naomi J Gadsby et al. Clin Infect Dis. .

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.

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References

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