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Comprehensive molecular testing for respiratory pathogens in community-acquired pneumonia

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Gadsby_2016_CID_Comprehensive_molecular_CC.pdf (232.2Kb)
Date
01/04/2016
Author
Gadsby , NJ
Russell , CD
McHugh, Martin Patrick
Mark , H
Conway Morris, A
Laurenson , IF
Hill , AT
Templeton , KE
Keywords
Community-acquired pneumonia
Bacterial load
Viral
Molecular testing
PCR
QR355 Virology
RB Pathology
DAS
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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.
Citation
Gadsby , NJ , Russell , CD , McHugh , M P , Mark , H , Conway Morris , A , Laurenson , IF , Hill , AT & Templeton , KE 2016 , ' Comprehensive molecular testing for respiratory pathogens in community-acquired pneumonia ' , Clinical Infectious Diseases , vol. 62 , no. 7 , pp. 817–823 . https://doi.org/10.1093/cid/civ1214
Publication
Clinical Infectious Diseases
Status
Peer reviewed
DOI
https://doi.org/10.1093/cid/civ1214
ISSN
1058-4838
Type
Journal article
Rights
Copyright © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited.
Description
Funding: This work was supported by the Chief Scientist Office (grant number ETM/250).
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  • University of St Andrews Research
URI
http://hdl.handle.net/10023/21047

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