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Respiratory infections: what to expect from molecular tools?

Performance of a PCR-based syndromic panel compared to routine culture and microscopy in patients suspected of pneumonia

April 21 • P4392

V. Andrews1, M. Pinholt1, U. Vest Schneider1/2, L. Søes1, K. Schønning1, G. Lisby1

1) Copenhagen University Hospital Hvidovre, Department of Clinical Microbiology, Hvidovre, Denmark
2) Department of Clinical Microbiology, Rigshospitalet, Denmark , Copenhagen, Denmark

Background: Syndromic testing for lower respiratory tract infections with BIOFIRE® FILMARRAY® Pneumonia Panel (PNplus) consists of a multiplex PCR with 27 pathogens and a turn-around-time of two hours. Routine diagnostic of bacterial pneumonia in the Capital Region of Denmark consist of culture preceded by microscopy for quality assessment of sputum. Turn-around-time and sensitivity of culture can be a limiting factor for targeted antimicrobial treatment. Hence, we evaluated PNplus against culture for analytical and clinical performance.

Materials/methods: From January to May 2019, 298 samples (sputum or endotracheal aspirates) were collected consecutively from hospitalized patients with suspected pneumonia. Samples were referred routinely to the Department of Clinical Microbiology (Copenhagen University Hospital Hvidovre) for culture and additional testing by BF.

Retrospectively, patients were categorized into “pneumonia” according to IDSA definition, “probable pneumonia” for patients without lung infiltrate but otherwise meeting the pneumonia criteria, and “not pneumonia”. Analytical performance was evaluated by bacterial pathogen concordance between the two methods. Clinical performance was determined regarding pneumonia/not pneumonia and detection of a positive/negative bacterial pathogen, and evaluated by sensitivity, positive predictive value (PPV), negative predictive value (NPV) and efficacy.

Patients with probable pneumonia were excluded in clinical performance calculations.

Results: 98 patients had pneumonia, 71 had probable pneumonia and 129 had not pneumonia.

Overall positive agreement between culture and PNplus was 42%. The rate increased to 67% when pathogens in lowest quantity (104 and 105 copies/mL) in PNplus were excluded.

Overall sensitivity of PNplus was improved from 73% to 89%, and for culture from 50% to 72%, when only high-quality samples as judged by microscopy were included in the analysis. For PNplus, PPV: 50%, NPV: 69% and efficacy: 57% were comparable to culture (PPV: 49%; NPV: 62%; efficacy: 56%); this increased slightly for both PNplus (PPV: 55%; NPV: 76%; efficacy:61) and culture (PPV: 53%; NPV: 62%; efficacy: 56%), when only high-quality samples were included.

Conclusions: PPV and NPV of both PNplus and culture were low. Both tests are therefore best used in patients in whom the pneumonia diagnosis has been established clinically. Indiscriminate use may be diagnostically misleading and a cause of inappropriate use of antibiotics.


Pneumonia Panel

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