Abstract
BackgroundFor the detection of respiratory pathogens, the sampling strategy may influence the diagnostic yield. Ideally, samples from the lower respiratory tract are collected, but they are difficult to obtain.ObjectivesIn this study, we compared the diagnostic yield in sputum and oropharyngeal samples (OPS) for the detection of respiratory pathogens in patients with community-acquired pneumonia (CAP), with the objective to optimize our diagnostic testing algorithm.MethodsMatched sputum samples, OPS, blood cultures, serum, and urine samples were taken from patients (>18 years) with CAP and tested for the presence of possible respiratory pathogens using bacterial cultures, PCR for 17 viruses and five bacteria and urinary antigen testing.ResultsWhen using only conventional methods, that is, blood cultures, sputum culture, urinary antigen tests, a pathogen was detected in 49·6% of patients (n = 57). Adding molecular detection assays increased the yield to 80%. A pathogen was detected in 77 of the 115 patients in OPS or sputum samples by PCR. The sensitivity of the OPS was lower than that of the sputum samples (57% versus 74%). In particular, bacterial pathogens were more often detected in sputum samples. The sensitivity of OPS for the detection of most viruses was higher than in sputum samples (72% versus 66%), except for human rhinovirus and respiratory syncytial virus.ConclusionAddition of PCR on both OPS and sputum samples significantly increased the diagnostic yield. For molecular detection of bacterial pathogens, a sputum sample is imperative, but for detection of most viral pathogens, an OPS is sufficient.
Highlights
Community-acquired pneumonia (CAP) remains a major cause of morbidity and mortality worldwide.[1]
Despite efforts to find evidence for bacterial and viral pathogens as etiological agents in patients with CAP, etiology remains elusive in up to 50% of the patients.[1,3,4,5]. Reasons reported for this low yield are use of antibiotics before collecting samples, sample type tested, and the diagnostic panel used for patient evaluation.[6,7,8]
Adding the full molecular diagnostic package increased the diagnostic yield to 80%
Summary
Community-acquired pneumonia (CAP) remains a major cause of morbidity and mortality worldwide.[1] Streptococcus pneumoniae, Mycoplasma pneumoniae, influenza A virus (InfA), respiratory syncytial virus (RSV), and adenoviruses (AdV) are recognized as important causes of CAP.[2,3] Despite efforts to find evidence for bacterial and viral pathogens as etiological agents in patients with CAP, etiology remains elusive in up to 50% of the patients.[1,3,4,5] Reasons reported for this low yield are use of antibiotics before collecting samples, sample type tested, and the diagnostic panel used for patient evaluation.[6,7,8] Diagnostic methods used range from culture (sputum, blood, throat swabs), antigen testing (e.g. urinary antigen testing), and molecular tests. Samples from the lower respiratory tract are collected, but they are difficult to obtain
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