Dataset Information

Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections.

ABSTRACT:

Background

PCR-based techniques for the diagnosis of community- acquired severe lower respiratory tract infections are becoming the standard of care. However, their relative ability to identify either atypical bacteria or viruses that cause LRTI from clinical samples from various sources is yet to be determined.

Objectives and study design

The aim of our study was to compare the diagnostic yield of nasopharyngeal aspirates with that of pulmonary samples for the etiological diagnosis of severe acute lower respiratory tract infections by multiplex PCR. Patients were adults with community-acquired pneumonia or acute exacerbation of chronic obstructive pulmonary disease.

Results

We obtained concordant results for 81 (79%) of the 103 pairs of samples. In 14 of the 22 discordant results, more pathogens were evidenced in the lower respiratory tract samples.

Conclusions

Pulmonary samples had a similar diagnostic sensitivity for virus detection by multiplex PCR as nasopharyngeal aspirates. In contrast, in our study, the diagnostic efficacy of pulmonary samples for Legionella pneumophila over simple aspirates was clearly superior.

SUBMITTER: Robert S

PROVIDER: S-EPMC7185397 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Publications

Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections.

Robert Sylvie S Lhommet Claire C Le Brun Cécile C Garot Denis D Legras Annick A Mankikian Julie J Goudeau Alain A

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 20180829

<h4>Background</h4>PCR-based techniques for the diagnosis of community- acquired severe lower respiratory tract infections are becoming the standard of care. However, their relative ability to identify either atypical bacteria or viruses that cause LRTI from clinical samples from various sources is yet to be determined.<h4>Objectives and study design</h4>The aim of our study was to compare the diagnostic yield of nasopharyngeal aspirates with that of pulmonary samples for the etiological diagnos ...[more]

PMID: 30195090

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Project description:Syndromic PCR-based analysis of lower respiratory tract (LRT) samples in patients with community-acquired pneumonia (CAP) improves the bacterial yield and time-to-results compared to culture-based methods. However, obtaining adequate sputum samples can be challenging and is frequently not prioritized in the emergency department (ED). In this study, we assess the concordance of microbiological detections between oropharyngeal- (OP) and LRT samples from patients presenting to the ED with CAP using a syndromic PCR-based respiratory panel [Biofire FilmArray Pneumonia plus (FAP plus)]. Paired OP- and high-quality LRT samples were collected from 103 patients with confirmed CAP, who had been included in a randomized controlled trial (NCT04660084) or a subsequent observational study at Haukeland University Hospital, and analyzed using the FAP plus. The LRT samples were obtained mainly by sputum induction (88%). Using the LRT samples as a reference standard, the positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement for the most common bacterial pathogens in CAP, Streptococcus pneumoniae and Haemophilus influenzae, were 85%, 99% and 95%, and 86%, 98% and 93%, respectively. For Moraxella catarrhalis, the PPA was lower (74%), while the NPA was 100%. For bacteria that are less likely causes of uncomplicated CAP (e.g., Staphylococcus aureus and Enterobacterales) the results were more divergent. In conclusion, the FAP plus detects the most common CAP pathogens S. pneumoniae and H. influenzae from OP samples with high PPAs and excellent NPAs when compared with LRT samples. For these pathogens, the PPAs for OP samples were higher than previous reports for nasopharyngeal samples. This suggests that analysis of OP samples with syndromic PCR panels could represent an alternative approach for rapid microbiological testing in the ED, especially in patients where LRT samples are difficult to obtain. Divergent results for bacteria that are less likely to cause uncomplicated CAP do, however, emphasize the need for clinical evaluation of positive test results.

Project description:Respiratory tract infections are major global health issues that require rapid and accurate diagnostic methods. Multiplex quantitative PCR (qPCR) is commonly used for pathogen detection in respiratory samples. However, the optimal specimen selection for detecting bacterial pathogens is not well-explored. We evaluated the detection rates of respiratory bacteria from nasopharyngeal swabs (NPS), sputum, and combined NPS and sputum samples using multiplex qPCR (Allplex PneumoBacter Assay, Seegene). Paired NPS and sputum samples from 219 patients with acute respiratory symptoms admitted to Korea University Anam Hospital were analyzed. qPCR was performed to detect seven respiratory bacteria: Bordetella parapertussis, Bordetella pertussis, Chlamydophila pneumoniae, Haemophilus influenzae, Legionella pneumophila, Mycoplasma pneumoniae, and Streptococcus pneumoniae. Combined NPS and sputum samples (n = 92) were created from 46 pairs of positive and 46 pairs of negative signals for NPS-alone and sputum-alone samples. Sputum samples (44.3%; 97/219) had a significantly higher positivity rate compared to NPS samples (21.0%; 46/219) (P < 0.001). The 92 combined samples identified a total of 65 bacterial nucleic acids. The detection rate for the combined samples was 86.2% (56/65), which was comparable to that of sputum alone (89.2%; 58/65) and higher than that of NPS samples (50.8%; 33/65). Combining NPS and sputum samples for PCR testing may offer an alternative for bacterial pathogen detection, providing rates comparable to those of sputum alone and greater sensitivity than that of NPS alone. This combined approach could be a cost-effective method to maximize diagnostic yield, reduce the need for multiple tests, and improve the management of respiratory infections.ImportanceThis study offers important insights into refining diagnostic strategies for respiratory bacterial infections using multiplex PCR. This study finds that combining sputum and nasopharyngeal swabs into a single tube could serve as an effective alternative for detecting respiratory bacteria in adults with acute respiratory illness.

Project description:BackgroundKlebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus are major bacterial causes of lower respiratory tract infections (LRTIs) globally, leading to substantial morbidity and mortality. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for their effective antibiotic therapy. In low-resourced settings, patients with LRTIs are prescribed antibiotics empirically while awaiting several days for culture results. Rapid pathogen and AMR gene detection could prompt optimal antibiotic use and improve outcomes.MethodsHere, we developed multiplex quantitative real-time PCR using EvaGreen dye and melting curve analysis to rapidly identify six major pathogens and fourteen AMR genes directly from respiratory samples. The reproducibility, linearity, limit of detection (LOD) of real-time PCR assays for pathogen detection were evaluated using DNA control mixes and spiked tracheal aspirate. The performance of RT-PCR assays was subsequently compared with the gold standard, conventional culture on 50 tracheal aspirate and sputum specimens of ICU patients.ResultsThe sensitivity of RT-PCR assays was 100% for K. pneumoniae, A. baumannii, P. aeruginosa, E. coli and 63.6% for S. aureus and the specificity ranged from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection of target bacteria was 1600 CFU/ml. The quantitative results from the PCR assays demonstrated 100% concordance with quantitative culture of tracheal aspirates. Compared to culture, PCR assays exhibited higher sensitivity in detecting mixed infections and S. pneumoniae. There was a high level of concordance between the detection of AMR gene and AMR phenotype in single infections.ConclusionsOur multiplex quantitative RT-PCR assays are fast and simple, but sensitive and specific in detecting six bacterial pathogens of LRTIs and their antimicrobial resistance genes and should be further evaluated for clinical utility.

Dataset Information

Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections.

Background

Objectives and study design

Results

Conclusions

Publications

Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections.

Similar Datasets

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