Comparison of rapid molecular testing methods for detecting respiratory viruses in emergency care: a prospective study

Markussen, Dagfinn Lunde; Grewal, Harleen M. S.; Knoop, Siri Tandberg; Serigstad, Sondre; Kommedal, Øyvind; Ebbesen, Marit Helen; Ulvestad, Elling; Bjørneklett, Rune

doi:10.1080/23744235.2021.2003857

Cited by 4 publications

(3 citation statements)

References 34 publications

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“…Furthermore, even though there was a small number of viral detections in this study, the data show a trend toward higher detection rates in LRT samples, resulting in a lower PPA. Indeed, and in line with previous investigations, four out of the 11 cases of rhino-/enterovirus were not detected in OP samples ( 12 , 38 ). All of these patients reported respiratory tract symptoms of more than one week's duration, supporting observations that URT samples may be most sensitive in the acute phase of a viral RTI while LRT samples can be more sensitive at a later stage, especially with development of LRT infections ( 39 , 40 ).…”

Section: Discussionsupporting

confidence: 90%

Diagnostic utility of oropharyngeal swabs as an alternative to lower respiratory tract samples for PCR-based syndromic testing in patients with community-acquired pneumonia

et al. 2023

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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.

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Section: Discussionsupporting

confidence: 90%

Diagnostic utility of oropharyngeal swabs as an alternative to lower respiratory tract samples for PCR-based syndromic testing in patients with community-acquired pneumonia

et al. 2023

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“…Access to rapid laboratory testing of a suitable panel of both viral and bacterial respiratory agents, according to the epidemiological situation, is important. Fast and pertinent microbiological testing is crucial to help clinicians make the right treatment decision for the patients’ benefit [ 44 ]. Rapid diagnostic testing is also needed to help decide on prompt isolation precautions to prevent nosocomial infections and can minimize unnecessary initiation of antibiotics and reduce the duration of antibiotic treatment, ultimately preventing the development of antibiotic resistance.…”

Section: Discussionmentioning

confidence: 99%

Antibiotic Consumption in a Cohort of Hospitalized Adults with Viral Respiratory Tract Infection

et al. 2023

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Development of antibiotic resistance, a threat to global health, is driven by inappropriate antibiotic usage. Respiratory tract infections (RTIs) are frequently treated empirically with antibiotics, despite the fact that a majority of the infections are caused by viruses. The purpose of this study was to determine the prevalence of antibiotic treatment in hospitalized adults with viral RTIs, and to investigate factors influencing the antibiotic decision-making. We conducted a retrospective observational study of patients ≥ 18 years, hospitalized in 2015–2018 with viral RTIs. Microbiological data were taken from the laboratory information system and information on antibiotic treatment drawn from the hospital records. To investigate decisions for prescribing antibiotic treatment, we evaluated relevant factors such as laboratory and radiological results, in addition to clinical signs. In 951 cases without secondary bacterial RTIs (median age 73 years, 53% female), 720 (76%) were prescribed antibiotic treatment, most frequently beta-lactamase-sensitive penicillins, but cephalosporins were prescribed as first-line in 16% of the cases. The median length of treatment (LOT) in the patients treated with antibiotics was seven days. Patients treated with antibiotics had an average of two days longer hospital stay compared to patients with no such treatment, but no difference in mortality was found. Our study revealed that there is still a role for antimicrobial stewardship to further improve antibiotic use in patients admitted for viral RTIs in a country with relatively low antibiotic consumption.

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“…Moreover, testing LRT samples may be useful in patients under clinical investigation whose NP swabs are negative [30]. To our knowledge, only a few studies [6,[30][31][32][33] have evaluated the diagnostic accuracy of the commercially available rapid RT-PCR kits for detecting SARS-CoV-2 RNA in these types of specimens. The protocol adopted for the pretreatment of LRT samples was judged to be efficient from the point of view of both sample handling time and test performance.…”

Section: Discussionmentioning

confidence: 99%

Comparative Diagnostic Accuracy of the STANDARD M10 Assay for the Molecular Diagnosis of SARS-CoV-2 in the Point-of-Care and Critical Care Settings

Domnich

Orsi

Trombetta

et al. 2022

JCM

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Accurate and rapid molecular diagnosis of COVID-19 is a crucial step to tackle the ongoing pandemic. The primary objective of this study was to estimate the real-world performance of the novel RT-PCR STANDARD M10 SARS-CoV-2 assay in a large number of nasopharyngeal (NP) specimens eluted in universal transport medium. The secondary objective was to evaluate the compatibility of this kit in testing NP samples eluted in an inactivated transport medium (essential for point-of-care testing) and lower respiratory tract (LRT) specimens, which are commonly collected in critical care. A total of 591 samples were analyzed. Compared with the standard extraction-based RT-PCR Allplex 2019-nCoV (time-to-result of 270 min), the sensitivities of the STANDARD M10 were 100% (95% CI: 98.1–100%), 95.5% (95% CI: 91.7–97.6%), and 99.5% (95% CI: 97.2–99.9%) for ≥1 gene, the ORF1ab gene, and the E gene, respectively, while the specificity was 100% (95% CI: 98.7–100%). The diagnostic accuracy was 100% in testing both NP samples eluted in an inactivated transport medium and LRT specimens. STANDARD M10 reliably detects SARS-CoV-2 in 60 min, may be used as a POC tool, and is suitable for testing LRT specimens in the critical care setting.

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Comparison of rapid molecular testing methods for detecting respiratory viruses in emergency care: a prospective study

Cited by 4 publications

References 34 publications

Diagnostic utility of oropharyngeal swabs as an alternative to lower respiratory tract samples for PCR-based syndromic testing in patients with community-acquired pneumonia

Diagnostic utility of oropharyngeal swabs as an alternative to lower respiratory tract samples for PCR-based syndromic testing in patients with community-acquired pneumonia

Antibiotic Consumption in a Cohort of Hospitalized Adults with Viral Respiratory Tract Infection

Comparative Diagnostic Accuracy of the STANDARD M10 Assay for the Molecular Diagnosis of SARS-CoV-2 in the Point-of-Care and Critical Care Settings

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