Multiplex Tests for Respiratory Tract Infections: The Direct Utility of the FilmArray Respiratory Panel in Emergency Department

Performance Assessment of a Multiplex Real-Time PCR Assay for Detection of Viruses Causing Respiratory Tract Infections

OBJECTIVES

Following the COVID-19 pandemic, global epidemiological trends demonstrate a return to pre-pandemic levels of respiratory syncytial virus (RSV) and influenza (Flu) A/B viruses. For the appropriate clinical management of viral infections, reliable and timely diagnosis is crucial. The clinical presentation of these respiratory viral infections shows significant overlaps; thus, the syndromic diagnosis of these infections becomes challenging. The goal of this study was to compare the performance of three multiplex real-time PCR-based platforms for the detection of SARS-CoV-2, Flu A, Flu B, and RSV.

MATERIALS AND METHODS

A retrospective study was performed on 200 de-identified nasopharyngeal and oropharyngeal specimens. All samples were tested simultaneously on three PCR-based platforms for the detection of SARS-CoV-2, Flu A, Flu B, and RSV: HealthTrackRx's real-time PCR Open Array® respiratory panel, TrueMark™ SARS-CoV-2, Flu A, Flu B, RSV Select Panel, and BioFire® RP2.1 Panel. The positive and negative predictive value of each test was evaluated at a 95% confidence interval.

RESULTS

Among the 200 tested samples, the TrueMark™ and OpenArray® laboratory-developed tests (LDTs) showed a 100% concordance for the detection of SARS-CoV-2, Flu A, Flu B, and RSV. Overall agreement of 100% was observed for nasopharyngeal samples between the laboratory-developed tests and FDA-approved BioFire® RP2.1 Panel. Diagnostic results for these four respiratory viruses, in clinical samples, between the LDTs and the FDA-approved comparator demonstrated full concordance.

CONCLUSIONS

Respiratory viral infections represent one of the major global healthcare burdens. Consequently, the accurate detection and surveillance of these viruses are critical, particularly when these viruses are known to co-circulate. The excellent performance and full concordance of the LDTs, with the BioFire® Respiratory RP2.1 panel, in detecting SARS-CoV-2, Flu A, Flu B, and RSV shows that these tests can be confidently implemented for the clinical testing of respiratory viral infections.

Evaluation of point-of-care multiplex polymerase chain reaction in guiding antibiotic treatment of patients acutely admitted with suspected community-acquired pneumonia in Denmark: A multicentre randomised controlled trial

BACKGROUND

Rapid and accurate detection of pathogens is needed in community-acquired pneumonia (CAP) to enable appropriate antibiotics and to slow the development of antibiotic resistance. We aimed to compare the effect of point-of-care (POC) polymerase chain reaction (PCR) detection of respiratory pathogens added to standard care with standard care only (SCO) on antibiotic prescriptions after acute hospital admission.

METHODS AND FINDINGS

We performed a superiority, parallel-group, open-label, multicentre, randomised controlled trial (RCT) in 3 Danish medical emergency departments (EDs) from March 2021 to February 2022. Adults acutely admitted with suspected CAP during the daytime on weekdays were included and randomly assigned (1:1) to POC-PCR (The Biofire FilmArray Pneumonia Panel plus added to standard care) or SCO (routine culture and, if requested by the attending physician, target-specific PCR) analysis of respiratory samples. We randomly assigned 294 patients with successfully collected samples (tracheal secretion 78.4% or expectorated sputum 21.6%) to POC-PCR (n = 148, 50.4%) or SCO (146, 49.6%). Patients and investigators owning the data were blinded to the allocation and test results. Outcome adjudicators and clinical staff at the ED were not blinded to allocation and test results but were together with the statistician, blinded to data management and analysis. Laboratory staff performing standard care analyses was blinded to allocation. The study coordinator was not blinded. Intention-to-treat and per protocol analysis were performed using logistic regression with Huber-White clustered standard errors for the prescription of antibiotic treatment. Loss to follow-up comprises 3 patients in the POC-PCR (2%) and none in the SCO group. Intention-to-treat analysis showed no difference in the primary outcome of prescriptions of no or narrow-spectrum antibiotics at 4 h after admission for the POC-PCR (n = 91, 62.8%) odds ratio (OR) 1.13; (95% confidence interval (CI) [0.96, 1.34] p = 0.134) and SCO (n = 87, 59.6%). Secondary outcomes showed that prescriptions were significantly more targeted at 4-h OR 5.68; (95% CI [2.49, 12.94] p < 0.001) and 48-h OR 4.20; (95% CI [1.87, 9.40] p < 0.001) and more adequate at 48-h OR 2.11; (95% CI [1.23, 3.61] p = 0.006) and on day 5 in the POC-PCR group OR 1.40; (95% CI [1.18, 1.66] p < 0.001). There was no difference between the groups in relation to intensive care unit (ICU) admissions OR 0.54; (95% CI [0.10, 2.91] p = 0.475), readmission within 30 days OR 0.90; (95% CI [0.43, 1.86] p = 0.787), length of stay (LOS) IRR 0.82; (95% CI [0.63, 1.07] p = 0.164), 30 days mortality OR 1.24; (95% CI [0.32, 4.82] p = 0.749), and in-hospital mortality OR 0.98; (95% CI [0.19, 5.06] p = 0.986).

CONCLUSIONS

In a setting with an already restrictive use of antibiotics, adding POC-PCR to the diagnostic setup did not increase the number of patients treated with narrow-spectrum or without antibiotics. POC-PCR may result in a more targeted and adequate use of antibiotics. A significant study limitation was the concurrent Coronavirus Disease 2019 (COVID-19) pandemic resulting in an unusually low transmission of respiratory virus.

TRIAL REGISTRATION

ClinicalTrials.gov (NCT04651712).

Clinical Characteristics Associated with Detected Respiratory Microorganism Employing Multiplex Nested PCR in Patients with Presumptive COVID-19 but Negative Molecular Results in Lima, Peru

The COVID-19 pandemic circumstances have varied the pathogens related to acute respiratory infections (ARI), and most specialists have ignored them due to SARS-CoV-2's similar symptomatology. We identify respiratory pathogens with multiplex PCR in samples with presumptive SARS-CoV-2 but negative RT-qPCR results. We performed a retrospective transversal study employing clinical data and nasopharyngeal swab samples from patients with suspected clinical SARS-CoV-2 infection and a negative PCR result in a private laboratory in Lima, Peru. The samples were analyzed using the FilmArray™ respiratory panel. Of 342 samples, we detected at least one pathogen in 50% of the samples. The main ones were rhinovirus (54.38%), influenza A(H3N2) (22.80%), and respiratory syncytial virus (RSV) (14.04%). The clinical characteristics were sore throat (70.18%), cough (58.48%), nasal congestion (56.43%), and fever (40.06%). Only 41.46% and 48.78% of patients with influenza met the definition of influenza-like illness (ILI) by the World Health Organization (WHO) (characterized by cough and fever) and the Centers for Disease Control and Prevention (CDC) (characterized by fever and cough and sore throat), respectively. A higher prevalence of influenza was associated with ILI by WHO (aPR: 2.331) and ILI by CDC (aPR: 1.892), which was not observed with other respiratory viruses. The clinical characteristic associated with the increased prevalence of rhinovirus was nasal congestion (aPR: 1.84). For patients with ARI and negative PCR results, the leading respiratory pathogens detected were rhinovirus, influenza, and RSV. Less than half of patients with influenza presented ILI, although its presence was specific to the disease.

Viral co-infections are associated with increased rates of hospitalization in those with influenza

Background

Influenza causes significant morbidity and mortality in the United States. Among patients infected with influenza, the presence of bacterial co‐infection is associated with worse clinical outcomes; less is known regarding the clinical importance of viral co‐infections. The objective of this study was to determine rates of viral co‐infections in emergency department (ED) patients with confirmed influenza and association of co‐infection with disease severity.

Methods

Secondary analysis of a biorepository and clinical database from a parent study where rapid influenza testing was implemented in four U.S. academic EDs, during the 2014–2015 influenza season. Patients were systematically tested for influenza virus using a validated clinical decision guideline. Demographic and clinical data were extracted from medical records; nasopharyngeal specimens from influenza‐positive patients were tested for viral co‐infections (ePlex, Genmark Diagnostics). Patterns of viral co‐infections were evaluated using chi‐square analysis. The association of viral co‐infection with hospital admission was assessed using univariate and multivariate regression.

Results

The overall influenza A/B positivity rate was 18.1% (1071/5919). Of the 999 samples with ePlex results, the prevalence of viral co‐infections was 7.9% (79/999). The most common viral co‐infection was rhinovirus/enterovirus (RhV/EV), at 3.9% (39/999). The odds of hospital admission (OR 2.33, 95% CI: 1.01–5.34) increased significantly for those with viral co‐infections (other than RhV/EV) versus those with influenza A infection only.

Conclusion

Presence of viral co‐infection (other than RhV/EV) in ED influenza A/B positive patients was independently associated with increased risk of hospital admission. Further research is needed to determine clinical utility of ED multiplex testing.

Identification of pathogens from the upper respiratory tract of adult emergency department patients at high risk for influenza complications in a pre-Sars-CoV-2 environment

The emergence of SARS-CoV-2 and subsequent COVID-19 pandemic highlights the morbidity and potential disease severity caused by respiratory viruses. To elucidate pathogen prevalence, etiology of coinfections and URIs from symptomatic adult Emergency department patients in a pre-SARS-CoV-2 environment, we evaluated specimens from four geographically diverse Emergency departments in the United States from 2013-2014 utilizing ePlex RP RUO cartridges (Genmark Diagnostics). The overall positivity was 30.1% (241/799), with 6.6% (16/241) coinfections. Noninfluenza pathogens from most to least common were rhinovirus/enterovirus, coronavirus, human metapneumovirus and RSV, respectively. Broad differences in disease prevalence and pathogen distributions were observed across geographic regions; the site with the highest detection rate (for both mono and coinfections) demonstrated the greatest pathogen diversity. A variety of respiratory pathogens and geographic variations in disease prevalence and copathogen type were observed. Further research is required to evaluate the clinical relevance of these findings, especially considering the SARS-CoV-2 pandemic and related questions regarding SARS-CoV-2 disease severity and the presence of co-infections.

Virus Coinfection is a Predictor of Radiologically Confirmed Pneumonia in Children with Bordetella pertussis Infection

Introduction

This study aimed to prospectively investigate the burden of pertussis in southeast Chinese children hospitalized with lower respiratory tract infection (LRTI) during a pertussis outbreak and to compare the outcomes of Bordetella pertussis infection with or without virus coinfections.

Methods

Children < 24 months of age hospitalized with LRTI were prospectively enrolled from January 2017 to December 2019. Demographic and clinical information were recorded, and respiratory tract samples were tested for the presence of B. pertussis and ten common viruses by polymerase chain reaction (PCR).

Results

Bordetella pertussis PCR was positive in 6.1% (202/4287) of the patients. Only 146 (72.3%) B. pertussis infections met the Centers for Disease Control and Prevention case definition for pertussis. Among the 202 subjects with B. pertussis infections, 81 (40.1%) were coinfected with at least 1 respiratory virus, with human rhinovirus being the most commonly detected virus (25.7%). No differences in clinical severity were observed between children with single B. pertussis infection and those with virus coinfection [odds ratio (OR) 0.75; 95% confidence interval (CI) 0.39–1.44]. However, children with virus coinfection were significantly more likely to present with radiologically confirmed pneumonia than those with a single B. pertussis infection (OR 2.62; CI 1.39–4.91).

Conclusions

Bordetella pertussis infection contributed to a high proportion of LRTI hospitalizations among southeast Chinese children. There were no significant differences in clinical severity between children with virus coinfection and single B. pertussis infection, although children coinfected with virus coinfection presented with pneumonia more frequently than those with single B. pertussis infection.

Electronic supplementary material

The online version of this article (10.1007/s40121-020-00376-5) contains supplementary material, which is available to authorized users.