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Rapid Molecular Detection and Differentiation of Influenza Viruses A and B
Published on: January 30, 2017
Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness
Pallavi Upadhyay1, Jairus Reddy1, Teddie Proctor2
1HealthTrackRx R&D Division, Denton, TX 76207, USA.
Abstract:
While COVID-19 has dominated Influenza-like illness (ILI) over the past few years, there are many other pathogens responsible for ILI. It is not uncommon to have coinfections with multiple pathogens in patients with ILI. The goal of this study was to identify the different organisms in symptomatic patients presenting with ILI using two different high throughput multiplex real time PCR platforms. Specimens were collected from 381 subjects presenting with ILI symptoms. All samples (nasal and nasopharyngeal swabs) were simultaneously tested on two expanded panel PCR platforms: Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, OpenArray™ plate (OA) (32 viral and bacterial targets); and Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, TaqMan™ Array card (TAC) (41 viral, fungal, and bacterial targets). Results were analyzed for concordance between the platforms and for identification of organisms responsible for the clinical presentation including possible coinfections. Very good agreement was observed between the two PCR platforms with 100% agreement for 12 viral and 3 bacterial pathogens. Of 381 specimens, approximately 58% of the samples showed the presence of at least one organism with an important incidence of co-infections (~36-40% of positive samples tested positive for two and more organisms). S. aureus was the most prevalent detected pathogen (~30%) followed by SARS-CoV-2 (~25%), Rhinovirus (~15%) and HHV6 (~10%). Co-infections between viruses and bacteria were the most common (~69%), followed by viral-viral (~23%) and bacterial-bacterial (~7%) co-infections. These results showed that coinfections are common in RTIs suggesting that syndromic panel based multiplex PCR tests could enable the identification of pathogens contributing to coinfections, help guide patient management thereby improving clinical outcomes and supporting antimicrobial stewardship.
Insights
Coinfections are common in respiratory infections, with over half of symptomatic patients harboring multiple pathogens. Multiplex PCR testing effectively identifies these coinfections, aiding in patient management and antimicrobial stewardship.
Area of Science:
- Clinical microbiology
- Infectious diseases
- Molecular diagnostics
Background:
- Influenza-like illness (ILI) is often caused by pathogens other than SARS-CoV-2.
- Coinfections with multiple pathogens are frequent in patients presenting with ILI.
Purpose of the Study:
- To identify various organisms causing ILI in symptomatic patients.
- To evaluate two multiplex real-time PCR platforms for pathogen detection and coinfection analysis.
Main Methods:
- Collected nasal and nasopharyngeal swabs from 381 patients with ILI symptoms.
- Tested samples using two PCR platforms: Applied Biosystems™ TrueMark™ Respiratory Panel 2.0 OpenArray™ plate (32 targets) and TaqMan™ Array card (41 targets).
- Analyzed results for platform concordance and identified coinfections.
Main Results:
- High agreement between the two PCR platforms was observed.
- Approximately 58% of samples detected at least one pathogen.
- Coinfections were prevalent (~36-40% of positive samples), with bacterial-viral coinfections being most common (~69%).
- Key pathogens identified included *S. aureus* (~30%), SARS-CoV-2 (~25%), Rhinovirus (~15%), and HHV6 (~10%).
Conclusions:
- Coinfections are a significant factor in respiratory tract infections (RTIs).
- Syndromic panel-based multiplex PCR tests are valuable for identifying coinfecting pathogens.
- Accurate pathogen identification can improve patient management, clinical outcomes, and antimicrobial stewardship.
