Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness

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 (TM) TrueMark (TM) Respiratory Panel 2.0, OpenArray (TM) plate (OA) (32 viral and bacterial targets); and Applied Biosystems (TM) TrueMark (TM) Respiratory Panel 2.0, TaqMan (TM) 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 (similar to 36-40% of positive samples tested positive for two and more organisms). S. aureus was the most prevalent detected pathogen (similar to 30%) followed by SARS-CoV-2 (similar to 25%), Rhinovirus (similar to 15%) and HHV6 (similar to 10%). Co-infections between viruses and bacteria were the most common (similar to 69%), followed by viral-viral (similar to 23%) and bacterial-bacterial (similar to 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.