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 p...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/13/12/2014 |
| _version_ | 1797595302119604224 |
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| author | Pallavi Upadhyay Jairus Reddy Teddie Proctor Oceane Sorel Harita Veereshlingam Manoj Gandhi Xuemei Wang Vijay Singh |
| author_facet | Pallavi Upadhyay Jairus Reddy Teddie Proctor Oceane Sorel Harita Veereshlingam Manoj Gandhi Xuemei Wang Vijay Singh |
| author_sort | Pallavi Upadhyay |
| collection | DOAJ |
| description | 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). <i>S. aureus</i> 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. |
| first_indexed | 2024-03-11T02:34:20Z |
| format | Article |
| id | doaj.art-1018b99812624c23ad35fbed1d0fa1c0 |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-11T02:34:20Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-1018b99812624c23ad35fbed1d0fa1c02023-11-18T09:59:55ZengMDPI AGDiagnostics2075-44182023-06-011312201410.3390/diagnostics13122014Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like IllnessPallavi Upadhyay0Jairus Reddy1Teddie Proctor2Oceane Sorel3Harita Veereshlingam4Manoj Gandhi5Xuemei Wang6Vijay Singh7HealthTrackRx R&D Division, Denton, TX 76207, USAHealthTrackRx R&D Division, Denton, TX 76207, USAThermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USAThermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USAThermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USAThermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USAThermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USAHealthTrackRx R&D Division, Denton, TX 76207, USAWhile 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). <i>S. aureus</i> 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.https://www.mdpi.com/2075-4418/13/12/2014respiratory tract infectionsCOVID-19influenza-like illnessmultiplex PCRsyndromic panels |
| spellingShingle | Pallavi Upadhyay Jairus Reddy Teddie Proctor Oceane Sorel Harita Veereshlingam Manoj Gandhi Xuemei Wang Vijay Singh Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness Diagnostics respiratory tract infections COVID-19 influenza-like illness multiplex PCR syndromic panels |
| title | Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness |
| title_full | Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness |
| title_fullStr | Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness |
| title_full_unstemmed | Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness |
| title_short | Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness |
| title_sort | expanded pcr panel testing for identification of respiratory pathogens and coinfections in influenza like illness |
| topic | respiratory tract infections COVID-19 influenza-like illness multiplex PCR syndromic panels |
| url | https://www.mdpi.com/2075-4418/13/12/2014 |
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