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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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Autores principales: Upadhyay, Pallavi, Reddy, Jairus, Proctor, Teddie, Sorel, Oceane, Veereshlingam, Harita, Gandhi, Manoj, Wang, Xuemei, Singh, Vijay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10297358/
https://www.ncbi.nlm.nih.gov/pubmed/37370910
http://dx.doi.org/10.3390/diagnostics13122014
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author Upadhyay, Pallavi
Reddy, Jairus
Proctor, Teddie
Sorel, Oceane
Veereshlingam, Harita
Gandhi, Manoj
Wang, Xuemei
Singh, Vijay
author_facet Upadhyay, Pallavi
Reddy, Jairus
Proctor, Teddie
Sorel, Oceane
Veereshlingam, Harita
Gandhi, Manoj
Wang, Xuemei
Singh, Vijay
author_sort Upadhyay, Pallavi
collection PubMed
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). 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.
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spelling pubmed-102973582023-06-28 Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness Upadhyay, Pallavi Reddy, Jairus Proctor, Teddie Sorel, Oceane Veereshlingam, Harita Gandhi, Manoj Wang, Xuemei Singh, Vijay Diagnostics (Basel) Article 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. MDPI 2023-06-09 /pmc/articles/PMC10297358/ /pubmed/37370910 http://dx.doi.org/10.3390/diagnostics13122014 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Upadhyay, Pallavi
Reddy, Jairus
Proctor, Teddie
Sorel, Oceane
Veereshlingam, Harita
Gandhi, Manoj
Wang, Xuemei
Singh, Vijay
Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness
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 Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10297358/
https://www.ncbi.nlm.nih.gov/pubmed/37370910
http://dx.doi.org/10.3390/diagnostics13122014
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