Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection

Identification of etiology remains a significant challenge in the diagnosis of infectious diseases, particularly in resource-poor settings. Viral, bacterial, and fungal pathogens, as well as parasites, play a role for many syndromes, and optimizing a single diagnostic system to detect a range of pat...

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Main Authors:	Diaz, Maureen H., Waller, Jessica L., Napoliello, Rebecca A., Islam, Md. Shahidul, Wolff, Bernard J., Burken, Daniel J., Holden, Rhiannon L., Srinivasan, Velusamy, Arvay, Melissa, McGee, Lesley, Oberste, M. Steven, Whitney, Cynthia G., Schrag, Stephanie J., Winchell, Jonas M., Saha, Samir K.
Format:	Online
Language:	English
Published:	Public Library of Science 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689704/

id	pubmed-3689704
recordtype	oai_dc
spelling	pubmed-36897042013-06-26 Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection Diaz, Maureen H. Waller, Jessica L. Napoliello, Rebecca A. Islam, Md. Shahidul Wolff, Bernard J. Burken, Daniel J. Holden, Rhiannon L. Srinivasan, Velusamy Arvay, Melissa McGee, Lesley Oberste, M. Steven Whitney, Cynthia G. Schrag, Stephanie J. Winchell, Jonas M. Saha, Samir K. Research Article Identification of etiology remains a significant challenge in the diagnosis of infectious diseases, particularly in resource-poor settings. Viral, bacterial, and fungal pathogens, as well as parasites, play a role for many syndromes, and optimizing a single diagnostic system to detect a range of pathogens is challenging. The TaqMan Array Card (TAC) is a multiple-pathogen detection method that has previously been identified as a valuable technique for determining etiology of infections and holds promise for expanded use in clinical microbiology laboratories and surveillance studies. We selected TAC for use in the Aetiology of Neonatal Infection in South Asia (ANISA) study for identifying etiologies of severe disease in neonates in Bangladesh, India, and Pakistan. Here we report optimization of TAC to improve pathogen detection and overcome technical challenges associated with use of this technology in a large-scale surveillance study. Specifically, we increased the number of assay replicates, implemented a more robust RT-qPCR enzyme formulation, and adopted a more efficient method for extraction of total nucleic acid from blood specimens. We also report the development and analytical validation of ten new assays for use in the ANISA study. Based on these data, we revised the study-specific TACs for detection of 22 pathogens in NP/OP swabs and 12 pathogens in blood specimens as well as two control reactions (internal positive control and human nucleic acid control) for each specimen type. The cumulative improvements realized through these optimization studies will benefit ANISA and perhaps other studies utilizing multiple-pathogen detection approaches. These lessons may also contribute to the expansion of TAC technology to the clinical setting. Public Library of Science 2013-06-21 /pmc/articles/PMC3689704/ /pubmed/23805203 http://dx.doi.org/10.1371/journal.pone.0066183 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Diaz, Maureen H. Waller, Jessica L. Napoliello, Rebecca A. Islam, Md. Shahidul Wolff, Bernard J. Burken, Daniel J. Holden, Rhiannon L. Srinivasan, Velusamy Arvay, Melissa McGee, Lesley Oberste, M. Steven Whitney, Cynthia G. Schrag, Stephanie J. Winchell, Jonas M. Saha, Samir K.
spellingShingle	Diaz, Maureen H. Waller, Jessica L. Napoliello, Rebecca A. Islam, Md. Shahidul Wolff, Bernard J. Burken, Daniel J. Holden, Rhiannon L. Srinivasan, Velusamy Arvay, Melissa McGee, Lesley Oberste, M. Steven Whitney, Cynthia G. Schrag, Stephanie J. Winchell, Jonas M. Saha, Samir K. Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection
author_facet	Diaz, Maureen H. Waller, Jessica L. Napoliello, Rebecca A. Islam, Md. Shahidul Wolff, Bernard J. Burken, Daniel J. Holden, Rhiannon L. Srinivasan, Velusamy Arvay, Melissa McGee, Lesley Oberste, M. Steven Whitney, Cynthia G. Schrag, Stephanie J. Winchell, Jonas M. Saha, Samir K.
author_sort	Diaz, Maureen H.
title	Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection
title_short	Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection
title_full	Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection
title_fullStr	Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection
title_full_unstemmed	Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection
title_sort	optimization of multiple pathogen detection using the taqman array card: application for a population-based study of neonatal infection
description	Identification of etiology remains a significant challenge in the diagnosis of infectious diseases, particularly in resource-poor settings. Viral, bacterial, and fungal pathogens, as well as parasites, play a role for many syndromes, and optimizing a single diagnostic system to detect a range of pathogens is challenging. The TaqMan Array Card (TAC) is a multiple-pathogen detection method that has previously been identified as a valuable technique for determining etiology of infections and holds promise for expanded use in clinical microbiology laboratories and surveillance studies. We selected TAC for use in the Aetiology of Neonatal Infection in South Asia (ANISA) study for identifying etiologies of severe disease in neonates in Bangladesh, India, and Pakistan. Here we report optimization of TAC to improve pathogen detection and overcome technical challenges associated with use of this technology in a large-scale surveillance study. Specifically, we increased the number of assay replicates, implemented a more robust RT-qPCR enzyme formulation, and adopted a more efficient method for extraction of total nucleic acid from blood specimens. We also report the development and analytical validation of ten new assays for use in the ANISA study. Based on these data, we revised the study-specific TACs for detection of 22 pathogens in NP/OP swabs and 12 pathogens in blood specimens as well as two control reactions (internal positive control and human nucleic acid control) for each specimen type. The cumulative improvements realized through these optimization studies will benefit ANISA and perhaps other studies utilizing multiple-pathogen detection approaches. These lessons may also contribute to the expansion of TAC technology to the clinical setting.
publisher	Public Library of Science
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689704/
_version_	1611988655439609856

Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection

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