Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry
Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have clos...
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| Format: | Online |
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Public Library of Science
2012
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3387173/ |
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pubmed-33871732012-07-05 Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry Sampath, Rangarajan Mulholland, Niveen Blyn, Lawrence B. Massire, Christian Whitehouse, Chris A. Waybright, Nicole Harter, Courtney Bogan, Joseph Miranda, Mary Sue Smith, David Baldwin, Carson Wolcott, Mark Norwood, David Kreft, Rachael Frinder, Mark Lovari, Robert Yasuda, Irene Matthews, Heather Toleno, Donna Housley, Roberta Duncan, David Li, Feng Warren, Robin Eshoo, Mark W. Hall, Thomas A. Hofstadler, Steven A. Ecker, David J. Research Article Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. Public Library of Science 2012-06-29 /pmc/articles/PMC3387173/ /pubmed/22768032 http://dx.doi.org/10.1371/journal.pone.0036528 Text en This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. 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 |
Sampath, Rangarajan Mulholland, Niveen Blyn, Lawrence B. Massire, Christian Whitehouse, Chris A. Waybright, Nicole Harter, Courtney Bogan, Joseph Miranda, Mary Sue Smith, David Baldwin, Carson Wolcott, Mark Norwood, David Kreft, Rachael Frinder, Mark Lovari, Robert Yasuda, Irene Matthews, Heather Toleno, Donna Housley, Roberta Duncan, David Li, Feng Warren, Robin Eshoo, Mark W. Hall, Thomas A. Hofstadler, Steven A. Ecker, David J. |
| spellingShingle |
Sampath, Rangarajan Mulholland, Niveen Blyn, Lawrence B. Massire, Christian Whitehouse, Chris A. Waybright, Nicole Harter, Courtney Bogan, Joseph Miranda, Mary Sue Smith, David Baldwin, Carson Wolcott, Mark Norwood, David Kreft, Rachael Frinder, Mark Lovari, Robert Yasuda, Irene Matthews, Heather Toleno, Donna Housley, Roberta Duncan, David Li, Feng Warren, Robin Eshoo, Mark W. Hall, Thomas A. Hofstadler, Steven A. Ecker, David J. Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry |
| author_facet |
Sampath, Rangarajan Mulholland, Niveen Blyn, Lawrence B. Massire, Christian Whitehouse, Chris A. Waybright, Nicole Harter, Courtney Bogan, Joseph Miranda, Mary Sue Smith, David Baldwin, Carson Wolcott, Mark Norwood, David Kreft, Rachael Frinder, Mark Lovari, Robert Yasuda, Irene Matthews, Heather Toleno, Donna Housley, Roberta Duncan, David Li, Feng Warren, Robin Eshoo, Mark W. Hall, Thomas A. Hofstadler, Steven A. Ecker, David J. |
| author_sort |
Sampath, Rangarajan |
| title |
Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry |
| title_short |
Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry |
| title_full |
Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry |
| title_fullStr |
Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry |
| title_full_unstemmed |
Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry |
| title_sort |
comprehensive biothreat cluster identification by pcr/electrospray-ionization mass spectrometry |
| description |
Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. |
| publisher |
Public Library of Science |
| publishDate |
2012 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3387173/ |
| _version_ |
1611540337275174912 |