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Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing

BACKGROUND: The anthrax letter attacks of 2001 highlighted the need for rapid identification of biothreat agents not only for epidemiological surveillance of the intentional outbreak but also for implementing appropriate countermeasures, such as antibiotic treatment, in a timely manner to prevent fu...

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Autores principales: Chen, Peter E., Willner, Kristin M., Butani, Amy, Dorsey, Shakia, George, Matroner, Stewart, Andrew, Lentz, Shannon M., Cook, Christopher E., Akmal, Arya, Price, Lance B., Keim, Paul S., Mateczun, Alfred, Brahmbhatt, Trupti N., Bishop-Lilly, Kimberly A., Zwick, Michael E., Read, Timothy D., Sozhamannan, Shanmuga
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928293/
https://www.ncbi.nlm.nih.gov/pubmed/20811637
http://dx.doi.org/10.1371/journal.pone.0012397
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author Chen, Peter E.
Willner, Kristin M.
Butani, Amy
Dorsey, Shakia
George, Matroner
Stewart, Andrew
Lentz, Shannon M.
Cook, Christopher E.
Akmal, Arya
Price, Lance B.
Keim, Paul S.
Mateczun, Alfred
Brahmbhatt, Trupti N.
Bishop-Lilly, Kimberly A.
Zwick, Michael E.
Read, Timothy D.
Sozhamannan, Shanmuga
author_facet Chen, Peter E.
Willner, Kristin M.
Butani, Amy
Dorsey, Shakia
George, Matroner
Stewart, Andrew
Lentz, Shannon M.
Cook, Christopher E.
Akmal, Arya
Price, Lance B.
Keim, Paul S.
Mateczun, Alfred
Brahmbhatt, Trupti N.
Bishop-Lilly, Kimberly A.
Zwick, Michael E.
Read, Timothy D.
Sozhamannan, Shanmuga
author_sort Chen, Peter E.
collection PubMed
description BACKGROUND: The anthrax letter attacks of 2001 highlighted the need for rapid identification of biothreat agents not only for epidemiological surveillance of the intentional outbreak but also for implementing appropriate countermeasures, such as antibiotic treatment, in a timely manner to prevent further casualties. It is clear from the 2001 cases that survival may be markedly improved by administration of antimicrobial therapy during the early symptomatic phase of the illness; i.e., within 3 days of appearance of symptoms. Microbiological detection methods are feasible only for organisms that can be cultured in vitro and cannot detect all genetic modifications with the exception of antibiotic resistance. Currently available immuno or nucleic acid-based rapid detection assays utilize known, organism-specific proteins or genomic DNA signatures respectively. Hence, these assays lack the ability to detect novel natural variations or intentional genetic modifications that circumvent the targets of the detection assays or in the case of a biological attack using an antibiotic resistant or virulence enhanced Bacillus anthracis, to advise on therapeutic treatments. METHODOLOGY/PRINCIPAL FINDINGS: We show here that the Roche 454-based pyrosequencing can generate whole genome draft sequences of deep and broad enough coverage of a bacterial genome in less than 24 hours. Furthermore, using the unfinished draft sequences, we demonstrate that unbiased identification of known as well as heretofore-unreported genetic modifications that include indels and single nucleotide polymorphisms conferring antibiotic and phage resistances is feasible within the next 12 hours. CONCLUSIONS/SIGNIFICANCE: Second generation sequencing technologies have paved the way for sequence-based rapid identification of both known and previously undocumented genetic modifications in cultured, conventional and newly emerging biothreat agents. Our findings have significant implications in the context of whole genome sequencing-based routine clinical diagnostics as well as epidemiological surveillance of natural disease outbreaks caused by bacterial and viral agents.
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spelling pubmed-29282932010-09-01 Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing Chen, Peter E. Willner, Kristin M. Butani, Amy Dorsey, Shakia George, Matroner Stewart, Andrew Lentz, Shannon M. Cook, Christopher E. Akmal, Arya Price, Lance B. Keim, Paul S. Mateczun, Alfred Brahmbhatt, Trupti N. Bishop-Lilly, Kimberly A. Zwick, Michael E. Read, Timothy D. Sozhamannan, Shanmuga PLoS One Research Article BACKGROUND: The anthrax letter attacks of 2001 highlighted the need for rapid identification of biothreat agents not only for epidemiological surveillance of the intentional outbreak but also for implementing appropriate countermeasures, such as antibiotic treatment, in a timely manner to prevent further casualties. It is clear from the 2001 cases that survival may be markedly improved by administration of antimicrobial therapy during the early symptomatic phase of the illness; i.e., within 3 days of appearance of symptoms. Microbiological detection methods are feasible only for organisms that can be cultured in vitro and cannot detect all genetic modifications with the exception of antibiotic resistance. Currently available immuno or nucleic acid-based rapid detection assays utilize known, organism-specific proteins or genomic DNA signatures respectively. Hence, these assays lack the ability to detect novel natural variations or intentional genetic modifications that circumvent the targets of the detection assays or in the case of a biological attack using an antibiotic resistant or virulence enhanced Bacillus anthracis, to advise on therapeutic treatments. METHODOLOGY/PRINCIPAL FINDINGS: We show here that the Roche 454-based pyrosequencing can generate whole genome draft sequences of deep and broad enough coverage of a bacterial genome in less than 24 hours. Furthermore, using the unfinished draft sequences, we demonstrate that unbiased identification of known as well as heretofore-unreported genetic modifications that include indels and single nucleotide polymorphisms conferring antibiotic and phage resistances is feasible within the next 12 hours. CONCLUSIONS/SIGNIFICANCE: Second generation sequencing technologies have paved the way for sequence-based rapid identification of both known and previously undocumented genetic modifications in cultured, conventional and newly emerging biothreat agents. Our findings have significant implications in the context of whole genome sequencing-based routine clinical diagnostics as well as epidemiological surveillance of natural disease outbreaks caused by bacterial and viral agents. Public Library of Science 2010-08-25 /pmc/articles/PMC2928293/ /pubmed/20811637 http://dx.doi.org/10.1371/journal.pone.0012397 Text en 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. 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.
spellingShingle Research Article
Chen, Peter E.
Willner, Kristin M.
Butani, Amy
Dorsey, Shakia
George, Matroner
Stewart, Andrew
Lentz, Shannon M.
Cook, Christopher E.
Akmal, Arya
Price, Lance B.
Keim, Paul S.
Mateczun, Alfred
Brahmbhatt, Trupti N.
Bishop-Lilly, Kimberly A.
Zwick, Michael E.
Read, Timothy D.
Sozhamannan, Shanmuga
Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing
title Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing
title_full Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing
title_fullStr Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing
title_full_unstemmed Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing
title_short Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing
title_sort rapid identification of genetic modifications in bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928293/
https://www.ncbi.nlm.nih.gov/pubmed/20811637
http://dx.doi.org/10.1371/journal.pone.0012397
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