Rapid identification of genetic modifications in bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing

Peter E. Chen, Kristin M. Willner, Amy Butani, Shakia Dorsey, Matroner George, Andrew Stewart, Shannon M. Lentz, Christopher E. Cook, Arya Akmal, Lance B. Price, Paul S Keim, Alfred Mateczun, Trupti N. Brahmbhatt, Kimberly A. Bishop-Lilly, Michael E. Zwick, Timothy D. Read, Shanmuga Sozhamannan

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article numbere12397
JournalPLoS One
Volume5
Issue number8
DOIs
StatePublished - 2010

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Bacillus anthracis
Bacilli
Microbial Drug Resistance
genetic engineering
Disease Outbreaks
Genes
Genome
Anti-Bacterial Agents
Bacterial Genomes
Assays
Anthrax
genome
antibiotics
Bacteriophages
Nucleic Acids
Single Nucleotide Polymorphism
Virulence
assays
Technology
anthrax

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Chen, P. E., Willner, K. M., Butani, A., Dorsey, S., George, M., Stewart, A., ... Sozhamannan, S. (2010). Rapid identification of genetic modifications in bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing. PLoS One, 5(8), [e12397]. https://doi.org/10.1371/journal.pone.0012397

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.

In: PLoS One, Vol. 5, No. 8, e12397, 2010.

Research output: Contribution to journalArticle

Chen, PE, Willner, KM, Butani, A, Dorsey, S, George, M, Stewart, A, Lentz, SM, Cook, CE, Akmal, A, Price, LB, Keim, PS, Mateczun, A, Brahmbhatt, TN, Bishop-Lilly, KA, Zwick, ME, Read, TD & Sozhamannan, S 2010, 'Rapid identification of genetic modifications in bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing', PLoS One, vol. 5, no. 8, e12397. https://doi.org/10.1371/journal.pone.0012397
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. In: PLoS One. 2010 ; Vol. 5, No. 8.
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abstract = "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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