title: Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America.
authors.forename: Peter E
authors.initials: PE
authors.lastname: Chen
authors.forename: Kristin M
authors.initials: KM
authors.lastname: Willner
authors.forename: Amy
authors.initials: A
authors.lastname: Butani
authors.forename: Shakia
authors.initials: S
authors.lastname: Dorsey
authors.forename: Matroner
authors.initials: M
authors.lastname: George
authors.forename: Andrew
authors.initials: A
authors.lastname: Stewart
authors.forename: Shannon M
authors.initials: SM
authors.lastname: Lentz
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Cook
authors.forename: Arya
authors.initials: A
authors.lastname: Akmal
authors.forename: Lance B
authors.initials: LB
authors.lastname: Price
authors.forename: Paul S
authors.initials: PS
authors.lastname: Keim
authors.forename: Alfred
authors.initials: A
authors.lastname: Mateczun
authors.forename: Trupti N
authors.initials: TN
authors.lastname: Brahmbhatt
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Bishop-Lilly
authors.forename: Michael E
authors.initials: ME
authors.lastname: Zwick
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Read
authors.forename: Shanmuga
authors.initials: S
authors.lastname: Sozhamannan
mesh_terms: D001408:Bacillus anthracis / Q000187:drug effects / Q000235:genetics* / Q000502:physiology / Q000821:virology; D001435:Bacteriophages / Q000502:physiology; D002939:Ciprofloxacin / Q000494:pharmacology; D019295:Computational Biology; D024881:Drug Resistance, Bacterial / Q000235:genetics; D004917:Erythromycin / Q000494:pharmacology; D016680:Genome, Bacterial / Q000235:genetics*; D007753:Laboratories; D009154:Mutation; D017422:Sequence Analysis, DNA / Q000379:methods*; D013997:Time Factors
chemical_list: D002939:Ciprofloxacin; D004917:Erythromycin
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