title: Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.
abstract: The rapid technological development in the field of parallel sequencing offers new opportunities when tracing and tracking microorganisms in the food and feed chain. If a bioterror organism is deliberately spread it is of crucial importance to get as much information as possible regarding the strain as fast as possible to aid the decision process and select suitable controls, tracing and tracking tools. A lot of efforts have been made to sequence multiple strains of potential bioterror organisms so there is a relatively large set of reference genomes available. This study is focused on how to use parallel sequencing for rapid phylogenomic analysis and screen for genetic modifications. A bioinformatic methodology has been developed to rapidly analyze sequence data with minimal post-processing. Instead of assembling the genome, defining genes, defining orthologous relations and calculating distances, the present method can achieve a similar high resolution directly from the raw sequence data. The method defines orthologous sequence reads instead of orthologous genes and the average similarity of the core genome (ASC) is calculated. The sequence reads from the core and from the non-conserved genomic regions can also be separated for further analysis. Finally, the comparison algorithm is used to visualize the phylogenomic diversity of the bacterial bioterror organisms Bacillus anthracis and Clostridium botulinum using heat plot diagrams.
authors.affiliation: Department of Bacteriology, National Veterinary Institute SVA, SE-751 89 Uppsala, Sweden. bo.segerman@sva.se
authors.forename: Bo
authors.initials: B
authors.lastname: Segerman
authors.forename: Dario
authors.initials: D
authors.lastname: De Medici
authors.forename: Monika
authors.initials: M
authors.lastname: Ehling Schulz
authors.forename: Patrick
authors.initials: P
authors.lastname: Fach
authors.forename: Lucia
authors.initials: L
authors.lastname: Fenicia
authors.forename: Martina
authors.initials: M
authors.lastname: Fricker
authors.forename: Peter
authors.initials: P
authors.lastname: Wielinga
authors.forename: Bart
authors.initials: B
authors.lastname: Van Rotterdam
authors.forename: Rickard
authors.initials: R
authors.lastname: Knutsson
mesh_terms: D000465:Algorithms; D000821:Animal Feed / Q000382:microbiology; D001408:Bacillus anthracis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D023482:Bioterrorism; D003014:Clostridium botulinum / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D005516:Food Microbiology / Q000379:methods*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D005810:Multigene Family; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012984:Software