title: Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia.
abstract: BACKGROUND
  Clostridium botulinum is a diverse group of bacteria characterized by the production of botulinum neurotoxin. Botulinum neurotoxins are classified into serotypes (BoNT/A-G), which are produced by six species/Groups of Clostridia, but the genetic background of the bacteria remains poorly understood. The purpose of this study was to use comparative genomics to provide insights into the genetic diversity and evolutionary history of bacteria that produce the potent botulinum neurotoxin.
  
  
  RESULTS
  Comparative genomic analyses of over 170 Clostridia genomes, including our draft genome assemblies for 59 newly sequenced Clostridia strains from six continents and publicly available genomic data, provided in-depth insights into the diversity and distribution of BoNT-producing bacteria. These newly sequenced strains included Group I and II strains that express BoNT/A,/B,/E, or/F as well as bivalent strains. BoNT-producing Clostridia and closely related Clostridia species were delineated with a variety of methods including 16S rRNA gene, concatenated marker genes, core genome and concatenated multi-locus sequencing typing (MLST) gene phylogenies that related whole genome sequenced strains to publicly available strains and sequence types. These analyses illustrated the phylogenetic diversity in each Group and the diversity of genomic backgrounds that express the same toxin type or subtype. Comparisons of the botulinum neurotoxin genes did not identify novel toxin types or variants.
  
  
  CONCLUSIONS
  This study represents one of the most comprehensive analyses of whole genome sequence data for Group I and II BoNT-producing strains. Read data and draft genome assemblies generated for 59 isolates will be a resource to the research community. Core genome phylogenies proved to be a powerful tool for differentiating BoNT-producing strains and can provide a framework for the study of these bacteria. Comparative genomic analyses of Clostridia species illustrate the diversity of botulinum-neurotoxin-producing strains and the plasticity of the genomic backgrounds in which bont genes are found.
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA. Chase.Williamson@nau.edu.
authors.forename: Charles H D
authors.initials: CH
authors.lastname: Williamson
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA. Jason.Sahl@nau.edu.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Sahl
authors.affiliation: Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA. theresa.j.smith.civ@mail.mil.
authors.forename: Theresa J
authors.initials: TJ
authors.lastname: Smith
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA. xie@lanl.gov.
authors.forename: Gary
authors.initials: G
authors.lastname: Xie
authors.affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA. btf@lanl.gov.
authors.forename: Brian T
authors.initials: BT
authors.lastname: Foley
authors.affiliation: Medical Countermeasures Technology, United States Army Medical Research and Material Command, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA. leonard.a.smith1.civ@mail.mil.
authors.forename: Leonard A
authors.initials: LA
authors.lastname: Smith
authors.affiliation: Área Microbiología, Departamento de Patología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Centro Universitario, (5500), Mendoza, Argentina. rafael.fernandez@fcm.uncu.edu.ar.
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Fernández
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland. miia.lindstrom@helsinki.fi.
authors.forename: Miia
authors.initials: M
authors.lastname: Lindström
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland. hannu.korkeala@helsinki.fi.
authors.forename: Hannu
authors.initials: H
authors.lastname: Korkeala
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA. Paul.Keim@nau.edu.
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA. Jeff.Foster@unh.edu.|Present Address: Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA. Jeff.Foster@unh.edu.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Foster
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA. khill@lanl.gov.
authors.forename: Karen
authors.initials: K
authors.lastname: Hill
mesh_terms: D015373:Bacterial Typing Techniques; D001905:Botulinum Toxins / Q000235:genetics*; D003013:Clostridium / Q000145:classification / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D005810:Multigene Family; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D001905:Botulinum Toxins