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 genesmore »
- Authors:
-
- Northern Arizona Univ., Flagstaff, AZ (United States). Center for Microbial Genetics and Genomics
- US Army Medical Research Inst. of Infectious Diseases, Fort Detrick, MD (United States)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Bioscience Div.
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Div.
- US Army Medical Research Inst of Infecgious Diseases, Fort Detrick, MD (United States). Medical Countermeasures Technology, US Army Medical Research and Material Command
- Área Microbiología, Departamento de Patología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Centro Universitario, Mendoza (Argentina)
- Univ. of Helsinki (Finland). Dept. of Food Hygiene and Environmental Health
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE; U.S. Department of Homeland Security
- OSTI Identifier:
- 1626797
- Grant/Contract Number:
- AC52-06NA25396; HSHQDC-10-C-00139; DHS-2010-ST-108-000019
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity; Clostridium botulinum; Botulinum neurotoxin; Whole genome sequence; Comparative
Citation Formats
Williamson, Charles H. D., Sahl, Jason W., Smith, Theresa J., Xie, Gary, Foley, Brian T., Smith, Leonard A., Fernández, Rafael A., Lindström, Miia, Korkeala, Hannu, Keim, Paul, Foster, Jeffrey, and Hill, Karen. Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia. United States: N. p., 2016.
Web. doi:10.1186/s12864-016-2502-z.
Williamson, Charles H. D., Sahl, Jason W., Smith, Theresa J., Xie, Gary, Foley, Brian T., Smith, Leonard A., Fernández, Rafael A., Lindström, Miia, Korkeala, Hannu, Keim, Paul, Foster, Jeffrey, & Hill, Karen. Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia. United States. https://doi.org/10.1186/s12864-016-2502-z
Williamson, Charles H. D., Sahl, Jason W., Smith, Theresa J., Xie, Gary, Foley, Brian T., Smith, Leonard A., Fernández, Rafael A., Lindström, Miia, Korkeala, Hannu, Keim, Paul, Foster, Jeffrey, and Hill, Karen. Thu .
"Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia". United States. https://doi.org/10.1186/s12864-016-2502-z. https://www.osti.gov/servlets/purl/1626797.
@article{osti_1626797,
title = {Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia},
author = {Williamson, Charles H. D. and Sahl, Jason W. and Smith, Theresa J. and Xie, Gary and Foley, Brian T. and Smith, Leonard A. and Fernández, Rafael A. and Lindström, Miia and Korkeala, Hannu and Keim, Paul and Foster, Jeffrey and Hill, Karen},
abstractNote = {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.},
doi = {10.1186/s12864-016-2502-z},
journal = {BMC Genomics},
number = 1,
volume = 17,
place = {United States},
year = {Thu Mar 03 00:00:00 EST 2016},
month = {Thu Mar 03 00:00:00 EST 2016}
}
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