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Smith TJ, Williamson CHD, Hill KK, Johnson SL, Xie G, Anniballi F, Auricchio B, Fernández RA, Caballero PA, Keim P, Sahl JW. The Distinctive Evolution of orfX Clostridium parabotulinum Strains and Their Botulinum Neurotoxin Type A and F Gene Clusters Is Influenced by Environmental Factors and Gene Interactions via Mobile Genetic Elements. Front Microbiol 2021; 12:566908. [PMID: 33716993 PMCID: PMC7952441 DOI: 10.3389/fmicb.2021.566908] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/08/2021] [Indexed: 12/30/2022] Open
Abstract
Of the seven currently known botulinum neurotoxin-producing species of Clostridium, C. parabotulinum, or C. botulinum Group I, is the species associated with the majority of human botulism cases worldwide. Phylogenetic analysis of these bacteria reveals a diverse species with multiple genomic clades. The neurotoxins they produce are also diverse, with over 20 subtypes currently represented. The existence of different bont genes within very similar genomes and of the same bont genes/gene clusters within different bacterial variants/species indicates that they have evolved independently. The neurotoxin genes are associated with one of two toxin gene cluster types containing either hemagglutinin (ha) genes or orfX genes. These genes may be located within the chromosome or extrachromosomal elements such as large plasmids. Although BoNT-producing C parabotulinum bacteria are distributed globally, they are more ubiquitous in certain specific geographic regions. Notably, northern hemisphere strains primarily contain ha gene clusters while southern hemisphere strains have a preponderance of orfX gene clusters. OrfX C. parabotulinum strains constitute a subset of this species that contain highly conserved bont gene clusters having a diverse range of bont genes. While much has been written about strains with ha gene clusters, less attention has been devoted to those with orfX gene clusters. The recent sequencing of 28 orfX C. parabotulinum strains and the availability of an additional 91 strains for analysis provides an opportunity to compare genomic relationships and identify unique toxin gene cluster characteristics and locations within this species subset in depth. The mechanisms behind the independent processes of bacteria evolution and generation of toxin diversity are explored through the examination of bacterial relationships relating to source locations and evidence of horizontal transfer of genetic material among different bacterial variants, particularly concerning bont gene clusters. Analysis of the content and locations of the bont gene clusters offers insights into common mechanisms of genetic transfer, chromosomal integration, and development of diversity among these genes.
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Affiliation(s)
- Theresa J Smith
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Charles H D Williamson
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Karen K Hill
- Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Gary Xie
- Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Fabrizio Anniballi
- Department of Food Safety, Nutrition and Veterinary Public Health, National Reference Centre for Botulism, Istituto Superiore di Sanità, Rome, Italy
| | - Bruna Auricchio
- Department of Food Safety, Nutrition and Veterinary Public Health, National Reference Centre for Botulism, Istituto Superiore di Sanità, Rome, Italy
| | - Rafael A Fernández
- Área Microbiología, Departamento de Patología, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Patricia A Caballero
- Área Microbiología, Departamento de Patología, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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Brunt J, van Vliet AHM, Carter AT, Stringer SC, Amar C, Grant KA, Godbole G, Peck MW. Diversity of the Genomes and Neurotoxins of Strains of Clostridium botulinum Group I and Clostridium sporogenes Associated with Foodborne, Infant and Wound Botulism. Toxins (Basel) 2020; 12:toxins12090586. [PMID: 32932818 PMCID: PMC7551954 DOI: 10.3390/toxins12090586] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 12/23/2022] Open
Abstract
Clostridium botulinum Group I and Clostridium sporogenes are closely related bacteria responsible for foodborne, infant and wound botulism. A comparative genomic study with 556 highly diverse strains of C. botulinum Group I and C. sporogenes (including 417 newly sequenced strains) has been carried out to characterise the genetic diversity and spread of these bacteria and their neurotoxin genes. Core genome single-nucleotide polymorphism (SNP) analysis revealed two major lineages; C. botulinum Group I (most strains possessed botulinum neurotoxin gene(s) of types A, B and/or F) and C. sporogenes (some strains possessed a type B botulinum neurotoxin gene). Both lineages contained strains responsible for foodborne, infant and wound botulism. A new C. sporogenes cluster was identified that included five strains with a gene encoding botulinum neurotoxin sub-type B1. There was significant evidence of horizontal transfer of botulinum neurotoxin genes between distantly related bacteria. Population structure/diversity have been characterised, and novel associations discovered between whole genome lineage, botulinum neurotoxin sub-type variant, epidemiological links to foodborne, infant and wound botulism, and geographic origin. The impact of genomic and physiological variability on the botulism risk has been assessed. The genome sequences are a valuable resource for future research (e.g., pathogen biology, evolution of C. botulinum and its neurotoxin genes, improved pathogen detection and discrimination), and support enhanced risk assessments and the prevention of botulism.
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Affiliation(s)
- Jason Brunt
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
- Gut Health and Food Safety, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (A.T.C.); (S.C.S.)
- Correspondence: (J.B.); (M.W.P.)
| | - Arnoud H. M. van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK;
| | - Andrew T. Carter
- Gut Health and Food Safety, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (A.T.C.); (S.C.S.)
| | - Sandra C. Stringer
- Gut Health and Food Safety, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (A.T.C.); (S.C.S.)
| | - Corinne Amar
- Gastrointestinal Pathogens Unit, National Infection Service, Public Health England, London NW9 5EQ, UK; (C.A.); (K.A.G.); (G.G.)
| | - Kathie A. Grant
- Gastrointestinal Pathogens Unit, National Infection Service, Public Health England, London NW9 5EQ, UK; (C.A.); (K.A.G.); (G.G.)
| | - Gauri Godbole
- Gastrointestinal Pathogens Unit, National Infection Service, Public Health England, London NW9 5EQ, UK; (C.A.); (K.A.G.); (G.G.)
| | - Michael W. Peck
- Gut Health and Food Safety, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (A.T.C.); (S.C.S.)
- Correspondence: (J.B.); (M.W.P.)
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Abstract
C. botulinum Groups I and II form botulinum neurotoxin and cause foodborne botulism. Increased knowledge of C. botulinum Group I and II genomes and neurotoxin diversity. Impact on food safety via improved surveillance and tracing/tracking during outbreaks. New insights into C. botulinum biology, food chain transmission, evolution.
The deadly botulinum neurotoxin formed by Clostridium botulinum is the causative agent of foodborne botulism. The increasing availability of C. botulinum genome sequences is starting to allow the genomic diversity of C. botulinum Groups I and II and their neurotoxins to be characterised. This information will impact on microbiological food safety through improved surveillance and tracing/tracking during outbreaks, and a better characterisation of C. botulinum Groups I and II, including the risk presented, and new insights into their biology, food chain transmission, and evolution.
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Williamson CHD, Sahl JW, Smith TJ, Xie G, Foley BT, Smith LA, Fernández RA, Lindström M, Korkeala H, Keim P, Foster J, Hill K. Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia. BMC Genomics 2016; 17:180. [PMID: 26939550 PMCID: PMC4778365 DOI: 10.1186/s12864-016-2502-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/18/2016] [Indexed: 11/24/2022] Open
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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2502-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charles H D Williamson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Jason W Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Theresa J Smith
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA.
| | - Gary Xie
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | - Brian T Foley
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | - Leonard A Smith
- 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.
| | - Rafael A Fernández
- Área Microbiología, Departamento de Patología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Centro Universitario, (5500), Mendoza, Argentina.
| | - Miia Lindström
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
| | - Hannu Korkeala
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Jeffrey Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA. .,Present Address: Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
| | - Karen Hill
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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Jaakkola K, Somervuo P, Korkeala H. Comparative Genomic Hybridization Analysis of Yersinia enterocolitica and Yersinia pseudotuberculosis Identifies Genetic Traits to Elucidate Their Different Ecologies. BIOMED RESEARCH INTERNATIONAL 2015; 2015:760494. [PMID: 26605338 PMCID: PMC4641178 DOI: 10.1155/2015/760494] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/28/2015] [Indexed: 12/22/2022]
Abstract
Enteropathogenic Yersinia enterocolitica and Yersinia pseudotuberculosis are both etiological agents for intestinal infection known as yersiniosis, but their epidemiology and ecology bear many differences. Swine are the only known reservoir for Y. enterocolitica 4/O:3 strains, which are the most common cause of human disease, while Y. pseudotuberculosis has been isolated from a variety of sources, including vegetables and wild animals. Infections caused by Y. enterocolitica mainly originate from swine, but fresh produce has been the source for widespread Y. pseudotuberculosis outbreaks within recent decades. A comparative genomic hybridization analysis with a DNA microarray based on three Yersinia enterocolitica and four Yersinia pseudotuberculosis genomes was conducted to shed light on the genomic differences between enteropathogenic Yersinia. The hybridization results identified Y. pseudotuberculosis strains to carry operons linked with the uptake and utilization of substances not found in living animal tissues but present in soil, plants, and rotting flesh. Y. pseudotuberculosis also harbors a selection of type VI secretion systems targeting other bacteria and eukaryotic cells. These genetic traits are not found in Y. enterocolitica, and it appears that while Y. pseudotuberculosis has many tools beneficial for survival in varied environments, the Y. enterocolitica genome is more streamlined and adapted to their preferred animal reservoir.
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Affiliation(s)
- Kaisa Jaakkola
- Department of Food Hygiene and Environmental Health, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland
| | - Panu Somervuo
- Department of Food Hygiene and Environmental Health, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland
| | - Hannu Korkeala
- Department of Food Hygiene and Environmental Health, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland
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Smith TJ, Hill KK, Raphael BH. Historical and current perspectives on Clostridium botulinum diversity. Res Microbiol 2015; 166:290-302. [PMID: 25312020 PMCID: PMC11302483 DOI: 10.1016/j.resmic.2014.09.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 09/24/2014] [Accepted: 09/24/2014] [Indexed: 11/19/2022]
Abstract
For nearly one hundred years, researchers have attempted to categorize botulinum neurotoxin-producing clostridia and the toxins that they produce according to biochemical characterizations, serological comparisons, and genetic analyses. Throughout this period the bacteria and their toxins have defied such attempts at categorization. Below is a description of both historic and current Clostridium botulinum strain and neurotoxin information that illustrates how each new finding has significantly added to the knowledge of the botulinum neurotoxin-containing clostridia and their diversity.
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Affiliation(s)
- Theresa J Smith
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Karen K Hill
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian H Raphael
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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Marshall KM, Nowaczyk L, Raphael BH, Skinner GE, Rukma Reddy N. Identification and genetic characterization of Clostridium botulinum serotype A strains from commercially pasteurized carrot juice. Food Microbiol 2014; 44:149-55. [PMID: 25084657 PMCID: PMC11302426 DOI: 10.1016/j.fm.2014.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/23/2014] [Accepted: 05/23/2014] [Indexed: 12/29/2022]
Abstract
Clostridium botulinum is an important foodborne pathogen capable of forming heat resistant endospores and producing deadly botulinum neurotoxins (BoNTs). In 2006, C. botulinum was responsible for an international outbreak of botulism attributed to the consumption of commercially pasteurized carrot juice. The purpose of this study was to isolate and characterize strains of C. botulinum from the adulterated product. Carrot juice bottles retrieved from the manufacturing facility were analyzed for the presence of BoNT and BoNT-producing isolates using DIG-ELISA. Toxigenic isolates from the carrot juice were analyzed using pulsed-field gel electrophoresis (PFGE) and DNA microarray analysis to determine their genetic relatedness to the original outbreak strains CDC51348 and CDC51303. PFGE revealed that isolates CJ4-1 and CJ10-1 shared an identical pulsotype with strain CDC51303, whereas isolate CJ5-1 displayed a unique restriction banding pattern. DNA microarray analysis identified several phage related genes unique to strain CJ5-1, and Southern hybridization analysis of XhoI digested and nondigested DNA showed their chromosomal location, while a homolog to pCLI_A009 of plasmid pCLI of C. botulinum serotype Langeland F, was located on a small plasmid. The acquisition or loss of bacteriophages and other mobile genetic elements among C. botulinum strains has epidemiological and evolutionary implications.
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Affiliation(s)
- Kristin M Marshall
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, 6502 South Archer Road, Bedford Park, IL 60501, USA.
| | - Louis Nowaczyk
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, 6502 South Archer Road, Bedford Park, IL 60501, USA.
| | - Brian H Raphael
- Centers for Disease Control and Prevention, 1600 Clifton Road, NE, Atlanta, GA 30329, USA.
| | - Guy E Skinner
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, 6502 South Archer Road, Bedford Park, IL 60501, USA.
| | - N Rukma Reddy
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, 6502 South Archer Road, Bedford Park, IL 60501, USA.
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Dahlsten E, Lindström M, Korkeala H. Mechanisms of food processing and storage-related stress tolerance in Clostridium botulinum. Res Microbiol 2014; 166:344-52. [PMID: 25303833 DOI: 10.1016/j.resmic.2014.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/26/2014] [Accepted: 09/26/2014] [Indexed: 12/28/2022]
Abstract
Vegetative cultures of Clostridium botulinum produce the extremely potent botulinum neurotoxin, and may jeopardize the safety of foods unless sufficient measures to prevent growth are applied. Minimal food processing relies on combinations of mild treatments, primarily to avoid deterioration of the sensory qualities of the food. Tolerance of C. botulinum to minimal food processing is well characterized. However, data on effects of successive treatments on robustness towards further processing is lacking. Developments in genetic manipulation tools and the availability of annotated genomes have allowed identification of genetic mechanisms involved in stress tolerance of C. botulinum. Most studies focused on low temperature, and the importance of various regulatory mechanisms in cold tolerance of C. botulinum has been demonstrated. Furthermore, novel roles in cold tolerance were shown for metabolic pathways under the control of these regulators. A role for secondary oxidative stress in tolerance to extreme temperatures has been proposed. Additionally, genetic mechanisms related to tolerance to heat, low pH, and high salinity have been characterized. Data on genetic stress-related mechanisms of psychrotrophic Group II C. botulinum strains are scarce; these mechanisms are of interest for food safety research and should thus be investigated. This minireview encompasses the importance of C. botulinum as a food safety hazard and its central physiological characteristics related to food-processing and storage-related stress. Special attention is given to recent findings considering genetic mechanisms C. botulinum utilizes in detecting and countering these adverse conditions.
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Affiliation(s)
- Elias Dahlsten
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P. O. Box 66, FI-00014 Helsinki, Finland.
| | - Miia Lindström
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P. O. Box 66, FI-00014 Helsinki, Finland.
| | - Hannu Korkeala
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P. O. Box 66, FI-00014 Helsinki, Finland.
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Whole-genome single-nucleotide-polymorphism analysis for discrimination of Clostridium botulinum group I strains. Appl Environ Microbiol 2014; 80:2125-32. [PMID: 24463972 DOI: 10.1128/aem.03934-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium botulinum is a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA(+) OrfX(-)) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA(-) OrfX(+)) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producing C. botulinum strains: two strains with the HA(+) OrfX(-) cluster (69A and 32A) and one strain with the HA(-) OrfX(+) cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly available C. botulinum group I strains revealed five distinct lineages. Strains 69A and 32A clustered with the C. botulinum type A1 Hall group, and strain CDC297 clustered with the C. botulinum type Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination of C. botulinum group I strains and demonstrates the utility of this analysis in quickly differentiating C. botulinum strains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.
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Popoff MR, Bouvet P. Genetic characteristics of toxigenic Clostridia and toxin gene evolution. Toxicon 2013; 75:63-89. [DOI: 10.1016/j.toxicon.2013.05.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 04/30/2013] [Accepted: 05/08/2013] [Indexed: 12/14/2022]
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The cold-induced two-component system CBO0366/CBO0365 regulates metabolic pathways with novel roles in group I Clostridium botulinum ATCC 3502 cold tolerance. Appl Environ Microbiol 2013; 80:306-19. [PMID: 24162575 DOI: 10.1128/aem.03173-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The two-component system CBO0366/CBO0365 was recently demonstrated to have a role in cold tolerance of group I Clostridium botulinum ATCC 3502. The mechanisms under its control, ultimately resulting in increased sensitivity to low temperature, are unknown. A transcriptomic analysis with DNA microarrays was performed to identify the differences in global gene expression patterns of the wild-type ATCC 3502 and a derivative mutant with insertionally inactivated cbo0365 at 37 and 15°C. Altogether, 150 or 141 chromosomal coding sequences (CDSs) were found to be differently expressed in the cbo0365 mutant at 37 or 15°C, respectively, and thus considered to be under the direct or indirect transcriptional control of the response regulator CBO0365. Of the differentially expressed CDSs, expression of 141 CDSs was similarly affected at both temperatures investigated, suggesting that the putative CBO0365 regulon was practically not affected by temperature. The regulon involved genes related to acetone-butanol-ethanol (ABE) fermentation, motility, arsenic resistance, and phosphate uptake and transport. Deteriorated growth at 17°C was observed for mutants with disrupted ABE fermentation pathway components (crt, bcd, bdh, and ctfA), arsenic detoxifying machinery components (arsC and arsR), or phosphate uptake mechanism components (phoT), suggesting roles for these mechanisms in cold tolerance of group I C. botulinum. Electrophoretic mobility shift assays showed recombinant CBO0365 to bind to the promoter regions of crt, arsR, and phoT, as well as to the promoter region of its own operon, suggesting direct DNA-binding transcriptional activation or repression as a means for CBO0365 in regulating these operons. The results provide insight to the mechanisms group I C. botulinum utilizes in coping with cold.
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Vanhomwegen J, Berthet N, Mazuet C, Guigon G, Vallaeys T, Stamboliyska R, Dubois P, Kennedy GC, Cole ST, Caro V, Manuguerra JC, Popoff MR. Application of high-density DNA resequencing microarray for detection and characterization of botulinum neurotoxin-producing clostridia. PLoS One 2013; 8:e67510. [PMID: 23818983 PMCID: PMC3688605 DOI: 10.1371/journal.pone.0067510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 05/22/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Clostridium botulinum and related clostridia express extremely potent toxins known as botulinum neurotoxins (BoNTs) that cause severe, potentially lethal intoxications in humans. These BoNT-producing bacteria are categorized in seven major toxinotypes (A through G) and several subtypes. The high diversity in nucleotide sequence and genetic organization of the gene cluster encoding the BoNT components poses a great challenge for the screening and characterization of BoNT-producing strains. METHODOLOGY/PRINCIPAL FINDINGS In the present study, we designed and evaluated the performances of a resequencing microarray (RMA), the PathogenId v2.0, combined with an automated data approach for the simultaneous detection and characterization of BoNT-producing clostridia. The unique design of the PathogenID v2.0 array allows the simultaneous detection and characterization of 48 sequences targeting the BoNT gene cluster components. This approach allowed successful identification and typing of representative strains of the different toxinotypes and subtypes, as well as the neurotoxin-producing C. botulinum strain in a naturally contaminated food sample. Moreover, the method allowed fine characterization of the different neurotoxin gene cluster components of all studied strains, including genomic regions exhibiting up to 24.65% divergence with the sequences tiled on the arrays. CONCLUSIONS/SIGNIFICANCE The severity of the disease demands rapid and accurate means for performing risk assessments of BoNT-producing clostridia and for tracing potentials sources of contamination in outbreak situations. The RMA approach constitutes an essential higher echelon component in a diagnostics and surveillance pipeline. In addition, it is an important asset to characterise potential outbreak related strains, but also environment isolates, in order to obtain a better picture of the molecular epidemiology of BoNT-producing clostridia.
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Affiliation(s)
- Jessica Vanhomwegen
- Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France
| | - Nicolas Berthet
- Institut Pasteur, Epidemiology and Pathophysiology of Oncogenic Viruses, Paris, France
- CNRS, UMR3569, Paris, France
| | | | - Ghislaine Guigon
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Tatiana Vallaeys
- CNRS – CC093 Université Montpellier II, UMR5119 Ecosystèmes lagunaires, Montpellier, France
| | - Rayna Stamboliyska
- Department of Biology II, University of Munich (LMU), Planegg-Martinsried, Germany
| | - Philippe Dubois
- Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France
| | - Giulia C. Kennedy
- Department of Research and Development, Veracyte, Inc., South San Francisco, California, United States of America
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
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Stringer SC, Carter AT, Webb MD, Wachnicka E, Crossman LC, Sebaihia M, Peck MW. Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum. BMC Genomics 2013; 14:333. [PMID: 23679073 PMCID: PMC3672017 DOI: 10.1186/1471-2164-14-333] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 05/14/2013] [Indexed: 11/17/2022] Open
Abstract
Background Clostridium botulinum is a group of four physiologically and phylogenetically distinct bacteria that produce botulinum neurotoxin. While studies have characterised variability between strains of Group I (proteolytic) C. botulinum, the genetic and physiological variability and relationships between strains within Group II (non-proteolytic) C. botulinum are not well understood. In this study the genome of Group II strain C. botulinum Eklund 17B (NRP) was sequenced and used to construct a whole genome DNA microarray. This was used in a comparative genomic indexing study to compare the relatedness of 43 strains of Group II C. botulinum (14 type B, 24 type E and 5 type F). These results were compared with characteristics determined from physiological tests. Results Whole genome indexing showed that strains of Group II C. botulinum isolated from a wide variety of environments over more than 75 years clustered together indicating the genetic background of Group II C. botulinum is stable. Further analysis showed that strains forming type B or type F toxin are closely related with only toxin cluster genes targets being unique to either type. Strains producing type E toxin formed a separate subset. Carbohydrate fermentation tests supported the observation that type B and F strains form a separate subset to type E strains. All the type F strains and most of type B strains produced acid from amylopectin, amylose and glycogen whereas type E strains did not. However, these two subsets did not differ strongly in minimum growth temperature or maximum NaCl concentration for growth. No relationship was found between tellurite resistance and toxin type despite all the tested type B and type F strains carrying tehB, while the sequence was absent or diverged in all type E strains. Conclusions Although Group II C. botulinum form a tight genetic group, genomic and physiological analysis indicates there are two distinct subsets within this group. All type B strains and type F strains are in one subset and all type E strains in the other.
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Affiliation(s)
- Sandra C Stringer
- Institute of Food Research (IFR), Norwich Research Park, Colney, Norwich NR4 7UA, UK.
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Singh AK, Stanker LH, Sharma SK. Botulinum neurotoxin: where are we with detection technologies? Crit Rev Microbiol 2012; 39:43-56. [PMID: 22676403 DOI: 10.3109/1040841x.2012.691457] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Because of its high toxicity, botulinum neurotoxin (BoNT) poses a significant risk to humans and it represents a possible biological warfare agent. Nevertheless, BoNT serotypes A and B are considered an effective treatment for a variety of neurological disorders. The growing applicability of BoNT as a drug, and its potential use as a biological threat agent, highlight the urgent need to develop sensitive detection assays and therapeutic counter measures. In the last decade, significant progress has been made in BoNT detection technologies but none have fully replaced the mouse lethality assay, the current "gold standard". Recently, new advances in robotics and the availability of new reagents have allowed development of methods for rapid toxin analysis. These technologies while promising need further refinement.
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Affiliation(s)
- Ajay K Singh
- Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
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15
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Raphael BH. Exploring genomic diversity in Clostridium botulinum using DNA microarrays. THE BOTULINUM JOURNAL 2012; 2:99-108. [PMID: 39130517 PMCID: PMC11310924 DOI: 10.1504/tbj.2012.050195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Rapid increases in the number of available Clostridium botulinum genome sequences have permitted the development of new molecular subtyping methods for this organism. Our laboratory has developed various DNA microarrays in an effort to differentiate strains based on differences in gene content. This review will focus on both high density comparative genomic hybridisation (CGH) microarrays and various focused (low density) oligonucleotide spotted microarrays. Comparison of gene content using DNA microarrays provides investigators with the ability to simultaneously differentiate unrelated strains and to identify strain variable genes. Such genes may play important roles in the pathogenesis, growth, and survival of this organism. Moreover, probes may be optimised as new genome sequences become available leading to improvements in the ability to characterise novel or unusual strains.
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Affiliation(s)
- Brian H Raphael
- National Botulism Laboratory Preparedness Team, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G-29, Atlanta, GA 30329, USA
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16
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Peck MW, Stringer SC, Carter AT. Clostridium botulinum in the post-genomic era. Food Microbiol 2010; 28:183-91. [PMID: 21315972 DOI: 10.1016/j.fm.2010.03.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 03/11/2010] [Accepted: 03/12/2010] [Indexed: 01/11/2023]
Abstract
Foodborne botulism is a severe neuroparalytic disease caused by consumption of botulinum neurotoxin formed by strains of proteolytic Clostridium botulinum and non-proteolytic C. botulinum during their growth in food. The botulinum neurotoxin is the most potent substance known, with as little as 30-100 ng potentially fatal, and consumption of just a few milligrams of neurotoxin-containing food is likely to be sufficient to cause illness and potentially death. In order to minimise the foodborne botulism hazard, it is necessary to extend understanding of the biology of these bacteria. This process has been recently advanced by genome sequencing and subsequent analysis. In addition to neurotoxin formation, endospore formation is also critical to the success of proteolytic C. botulinum and non-proteolytic C. botulinum as foodborne pathogens. The endospores are highly resistant, and enable survival of adverse treatments such as heating. To better control the botulinum neurotoxin-forming clostridia, it is important to understand spore resistance mechanisms, and the physiological processes involved in germination and lag phase during recovery from this dormant state.
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Affiliation(s)
- Michael W Peck
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK.
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17
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Artin I, Mason DR, Pin C, Schelin J, Peck MW, Holst E, Rådström P, Carter AT. Effects of carbon dioxide on growth of proteolytic Clostridium botulinum, its ability to produce neurotoxin, and its transcriptome. Appl Environ Microbiol 2010; 76:1168-72. [PMID: 20038699 PMCID: PMC2820955 DOI: 10.1128/aem.02247-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 12/14/2009] [Indexed: 01/02/2023] Open
Abstract
The antimicrobial gas carbon dioxide is frequently used in modified atmosphere packaging. In the present study, the effects of CO2 (10 to 70%, vol/vol) on gene expression (measured using quantitative reverse transcription-PCR and a whole-genome DNA microarray) and neurotoxin formation (measured using an enzyme-linked immunosorbent assay [ELISA]) by proteolytic Clostridium botulinum type A1 strain ATCC 3502 were studied during the growth cycle. Interestingly, in marked contrast to the situation with nonproteolytic C. botulinum types B and E, CO2 had little effect on any of these parameters. At all CO2 concentrations, relative expression of neurotoxin cluster genes peaked in the transition between exponential and stationary phases, with evidence of a second rise in expression in late stationary phase. Microarray analysis enabled identification of coding sequences whose expression profiles matched those of the neurotoxin cluster. Further research is needed to determine whether these are connected to neurotoxin formation or are merely growth phase associated.
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Affiliation(s)
- Ingrid Artin
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - David R. Mason
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Carmen Pin
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jenny Schelin
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Michael W. Peck
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Elisabet Holst
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Peter Rådström
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Andrew T. Carter
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Raphael BH, Joseph LA, McCroskey LM, Lúquez C, Maslanka SE. Detection and differentiation of Clostridium botulinum type A strains using a focused DNA microarray. Mol Cell Probes 2010; 24:146-53. [PMID: 20056143 DOI: 10.1016/j.mcp.2009.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/11/2009] [Accepted: 12/24/2009] [Indexed: 10/20/2022]
Abstract
A focused oligonucleotide microarray featuring 62 probes targeting strain variable regions of the Clostridium botulinum strain ATCC 3502 genome sequence was developed to differentiate C. botulinum type A strains. The strain variable regions were selected from deletions identified among a panel of 10 type A strains compared to the strain ATCC 3502 genome sequence using high density comparative genomic hybridization microarrays. The focused microarray also featured specific probes for the detection of the neurotoxin genes of various serotypes (A-G), toxin gene cluster components (ha70 and orfX1), and fldB as a marker for proteolytic clostridia (Group I). Eight pairs of strains selected from separate type A botulism outbreaks were included in the 27 subtype A1-A4 strains examined in this study. Each outbreak related strain pair consisted of strains isolated from different sources (stool and food). Of the eight outbreak related strain pairs, six groups of strains with indistinguishable hybridization patterns were identified. Outbreak related strains were shown to have identical hybridization patterns. Strain pairs from three separate outbreaks involving strains harboring both the type A neurotoxin gene (bont/A) and an unexpressed type B neurotoxin gene (bont/B) shared the same probe hybridization profile. The focused microarray format provides a rapid approach for neurotoxin gene detection and preliminary determination of the relatedness of strains isolated from different sources.
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Affiliation(s)
- Brian H Raphael
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
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Hill KK, Xie G, Foley BT, Smith TJ, Munk AC, Bruce D, Smith LA, Brettin TS, Detter JC. Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. BMC Biol 2009; 7:66. [PMID: 19804621 PMCID: PMC2764570 DOI: 10.1186/1741-7007-7-66] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 10/05/2009] [Indexed: 12/04/2022] Open
Abstract
Background Clostridium botulinum is a taxonomic designation for at least four diverse species that are defined by the expression of one (monovalent) or two (bivalent) of seven different C. botulinum neurotoxins (BoNTs, A-G). The four species have been classified as C. botulinum Groups I-IV. The presence of bont genes in strains representing the different Groups is probably the result of horizontal transfer of the toxin operons between the species. Results Chromosome and plasmid sequences of several C. botulinum strains representing A, B, E and F serotypes and a C. butyricum type E strain were compared to examine their genomic organization, or synteny, and the location of the botulinum toxin complex genes. These comparisons identified synteny among proteolytic (Group I) strains or nonproteolytic (Group II) strains but not between the two Groups. The bont complex genes within the strains examined were not randomly located but found within three regions of the chromosome or in two specific sites within plasmids. A comparison of sequences from a Bf strain revealed homology to the plasmid pCLJ with similar locations for the bont/bv b genes but with the bont/a4 gene replaced by the bont/f gene. An analysis of the toxin cluster genes showed that many recombination events have occurred, including several events within the ntnh gene. One such recombination event resulted in the integration of the bont/a1 gene into the serotype toxin B ha cluster, resulting in a successful lineage commonly associated with food borne botulism outbreaks. In C. botulinum type E and C. butyricum type E strains the location of the bont/e gene cluster appears to be the result of insertion events that split a rarA, recombination-associated gene, independently at the same location in both species. Conclusion The analysis of the genomic sequences representing different strains reveals the presence of insertion sequence (IS) elements and other transposon-associated proteins such as recombinases that could facilitate the horizontal transfer of the bonts; these events, in addition to recombination among the toxin complex genes, have led to the lineages observed today within the neurotoxin-producing clostridia.
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Affiliation(s)
- Karen K Hill
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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