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Marinier E, Zaheer R, Berry C, Weedmark KA, Domaratzki M, Mabon P, Knox NC, Reimer AR, Graham MR, Chui L, Patterson-Fortin L, Zhang J, Pagotto F, Farber J, Mahony J, Seyer K, Bekal S, Tremblay C, Isaac-Renton J, Prystajecky N, Chen J, Slade P, Van Domselaar G. Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations. Nucleic Acids Res 2017; 45:e159. [PMID: 29048594 PMCID: PMC5737611 DOI: 10.1093/nar/gkx702] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 08/01/2017] [Indexed: 11/13/2022] Open
Abstract
The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models. Neptune uses parallel computing to efficiently identify and extract these loci from draft genome assemblies without requiring multiple sequence alignments or other computationally expensive comparative sequence analyses. Tests on simulated and real datasets showed that Neptune rapidly identifies regions that are both sensitive and specific. We demonstrate that this system can identify trait-specific loci from different bacterial lineages. Neptune is broadly applicable for comparative bacterial analyses, yet will particularly benefit pathogenomic applications, owing to efficient and sensitive discovery of differentially abundant genomic loci. The software is available for download at: http://github.com/phac-nml/neptune.
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Affiliation(s)
- Eric Marinier
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Rahat Zaheer
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Kelly A Weedmark
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Michael Domaratzki
- Department of Computer Science, University of Manitoba, 66 Chancellors Circle, Winnipeg, MB R3T 2N2, Canada
| | - Philip Mabon
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Natalie C Knox
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Aleisha R Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Morag R Graham
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
| | - Linda Chui
- Provincial Laboratory for Public Health, 8440 112 St NW, Edmonton, AB T6G 2P4, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, 116 St. and 85 Ave., Edmonton, AB T6G 2R3, Canada
| | - Laura Patterson-Fortin
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St. and 85 Ave., Edmonton, AB T6G 2R3, Canada
| | - Jian Zhang
- Alberta Innovates-Technology Futures, 250 Karl Clark Road, Edmonton, AB T6N 1E4, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, Tunney's Pasture, Ottawa, ON K1A 0K9, Canada
| | - Jeff Farber
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, Tunney's Pasture, Ottawa, ON K1A 0K9, Canada
| | - Jim Mahony
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Karine Seyer
- Canadian Food Inspection Agency, St. Hyacinthe Laboratory, 3400 Boulevard Casavant O, Saint-Hyacinthe, QC J2S 8E3, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, 20045 Ch Ste-Marie, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada.,Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Pavillon Roger-Gaudry, Université de Montréal, C.P. 6128, Succ. Centre-ville Montréal, QC H3C 3J7, Canada
| | - Cécile Tremblay
- Laboratoire de santé publique du Québec, 20045 Ch Ste-Marie, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada.,Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Pavillon Roger-Gaudry, Université de Montréal, C.P. 6128, Succ. Centre-ville Montréal, QC H3C 3J7, Canada
| | - Judy Isaac-Renton
- BC Public Health and Microbiology Reference Laboratory, 655 W. 12th Avenue, Vancouver, BC V5Z 4R4, Canada
| | - Natalie Prystajecky
- BC Public Health and Microbiology Reference Laboratory, 655 W. 12th Avenue, Vancouver, BC V5Z 4R4, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227 - 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Jessica Chen
- Department of Food Science, Food, Nutrition and Health, University of British Columbia, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada
| | - Peter Slade
- Maple Leaf Foods, 6897 Financial Drive, Mississauga, ON L5N 0A8, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
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Carter AT, Austin JW, Weedmark KA, Peck MW. Evolution of Chromosomal Clostridium botulinum Type E Neurotoxin Gene Clusters: Evidence Provided by Their Rare Plasmid-Borne Counterparts. Genome Biol Evol 2016; 8:540-55. [PMID: 26936890 PMCID: PMC4824171 DOI: 10.1093/gbe/evw017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Analysis of more than 150 Clostridium botulinum Group II type E genomes identified a small fraction (6%) where neurotoxin-encoding genes were located on plasmids. Seven closely related (134–144 kb) neurotoxigenic plasmids of subtypes E1, E3, and E10 were characterized; all carried genes associated with plasmid mobility via conjugation. Each plasmid contained the same 24-kb neurotoxin cluster cassette (six neurotoxin cluster and six flanking genes) that had split a helicase gene, rather than the more common chromosomal rarA. The neurotoxin cluster cassettes had evolved as separate genetic units which had either exited their chromosomal rarA locus in a series of parallel events, inserting into the plasmid-borne helicase gene, or vice versa. A single intact version of the helicase gene was discovered on a nonneurotoxigenic form of this plasmid. The observed low frequency for the plasmid location may reflect one or more of the following: 1) Less efficient recombination mechanism for the helicase gene target, 2) lack of suitable target plasmids, and 3) loss of neurotoxigenic plasmids. Type E1 and E10 plasmids possessed a Clustered Regularly Interspaced Short Palindromic Repeats locus with spacers that recognized C. botulinum Group II plasmids, but not C. botulinum Group I plasmids, demonstrating their long-term separation. Clostridium botulinum Group II type E strains also carry nonneurotoxigenic plasmids closely related to C. botulinum Group II types B and F plasmids. Here, the absence of neurotoxin cassettes may be because recombination requires both a specific mechanism and specific target sequence, which are rarely found together.
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Affiliation(s)
- Andrew T Carter
- Gut Health and Food Safety, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - John W Austin
- Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Kelly A Weedmark
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Michael W Peck
- Gut Health and Food Safety, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
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Carter AT, Austin JW, Weedmark KA, Corbett C, Peck MW. Three classes of plasmid (47-63 kb) carry the type B neurotoxin gene cluster of group II Clostridium botulinum. Genome Biol Evol 2015; 6:2076-87. [PMID: 25079343 PMCID: PMC4231633 DOI: 10.1093/gbe/evu164] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pulsed-field gel electrophoresis and DNA sequence analysis of 26 strains of Group II (nonproteolytic) Clostridium botulinum type B4 showed that 23 strains carried their neurotoxin gene cluster on a 47–63 kb plasmid (three strains lacked any hybridization signal for the neurotoxin gene, presumably having lost their plasmid). Unexpectedly, no neurotoxin genes were found on the chromosome. This apparent constraint on neurotoxin gene transfer to the chromosome stands in marked contrast to Group I C. botulinum, in which neurotoxin gene clusters are routinely found in both locations. The three main classes of type B4 plasmid identified in this study shared different regions of homology, but were unrelated to any Group I or Group III plasmid. An important evolutionary aspect firmly links plasmid class to geographical origin, with one class apparently dominant in marine environments, whereas a second class is dominant in European terrestrial environments. A third class of plasmid is a hybrid between the other two other classes, providing evidence for contact between these seemingly geographically separated populations. Mobility via conjugation has been previously demonstrated for the type B4 plasmid of strain Eklund 17B, and similar genes associated with conjugation are present in all type B4 plasmids now described. A plasmid toxin–antitoxin system pemI gene located close to the neurotoxin gene cluster and conserved in each type B4 plasmid class may be important in understanding the mechanism which regulates this unique and unexpected bias toward plasmid-borne neurotoxin genes in Group II C. botulinum type B4.
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Affiliation(s)
- Andrew T Carter
- Gut Health and Food Safety, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - John W Austin
- Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kelly A Weedmark
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Cindi Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael W Peck
- Gut Health and Food Safety, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
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Corbett CR, Ballegeer E, Weedmark KA, Elias MD, Al-Saleem FH, Ancharski DM, Simpson LL, Berry JD. Epitope characterization of sero-specific monoclonal antibody to Clostridium botulinum neurotoxin type A. Hybridoma (Larchmt) 2012; 30:503-10. [PMID: 22149274 DOI: 10.1089/hyb.2011.0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Botulinum neurotoxins (BoNTs) are extremely potent toxins that can contaminate foods and are a public health concern. Anti-BoNT antibodies have been described that are capable of detecting BoNTs; however there still exists a need for accurate and sensitive detection capabilities for BoNTs. Herein, we describe the characterization of a panel of eight monoclonal antibodies (MAbs) generated to the non-toxic receptor-binding domain of BoNT/A (H(C)50/A) developed using a high-throughput screening approach. In two independent hybridoma fusions, two groups of four IgG MAbs were developed against recombinant H(C)50/A. Of these eight, only a single MAb, F90G5-3, bound to the whole BoNT/A protein and was characterized further. The F90G5-3 MAb slightly prolonged time to death in an in vivo mouse bioassay and was mapped by pepscan to a peptide epitope in the N-terminal subdomain of H(C)50/A (H(CN)25/A) comprising amino acid residues (985)WTLQDTQEIKQRVVF(999), an epitope that is highly immunoreactive in humans. Furthermore, we demonstrate that F90G5-3 binds BoNT/A with nanomolar efficiency. Together, our results indicate that F90G5-3 is of potential value as a diagnostic immunoreagent for BoNT/A capture assay development and bio-forensic analysis.
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Affiliation(s)
- Cindi R Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Mannitoba, Canada.
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