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Gélis-Jeanvoine S, Canette A, Gohar M, Caradec T, Lemy C, Gominet M, Jacques P, Lereclus D, Slamti L. Genetic and functional analyses of krs, a locus encoding kurstakin, a lipopeptide produced by Bacillus thuringiensis. Res Microbiol 2016; 168:356-368. [PMID: 27353188 DOI: 10.1016/j.resmic.2016.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/23/2016] [Accepted: 06/06/2016] [Indexed: 11/17/2022]
Abstract
Bacteria of the Bacillus genus are able to synthesize several families of lipopeptides. These small molecules are the product of non-ribosomal peptide synthetases. In 2000, it was found that Bacillus thuringiensis, an entomopathogenic bacterium of the Bacillus cereus group, produced a previously unknown lipopeptide: kurstakin. Genomic analyses reveal that the krs locus, encoding the kurstakin synthetases, is specific to the B. cereus group, but is unevenly distributed within this group. Previous work showed that krs transcription requires the necrotrophism quorum-sensor NprR. Here, we demonstrated that the genes of the krs locus form an operon and we defined its transcription start site. Following krs transcription at the population and single-cell levels in multiple culture conditions, we depicted a condition-dependent transcription pattern, indicating that production of kurstakin is subject to environmental regulation. Consistent with this idea, we found krs transcription to be regulated by another master regulator, Spo0A, suggesting that krs expression is fine-tuned by integrating multiple signals. We also reported an unknown DNA palindrome in the krs promoter region that modulates krs expression. Due to their surfactant properties, lipopeptides could play several physiological roles. We showed that the krs locus was required for proper biofilm structuration.
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Affiliation(s)
| | - Alexis Canette
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Michel Gohar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Thibault Caradec
- University of Lille, EA 7394, ICV-Institut Charles Viollette, ProBioGEM Team, Polytech'Lille, Avenue Langevin, 59655 Villeneuve d'Ascq, France.
| | - Christelle Lemy
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Myriam Gominet
- Institut Pasteur, CNRS URA 2172, Unité de Biologie des Bactéries Pathogènes à Gram positif, 75015 Paris, France.
| | - Philippe Jacques
- University of Lille, EA 7394, ICV-Institut Charles Viollette, ProBioGEM Team, Polytech'Lille, Avenue Langevin, 59655 Villeneuve d'Ascq, France.
| | - Didier Lereclus
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Leyla Slamti
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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102
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Phylogenetic Characteristics of Anthrax Outbreaks in Liaoning Province, China, 2001-2015. PLoS One 2016; 11:e0157496. [PMID: 27299730 PMCID: PMC4907462 DOI: 10.1371/journal.pone.0157496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 05/30/2016] [Indexed: 11/19/2022] Open
Abstract
Anthrax is a continuous threat in China, especially in rural regions. In July 2015, an anthrax outbreak occurred in Xifeng County, Liaoning Province. A total of 10 cutaneous anthrax cases were reported, with 210 people under medical observation. In this study, the general characteristics of human anthrax outbreak occurred in Liaoning Province were described, and all cases were caused by butchering and contacting sick animal. Meanwhile, the phylogenetic relationship between outbreak-related isolates/samples of the year 2015 and previous Bacillus anthracis strains was analyzed by means of canonical single nucleotide polymorphisms (canSNP), multiple-locus variable-number tandem repeat analysis (MLVA) with 15 markers and single-nucleotide repeats (SNR) analysis. There are two canSNP subgroups found in Liaoning, A.Br.001/002 and A.Br.Ames, and a total of six MLVA 15 genotypes and five SNR genotypes were observed. The strain collected from anthrax outbreak in Xifeng County in 2015 was classified as A.Br.001/002 subgroup and identified as MLVA15-29 genotype, with same SNR profile (CL10: 17, CL12: 15, CL33: 29, and CL35: 13). So we conclude that the same clone of B.anthracis caused the anthrax outbreak in Xifeng County in 2015, and this clone is different to previous isolates. Strengthening public health education in China is one of the most important measures to prevent and control anthrax.
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Rume FI, Affuso A, Serrecchia L, Rondinone V, Manzulli V, Campese E, Di Taranto P, Biswas PK, Ahsan CR, Yasmin M, Fasanella A, Hugh-Jones M. Genotype Analysis of Bacillus anthracis Strains Circulating in Bangladesh. PLoS One 2016; 11:e0153548. [PMID: 27082248 PMCID: PMC4833350 DOI: 10.1371/journal.pone.0153548] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/31/2016] [Indexed: 11/30/2022] Open
Abstract
In Bangladesh, anthrax, caused by the bacterium Bacillus anthracis, is considered an endemic disease affecting ruminants with sporadic zoonotic occurrences in humans. Due to the lack of knowledge about risks from an incorrect removal of infected carcasses, the disease is not properly monitored, and because of the socio-economic conditions, the situation is under-reported and under-diagnosed. For sensitive species, anthrax represents a fatal outcome with sudden death and sometimes bleeding from natural orifices. The most common source of infection for ruminants is ingestion of spores during grazing in contaminated pastures or through grass and water contaminated with anthrax spores. Domestic cattle, sheep and goats can also become infected through contaminated bone meal (used as feed) originating from anthrax-infected carcasses. The present investigation was conducted to isolate B. anthracis organisms from 169 samples (73 soil, 1 tissue, 4 bone and 91 bone meal samples) collected from 12 different districts of Bangladesh. The sampling was carried out from 2012 to 2015. Twelve samples resulted positive for B. anthracis. Biomolecular analyses were conducted starting from the Canonical Single Nucleotide Polymorphism (CanSNP) to analyze the phylogenetic origin of strains. The analysis of genotype, obtained through the Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) with the analysis of 15 Variable Number Tandem Repeats (VNTR), demonstrated four different genotypes: two of them were previously identified in the district of Sirajganj. The sub-genotyping, conducted with Single Nucleotide Repeats analysis, revealed the presence of eight subgenotypes. The data of the present study concluded that there was no observed correlation between imported cattle feed and anthrax occurrence in Bangladesh and that the remarkable genetic variations of B. anthracis were found in the soil of numerous outbreaks in this country.
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Affiliation(s)
- Farzana Islam Rume
- Department of Microbiology, Dhaka University. Dhaka, Bangladesh
- Department of Microbiology & Virology, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Alessia Affuso
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
- * E-mail:
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Viviana Manzulli
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Emanuele Campese
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Pietro Di Taranto
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Paritosh Kumar Biswas
- Department of Microbiology & Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | | | - Mahmuda Yasmin
- Department of Microbiology, Dhaka University. Dhaka, Bangladesh
| | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Martin Hugh-Jones
- School of the Coast & Environment, Louisiana State University, Baton Rouge, United States of America
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104
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Genome Sequence of Bacillus anthracis Strain Stendal, Isolated from an Anthrax Outbreak in Cattle in Germany. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00219-16. [PMID: 27056225 PMCID: PMC4824258 DOI: 10.1128/genomea.00219-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In July 2012, an anthrax outbreak occurred among cattle in northern Germany resulting in ten losses. Here, we report the draft genome sequence of Bacillus anthracis strain Stendal, isolated from one of the diseased cows.
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105
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Quantitative Determination of Lethal Toxin Proteins in Culture Supernatant of Human Live Anthrax Vaccine Bacillus anthracis A16R. Toxins (Basel) 2016; 8:toxins8030056. [PMID: 26927174 PMCID: PMC4810201 DOI: 10.3390/toxins8030056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/26/2022] Open
Abstract
Bacillus anthracis (B. anthracis) is the etiological agent of anthrax affecting both humans and animals. Anthrax toxin (AT) plays a major role in pathogenesis. It includes lethal toxin (LT) and edema toxin (ET), which are formed by the combination of protective antigen (PA) and lethal factor (LF) or edema factor (EF), respectively. The currently used human anthrax vaccine in China utilizes live-attenuated B. anthracis spores (A16R; pXO1+, pXO2−) that produce anthrax toxin but cannot produce the capsule. Anthrax toxins, especially LT, have key effects on both the immunogenicity and toxicity of human anthrax vaccines. Thus, determining quantities and biological activities of LT proteins expressed by the A16R strain is meaningful. Here, we explored LT expression patterns of the A16R strain in culture conditions using another vaccine strain Sterne as a control. We developed a sandwich ELISA and cytotoxicity-based method for quantitative detection of PA and LF. Expression and degradation of LT proteins were observed in culture supernatants over time. Additionally, LT proteins expressed by the A16R and Sterne strains were found to be monomeric and showed cytotoxic activity, which may be the main reason for side effects of live anthrax vaccines. Our work facilitates the characterization of anthrax vaccines components and establishment of a quality control standard for vaccine production which may ultimately help to ensure the efficacy and safety of the human anthrax vaccine A16R.
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Vergnaud G, Girault G, Thierry S, Pourcel C, Madani N, Blouin Y. Comparison of French and Worldwide Bacillus anthracis Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade. PLoS One 2016; 11:e0146216. [PMID: 26901621 PMCID: PMC4763433 DOI: 10.1371/journal.pone.0146216] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
Background Bacillus anthracis, the highly dangerous zoonotic bacterial pathogen species is currently composed of three genetic groups, called A, B and C. Group A is represented worldwide whereas group B is present essentially in Western Europe and Southern Africa. Only three strains from group C have been reported. This knowledge is derived from the genotyping of more than 2000 strains collected worldwide. Strains from both group A and group B are present in France. Previous investigations showed that the majority of sporadic French strains belong to the so-called A.Br.011/009 group A clade and define a very remarkable polytomy with six branches. Here we explore the significance of this polytomy by comparing the French B. anthracis lineages to worldwide lineages. We take advantage of whole genome sequence data previously determined for 122 French strains and 45 strains of various origins. Results A total of 6690 SNPs was identified among the available dataset and used to draw the phylogeny. The phylogeny of the French B group strains which belongs to B.Br.CNEVA indicates an expansion from the south-east part of France (the Alps) towards the south-west (Massif-Central and Pyrenees). The relatively small group A strains belonging to A.Br.001/002 results from at least two independent introductions. Strikingly, the data clearly demonstrates that the currently predominant B. anthracis lineage in North America, called WNA for Western North American, is derived from one branch of the A.Br.011/009 polytomy predominant in France. Conclusions/Significance The present work extends the range of observed substitution rate heterogeneity within B. anthracis, in agreement with its ecology and in contrast with some other pathogens. The population structure of the six branches A.Br.011/009 polytomy identified in France, diversity of branch length, and comparison with the WNA lineage, suggests that WNA is of post-Columbian and west European origin, with France as a likely source. Furthermore, it is tempting to speculate that the polytomy’s most recent common ancestor -MRCA- dates back to the Hundred Years' war between France and England started in the mid-fourteenth century. These events were associated in France with deadly epidemics and major economic and social changes.
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Affiliation(s)
- Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
- * E-mail:
| | - Guillaume Girault
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Simon Thierry
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Nora Madani
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Yann Blouin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
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107
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Mullins JC, Van Ert M, Hadfield T, Nikolich MP, Hugh-Jones ME, Blackburn JK. Spatio-temporal patterns of an anthrax outbreak in white-tailed deer, Odocoileus virginanus, and associated genetic diversity of Bacillus anthracis. BMC Ecol 2015; 15:23. [PMID: 26669305 PMCID: PMC4681179 DOI: 10.1186/s12898-015-0054-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 11/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anthrax, a soil-borne zoonosis caused by the bacterium Bacillus anthracis, is enzootic in areas of North America with frequent outbreaks in west Texas. Despite a long history of study, pathogen transmission during natural outbreaks remains poorly understood. Here we combined case-level spatio-temporal analysis and high resolution genotyping to investigate anthrax transmission dynamics. Carcass locations from a single white-tailed deer, Odocoileus virginanus, outbreak were analyzed for spatial clustering using K-function analysis and directionality with trend surface analysis and the direction test. RESULTS The directionalities were compared to results of high resolution genotyping. The results of the spatial clustering analyses, combined with deer movement data, suggest anthrax transmission events occur within limited spatial areas, with carcass locations occurring within the activity space of adjacent cases. The directionality of the outbreak paralleled adjacent dry river beds. Isolates from the outbreak were represented by a single genotype based on multiple locus variable number tandem repeat analysis (MLVA); four sub-genotypes were identified using single nucleotide repeat (SNR) analysis. CONCLUSIONS Areas of high transmission agreed spatially with areas of higher SNR genetic diversity; however, SNRs did not provide clear evidence of linear transmission. Overlap of case home ranges provides spatial and temporal support for localized transmission, which may include the role of necrophagous or hematophagous flies in outbreaks in this region. These results emphasize the need for active surveillance and prompt cleanup of anthrax carcasses to control anthrax both during outbreaks and between seasons.
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Affiliation(s)
- Jocelyn C Mullins
- Department of Geography, Spatial Epidemiology and Ecology Research Laboratory, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, USA.
| | - Matthew Van Ert
- Department of Geography, Spatial Epidemiology and Ecology Research Laboratory, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, USA.
| | - Ted Hadfield
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.
| | - Mikeljon P Nikolich
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Martin E Hugh-Jones
- Department of Environmental Sciences, School of the Coast and Environment, Louisiana State University, Baton Rouge, LA, USA.
| | - Jason K Blackburn
- Department of Geography, Spatial Epidemiology and Ecology Research Laboratory, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, USA.
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108
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D'Amelio E, Gentile B, Lista F, D'Amelio R. Historical evolution of human anthrax from occupational disease to potentially global threat as bioweapon. ENVIRONMENT INTERNATIONAL 2015; 85:133-146. [PMID: 26386727 DOI: 10.1016/j.envint.2015.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Abstract
PURPOSE Anthrax is caused by Bacillus anthracis, which can naturally infect livestock, wildlife and occupationally exposed humans. However, for its resistance due to spore formation, ease of dissemination, persistence in the environment and high virulence, B. anthracis has been considered the most serious bioterrorism agent for a long time. During the last century anthrax evolved from limited natural disease to potentially global threat if used as bioweapon. Several factors may mitigate the consequences of an anthrax attack, including 1. the capability to promptly recognize and manage the illness and its public health consequences; 2. the limitation of secondary contamination risk through an appropriate decontamination; and 3. the evolution of genotyping methods (for microbes characterization at high resolution level) that can influence the course and/or focus of investigations, impacting the response of the government to an attack. METHODS A PubMed search has been done using the key words “bioterrorism anthrax”. RESULTS Over one thousand papers have been screened and the most significant examined to present a comprehensive literature review in order to discuss the current knowledge and strategies in preparedness for a possible deliberate release of B. anthracis spores and to indicate the most current and complete documents in which to deepen. CONCLUSIONS The comprehensive analysis of the two most relevant unnatural anthrax release events, Sverdlovsk in the former Soviet Union (1979) and the contaminated letters in the USA (2001), shows that inhalational anthrax may easily and cheaply be spread resulting in serious consequences. The damage caused by an anthrax attack can be limited if public health organization, first responders, researchers and investigators will be able to promptly manage anthrax cases and use new technologies for decontamination methods and in forensic microbiology.
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Affiliation(s)
| | - Bernardina Gentile
- Histology and Molecular Biology Section, Army Medical Research Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
| | - Florigio Lista
- Histology and Molecular Biology Section, Army Medical Research Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
| | - Raffaele D'Amelio
- Sapienza University of Rome, Department of Clinical and Molecular Medicine, S. Andrea University Hospital, Via di Grottarossa 1039, 00189 Rome, Italy.
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109
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Pullan ST, Pearson TR, Latham J, Mason J, Atkinson B, Silman NJ, Marston CK, Sahl JW, Birdsell D, Hoffmaster AR, Keim P, Vipond R. Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case. Microb Genom 2015; 1:e000039. [PMID: 28348823 PMCID: PMC5320680 DOI: 10.1099/mgen.0.000039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/08/2015] [Indexed: 11/18/2022] Open
Abstract
There have been two anthrax cases affecting people that played and/or made animal-skin drums in the UK during the last 10 years, with single fatal occurrences in Scotland in 2006 and London in 2008. Investigations by the Health Protection Agency (now Public Health England) employing multi-locus-variable number tandem repeat analysis had previously linked the clinical cases to spores associated with animal skins and drums the patients had been in contact with. In this study, whole-genome sequencing of 23 Bacillus anthracis isolates harvested during the investigations was performed. High-quality draft assemblies of these genomes provided greater characterization of the B. anthracis strains present and placed them all upon a new branch of the global phylogeny. Although closely related, the clinical isolates from the two events, and another isolated from a drum-skin-associated case in New York in 2006, were distinct from each other. Multiple distinct genotypes were found during both investigations, implying either multiple contamination events or a single heterogeneous contamination. One environmental isolate from the Scottish incident was more closely related to London isolates than to the other Scottish isolates. As B. anthracis of this subgroup was present at both geographically and temporally distinct events, it may be more widespread at the source of contamination. All isolates were distinct from currently characterized West African strains, despite this being the likely origin of the drums and hides, therefore adding to our knowledge of B. anthracis diversity in the region.
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Affiliation(s)
- Steven T Pullan
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Talima R Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Jennie Latham
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Joanne Mason
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Barry Atkinson
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Nigel J Silman
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Chung K Marston
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jason W Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Dawn Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Alex R Hoffmaster
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Richard Vipond
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
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Keim P, Grunow R, Vipond R, Grass G, Hoffmaster A, Birdsell DN, Klee SR, Pullan S, Antwerpen M, Bayer BN, Latham J, Wiggins K, Hepp C, Pearson T, Brooks T, Sahl J, Wagner DM. Whole Genome Analysis of Injectional Anthrax Identifies Two Disease Clusters Spanning More Than 13 Years. EBioMedicine 2015; 2:1613-8. [PMID: 26870786 PMCID: PMC4740342 DOI: 10.1016/j.ebiom.2015.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/24/2015] [Accepted: 10/02/2015] [Indexed: 12/30/2022] Open
Abstract
Background Anthrax is a rare disease in humans but elicits great public fear because of its past use as an agent of bioterrorism. Injectional anthrax has been occurring sporadically for more than ten years in heroin consumers across multiple European countries and this outbreak has been difficult to trace back to a source. Methods We took a molecular epidemiological approach in understanding this disease outbreak, including whole genome sequencing of Bacillus anthracis isolates from the anthrax victims. We also screened two large strain repositories for closely related strains to provide context to the outbreak. Findings Analyzing 60 Bacillus anthracis isolates associated with injectional anthrax cases and closely related reference strains, we identified 1071 Single Nucleotide Polymorphisms (SNPs). The synapomorphic SNPs (350) were used to reconstruct phylogenetic relationships, infer likely epidemiological sources and explore the dynamics of evolving pathogen populations. Injectional anthrax genomes separated into two tight clusters: one group was exclusively associated with the 2009–10 outbreak and located primarily in Scotland, whereas the second comprised more recent (2012–13) cases but also a single Norwegian case from 2000. Interpretation Genome-based differentiation of injectional anthrax isolates argues for at least two separate disease events spanning > 12 years. The genomic similarity of the two clusters makes it likely that they are caused by separate contamination events originating from the same geographic region and perhaps the same site of drug manufacturing or processing. Pathogen diversity within single patients challenges assumptions concerning population dynamics of infecting B. anthracis and host defensive barriers for injectional anthrax. Funding This work was supported by the United States Department of Homeland Security grant no. HSHQDC-10-C-00,139 and via a binational cooperative agreement between the United States Government and the Government of Germany. This work was supported by funds from the German Ministry of Defense (Sonderforschungsprojekt 25Z1-S-431,214). Support for sequencing was also obtained from Illumina, Inc. These sources had no role in the data generation or interpretation, and had not role in the manuscript preparation. Panel 1: Research in Context Systematic Review We searched PubMed for any article published before Jun. 17, 2015, with the terms “Bacillus anthracis” and “heroin”, or “injectional anthrax”. Other than our previously published work (Price et al., 2012), we found no other relevant studies on elucidating the global phylogenetic relationships of B. anthracis strains associated with injectional anthrax caused by recreational heroin consumption of spore-contaminated drug. There were, however, publically available genome sequences of two strains involved (Price et al., 2012, Grunow et al., 2013) and the draft genome sequence of Bacillus anthracis UR-1, isolated from a German heroin user (Ruckert et al., 2012) with only limited information on the genotyping of closely related strains (Price et al., 2012, Grunow et al., 2013). Lay Person Interpretation Injectional anthrax has been plaguing heroin drug users across Europe for more than 10 years. In order to better understand this outbreak, we assessed genomic relationships of all available injectional anthrax strains from four countries spanning a > 12 year period. Very few differences were identified using genome-based analysis, but these differentiated the isolates into two distinct clusters. This strongly supports a hypothesis of at least two separate anthrax spore contamination events perhaps during the drug production processes. Identification of two events would not have been possible from standard epidemiological analysis. These comprehensive data will be invaluable for classifying future injectional anthrax isolates and for future geographic attribution. Whole genome sequences of injectional anthrax B. anthracis isolates fall in two tight but distinct genomic clusters. The distinct genomic clusters are consistent with two or more disease events that overlap in time and space. Defining pathogen clusters will lead to better public health responses to difficult to track disease outbreaks.
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Affiliation(s)
- Paul Keim
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; The Pathogen Genomics Division, The Translational Genomics Research Institute, 3051 W. Shamrell Blvd, Suite 106, Flagstaff, AZ 86001 USA
| | | | - Richard Vipond
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Alex Hoffmaster
- The Center for Disease Control and Prevention, Atlanta, GA, USA
| | - Dawn N Birdsell
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| | | | - Steven Pullan
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Markus Antwerpen
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom
| | - Brittany N Bayer
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| | - Jennie Latham
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom
| | - Kristin Wiggins
- The Pathogen Genomics Division, The Translational Genomics Research Institute, 3051 W. Shamrell Blvd, Suite 106, Flagstaff, AZ 86001 USA
| | - Crystal Hepp
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| | - Talima Pearson
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| | - Tim Brooks
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Jason Sahl
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; The Pathogen Genomics Division, The Translational Genomics Research Institute, 3051 W. Shamrell Blvd, Suite 106, Flagstaff, AZ 86001 USA
| | - David M Wagner
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
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Abstract
Fifty complete Bacillus genome sequences and associated plasmids were compared using the “feature frequency profile” (FFP) method. The resulting whole-genome phylogeny supports the placement of three Bacillus species (B. thuringiensis, B. anthracis and B. cereus) as a single clade. The monophyletic status of B. anthracis was strongly supported by the analysis. FFP proved to be more effective in inferring the phylogeny of Bacillus than methods based on single gene sequences [16s rRNA gene, GryB (gyrase subunit B) and AroE (shikimate-5-dehydrogenase)] analyses. The findings of FFP analysis were verified using kSNP v2 (alignment-free sequence analysis method) and Harvest suite (core genome sequence alignment method).
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112
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Derzelle S, Girault G, Kokotovic B, Angen Ø. Whole Genome-Sequencing and Phylogenetic Analysis of a Historical Collection of Bacillus anthracis Strains from Danish Cattle. PLoS One 2015; 10:e0134699. [PMID: 26317972 PMCID: PMC4552859 DOI: 10.1371/journal.pone.0134699] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/13/2015] [Indexed: 11/28/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is known as one of the most genetically monomorphic species. Canonical single-nucleotide polymorphism (SNP) typing and whole-genome sequencing were used to investigate the molecular diversity of eleven B. anthracis strains isolated from cattle in Denmark between 1935 and 1988. Danish strains were assigned into five canSNP groups or lineages, i.e. A.Br.001/002 (n = 4), A.Br.Ames (n = 2), A.Br.008/011 (n = 2), A.Br.005/006 (n = 2) and A.Br.Aust94 (n = 1). The match with the A.Br.Ames lineage is of particular interest as the occurrence of such lineage in Europe is demonstrated for the first time, filling an historical gap within the phylogeography of the lineage. Comparative genome analyses of these strains with 41 isolates from other parts of the world revealed that the two Danish A.Br.008/011 strains were related to the heroin-associated strains responsible for outbreaks of injection anthrax in drug users in Europe. Eight novel diagnostic SNPs that specifically discriminate the different sub-groups of Danish strains were identified and developed into PCR-based genotyping assays.
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Affiliation(s)
- Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Maisons-Alfort, France
| | - Guillaume Girault
- University Paris-Est, Anses, Animal Health Laboratory, Maisons-Alfort, France
| | - Branko Kokotovic
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Øystein Angen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
- * E-mail:
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113
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Zhou W, Sun Y, Zhu L, Zhou B, Liu J, Ji X, Wang X, Wang N, Gu G, Feng S, Qian J, Guo X. Investigation of Anthrax Cases in North-East China, 2010-2014. PLoS One 2015; 10:e0135777. [PMID: 26308449 PMCID: PMC4550413 DOI: 10.1371/journal.pone.0135777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/24/2015] [Indexed: 12/04/2022] Open
Abstract
We determined the genotypes of seven Bacillus anthracis strains that were recovered from nine anthrax outbreaks in North-East China from 2010 to 2014, and two approved vaccine strains that are currently in use in China. The causes of these cases were partly due to local farmers being unaware of the presence of anthrax, and butchers with open wounds having direct contact with anthrax-contaminated meat products. The genotype of five of the seven recovered strains was A.Br.001/002 sub-lineage, which was concordant with previously published research. The remaining two cases belongs to the A.Br.Ames sub-lineage. Both of these strains displayed an identical SNR pattern, which was the first time that this genotype was identified in North-East China. Strengthening education in remote villages of rural China is an important activity aimed at fostering attempts to prevent and control anthrax. The genotype of the vaccine strain Anthrax Spore Vaccine No.II was A.Br.008/009 and A.Br.001/002 for the vaccine strain Anthrax Spore Vaccine Non-capsulated. Further studies of their characteristics are clearly warranted.
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Affiliation(s)
- Wei Zhou
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Yang Sun
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Lingwei Zhu
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Bo Zhou
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Jun Liu
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Xue Ji
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Xiaofeng Wang
- Animal Diseases Control and Prevention Centre of Jilin Province, Jilin, China
| | - Nan Wang
- Animal Diseases Control and Prevention Centre of Jilin Province, Jilin, China
| | - Guibo Gu
- Animal Diseases Control and Prevention Centre of Liaoning Province, Liaoning, China
| | - Shuzhang Feng
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Jun Qian
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Xuejun Guo
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
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114
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Blackburn JK, Odugbo MO, Van Ert M, O’Shea B, Mullins J, Perrenten V, Maho A, Hugh-Jones M, Hadfield T. Bacillus anthracis Diversity and Geographic Potential across Nigeria, Cameroon and Chad: Further Support of a Novel West African Lineage. PLoS Negl Trop Dis 2015; 9:e0003931. [PMID: 26291625 PMCID: PMC4546381 DOI: 10.1371/journal.pntd.0003931] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/23/2015] [Indexed: 01/11/2023] Open
Abstract
Zoonoses, diseases affecting both humans and animals, can exert tremendous pressures on human and veterinary health systems, particularly in resource limited countries. Anthrax is one such zoonosis of concern and is a disease requiring greater public health attention in Nigeria. Here we describe the genetic diversity of Bacillus anthracis in Nigeria and compare it to Chad, Cameroon and a broader global dataset based on the multiple locus variable number tandem repeat (MLVA-25) genetic typing system. Nigerian B. anthracis isolates had identical MLVA genotypes and could only be resolved by measuring highly mutable single nucleotide repeats (SNRs). The Nigerian MLVA genotype was identical or highly genetically similar to those in the neighboring countries, confirming the strains belong to this unique West African lineage. Interestingly, sequence data from a Nigerian isolate shares the anthrose deficient genotypes previously described for strains in this region, which may be associated with vaccine evasion. Strains in this study were isolated over six decades, indicating a high level of temporal strain stability regionally. Ecological niche models were used to predict the geographic distribution of the pathogen for all three countries. We describe a west-east habitat corridor through northern Nigeria extending into Chad and Cameroon. Ecological niche models and genetic results show B. anthracis to be ecologically established in Nigeria. These findings expand our understanding of the global B. anthracis population structure and can guide regional anthrax surveillance and control planning. Anthrax, caused by the soil-borne bacterium Bacillus anthracis, is a disease with important public health and national security implications globally. Understanding the global genetic diversity of the pathogen is important for epidemiological and forensic investigations of anthrax events. Toward this, we describe B. anthracis genetic diversity in Nigeria and confirm it belongs to a unique West African genetic group not yet reported beyond neighboring Cameroon and Chad and Mali. This refines the global phylogeny of B. anthracis, allowing the development of more accurate diagnostics. We coupled these efforts with ecological niche modeling to map the geographic distribution of this strain group across the region. Suitable habitat for the pathogen is predicted across central Nigeria from west to east into Cameroon and Chad. Understanding the geography of B. anthracis plays an important role in informing public health by targeting disease control to high risk regions. This is particularly important in resource limited areas where intervention strategies are constrained and zoonotic disease risk is high.
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Affiliation(s)
- Jason K. Blackburn
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Moses Ode Odugbo
- Bacterial Research Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Matthew Van Ert
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Bob O’Shea
- MRI Global, Palm Bay, Florida, United States of America
| | - Jocelyn Mullins
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Vincent Perrenten
- Institute of Veterinary Bacteriology, University of Berne, Berne, Switzerland
| | - Angaya Maho
- Laboratoire de Recherches Vétérinaires et Zootechniques, N’Djaména, Chad
| | - Martin Hugh-Jones
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Ted Hadfield
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- MRI Global, Palm Bay, Florida, United States of America
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115
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Braun P, Grass G, Aceti A, Serrecchia L, Affuso A, Marino L, Grimaldi S, Pagano S, Hanczaruk M, Georgi E, Northoff B, Schöler A, Schloter M, Antwerpen M, Fasanella A. Microevolution of Anthrax from a Young Ancestor (M.A.Y.A.) Suggests a Soil-Borne Life Cycle of Bacillus anthracis. PLoS One 2015; 10:e0135346. [PMID: 26266934 PMCID: PMC4534099 DOI: 10.1371/journal.pone.0135346] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/15/2015] [Indexed: 01/10/2023] Open
Abstract
During an anthrax outbreak at the Pollino National Park (Basilicata, Italy) in 2004, diseased cattle were buried and from these anthrax-foci Bacillus anthracis endospores still diffuse to the surface resulting in local accumulations. Recent data suggest that B. anthracis multiplies in soil outside the animal-host body. This notion is supported by the frequent isolation of B. anthracis from soil lacking one or both virulence plasmids. Such strains represent an evolutionary dead end, as they are likely no longer able to successfully infect new hosts. This loss of virulence plasmids is explained most simply by postulating a soil-borne life cycle of the pathogen. To test this hypothesis we investigated possible microevolution at two natural anthrax foci from the 2004 outbreak. If valid, then genotypes of strains isolated from near the surface at these foci should be on a different evolutionary trajectory from those below residing in deeper-laying horizons close to the carcass. Thus, the genetic diversity of B. anthracis isolates was compared conducting Progressive Hierarchical Resolving Assays using Nucleic Acids (PHRANA) and next generation Whole Genome Sequencing (WGS). PHRANA was not discriminatory enough to resolve the fine genetic relationships between the isolates. Conversely, WGS of nine isolates from near-surface and nine from near-carcass revealed five isolate specific SNPs, four of which were found only in different near-surface isolates. In support of our hypothesis, one surface-isolate lacked plasmid pXO1 and also harbored one of the unique SNPs. Taken together, our results suggest a limited soil-borne life cycle of B. anthracis.
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Affiliation(s)
- Peter Braun
- Bundeswehr Institute of Microbiology, Munich, Germany
- Technische Universität München, Wissenschaftszentrum Weihenstephan, Chair for Soil Ecology, Freising, Germany
| | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Angela Aceti
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Alessia Affuso
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Leonardo Marino
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Stefania Grimaldi
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Stefania Pagano
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | | | - Enrico Georgi
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Bernd Northoff
- Bundeswehr Institute of Microbiology, Munich, Germany
- Ludwig Maximilians Universität München, Institute for Laboratory Medicine, Munich, Germany
| | - Anne Schöler
- German Research Center for Environmental Health, Research Unit for Environmental Genomics, Neuherberg, Germany
| | - Michael Schloter
- Technische Universität München, Wissenschaftszentrum Weihenstephan, Chair for Soil Ecology, Freising, Germany
- German Research Center for Environmental Health, Research Unit for Environmental Genomics, Neuherberg, Germany
| | | | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
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116
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Califf KJ, Keim PS, Wagner DM, Sahl JW. Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics. Microb Genom 2015; 1:e000028. [PMID: 28348813 PMCID: PMC5320571 DOI: 10.1099/mgen.0.000028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/06/2015] [Indexed: 12/13/2022] Open
Abstract
Yersinia pestis, the causative agent of plague, is best known for historical pandemics, but still actively causes disease in many parts of the world. Y. pestis is a recently derived clone of the pathogenic species Yersinia pseudotuberculosis, but is more associated with human infection. Numerous studies have documented genomic changes since the two species differentiated, although all of these studies used a relatively small sample set for defining these differences. In this study, we compared the complete genomic content between a diverse set of Y. pestis and Y. pseudotuberculosis genomes, and identified unique loci that could serve as diagnostic markers or for better understanding the evolution and pathogenesis of each group. Comparative genomics analyses also identified subtle variations in gene content between individual monophyletic clades within these species, based on a core genome single nucleotide polymorphism phylogeny that would have been undetected in a less comprehensive genome dataset. We also screened loci that were identified in other published studies as unique to either species and generally found a non-uniform distribution, suggesting that the assignment of these unique genes to either species should be re-evaluated in the context of current sequencing efforts. Overall, this study provides a high-resolution view into the genomic differences between Y. pestis and Y. pseudotuberculosis, demonstrating fine-scale differentiation and unique gene composition in both species.
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Affiliation(s)
- Katy J. Califf
- Microbial Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul S. Keim
- Microbial Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - David M. Wagner
- Microbial Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W. Sahl
- Microbial Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
- Translational Genomics Research Institute, Flagstaff, AZ, USA
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117
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Abstract
Anthrax is caused by the spore-forming, gram-positive bacterium Bacillus anthracis. The bacterium's major virulence factors are (a) the anthrax toxins and (b) an antiphagocytic polyglutamic capsule. These are encoded by two large plasmids, the former by pXO1 and the latter by pXO2. The expression of both is controlled by the bicarbonate-responsive transcriptional regulator, AtxA. The anthrax toxins are three polypeptides-protective antigen (PA), lethal factor (LF), and edema factor (EF)-that come together in binary combinations to form lethal toxin and edema toxin. PA binds to cellular receptors to translocate LF (a protease) and EF (an adenylate cyclase) into cells. The toxins alter cell signaling pathways in the host to interfere with innate immune responses in early stages of infection and to induce vascular collapse at late stages. This review focuses on the role of anthrax toxins in pathogenesis. Other virulence determinants, as well as vaccines and therapeutics, are briefly discussed.
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Affiliation(s)
- Mahtab Moayeri
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892; , , , ,
| | - Stephen H Leppla
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892; , , , ,
| | - Catherine Vrentas
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892; , , , ,
| | - Andrei P Pomerantsev
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892; , , , ,
| | - Shihui Liu
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892; , , , ,
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118
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Molecular characterization of the circulating Bacillus anthracis in Jordan. Trop Anim Health Prod 2015; 47:1621-4. [PMID: 26156620 DOI: 10.1007/s11250-015-0882-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 06/29/2015] [Indexed: 10/23/2022]
Abstract
To understand the biomolecular charcteristics of Bacillus anthracis in Jordan, 20 blood smear slides from dead animals with suspected anthrax were analyzed using conventional and molecular approaches. All slides were positive for B. anthracis by conventional staining but no growth of the organism on selective media was detected. However, of the 20 samples, 16 were B. anthracis DNA-positive using polymerase chain reaction (PCR). Seven samples provided enough quantity and quality of DNA, and their multilocus variable tandem repeat analysis (MLVA)-15 loci analysis revealed two different genotypes. All genotypes were belonging to A.B..r. 008/009 which is very common in Asia and Europe. Single nucleotide repeat (SNR) analysis revealed that there were no sub genotypes. Molecular diagnosis of animal anthrax in Jordan is not used routinely; henceforth, official diagnosis of anthrax is based on the observation of the slides by optical microscope and this can often cause reading errors. Therefore, the prevalence of the disease in Jordan might be slightly lower than that reported by the official bodies.
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119
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Thapa NK, Wangdi K, Dorji T, Dorjee J, Marston CK, Hoffmaster AR. Investigation and control of anthrax outbreak at the human-animal interface, Bhutan, 2010. Emerg Infect Dis 2015; 20:1524-6. [PMID: 25147965 PMCID: PMC4178414 DOI: 10.3201/eid2009.140181] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 2010, we investigated anthrax outbreak in Bhutan. A total of 43 domestic animals died, and cutaneous anthrax developed in 9 persons, and 1 died. All affected persons had contact with the carcasses of infected animals. Comprehensive preparedness and response guidelines are needed to increase public awareness of anthrax in Bhutan.
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120
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Seyed-Mohamadi S, Moradi Bidhendi S, Tadayon K, Ghaderi R. Genetic Characterization of Bacillus anthracis 17 JB strain. IRANIAN JOURNAL OF MICROBIOLOGY 2015; 7:168-72. [PMID: 26668705 PMCID: PMC4676987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND AND OBJECTIVES Bacillus anthracis is one of the most homogenous bacteria ever described. Some level of diversity. Bacillus anthracis 17JB is a laboratory strain It is broadly used as a challenge strain in guinea pigs for potency test of anthrax vaccine. MATERIAL AND METHODS This work describes genetic characterization of B. anthracis 17 JB strain using the SNPs and MLVA genotyping. RESULTS AND CONCLUSION In SNPs typing, the originally French 17JB strain represented the A.Br. 008/009 subgroup. In Levy's genotyping method, 843, 451 and 864 bp long fragments were identified at AA03, AJ03 and AA07 loci, respectively. In the vaccine manufacturer perspective these findings are much valuable on their own account, but similar research is required to extend molecular knowledge of B. anthracis epidemiology in Persia.
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Affiliation(s)
| | - Soheila Moradi Bidhendi
- Department of Microbiology, Razi Institute, Karaj, Iran,Corresponding author: Soheila Moradi Bidhendi, PhD. Tel: +98-26-34502892, E-mail:
| | - Keyvan Tadayon
- Department of Aerobic Veterinary Bacteria, Razi Institute, Karaj, Iran
| | - Rainak Ghaderi
- Department of Aerobic Veterinary Bacteria, Razi Institute, Karaj, Iran
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121
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Derzelle S, Girault G, Roest HIJ, Koene M. Molecular diversity of Bacillus anthracis in the Netherlands: Investigating the relationship to the worldwide population using whole-genome SNP discovery. INFECTION GENETICS AND EVOLUTION 2015; 32:370-6. [DOI: 10.1016/j.meegid.2015.03.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 01/01/2023]
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122
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Ehrhardt CJ, Murphy DL, Robertson JM, Bannan JD. Fatty Acid Profiles for Differentiating Growth Medium Formulations Used to Culture Bacillus cereus T-strain Spores. J Forensic Sci 2015; 60:1022-9. [PMID: 25854710 DOI: 10.1111/1556-4029.12771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/20/2014] [Accepted: 07/21/2014] [Indexed: 12/31/2022]
Abstract
Microbial biomarkers that indicate aspects of an organism's growth conditions are important targets of forensic research. In this study, we examined fatty acid composition as a signature for the types of complex nutrients in the culturing medium. Bacillus cereus T-strain spores were grown in medium formulations supplemented with one of the following: peptone (meat protein), tryptone (casein protein), soy protein, and brain-heart infusion. Cellular biomass was profiled with fatty acid methyl ester (FAME) analysis. Results showed peptone cultures produced spores enriched in straight-chained lipids. Tryptone cultures produced spores enriched in branched-odd lipids when compared with peptone, soy, and brain-heart formulations. The observed FAME variation was used to construct a set of discriminant functions that could help identify the nutrients in a culturing recipe for an unknown spore sample. Blinded classification tests were most successful for spores grown on media containing peptone and tryptone, showing 88% and 100% correct identification, respectively.
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Affiliation(s)
- Christopher J Ehrhardt
- Department of Forensic Science, Virginia Commonwealth University, Grace E. Harris Hall South, 1015 Floyd Avenue, Richmond, VA
| | - Devonie L Murphy
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation, Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135.,Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation, Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135
| | - James M Robertson
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation, Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135
| | - Jason D Bannan
- Biological Program Science Advisor, Federal Bureau of Investigation, Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135
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123
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Brézillon C, Haustant M, Dupke S, Corre JP, Lander A, Franz T, Monot M, Couture-Tosi E, Jouvion G, Leendertz FH, Grunow R, Mock ME, Klee SR, Goossens PL. Capsules, toxins and AtxA as virulence factors of emerging Bacillus cereus biovar anthracis. PLoS Negl Trop Dis 2015; 9:e0003455. [PMID: 25830379 PMCID: PMC4382292 DOI: 10.1371/journal.pntd.0003455] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 12/04/2014] [Indexed: 11/18/2022] Open
Abstract
Emerging B. cereus strains that cause anthrax-like disease have been isolated in Cameroon (CA strain) and Côte d’Ivoire (CI strain). These strains are unusual, because their genomic characterisation shows that they belong to the B. cereus species, although they harbour two plasmids, pBCXO1 and pBCXO2, that are highly similar to the pXO1 and pXO2 plasmids of B. anthracis that encode the toxins and the polyglutamate capsule respectively. The virulence factors implicated in the pathogenicity of these B. cereus bv anthracis strains remain to be characterised. We tested their virulence by cutaneous and intranasal delivery in mice and guinea pigs; they were as virulent as wild-type B. anthracis. Unlike as described for pXO2-cured B. anthracis, the CA strain cured of the pBCXO2 plasmid was still highly virulent, showing the existence of other virulence factors. Indeed, these strains concomitantly expressed a hyaluronic acid (HA) capsule and the B. anthracis polyglutamate (PDGA) capsule. The HA capsule was encoded by the hasACB operon on pBCXO1, and its expression was regulated by the global transcription regulator AtxA, which controls anthrax toxins and PDGA capsule in B. anthracis. Thus, the HA and PDGA capsules and toxins were co-regulated by AtxA. We explored the respective effect of the virulence factors on colonisation and dissemination of CA within its host by constructing bioluminescent mutants. Expression of the HA capsule by itself led to local multiplication and, during intranasal infection, to local dissemination to the adjacent brain tissue. Co-expression of either toxins or PDGA capsule with HA capsule enabled systemic dissemination, thus providing a clear evolutionary advantage. Protection against infection by B. cereus bv anthracis required the same vaccination formulation as that used against B. anthracis. Thus, these strains, at the frontier between B. anthracis and B. cereus, provide insight into how the monomorphic B. anthracis may have emerged. Anthrax is caused by the bacterium Bacillus anthracis that affects all mammals worldwide. It emerged more than 10,000 years ago from a Bacillus cereus precursor. In the past decade, B. cereus bacteria were isolated in the USA from anthrax-like pneumonia cases. They harbour one virulence plasmid very similar to the toxin–encoding plasmid of B. anthracis. Recently, an anthrax-like disease in great apes in Africa was caused by emerging B. cereus strains, named B. cereus biovar anthracis. These strains are atypical as they possess both plasmids coding for toxin and capsule similar to those so far found only in B. anthracis. These unusual pathogenic B. cereus are currently neglected. We explored the virulence of these pathogens and their colonisation and dissemination capacity within the murine host. We found that these toxinogenic strains harbour two capsules, the classical B. anthracis capsule and an additional polysaccharidic capsule. This latter capsule confers virulence alone or in combination with toxins. Both capsules are concomitantly expressed, under the control of a common global regulator and host signals. Our results show that acquisition of new genetic information by these B. cereus clearly gives them a selective advantage, favouring their dissemination within infected hosts and the environment.
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Affiliation(s)
| | - Michel Haustant
- Institut Pasteur, Pathogénie des Toxi-Infections Bactériennes, Paris, France
| | - Susann Dupke
- Robert Koch-Institut, Centre for Biological Threats and Special Pathogens (ZBS 2), Berlin, Germany
| | - Jean-Philippe Corre
- Institut Pasteur, Pathogénie des Toxi-Infections Bactériennes, Paris, France
| | - Angelika Lander
- Robert Koch-Institut, Centre for Biological Threats and Special Pathogens (ZBS 2), Berlin, Germany
| | - Tatjana Franz
- Robert Koch-Institut, Centre for Biological Threats and Special Pathogens (ZBS 2), Berlin, Germany
| | - Marc Monot
- Institut Pasteur, Pathogenèse des bactéries anaérobies, Paris, France
| | | | - Gregory Jouvion
- Institut Pasteur, Unité Histopathologie Humaine et Modèles Animaux, Paris, France
| | - Fabian H. Leendertz
- Robert Koch-Institut, Epidemiology of Highly Pathogenic Microorganisms (P 3), Berlin, Germany
| | - Roland Grunow
- Robert Koch-Institut, Centre for Biological Threats and Special Pathogens (ZBS 2), Berlin, Germany
| | - Michèle E. Mock
- Institut Pasteur, Pathogénie des Toxi-Infections Bactériennes, Paris, France
| | - Silke R. Klee
- Robert Koch-Institut, Centre for Biological Threats and Special Pathogens (ZBS 2), Berlin, Germany
- * E-mail: (SRK); (PLG)
| | - Pierre L. Goossens
- Institut Pasteur, Pathogénie des Toxi-Infections Bactériennes, Paris, France
- * E-mail: (SRK); (PLG)
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Janzen TW, Thomas MC, Goji N, Shields MJ, Hahn KR, Amoako KK. Rapid detection method for Bacillus anthracis using a combination of multiplexed real-time PCR and pyrosequencing and its application for food biodefense. J Food Prot 2015; 78:355-61. [PMID: 25710151 DOI: 10.4315/0362-028x.jfp-14-216] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Bacillus anthracis, the causative agent of anthrax, has the capacity to form highly resilient spores as part of its life cycle. The potential for the dissemination of these spores using food as a vehicle is a huge public health concern and, hence, requires the development of a foodborne bioterrorism response approach. In this work, we address a critical gap in food biodefense by presenting a novel, combined, sequential method involving the use of real-time PCR and pyrosequencing for the rapid, specific detection of B. anthracis spores in three food matrices: milk, apple juice, and bottled water. The food samples were experimentally inoculated with 40 CFU ml(-1), and DNA was extracted from the spores and analyzed after immunomagnetic separation. Applying the combination of multiplex real-time PCR and pyrosequencing, we successfully detected the presence of targets on both of the virulence plasmids and the chromosome. The results showed that DNA amplicons generated from a five-target multiplexed real-time PCR detection using biotin-labeled primers can be used for single-plex pyrosequencing detection. The combined use of multiplexed real-time PCR and pyrosequencing is a novel, rapid detection method for B. anthracis from food and provides a tool for accurate, quantitative identification with potential biodefense applications.
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Affiliation(s)
- Timothy W Janzen
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Matthew C Thomas
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Noriko Goji
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Michael J Shields
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Kristen R Hahn
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Kingsley K Amoako
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4.
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Derzelle S. Single-nucleotide polymorphism discrimination using high-resolution melting analysis for the genotyping of Bacillus anthracis. Methods Mol Biol 2015; 1247:361-371. [PMID: 25399109 DOI: 10.1007/978-1-4939-2004-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
High-resolution melting (HRM) is a post-PCR technique that determines with high precision the melt profile of PCR products using a new generation of double-stranded DNA-binding dyes and accurate fluorescence data acquisition over small temperature increments. The method can be used to interrogate small sets of single-nucleotide polymorphisms (SNPs). Here, we describe a simple and cost-effective HRM-based method for the screening of 14 phylogenetically informative SNPs within the genome of Bacillus anthracis that subtype the species into 13 major sublineages or subgroups. Fourteen monoplex and seven duplex SNP-discrimination assays have been designed. We detail the parameters most important for the successful application of HRM for B. anthracis genotyping.
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Affiliation(s)
- Sylviane Derzelle
- Bacterial Zoonosis Unit, Animal Health Laboratory, University Paris-Est, Anses, 23 Avenue du Général de Gaulle, 94706, Maisons-Alfort Cedex, France,
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Rouli L, MBengue M, Robert C, Ndiaye M, La Scola B, Raoult D. Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium. New Microbes New Infect 2014; 2:161-9. [PMID: 25566394 PMCID: PMC4265047 DOI: 10.1002/nmi2.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/04/2014] [Accepted: 08/08/2014] [Indexed: 01/31/2023] Open
Abstract
Bacillus anthracis is the causative agent of anthrax and is classified as a
‘Category A’ biological weapon. Six complete genomes of
B. anthracis (A0248, Ames, Ames Ancestor, CDC684, H0491, and Sterne) are
currently available. In this report, we add three African strain genomes: Sen2Col2, Sen3 and Gmb1.
To study the pan-genome of B. anthracis, we used bioinformatics tools, such
as Cluster of Orthologous Groups, and performed phylogenetic analysis. We found that the three
African strains contained the pX01 and pX02 plasmids, the nonsense mutation in the
plcR gene and the four known prophages. These strains are most similar to the
CDC684 strain and belong to the A cluster. We estimated that the
B. anthracis pan-genome has 2893 core genes (99% of the genome size)
and 85 accessory genes. We validated the hypothesis that B. anthracis has a
closed pan-genome and found that the three African strains carry the two plasmids associated with
bacterial virulence. The pan-genome nature of B. anthracis confirms its lack
of exchange (similar to Clostridium tetani) and supports its exclusively pathogenic
role, despite its survival in the environment. Moreover, thanks to the study of the core content
single nucleotide polymorphisms, we can see that our three African strains diverged very recently
from the other B. anthracis strains.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - M MBengue
- Laboratoire National d'Elevage et des Recherches Vétérinaires (LNERV), Institut Sénégalais de Recherches Agricoles (ISRA) Hann, Dakar, Senegal
| | - C Robert
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - M Ndiaye
- Laboratoire de Biologie Cellulaire, Faculté des Sciences et Techniques de l'Université Cheikh Anta DIOP de Dakar (UCAD) Dakar, Senegal
| | - B La Scola
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
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TaqMan real-time PCR assays for single-nucleotide polymorphisms which identify Francisella tularensis and its subspecies and subpopulations. PLoS One 2014; 9:e107964. [PMID: 25238067 PMCID: PMC4169575 DOI: 10.1371/journal.pone.0107964] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/18/2014] [Indexed: 01/01/2023] Open
Abstract
Francisella tularensis, the etiologic agent of tularemia and a Class A Select Agent, is divided into three subspecies and multiple subpopulations that differ in virulence and geographic distribution. Given these differences, there is a need to rapidly and accurately determine if a strain is F. tularensis and, if it is, assign it to subspecies and subpopulation. We designed TaqMan real-time PCR genotyping assays using eleven single nucleotide polymorphisms (SNPs) that were potentially specific to closely related groups within the genus Francisella, including numerous subpopulations within F. tularensis species. We performed extensive validation studies to test the specificity of these SNPs to particular populations by screening the assays across a set of 565 genetically and geographically diverse F. tularensis isolates and an additional 21 genetic near-neighbor (outgroup) isolates. All eleven assays correctly determined the genetic groups of all 565 F. tularensis isolates. One assay differentiates F. tularensis, F. novicida, and F. hispaniensis from the more genetically distant F. philomiragia and Francisella-like endosymbionts. Another assay differentiates F. tularensis isolates from near neighbors. The remaining nine assays classify F. tularensis-confirmed isolates into F. tularensis subspecies and subpopulations. The genotyping accuracy of these nine assays diminished when tested on outgroup isolates (i.e. non F. tularensis), therefore a hierarchical approach of assay usage is recommended wherein the F. tularensis-specific assay is used before the nine downstream assays. Among F. tularensis isolates, all eleven assays were highly sensitive, consistently amplifying very low concentrations of DNA. Altogether, these eleven TaqMan real-time PCR assays represent a highly accurate, rapid, and sensitive means of identifying the species, subspecies, and subpopulation of any F. tularensis isolate if used in a step-wise hierarchical scheme. These assays would be very useful in clinical, epidemiological, and/or forensic investigations involving F. tularensis.
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Genome Sequence of Bacillus anthracis STI, a Sterne-Like Georgian/Soviet Vaccine Strain. GENOME ANNOUNCEMENTS 2014; 2:2/5/e00853-14. [PMID: 25237016 PMCID: PMC4172265 DOI: 10.1128/genomea.00853-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Bacillus anthracis strain STI is a Soviet vaccine strain that lacks the pXO2 plasmid. Previous data indicate that this isolate forms a new branch within the B. anthracis sub-group originally identified as A. Br.008/009.
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129
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Kingston JJ, Majumder S, Uppalapati SR, Makam SS, Urs RM, Murali HS, Batra HV. Anthrax Outbreak Among Cattle and its Detection by Extractable Antigen 1 (EA1) Based Sandwich ELISA and Immuno PCR. Indian J Microbiol 2014. [DOI: 10.1007/s12088-014-0494-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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130
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Hanczaruk M, Reischl U, Holzmann T, Frangoulidis D, Wagner DM, Keim PS, Antwerpen MH, Meyer H, Grass G. Injectional anthrax in heroin users, Europe, 2000-2012. Emerg Infect Dis 2014; 20:322-3. [PMID: 24447525 PMCID: PMC3901468 DOI: 10.3201/eid2002.120921] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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132
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Source tracking of an anthrax outbreak in northeastern China using complete genome analysis and MLVA genotyping. Eur J Clin Microbiol Infect Dis 2014; 34:89-100. [DOI: 10.1007/s10096-014-2195-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/22/2014] [Indexed: 11/26/2022]
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Draft Genomes of Three Strains Representative of the Bacillus anthracis Diversity Found in France. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00736-14. [PMID: 25081258 PMCID: PMC4118061 DOI: 10.1128/genomea.00736-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genomes of three Bacillus anthracis strains isolated in France: 08-8_20 (A.Br.001/002), 99-100 (A.Br.011/009), and 00-82 (B.Br CNEVA). The total lengths of assemblies are 5,440,708 bp, 5,446,472 bp, and 5,436,014 bp for 08-8_20, 99-100, and 00-82, respectively.
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Khmaladze E, Birdsell DN, Naumann AA, Hochhalter CB, Seymour ML, Nottingham R, Beckstrom-Sternberg SM, Beckstrom-Sternberg J, Nikolich MP, Chanturia G, Zhgenti E, Zakalashvili M, Malania L, Babuadze G, Tsertsvadze N, Abazashvili N, Kekelidze M, Tsanava S, Imnadze P, Ganz HH, Getz WM, Pearson O, Gajer P, Eppinger M, Ravel J, Wagner DM, Okinaka RT, Schupp JM, Keim P, Pearson T. Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes. PLoS One 2014; 9:e102651. [PMID: 25047912 PMCID: PMC4105404 DOI: 10.1371/journal.pone.0102651] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 06/21/2014] [Indexed: 11/19/2022] Open
Abstract
Sequence analyses and subtyping of Bacillus anthracis strains from Georgia reveal a single distinct lineage (Aust94) that is ecologically established. Phylogeographic analysis and comparisons to a global collection reveals a clade that is mostly restricted to Georgia. Within this clade, many groups are found around the country, however at least one subclade is only found in the eastern part. This pattern suggests that dispersal into and out of Georgia has been rare and despite historical dispersion within the country, for at least for one lineage, current spread is limited.
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Affiliation(s)
- Ekaterine Khmaladze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Dawn N. Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Amber A. Naumann
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Christian B. Hochhalter
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Meagan L. Seymour
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne Nottingham
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - James Beckstrom-Sternberg
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mikeljon P. Nikolich
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Gvantsa Chanturia
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Ekaterine Zhgenti
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | | | - Lile Malania
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Giorgi Babuadze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | | | | | - Merab Kekelidze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Shota Tsanava
- National Center for Disease Control and Public Health, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Paata Imnadze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Holly H. Ganz
- Department Environmental Science Policy and Management, University of California, Berkeley, California, United States of America
| | - Wayne M. Getz
- Department Environmental Science Policy and Management, University of California, Berkeley, California, United States of America
| | - Ofori Pearson
- US Geological Survey, Denver Federal Center, Denver, Colorado, United States of America
| | - Pawel Gajer
- Institute for Genome Sciences, Baltimore, Maryland, United States of America
| | - Mark Eppinger
- Institute for Genome Sciences, Baltimore, Maryland, United States of America
- University of Texas at San Antonio, Texas, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, Baltimore, Maryland, United States of America
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard T. Okinaka
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Schupp
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
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135
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Derzelle S, Thierry S. Genetic diversity of Bacillus anthracis in Europe: genotyping methods in forensic and epidemiologic investigations. Biosecur Bioterror 2014; 11 Suppl 1:S166-76. [PMID: 23971802 DOI: 10.1089/bsp.2013.0003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacillus anthracis, the etiological agent of anthrax, a zoonosis relatively common throughout the world, can be used as an agent of bioterrorism. In naturally occurring outbreaks and in criminal release of this pathogen, a fast and accurate diagnosis is crucial to an effective response. Microbiological forensics and epidemiologic investigations increasingly rely on molecular markers, such as polymorphisms in DNA sequence, to obtain reliable information regarding the identification or source of a suspicious strain. Over the past decade, significant research efforts have been undertaken to develop genotyping methods with increased power to differentiate B. anthracis strains. A growing number of DNA signatures have been identified and used to survey B. anthracis diversity in nature, leading to rapid advances in our understanding of the global population of this pathogen. This article provides an overview of the different phylogenetic subgroups distributed across the world, with a particular focus on Europe. Updated information on the anthrax situation in Europe is reported. A brief description of some of the work in progress in the work package 5.1 of the AniBioThreat project is also presented, including (1) the development of a robust typing tool based on a suspension array technology and multiplexed single nucleotide polymorphisms scoring and (2) the typing of a collection of DNA from European isolates exchanged between the partners of the project. The know-how acquired will contribute to improving the EU's ability to react rapidly when the identity and real origin of a strain need to be established.
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136
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Recent literature review of soil processing methods for recovery of Bacillus anthracis spores. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0932-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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137
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Thierry S, Tourterel C, Le Flèche P, Derzelle S, Dekhil N, Mendy C, Colaneri C, Vergnaud G, Madani N. Genotyping of French Bacillus anthracis strains based on 31-loci multi locus VNTR analysis: epidemiology, marker evaluation, and update of the internet genotype database. PLoS One 2014; 9:e95131. [PMID: 24901417 PMCID: PMC4046976 DOI: 10.1371/journal.pone.0095131] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 03/24/2014] [Indexed: 12/28/2022] Open
Abstract
Background Bacillus anthracis is known to have low genetic variability. In spite of this lack of diversity, multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) and single nucleotide polymorphisms (SNPs) including the canonical SNPs assay (canSNP) have proved to be highly effective to differentiate strains. Five different MLVA schemes based on a collection of 31 VNTR loci (MLVA8, MLVA15, MLVA20, MLVA25 and MLVA31) with increased resolving power have been described. Results MLVA31 was applied to characterize the French National Reference Laboratory collection. The total collection of 130 strains is resolved in 35 genotypes. The 119 veterinary and environmental strains collection in France were resolved into 26 genotypes belonging to three canSNP lineages and four MLVA clonal complexes (CCs) with particular geographical clustering. A subset of seven loci (MLVA7) is proposed to constitute a first line assay. The loci are compatible with moderate resolution equipment such as agarose gel electrophoresis and show a good congruence value with MLVA31. The associated MLVA and SNP data was imported together with published genotyping data by taking advantage of major enhancements to the MLVAbank software and web site. Conclusions The present report provides a wide coverage of the genetic diversity of naturally occurring B. anthracis strains in France as can be revealed by MLVA. The data obtained suggests that once such coverage is achieved, it becomes possible to devise optimized first-line MLVA assays comprising a sufficiently low number of loci to be typed either in one multiplex PCR or on agarose gels. Such a selection of seven loci is proposed here, and future similar investigations in additional countries will indicate to which extend the same selection can be used worldwide as a common minimum set. It is hoped that this approach will contribute to an efficient and low-cost routine surveillance of important pathogens for biosecurity such as B. anthracis.
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Affiliation(s)
- Simon Thierry
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Christophe Tourterel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Philippe Le Flèche
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Division of Analytical Microbiology, DGA CBRN Defence, Vert le Petit, France
| | - Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Neira Dekhil
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Christiane Mendy
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Cécile Colaneri
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Gilles Vergnaud
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- DGA/MRIS- Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France
| | - Nora Madani
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
- * E-mail:
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Girault G, Blouin Y, Vergnaud G, Derzelle S. High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery. BMC Genomics 2014; 15:288. [PMID: 24734872 PMCID: PMC4023602 DOI: 10.1186/1471-2164-15-288] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/09/2014] [Indexed: 11/10/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) are ideal signatures for subtyping monomorphic pathogens such as Bacillus anthracis. Here we report the use of next-generation sequencing technology to investigate the historical, geographic and genetic diversity of Bacillus anthracis in France. 122 strains isolated over a 60-years period throughout the country were whole-genome sequenced and comparative analyses were carried out with a focus on SNPs discovery to discriminate regional sub-groups of strains. Results A total of 1581 chromosomal SNPs precisely establish the phylogenetic relationships existing between the French strains. Phylogeography patterns within the three canSNP sub-lineages present in France (i.e. B.Br.CNEVA, A.Br.011/009 and A.Br.001/002) were observed. One of the more remarkable findings was the identification of a variety of genotypes within the A.Br.011/009 sub-group that are persisting in the different regions of France. The 560 SNPs defining the A.Br.011/009- affiliated French strains split the Trans-Eurasian sub-group into six distinct branches without any intermediate nodes. Distinct sub-branches, with some geographic clustering, were resolved. The 345 SNPs defining the major B.Br CNEVA sub-lineage clustered three main phylogeographic clades, the Alps, the Pyrenees, and the Massif Central, with a small Saône-et-Loire sub-cluster nested within the latter group. The French strains affiliated to the minor A.Br.001/002 group were characterized by 226 SNPs. All recent isolates collected from the Doubs department were closely related. Identification of SNPs from whole-genome sequences facilitates high-resolution strain tracking and provides the level of discrimination required for outbreak investigations. Eight diagnostic SNPs, representative of the main French-specific phylogeographic clusters, were therefore selected and developed into high-resolution melting SNP discriminative assays. Conclusions This work has established one of the most accurate phylogenetic reconstruction of B. anthracis population structure in a country. An extensive next-generation sequencing (NGS) dataset of 122 French strains have been created that allowed the identification of novel diagnostic SNPs useful to rapidly determine the geographic origin of any strain found in France.
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Affiliation(s)
| | | | | | - Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort 94706, France.
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Lärkeryd A, Myrtennäs K, Karlsson E, Dwibedi CK, Forsman M, Larsson P, Johansson A, Sjödin A. CanSNPer: a hierarchical genotype classifier of clonal pathogens. Bioinformatics 2014; 30:1762-4. [PMID: 24574113 DOI: 10.1093/bioinformatics/btu113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SUMMARY Advances in typing methodologies have recently reformed the field of molecular epidemiology of pathogens. The falling cost of sequencing technologies is creating a deluge of whole genome sequencing data that burdens bioinformatics resources and tool development. In particular, single nucleotide polymorphisms in core genomes of pathogens are recognized as the most important markers for inferring genetic relationships because they are evolutionarily stable and amenable to high-throughput detection methods. Sequence data will provide an excellent opportunity to extend our understanding of infectious disease when the challenge of extracting knowledge from available sequence resources is met. Here, we present an efficient and user-friendly genotype classification pipeline, CanSNPer, based on an easily expandable database of predefined canonical single nucleotide polymorphisms. AVAILABILITY AND IMPLEMENTATION All documentation and Python-based source code for the CanSNPer are freely available at http://github.com/adrlar/CanSNPer.
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Affiliation(s)
- Adrian Lärkeryd
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Kerstin Myrtennäs
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Edvin Karlsson
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Chinmay Kumar Dwibedi
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, SwedenDepartment of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Mats Forsman
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Pär Larsson
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Andreas Sjödin
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, SwedenDepartment of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
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140
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Marakeby H, Badr E, Torkey H, Song Y, Leman S, Monteil CL, Heath LS, Vinatzer BA. A system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature. PLoS One 2014; 9:e89142. [PMID: 24586551 PMCID: PMC3931686 DOI: 10.1371/journal.pone.0089142] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/14/2014] [Indexed: 11/29/2022] Open
Abstract
A broadly accepted and stable biological classification system is a prerequisite for biological sciences. It provides the means to describe and communicate about life without ambiguity. Current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. The current system is thus inadequate to classify and name the immense genetic diversity within species that is now being revealed by genome sequencing on a daily basis. To address this lack of a general intra-species classification and naming system adequate for today's speed of discovery of new diversity, we propose a classification and naming system that is exclusively based on genome similarity and that is suitable for automatic assignment of codes to any genome-sequenced organism without requiring any phenotypic or phylogenetic analysis. We provide examples demonstrating that genome similarity-based codes largely align with current taxonomic groups at many different levels in bacteria, animals, humans, plants, and viruses. Importantly, the proposed approach is only slightly affected by the order of code assignment and can thus provide codes that reflect similarity between organisms and that do not need to be revised upon discovery of new diversity. We envision genome similarity-based codes to complement current biological nomenclature and to provide a universal means to communicate unambiguously about any genome-sequenced organism in fields as diverse as biodiversity research, infectious disease control, human and microbial forensics, animal breed and plant cultivar certification, and human ancestry research.
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Affiliation(s)
- Haitham Marakeby
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Eman Badr
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Hanaa Torkey
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Yuhyun Song
- Department of Statistics, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Scotland Leman
- Department of Statistics, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Caroline L. Monteil
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
- INRA, UR0407 Pathologie Végétale; Montfavet, France
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
- This Genomic Life Inc., Blacksburg, Virginia, United States of America
| | - Boris A. Vinatzer
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
- This Genomic Life Inc., Blacksburg, Virginia, United States of America
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141
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Ågren J, Finn M, Bengtsson B, Segerman B. Microevolution during an Anthrax outbreak leading to clonal heterogeneity and penicillin resistance. PLoS One 2014; 9:e89112. [PMID: 24551231 PMCID: PMC3923885 DOI: 10.1371/journal.pone.0089112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/18/2014] [Indexed: 12/22/2022] Open
Abstract
Anthrax is a bacterial disease primarily affecting grazing animals but it can also cause severe disease in humans. We have used genomic epidemiology to study microevolution of the bacterium in a confined outbreak in cattle which involved emergence of an antibiotic-resistant phenotype. At the time of death, the animals contained a heterogeneous population of Single Nucleotide Variants (SNVs), some being clonal but most being subclonal. We found that independent isolates from the same carcass had similar levels of SNV differences as isolates from different animals. Furthermore the relative levels of subclonal populations were different in different locations in the same carcass. The heterogeneity appeared to be derived in part from heterogeneity in the infectious dose. The resistance phenotype was linked to clonal mutations in an anti-sigma factor gene and in one case was preceded by an acquisition of a hypermutator phenotype. In another animal, small subclonal populations were observed with counteracting mutations that had turned off the resistance genes. In summary, this study shows the importance of accounting for both acquired and inherited heterogeneity when doing high-resolution infection tracing and when estimating the risks associated with penicillin treatment.
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Affiliation(s)
- Joakim Ågren
- Department of Bacteriology, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Maria Finn
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Björn Bengtsson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Bo Segerman
- Department of Bacteriology, National Veterinary Institute (SVA), Uppsala, Sweden
- * E-mail:
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142
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Selvaraj C, Sivakamavalli J, Baskaralingam V, Singh SK. Virtual screening of LPXTG competitive SrtA inhibitors targeting signal transduction mechanism in Bacillus anthracis: a combined experimental and theoretical study. J Recept Signal Transduct Res 2014; 34:221-32. [PMID: 24490975 DOI: 10.3109/10799893.2013.876044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Members of the sortase enzyme super family decorate the surfaces of Bacillus anthracis cell wall with proteins that play key roles in microbial pathogenesis and its biofilm formation. Bacillus anthracis Sortase-A (Ba-SrtA) is a potential target for new therapeutics as it is required for B. anthracis survival and replication within macrophages. An understanding of the binding site pocket and substrate recognition mechanism by SrtA enzymes may serve to be beneficial in the rational development of sortase inhibitors. Here, the LPXTG signal peptide-based competitive inhibitors are screened against the Ba-SrtA and compounds with reasonable inhibition, specificity, and mechanisms of inactivation of SrtA have been covered. The screened compounds are experimentally validated against the phylogenetically similar Gram-positive pathogen B. cereus. In situ microscopic visualizations suggest that these screened compounds showed the microbial and biofilm inhibitory activity against B. cereus. It facilitates the further development of these molecules into useful anti-infective agents to treat infections caused by B. anthracis and other Gram-positive pathogens. These results provide insight into basic design principles for generating new clinically relevant lead molecules. It also provides an alternative strategy where a screened ligand molecule can be used in combination to battle increasingly against the Gram-positive pathogens.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University , Karaikudi, Tamil Nadu , India and
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143
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Hanczaruk M, Reischl U, Holzmann T, Frangoulidis D, Wagner DM, Keim PS, Antwerpen MH, Meyer H, Grass G. Injectional Anthrax in Heroin Users, Europe, 2000–2012. Emerg Infect Dis 2014. [DOI: 10.3201/eid1302/120921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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144
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Karlsson E, Macellaro A, Byström M, Forsman M, Frangoulidis D, Janse I, Larsson P, Lindgren P, Öhrman C, van Rotterdam B, Sjödin A, Myrtennäs K. Eight new genomes and synthetic controls increase the accessibility of rapid melt-MAMA SNP typing of Coxiella burnetii. PLoS One 2014; 9:e85417. [PMID: 24465554 PMCID: PMC3897454 DOI: 10.1371/journal.pone.0085417] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/26/2013] [Indexed: 11/19/2022] Open
Abstract
The case rate of Q fever in Europe has increased dramatically in recent years, mainly because of an epidemic in the Netherlands in 2009. Consequently, there is a need for more extensive genetic characterization of the disease agent Coxiella burnetii in order to better understand the epidemiology and spread of this disease. Genome reference data are essential for this purpose, but only thirteen genome sequences are currently available. Current methods for typing C. burnetii are criticized for having problems in comparing results across laboratories, require the use of genomic control DNA, and/or rely on markers in highly variable regions. We developed in this work a method for single nucleotide polymorphism (SNP) typing of C. burnetii isolates and tissue samples based on new assays targeting ten phylogenetically stable synonymous canonical SNPs (canSNPs). These canSNPs represent previously known phylogenetic branches and were here identified from sequence comparisons of twenty-one C. burnetii genomes, eight of which were sequenced in this work. Importantly, synthetic control templates were developed, to make the method useful to laboratories lacking genomic control DNA. An analysis of twenty-one C. burnetii genomes confirmed that the species exhibits high sequence identity. Most of its SNPs (7,493/7,559 shared by >1 genome) follow a clonal inheritance pattern and are therefore stable phylogenetic typing markers. The assays were validated using twenty-six genetically diverse C. burnetii isolates and three tissue samples from small ruminants infected during the epidemic in the Netherlands. Each sample was assigned to a clade. Synthetic controls (vector and PCR amplified) gave identical results compared to the corresponding genomic controls and are viable alternatives to genomic DNA. The results from the described method indicate that it could be useful for cheap and rapid disease source tracking at non-specialized laboratories, which requires accurate genotyping, assay accessibility and inter-laboratory comparisons.
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Affiliation(s)
- Edvin Karlsson
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Anna Macellaro
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Mona Byström
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | | | - Ingmar Janse
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Pär Larsson
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Petter Lindgren
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Bart van Rotterdam
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Andreas Sjödin
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Kerstin Myrtennäs
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
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145
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Single nucleotide repeat analysis of B. anthracis isolates in Canada through comparison of pyrosequencing and Sanger sequencing. Vet Microbiol 2014; 169:228-32. [PMID: 24485934 DOI: 10.1016/j.vetmic.2013.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/16/2013] [Accepted: 12/21/2013] [Indexed: 11/23/2022]
Abstract
Several technology platforms have been developed to resolve the phylogenetic placement of B. anthracis. However, these methods lack the resolution to identify differences between closely related strains within an outbreak due to the highly clonal nature of B. anthracis. Single Nucleotide Repeats (SNRs) are a type of rapidly evolving genetic marker that can be used to track epidemiological distribution in the event of an outbreak. Four SNR targets were used to detect and type 35 B. anthracis isolates in our collection; 18 from across Canada obtained between 1972 and 2005 and 17 from the 2006 Anthrax outbreak in north eastern Saskatchewan. A control sequence was developed for pyrosequencing which yielded consistent and accurate reads of SNRs. However, when DNA from the isolates was tested using pyrosequencing the results were inconsistent and did not reflect the number of SNRs obtained by Sanger sequencing. The SNR numbers derived from the Sanger sequencing show two of the four SNR loci could provide information on subtype, whereas the other two were not discriminatory. There is variation in SNRs between strains isolated from different outbreaks, the subset of 2006 outbreak strains showed very little difference in SNR number, and thus suggests low diversity among the strains sampled from the same outbreak.
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146
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Chenau J, Fenaille F, Caro V, Haustant M, Diancourt L, Klee SR, Junot C, Ezan E, Goossens PL, Becher F. Identification and validation of specific markers of Bacillus anthracis spores by proteomics and genomics approaches. Mol Cell Proteomics 2013; 13:716-32. [PMID: 24379445 DOI: 10.1074/mcp.m113.032946] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bacillus anthracis is the causative bacteria of anthrax, an acute and often fatal disease in humans. The infectious agent, the spore, represents a real bioterrorism threat and its specific identification is crucial. However, because of the high genomic relatedness within the Bacillus cereus group, it is still a real challenge to identify B. anthracis spores confidently. Mass spectrometry-based tools represent a powerful approach to the efficient discovery and identification of such protein markers. Here we undertook comparative proteomics analyses of Bacillus anthracis, cereus and thuringiensis spores to identify proteoforms unique to B. anthracis. The marker discovery pipeline developed combined peptide- and protein-centric approaches using liquid chromatography coupled to tandem mass spectrometry experiments using a high resolution/high mass accuracy LTQ-Orbitrap instrument. By combining these data with those from complementary bioinformatics approaches, we were able to highlight a dozen novel proteins consistently observed across all the investigated B. anthracis spores while being absent in B. cereus/thuringiensis spores. To further demonstrate the relevance of these markers and their strict specificity to B. anthracis, the number of strains studied was extended to 55, by including closely related strains such as B. thuringiensis 9727, and above all the B. cereus biovar anthracis CI, CA strains that possess pXO1- and pXO2-like plasmids. Under these conditions, the combination of proteomics and genomics approaches confirms the pertinence of 11 markers. Genes encoding these 11 markers are located on the chromosome, which provides additional targets complementary to the commonly used plasmid-encoded markers. Last but not least, we also report the development of a targeted liquid chromatography coupled to tandem mass spectrometry method involving the selection reaction monitoring mode for the monitoring of the 4 most suitable protein markers. Within a proof-of-concept study, we demonstrate the value of this approach for the further high throughput and specific detection of B. anthracis spores within complex samples.
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Affiliation(s)
- Jérôme Chenau
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France
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147
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Maâtallah M, Bakhrouf A, Habeeb MA, Turlej-Rogacka A, Iversen A, Pourcel C, Sioud O, Giske CG. Four genotyping schemes for phylogenetic analysis of Pseudomonas aeruginosa: comparison of their congruence with multi-locus sequence typing. PLoS One 2013; 8:e82069. [PMID: 24349186 PMCID: PMC3859543 DOI: 10.1371/journal.pone.0082069] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/21/2013] [Indexed: 11/28/2022] Open
Abstract
Several molecular typing schemes have been proposed to differentiate among isolates and clonal groups, and hence establish epidemiological or phylogenetic links. It has been widely accepted that multi-locus sequence typing (MLST) is the gold standard for phylogenetic typing/long-term epidemiological surveillance, but other recently described methods may be easier to carry out, especially in settings with limited access to DNA sequencing. Comparing the performance of such techniques to MLST is therefore of relevance. A study was therefore carried out with a collection of P. aeruginosa strains (n = 133) typed by four typing schemes: MLST, multiple-locus variable number tandem repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE) and the commercial DiversiLab microbial typing system (DL). The aim of this study was to compare the results of each typing method with MLST. The Simpson's indices of diversity were 0.989, 0.980, 0.961 and 0.906 respectively for PFGE, MLVA, DL and MLST. The congruence between techniques was measured by the adjusted Wallace index (W): this coefficient indicates the probability that a pair of isolates which is assigned to the same type by one typing method is also typed as identical by the other. In this context, the congruence between techniques was recorded as follow: MLVA-type to predict MLST-type (93%), PFGE to MLST (92%), DL to MLST (64.2%), PFGE to MLVA (63.5%) and PFGE to DL (61.7%). Conversely, for all above combinations, prediction was very poor. The congruence was increased at the clonal complex (CC) level. MLST is regarded the gold standard for phylogenetic classification of bacteria, but is rather laborious to carry out in many settings. Our data suggest that MLVA can predict the MLST-type with high accuracy, and even higher when studying the clonal complex level. Of the studied three techniques MLVA was therefore the best surrogate method to predict MLST.
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Affiliation(s)
- Makaoui Maâtallah
- Laboratoire d'Analyse, Traitement et Valorisation des Polluants de l'Environnement et des Produits, Faculté de Pharmacie, Monastir, Tunisia
| | - Amina Bakhrouf
- Laboratoire d'Analyse, Traitement et Valorisation des Polluants de l'Environnement et des Produits, Faculté de Pharmacie, Monastir, Tunisia
| | - Muhammed Asif Habeeb
- Clinical Microbiology L2:02, MTC – Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Agata Turlej-Rogacka
- Clinical Microbiology L2:02, MTC – Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Aina Iversen
- Clinical Microbiology L2:02, MTC – Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Christine Pourcel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, Orsay, France
- CNRS, Orsay, France
| | - Olfa Sioud
- Laboratoire de Microbiologie CHU Fattouma Bourguiba, Monastir, Tunisia
| | - Christian G. Giske
- Clinical Microbiology L2:02, MTC – Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
- * E-mail:
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148
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Host-nonspecific iron acquisition systems and virulence in the zoonotic serovar of Vibrio vulnificus. Infect Immun 2013; 82:731-44. [PMID: 24478087 DOI: 10.1128/iai.01117-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The zoonotic serovar of Vibrio vulnificus (known as biotype 2 serovar E) is the etiological agent of human and fish vibriosis. The aim of the present work was to discover the role of the vulnibactin- and hemin-dependent iron acquisition systems in the pathogenicity of this zoonotic serovar under the hypothesis that both are host-nonspecific virulence factors. To this end, we selected three genes for three outer membrane receptors (vuuA, a receptor for ferric vulnibactin, and hupA and hutR, two hemin receptors), obtained single and multiple mutants as well as complemented strains, and tested them in a series of in vitro and in vivo assays, using eels and mice as animal models. The overall results confirm that hupA and vuuA, but not hutR, are host-nonspecific virulence genes and suggest that a third undescribed host-specific plasmid-encoded system could also be used by the zoonotic serovar in fish. hupA and vuuA were expressed in the internal organs of the animals in the first 24 h of infection, suggesting that they may be needed to achieve the population size required to trigger fatal septicemia. vuuA and hupA were sequenced in strains representative of the genetic diversity of this species, and their phylogenies were reconstructed by multilocus sequence analysis of selected housekeeping and virulence genes as a reference. Given the overall results, we suggest that both genes might form part of the core genes essential not only for disease development but also for the survival of this species in its natural reservoir, the aquatic environment.
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149
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A multiplex bead-based suspension array assay for interrogation of phylogenetically informative single nucleotide polymorphisms for Bacillus anthracis. J Microbiol Methods 2013; 95:357-65. [DOI: 10.1016/j.mimet.2013.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 10/06/2013] [Indexed: 11/24/2022]
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150
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Mullins JC, Garofolo G, Van Ert M, Fasanella A, Lukhnova L, Hugh-Jones ME, Blackburn JK. Ecological niche modeling of Bacillus anthracis on three continents: evidence for genetic-ecological divergence? PLoS One 2013; 8:e72451. [PMID: 23977300 PMCID: PMC3747089 DOI: 10.1371/journal.pone.0072451] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/16/2013] [Indexed: 11/18/2022] Open
Abstract
We modeled the ecological niche of a globally successful Bacillus anthracis sublineage in the United States, Italy and Kazakhstan to better understand the geographic distribution of anthrax and potential associations between regional populations and ecology. Country-specific ecological-niche models were developed and reciprocally transferred to the other countries to determine if pathogen presence could be accurately predicted on novel landscapes. Native models accurately predicted endemic areas within each country, but transferred models failed to predict known occurrences in the outside countries. While the effects of variable selection and limitations of the genetic data should be considered, results suggest differing ecological associations for the B. anthracis populations within each country and may reflect niche specialization within the sublineage. Our findings provide guidance for developing accurate ecological niche models for this pathogen; models should be developed regionally, on the native landscape, and with consideration to population genetics. Further genomic analysis will improve our understanding of the genetic-ecological dynamics of B. anthracis across these countries and may lead to more refined predictive models for surveillance and proactive vaccination programs. Further studies should evaluate the impact of variable selection of native and transferred models.
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Affiliation(s)
- Jocelyn C. Mullins
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Giuliano Garofolo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
- Anthrax Reference Institute of Italy, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Matthew Van Ert
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Antonio Fasanella
- Anthrax Reference Institute of Italy, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Larisa Lukhnova
- Anthrax Laboratory, Kazakh Science Center for Quarantine and Zoonotic Diseases, Almaty, Kazakhstan
| | - Martin E. Hugh-Jones
- Department of Environmental Sciences, School of the Coast and Environment, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jason K. Blackburn
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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