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Bassy O, Antwerpen M, Ortega-García MV, Ortega-Sánchez MJ, Bouzada JA, Cabria-Ramos JC, Grass G. Spanish Outbreak Isolates Bridge Phylogenies of European and American Bacillus anthracis. Microorganisms 2023; 11:microorganisms11040889. [PMID: 37110312 PMCID: PMC10146487 DOI: 10.3390/microorganisms11040889] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023] Open
Abstract
The geographical origin of a major present-day phylogenetic group (A branch WNA; A.Br.WNA) of American Bacillus anthracis is controversial. One hypothesis postulated that the anthrax pathogen reached North America via a then-existing land bridge from northeastern Asia thousands of years ago. A competing hypothesis suggested that B. anthracis was introduced to America a couple of hundred years ago, related to European colonization. The latter view is strongly supported by genomic analysis of a group of French B. anthracis isolates that are phylogenetically closely related to the North American strains of the A branch A.Br.WNA clade. In addition, three West African strains also belong to this relationship group. Recently, we have added a Spanish strain to these close relatives of the WNA lineage of American B. anthracis. Nevertheless, the diversity of Spanish B. anthracis remains largely unexplored, and phylogenetic links to European or American relatives are not well resolved. Here, we genome sequenced and characterized 29 new B. anthracis isolates (yielding 18 unique genotypes) from outbreaks in west central and central Spain in 2021. Applying comparative chromosomal analysis, we placed the chromosomes of these isolates within the established phylogeny of the A.Br.008/009 (A.Br.TEA) canonical SNP group. From this analysis, a new sub-clade, named A.Br.11/ESPc, emerged that constitutes a sister group of American A.Br.WNA.
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Affiliation(s)
- Olga Bassy
- Chemical, Biological, Radiological and Nuclear (CBRN) Defence Systems Department, Campus La Marañosa, Instituto Nacional de Técnica Aeroespacial “Esteban Terradas” (INTA), 28330 San Martín de la Vega, Madrid, Spain
| | - Markus Antwerpen
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany
| | - María Victoria Ortega-García
- Chemical, Biological, Radiological and Nuclear (CBRN) Defence Systems Department, Campus La Marañosa, Instituto Nacional de Técnica Aeroespacial “Esteban Terradas” (INTA), 28330 San Martín de la Vega, Madrid, Spain
| | - María Jesús Ortega-Sánchez
- Laboratorio Central de Sanidad Animal (LCSA), Ministerio de Agricultura Pesca y Alimentación (MAPA), 18320 Santa Fe, Granada, Spain
| | - José Antonio Bouzada
- Laboratorio Central de Veterinaria, Ministerio de Agricultura Pesca y Alimentación (MAPA), 28110 Algete, Madrid, Spain
| | - Juan Carlos Cabria-Ramos
- Chemical, Biological, Radiological and Nuclear (CBRN) Defence Systems Department, Campus La Marañosa, Instituto Nacional de Técnica Aeroespacial “Esteban Terradas” (INTA), 28330 San Martín de la Vega, Madrid, Spain
| | - Gregor Grass
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany
- Correspondence: ; Tel.: +49-992692-3981
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Braun P, Beyer W, Hanczaruk M, Riehm JM, Antwerpen M, Otterbein C, Oesterheld J, Grass G. Reoccurring bovine anthrax in Germany on the same pasture after 12 years. J Clin Microbiol 2022;:jcm0229121. [PMID: 35195442 DOI: 10.1128/jcm.02291-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The zoonotic disease anthrax, caused by the endospore-forming bacterium Bacillus anthracis, is very rare in Germany. In the state of Bavaria, the last case occurred in July of 2009, resulting in four dead cows. In August of 2021, the disease reemerged after heavy rains, killing one gestating cow. Notably, both outbreaks affected the same pasture, suggesting a close epidemiological connection. B. anthracis could be grown from blood culture, and the presence of both virulence plasmids (pXO1 and pXO2) was confirmed by PCR. Also, recently developed diagnostic tools enabled rapid detection of B. anthracis cells and nucleic acids directly in clinical samples. The complete genome of the strain isolated from blood, designated BF-5, was DNA sequenced and phylogenetically grouped within the B.Br.CNEVA clade, which is typical for European B. anthracis strains. The genome was almost identical to BF-1, the isolate from 2009, separated only by three single nucleotide polymorphisms (SNPs) on the chromosome, one on plasmid pXO2 and three indel regions. Further, B. anthracis DNA was detected by PCR from soil samples taken from spots in the pasture where the cow had fallen. New tools based on phage receptor-binding proteins enabled the microscopic detection and isolation of B. anthracis directly from soil samples. These environmental isolates were genotyped and found to be identical to BF-5 in terms of SNPs. Therefore, it seems that the BF-5 genotype is currently the prevalent one at the affected premises. The area contaminated by the cadaver was subsequently disinfected with formaldehyde.
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Brangsch H, Golovko A, Pinchuk N, Deriabin O, Kyselova T, Linde J, Melzer F, Elschner MC. Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques. Microorganisms 2022; 10:microorganisms10020461. [PMID: 35208915 PMCID: PMC8875922 DOI: 10.3390/microorganisms10020461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining long- and short-read next-generation sequencing techniques, highly accurate genomes were reconstructed, enabling detailed in silico genotyping. Thus, the strains could be assigned to the Tsiankovskii subgroup of the “TransEurAsia” clade, which is commonly found in this region. Their high genetic similarity suggests that the four strains are members of the endemic population whose progenitor was once introduced in the Ukraine and bordering regions. This study provides information on B. anthracis strains from a region where there is little knowledge of the local population, thereby adding to the picture of global B. anthracis genotype distribution. We also emphasize the importance of surveillance and prevention methods regarding anthrax outbreaks, as other studies predicted a higher number of cases in the future due to global warming.
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Affiliation(s)
- Hanka Brangsch
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
- Correspondence:
| | - Anatolii Golovko
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Nataliia Pinchuk
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Oleg Deriabin
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Tetiana Kyselova
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Jörg Linde
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| | - Falk Melzer
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| | - Mandy Carolina Elschner
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
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Abdel-Glil MY, Chiaverini A, Garofolo G, Fasanella A, Parisi A, Harmsen D, Jolley KA, Elschner MC, Tomaso H, Linde J, Galante D. A Whole-Genome-Based Gene-by-Gene Typing System for Standardized High-Resolution Strain Typing of Bacillus anthracis. J Clin Microbiol 2021; 59:e0288920. [PMID: 33827898 DOI: 10.1128/JCM.02889-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequencing (WGS) has been established for bacterial subtyping and is regularly used to study pathogen transmission, to investigate outbreaks, and to perform routine surveillance. Core-genome multilocus sequence typing (cgMLST) is a bacterial subtyping method that uses WGS data to provide a high-resolution strain characterization. This study aimed at developing a novel cgMLST scheme for Bacillus anthracis, a notorious pathogen that causes anthrax in livestock and humans worldwide. The scheme comprises 3,803 genes that were conserved in 57 B. anthracis genomes spanning the whole phylogeny. The scheme has been evaluated and applied to 584 genomes from 50 countries. On average, 99.5% of the cgMLST targets were detected. The cgMLST results confirmed the classical canonical single-nucleotide-polymorphism (SNP) grouping of B. anthracis into major clades and subclades. Genetic distances calculated based on cgMLST were comparable to distances from whole-genome-based SNP analysis with similar phylogenetic topology and comparable discriminatory power. Additionally, the application of the cgMLST scheme to anthrax outbreaks from Germany and Italy led to a definition of a cutoff threshold of five allele differences to trace epidemiologically linked strains for cluster typing and transmission analysis. Finally, the association of two clusters of B. anthracis with human cases of injectional anthrax in four European countries was confirmed using cgMLST. In summary, this study presents a novel cgMLST scheme that provides high-resolution strain genotyping for B. anthracis. This scheme can be used in parallel with SNP typing methods to facilitate rapid and harmonized interlaboratory comparisons, essential for global surveillance and outbreak analysis. The scheme is publicly available for application by users, including those with little bioinformatics knowledge.
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Stone NE, Nunnally AE, Roe CC, Hornstra HM, Wagner DM, Sahl JW. Complete Genome Sequence of Peptacetobacter (Clostridium) hiranonis Strain DGF055142, Isolated from Dog Feces from Flagstaff, Arizona, USA, 2019. Microbiol Resour Announc 2021; 10:e00067-21. [PMID: 33664150 DOI: 10.1128/MRA.00067-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A single-chromosome closed genome of Peptacetobacter (Clostridium) hiranonis strain DGF055142 was generated using Illumina MiSeq short reads paired with Oxford Nanopore MinION long reads. This isolate was obtained from a canine in Flagstaff, Arizona, in 2019. Peptacetobacter (C.) hiranonis was hypothesized to contribute to canine Clostridium difficile infection resistance. A single-chromosome closed genome of Peptacetobacter (Clostridium) hiranonis strain DGF055142 was generated using Illumina MiSeq short reads paired with Oxford Nanopore MinION long reads. This isolate was obtained from a canine in Flagstaff, Arizona, in 2019. Peptacetobacter (C.) hiranonis was hypothesized to contribute to canine Clostridium difficile infection resistance.
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Thouret JM, Rogeaux O, Beaudouin E, Levast M, Ramisse V, Biot FV, Valade E, Thibault F, Gorgé O, Tournier JN. Case Report of an Injectional Anthrax in France, 2012. Microorganisms 2020; 8:microorganisms8070985. [PMID: 32630109 PMCID: PMC7409126 DOI: 10.3390/microorganisms8070985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 11/26/2022] Open
Abstract
(1) Background: Bacillus anthracis is a spore-forming, Gram-positive bacterium causing anthrax, a zoonosis affecting mainly livestock. When occasionally infecting humans, B. anthracis provokes three different clinical forms: cutaneous, digestive and inhalational anthrax. More recently, an injectional anthrax form has been described in intravenous drug users. (2) Case presentation: We report here the clinical and microbiological features, as well as the strain phylogenetic analysis, of the only injectional anthrax case observed in France so far. A 27-year-old patient presented a massive dermohypodermatitis with an extensive edema of the right arm, and the development of drug-resistant shocks. After three weeks in an intensive care unit, the patient recovered, but the microbiological identification of B. anthracis was achieved after a long delay. (3) Conclusions: Anthrax diagnostic may be difficult clinically and microbiologically. The phylogenetic analysis of the Bacillus anthracis strain PF1 confirmed its relatedness to the injectional anthrax European outbreak group-II.
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Affiliation(s)
- Jean-Marc Thouret
- Centre Hospitalier Centre Hospitalier Métropole Savoie, rue Lucien Bizet, 73000 Chambéry, France; (J.-M.T.); (O.R.); (E.B.); (M.L.)
| | - Olivier Rogeaux
- Centre Hospitalier Centre Hospitalier Métropole Savoie, rue Lucien Bizet, 73000 Chambéry, France; (J.-M.T.); (O.R.); (E.B.); (M.L.)
| | - Emmanuel Beaudouin
- Centre Hospitalier Centre Hospitalier Métropole Savoie, rue Lucien Bizet, 73000 Chambéry, France; (J.-M.T.); (O.R.); (E.B.); (M.L.)
| | - Marion Levast
- Centre Hospitalier Centre Hospitalier Métropole Savoie, rue Lucien Bizet, 73000 Chambéry, France; (J.-M.T.); (O.R.); (E.B.); (M.L.)
| | - Vincent Ramisse
- DGA Maîtrise NRBC, 5 rue Lavoisier, 91710 Vert le Petit, France;
| | - Fabrice V. Biot
- CNR-LE Charbon (National Reference Laboratory for Anthrax), Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91220 Brétigny sur Orge, France; (F.V.B.); (E.V.); (F.T.); (O.G.)
- Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91220 Brétigny sur Orge, France
| | - Eric Valade
- CNR-LE Charbon (National Reference Laboratory for Anthrax), Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91220 Brétigny sur Orge, France; (F.V.B.); (E.V.); (F.T.); (O.G.)
- Direction Centrale du Service de Santé des Armées, 60 Boulevard du Général Martial Valin, 75015 Paris, France
- Ecole du Val-de-Grâce, 1 Place Alphonse Laveran, 75 005 Paris, France
| | - François Thibault
- CNR-LE Charbon (National Reference Laboratory for Anthrax), Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91220 Brétigny sur Orge, France; (F.V.B.); (E.V.); (F.T.); (O.G.)
| | - Olivier Gorgé
- CNR-LE Charbon (National Reference Laboratory for Anthrax), Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91220 Brétigny sur Orge, France; (F.V.B.); (E.V.); (F.T.); (O.G.)
- Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91220 Brétigny sur Orge, France
| | - Jean-Nicolas Tournier
- CNR-LE Charbon (National Reference Laboratory for Anthrax), Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91220 Brétigny sur Orge, France; (F.V.B.); (E.V.); (F.T.); (O.G.)
- Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91220 Brétigny sur Orge, France
- Ecole du Val-de-Grâce, 1 Place Alphonse Laveran, 75 005 Paris, France
- Correspondence: ; Tel.: +33-178-65-1065
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Antwerpen M, Beyer W, Bassy O, Ortega-García MV, Cabria-Ramos JC, Grass G, Wölfel R. Phylogenetic Placement of Isolates Within the Trans-Eurasian Clade A.Br.008/009 of Bacillus anthracis. Microorganisms 2019; 7:E689. [PMID: 31842497 DOI: 10.3390/microorganisms7120689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022] Open
Abstract
The largest phylogenetic lineage known to date of the anthrax pathogen Bacillus anthracis is the wide-spread, so-called Trans-Eurasian clade systematically categorized as the A.Br.008/009 group sharing two defining canonical single-nucleotide polymorphisms (canSNP). In this study, we genome-sequenced a collection of 35 B. anthracis strains of this clade, derived from human infections, animal outbreaks or soil, mostly from European countries isolated between 1936 and 2008. The new data were subjected to comparative chromosomal analysis, together with 75 B. anthracis genomes available in public databases, and the relative placements of these isolates were determined within the global phylogeny of the A.Br.008/009 canSNP group. From this analysis, we have detected 3754 chromosomal SNPs, allowing the assignation of the new chromosomal sequences to established sub-clades, to define new sub-clades, such as two new Spanish, one Bulgarian or one German group(s), or to introduce orphan lineages. SNP-based results were compared with that of a multilocus variable number of tandem repeat analysis (MLVA). This analysis indicated that MLVA typing might provide additional information in cases when genomics yields identical genotypes or shows only minor differences. Introducing the delayed mismatch amplification assay (DMAA) PCR-analysis, we developed a cost-effective method to interrogate for a set of ten phylogenetically informative SNPs within genomes of A.Br.008/009 canSNP clade strains of B. anthracis. By this approach, additional 32 strains could be assigned to five of ten defined clades.
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Cocking JH, Deberg M, Schupp J, Sahl J, Wiggins K, Porty A, Hornstra HM, Hepp C, Jardine C, Furstenau TN, Schulte-Hostedde A, Fofanov VY, Pearson T. Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples. Genomics 2019; 112:1872-1878. [PMID: 31678592 DOI: 10.1016/j.ygeno.2019.10.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 10/05/2019] [Accepted: 10/09/2019] [Indexed: 10/25/2022]
Abstract
Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism's diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations.
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Affiliation(s)
- Jill Hager Cocking
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America.
| | - Michael Deberg
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Jim Schupp
- Pathogen and Microbiome Division, TGen North, Flagstaff, AZ, United States of America.
| | - Jason Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America.
| | - Kristin Wiggins
- Pathogen and Microbiome Division, TGen North, Flagstaff, AZ, United States of America.
| | - Ariel Porty
- Department of Biology, Laurentian University, Sudbury, Ontario, Canada.
| | - Heidie M Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America.
| | - Crystal Hepp
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America.
| | - Claire Jardine
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada.
| | - Tara N Furstenau
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America.
| | | | - Viacheslav Y Fofanov
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America.
| | - Talima Pearson
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America.
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Timofeev V, Bahtejeva I, Mironova R, Titareva G, Lev I, Christiany D, Borzilov A, Bogun A, Vergnaud G. Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS One 2019; 14:e0209140. [PMID: 31116737 DOI: 10.1101/486290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/07/2019] [Indexed: 05/28/2023] Open
Abstract
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, and whole genome sequence analysis showed that it is most closely related to the Yamal strains in spite of the remoteness of Yamal from Yakutia. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in the B. anthracis species. The geographic distribution of the strains belonging to A.Br.008/011 is suggesting that the polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
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Affiliation(s)
- Vitalii Timofeev
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Irina Bahtejeva
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Raisa Mironova
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Galina Titareva
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Igor Lev
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - David Christiany
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Alexander Borzilov
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Alexander Bogun
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
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10
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Timofeev V, Bahtejeva I, Mironova R, Titareva G, Lev I, Christiany D, Borzilov A, Bogun A, Vergnaud G. Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS One 2019; 14:e0209140. [PMID: 31116737 DOI: 10.1371/journal.pone.0209140] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/07/2019] [Indexed: 12/24/2022] Open
Abstract
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, and whole genome sequence analysis showed that it is most closely related to the Yamal strains in spite of the remoteness of Yamal from Yakutia. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in the B. anthracis species. The geographic distribution of the strains belonging to A.Br.008/011 is suggesting that the polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
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11
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Okutani A, Inoue S, Morikawa S. Comparative genomics and phylogenetic analysis of Bacillus anthracis strains isolated from domestic animals in Japan. Infect Genet Evol 2019; 71:128-139. [PMID: 30928604 DOI: 10.1016/j.meegid.2019.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 11/30/2022]
Abstract
Anthrax, caused by Bacillus anthracis, is a severe zoonosis with a great impact on both human and animal health. In the present study, we identified the phylogenetic relationships among 16 Japanese strains of B. anthracis, including eight bovine strains, two equine strains, five swine strains, and one former vaccine strain, using in silico canonical single nucleotide polymorphism (canSNP) and core genome SNP analyses. The results of our in silico canSNP analysis suggest that these 16 Japanese strains could be divided into four lineages: i) one equine strain in A.Br.Ames, ii) one equine and six bovine strains in A.Br.001/002, iii) five swine and one bovine strain in A.Br.Aust94, and iv) one bovine and one vaccine strain in A.Br.008/011. A comparison with non-Japanese B. anthracis strains revealed a total of 3787 SNPs identified from the whole genome sequences of the Japanese strains; these SNP data were subjected to a phylogenetic analysis using the maximum parsimony (MP) method. Our core genome SNP analysis was also able to detect differences of a few chromosomal SNPs across clonal strains from the same cases that had different storage and passage histories. Additionally, our whole genome SNP analysis clearly indicated that the Japanese swine anthrax cases of 1982 were caused by at least three independent strains; however, their phylogeny revealed no clear relationship with swine strains from other countries. The bovine strain belonging to the A.Br.008/011 lineage differed from a former Japanese vaccine strain by only 12 SNPs. Together with the phylogenic results and epidemiological circumstances, the diversity of strains reveals that the B. anthracis available in Japan probably resulted from multiple relatively recent import events, rather than reflecting the persistence of a more ancient ecologically established group.
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Affiliation(s)
- Akiko Okutani
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Satoshi Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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Eremenko EI, Ryazanova AG, Pisarenko SV, Aksenova LY, Semenova OV, Koteneva EA, Tsygankova OI, Kovalev DA, Golovinskaya TM, Chmerenko DK, Kulichenko AN. Comparative Analysis of Genotyping Methods for Bacillus anthracis. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541901006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Pullan ST, Miles RW, Lewandowski K, Vipond R. Closed Genome Sequence Obtained Using Hybrid Nanopore/Illumina Assembly of a Bacillus anthracis Isolate from an Animal-Skin-Drum-Associated Anthrax Case in the United Kingdom. Microbiol Resour Announc 2018; 7. [PMID: 30533686 PMCID: PMC6256555 DOI: 10.1128/mra.00802-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/29/2018] [Indexed: 11/24/2022] Open
Abstract
Hybrid de novo assembly of Illumina/Nanopore reads produced a complete closed genome sequence of the chromosome and two virulence plasmids of a Bacillus anthracis isolate from a fatal anthrax case in the United Kingdom linked to imported animal skins/drums; this provides a high-quality representative sequence for this lineage. Hybrid de novo assembly of Illumina/Nanopore reads produced a complete closed genome sequence of the chromosome and two virulence plasmids of a Bacillus anthracis isolate from a fatal anthrax case in the United Kingdom linked to imported animal skins/drums; this provides a high-quality representative sequence for this lineage.
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Lienemann T, Beyer W, Pelkola K, Rossow H, Rehn A, Antwerpen M, Grass G. Genotyping and phylogenetic placement of Bacillus anthracis isolates from Finland, a country with rare anthrax cases. BMC Microbiol 2018; 18:102. [PMID: 30176810 PMCID: PMC6122712 DOI: 10.1186/s12866-018-1250-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/27/2018] [Indexed: 11/24/2022] Open
Abstract
Background Anthrax, the zoonotic disease caused by the gram-positive bacterium Bacillus anthracis, is nowadays rare in northern parts of Europe including Finland and Scandinavia. Only two minor outbreaks of anthrax in 1988 and in 2004 and one sporadic infection in 2008 have been detected in animals in Finland since the 1970’s. Here, we report on two Finnish B. anthracis strains that were isolated from spleen and liver of a diseased calf related to the outbreak in 1988 (strain HKI4363/88) and from a local scrotum and testicle infection of a bull in 2008 (strain BA2968). These infections occurred in two rural Finnish regions, i.e., Ostrobothnia in western Finland and Päijänne Tavastia in southern Finland, respectively. Results The isolates were genetically characterized by PCR-based methods such as multilocus variable number of tandem repeat analysis (MLVA) and whole genome-sequence analysis (WGS). Phylogenetic comparison of the two strains HKI4363/88 and BA2968 by chromosomal single nucleotide polymorphism (SNP) analysis grouped these organisms within their relatives of the minor canonical A-branch canSNP-group A.Br.003/004 (A.Br.V770) or canonical B-branch B.Br.001/002, respectively. Strain HKI4363/88 clustered relatively closely with other members of the A.Br.003/004 lineage from Europe, South Africa, and South America. In contrast, strain BA2968 clearly constituted a new sublineage within B.Br.001/002 with its closest relative being HYO01 from South Korea. Conclusions Our results suggest that Finland harbors both unique (autochthonous) and more widely distributed, common clades of B. anthracis. We suspect that members of the common clades such as strains HKI4363/88 have been introduced only recently by anthropogenic activities involving importation of contaminated animal products. On the other hand, autochthonous strains such as isolate BA2968 probably have an older history of their introduction into Finland as evidenced by a high number of single nucleotide variant sites in their genomes. Electronic supplementary material The online version of this article (10.1186/s12866-018-1250-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taru Lienemann
- Finnish Food Safety Authority (Evira), Veterinary Bacteriology and Pathology Research Unit, Helsinki, Finland
| | | | - Kirsti Pelkola
- Finnish Food Safety Authority (Evira), Veterinary Bacteriology and Pathology Research Unit, Helsinki, Finland
| | - Heidi Rossow
- Finnish Food Safety Authority (Evira), Risk Assessment Research Unit, Helsinki, Finland
| | | | | | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany.
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15
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Fleshman A, Mullins K, Sahl J, Hepp C, Nieto N, Wiggins K, Hornstra H, Kelly D, Chan TC, Phetsouvanh R, Dittrich S, Panyanivong P, Paris D, Newton P, Richards A, Pearson T. Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity. Microb Genom 2018; 4. [PMID: 30035711 PMCID: PMC6202447 DOI: 10.1099/mgen.0.000199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.
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Affiliation(s)
- Amy Fleshman
- 1Northern Arizona University, Flagstaff, AZ, USA
| | | | - Jason Sahl
- 1Northern Arizona University, Flagstaff, AZ, USA
| | - Crystal Hepp
- 1Northern Arizona University, Flagstaff, AZ, USA
| | - Nathan Nieto
- 1Northern Arizona University, Flagstaff, AZ, USA
| | | | | | - Daryl Kelly
- 2Naval Medical Research Center, Silver Spring, MD, USA.,3The Ohio State University, Columbus, OH, USA
| | | | - Rattanaphone Phetsouvanh
- 4Lao-Oxford-Mahosot Hospital-Wellcome Trust, Research Unit, Mahosot Hospital, Vientiane, Vientiane, Lao People's Democratic Republic
| | - Sabine Dittrich
- 5University of Oxford, Centre for Tropical Medicine and Global Health, Oxford, UK.,6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,7Foundation of Innovative New Diagnostics, Geneva, Switzerland
| | - Phonepasith Panyanivong
- 6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Daniel Paris
- 8Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.,9Swiss Tropical and Public Health Institute, Basel, Switzerland.,10University of Basel, Basel, Switzerland
| | - Paul Newton
- 5University of Oxford, Centre for Tropical Medicine and Global Health, Oxford, UK.,6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Allen Richards
- 2Naval Medical Research Center, Silver Spring, MD, USA.,11Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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Pilo P, Frey J. Pathogenicity, population genetics and dissemination of Bacillus anthracis. Infect Genet Evol 2018; 64:115-125. [PMID: 29935338 DOI: 10.1016/j.meegid.2018.06.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 12/30/2022]
Abstract
Bacillus anthracis, the etiological agent of anthrax, procures its particular virulence by a capsule and two AB type toxins: the lethal factor LF and the edema factor EF. These toxins primarily disable immune cells. Both toxins are translocated to the host cell by the adhesin-internalin subunit called protective antigen PA. PA enables LF to reach intra-luminal vesicles, where it remains active for long periods. Subsequently, LF translocates to non-infected cells, leading to inefficient late therapy of anthrax. B. anthracis undergoes slow evolution because it alternates between vegetative and long spore phases. Full genome sequence analysis of a large number of worldwide strains resulted in a robust evolutionary reconstruction of this bacterium, showing that B. anthracis is split in three main clades: A, B and C. Clade A efficiently disseminated worldwide underpinned by human activities including heavy intercontinental trade of goat and sheep hair. Subclade A.Br.WNA, which is widespread in the Northern American continent, is estimated to have split from clade A reaching the Northern American continent in the late Pleistocene epoch via the former Bering Land Bridge and further spread from Northwest southwards. An alternative hypothesis is that subclade A.Br.WNA. evolved from clade A.Br.TEA tracing it back to strains from Northern France that were assumingly dispatched by European explorers that settled along the St. Lawrence River. Clade B established mostly in Europe along the alpine axis where it evolved in association with local cattle breeds and hence displays specific geographic subclusters. Sequencing technologies are also used for forensic applications to trace unintended or criminal acts of release of B. anthracis. Under natural conditions, B. anthracis generally affects domesticated and wild ruminants in arid ecosystems. The more recently discovered B. cereus biovar anthracis spreads in tropical forests, where it threatens particularly endangered primate populations.
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Affiliation(s)
- Paola Pilo
- Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Bern, Switzerland.
| | - Joachim Frey
- Dean's Office, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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17
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Pauker VI, Thoma BR, Grass G, Bleichert P, Hanczaruk M, Zöller L, Zange S. Improved Discrimination of Bacillus anthracis from Closely Related Species in the Bacillus cereus Sensu Lato Group Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2018; 56:e01900-17. [PMID: 29514939 DOI: 10.1128/JCM.01900-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Discrimination of highly pathogenic bacteria, such as Bacillus anthracis, from closely related species based on molecular biological methods is challenging. We applied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to a collection of B. anthracis strains and close relatives in order to significantly improve the statistical confidence of identification results for this group of bacteria. Protein mass spectra of 189 verified and diverse Bacillus strains of the Bacillus cereus sensu lato group were generated using MALDI-TOF MS and subsequently analyzed with supervised and unsupervised statistical methods, such as shrinkage discriminant analysis (SDA) and principal-component analysis (PCA). We aimed at identifying specific biomarkers in the protein spectra of B. anthracis not present in closely related Bacillus species. We could identify 7, 10, 18, and 14 B. anthracis-specific biomarker candidates that were absent in B. cereus, B. mycoides, B. thuringiensis, and B. weihenstephanensis strains, respectively. Main spectra (MSP) of a defined collection of Bacillus strains were compiled using the Bruker Biotyper software and added to an in-house reference library. Reevaluation of this library with 15 hitherto untested strains of B. anthracis and B. cereus yielded improved score values. The B. anthracis strains were identified with score values between 2.33 and 2.55 using the in-house database, while the same strains were identified with scores between 1.94 and 2.37 using the commercial database, and no false-positive identifications occurred using the in-house database.
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18
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Kalinowski J, Ahrens B, Al-dilaimi A, Winkler A, Wibberg D, Schleenbecker U, Rückert C, Wölfel R, Grass G. Isolation and whole genome analysis of endospore-forming bacteria from heroin. Forensic Sci Int Genet 2018; 32:1-6. [DOI: 10.1016/j.fsigen.2017.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 11/17/2022]
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Walter MC, Zwirglmaier K, Vette P, Holowachuk SA, Stoecker K, Genzel GH, Antwerpen MH. MinION as part of a biomedical rapidly deployable laboratory. J Biotechnol 2017; 250:16-22. [DOI: 10.1016/j.jbiotec.2016.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
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Stone NE, Sidak-Loftis LC, Sahl JW, Vazquez AJ, Wiggins KB, Gillece JD, Hicks ND, Schupp JM, Busch JD, Keim P, Wagner DM. More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes. PLoS One 2016; 11:e0164504. [PMID: 27723795 PMCID: PMC5056695 DOI: 10.1371/journal.pone.0164504] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/26/2016] [Indexed: 12/18/2022] Open
Abstract
Nosocomial acquisition of Clostridium difficile is well documented, yet recent studies have highlighted the importance of community acquired infections and identified community associated reservoirs for this pathogen. Multiple studies have implicated companion pets and farm animals as possible sources of community acquired C. difficile infections in humans. To explore the potential role of pet dogs in human C. difficile infections we systematically collected canine fecal samples (n = 197) in Flagstaff, AZ. Additionally, nineteen fecal samples were collected at a local veterinary clinic from diarrheic dogs. We used these combined samples to investigate important questions regarding C. difficile colonization in pet canines: 1) What is the prevalence and diversity of C. difficile in this companion pet population, and 2) Do C. difficile isolates collected from canines genetically overlap with isolates that cause disease in humans? We used a two-step sequence typing approach, including multilocus sequence typing to determine the overall genetic diversity of C. difficile present in Flagstaff canines, and whole-genome sequencing to assess the fine-scale diversity patterns within identical multilocus sequence types from isolates obtained within and among multiple canine hosts. We detected C. difficile in 17% of the canine fecal samples with 10% containing toxigenic strains that are known to cause human disease. Sequencing analyses revealed similar genotypes in dogs and humans. These findings suggest that companion pets are a potential source of community acquired C. difficile infections in humans.
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Affiliation(s)
- Nathan E. Stone
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, United States of America
| | - Lindsay C. Sidak-Loftis
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, United States of America
| | - Jason W. Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, United States of America
| | - Adam J. Vazquez
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, United States of America
| | - Kristin B. Wiggins
- Translational Genomics Research Institute, Flagstaff, AZ, 86001, United States of America
| | - John D. Gillece
- Translational Genomics Research Institute, Flagstaff, AZ, 86001, United States of America
| | - Nathan D. Hicks
- Translational Genomics Research Institute, Flagstaff, AZ, 86001, United States of America
| | - James M. Schupp
- Translational Genomics Research Institute, Flagstaff, AZ, 86001, United States of America
| | - Joseph D. Busch
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, United States of America
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, United States of America
- Translational Genomics Research Institute, Flagstaff, AZ, 86001, United States of America
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, United States of America
- * E-mail:
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21
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Sahl JW, Pearson T, Okinaka R, Schupp JM, Gillece JD, Heaton H, Birdsell D, Hepp C, Fofanov V, Noseda R, Fasanella A, Hoffmaster A, Wagner DM, Keim P. A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens. mBio 2016; 7:e01501-16. [PMID: 27677796 DOI: 10.1128/mBio.01501-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Anthrax is a zoonotic disease that occurs naturally in wild and domestic animals but has been used by both state-sponsored programs and terrorists as a biological weapon. A Soviet industrial production facility in Sverdlovsk, USSR, proved deficient in 1979 when a plume of spores was accidentally released and resulted in one of the largest known human anthrax outbreaks. In order to understand this outbreak and others, we generated a Bacillus anthracis population genetic database based upon whole-genome analysis to identify all single-nucleotide polymorphisms (SNPs) across a reference genome. Phylogenetic analysis has defined three major clades (A, B, and C), B and C being relatively rare compared to A. The A clade has numerous subclades, including a major polytomy named the trans-Eurasian (TEA) group. The TEA radiation is a dominant evolutionary feature of B. anthracis, with many contemporary populations having resulted from a large spatial dispersal of spores from a single source. Two autopsy specimens from the Sverdlovsk outbreak were deep sequenced to produce draft B. anthracis genomes. This allowed the phylogenetic placement of the Sverdlovsk strain into a clade with two Asian live vaccine strains, including the Russian Tsiankovskii strain. The genome was examined for evidence of drug resistance manipulation or other genetic engineering, but none was found. The Soviet Sverdlovsk strain genome is consistent with a wild-type strain from Russia that had no evidence of genetic manipulation during its industrial production. This work provides insights into the world’s largest biological weapons program and provides an extensive B. anthracis phylogenetic reference. The 1979 Russian anthrax outbreak resulted from an industrial accident at the Soviet anthrax spore production facility in the city of Sverdlovsk. Deep genomic sequencing of two autopsy specimens generated a draft genome and phylogenetic placement of the Soviet Sverdlovsk anthrax strain. While it is known that Soviet scientists had genetically manipulated Bacillus anthracis with the potential to evade vaccine prophylaxis and antibiotic therapeutics, there was no genomic evidence of this from the Sverdlovsk production strain genome. The whole-genome SNP genotype of the Sverdlovsk strain was used to precisely identify it and its close relatives in the context of an extensive global B. anthracis strain collection. This genomic identity can now be used for forensic tracking of this weapons material on a global scale and for future anthrax investigations.
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Barragan V, Sahl JW, Wiggins K, Chiriboga J, Salinas A, Cantos NE, Loor MN, Intriago BI, Morales M, Trueba G, Pearson T. Draft Genome Sequence of the First Pathogenic Leptospira Isolates from Ecuador. Genome Announc 2016; 4:e00271-16. [PMID: 27151788 DOI: 10.1128/genomeA.00271-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pathogenic Leptospira spp. cause leptospirosis upon contact with mucosa through wounds or ingestion, leading to headaches, fever, jaundice, kidney or liver failure, or death in about 1.3 million people each year. Here, we present the draft genomes of one L. santarosai isolate and two L. interrogans isolates from Ecuador.
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23
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Affiliation(s)
- Paola Pilo
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
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