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Kozytska T, Bassiouny M, Chechet O, Ordynska D, Galante D, Neubauer H, Wareth G. Retrospective Analysis of Official Data on Anthrax in Europe with a Special Reference to Ukraine. Microorganisms 2023; 11:1294. [PMID: 37317268 DOI: 10.3390/microorganisms11051294] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Anthrax is an acute infectious zoonotic disease caused by Bacillus anthracis that mostly affects grazing livestock and wildlife. Furthermore, B. anthracis is considered one of the most important biological agents of bioterrorism that could also be potentially misused in biological weapons. The distribution of anthrax in domestic animals and wildlife in Europe with a particular focus on Ukraine as a country of war was analyzed. Between 2005 and 2022, 267 anthrax cases were registered at the World Organization of Animal Health (WOAH) in animals in Europe, including 251 cases in domestic animals and 16 in wildlife. The highest numbers of cases were recorded in 2005 and 2016 followed by 2008, and the highest numbers of registered cases were reported from Albania, Russia, and Italy. In Ukraine, anthrax is currently a sporadic infection. Since 2007, 28 notifications were registered, with isolates mainly from soil samples. The highest number of confirmed anthrax cases was registered in 2018, and Odesa, which is close to Moldova, had the highest number of cases, followed by the Cherkasy region. The presence of thousands of biothermal pits and burial grounds of fallen cattle nationwide favors the re-emergence of new foci. Most confirmed cases were in cattle; however, single cases were confirmed in dogs, horses, and pigs. Further investigation of the disease in wildlife and in environmental samples is needed. The genetic analysis of isolates, investigation of susceptibility to antimicrobial compounds, and determination of virulence and pathogenicity factors are required in this volatile region of the world for awareness raising and preparedness.
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Affiliation(s)
- Tamara Kozytska
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany
- State Research Institute for Laboratory Diagnostics and Veterinary and Sanitary Expertise, State Service of Ukraine for Food Safety and Consumer Protection, 30, Donetska St., 03151 Kyiv, Ukraine
| | - Marwa Bassiouny
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany
| | - Olha Chechet
- State Research Institute for Laboratory Diagnostics and Veterinary and Sanitary Expertise, State Service of Ukraine for Food Safety and Consumer Protection, 30, Donetska St., 03151 Kyiv, Ukraine
| | - Diana Ordynska
- State Research Institute for Laboratory Diagnostics and Veterinary and Sanitary Expertise, State Service of Ukraine for Food Safety and Consumer Protection, 30, Donetska St., 03151 Kyiv, Ukraine
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Anthrax Reference Institute of Italy, Via Manfredonia 20, 71121 Foggia, Italy
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany
| | - Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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Lyu Y, Wang D, Yuan L, Feng E, Zhu L, Pan C, Guo Y, Liu X, Wang H. Rapid Identification of Bacillus anthracis In Silico and On-Site Using Novel Single-Nucleotide Polymorphisms. Microbiol Spectr 2022; 10:e0228521. [PMID: 35575735 PMCID: PMC9241702 DOI: 10.1128/spectrum.02285-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis is a spore-forming bacterium that causes life-threatening infections in animals and humans and has been used as a bioterror agent. Rapid and reliable detection and identification of B. anthracis are of primary interest for both medical and biological threat-surveillance purposes. Few chromosomal sequences provide enough polymorphisms to clearly distinguish B. anthracis from closely related species. We analyzed 18 loci of the chromosome of B. anthracis and discovered eight novel single-nucleotide polymorphism (SNP) sites that can be used for the specific identification of B. anthracis. Using these SNP sites, we developed software-named AGILE V1.1 (anthracis genome-based identification with high-fidelity E-probe)-for easy, user-friendly identification of B. anthracis from whole-genome sequences. We also developed a recombinase polymerase amplification-Cas12a-based method that uses nucleic acid extracts for the specific, rapid, in-the-field identification of B. anthracis based on these SNPs. Via this method and B. anthracis-specific CRISPR RNAs for the target CR5_2, CR5_1, and Ba813 SNPs, we clearly detected 5 aM genomic DNA. This study provides two simple and reliable methods suitable for use in local hospitals and public health programs for the detection of B. anthracis. IMPORTANCE Bacillus anthracis is the etiologic agent of anthrax, a fatal disease and a potential biothreat. A specific, accurate, and rapid method is urgently required for the identification of B. anthracis. We demonstrate the potential of using eight novel SNPs for the rapid and accurate detection of B. anthracis via in silico and laboratory-based testing methods. Our findings have important implications for public health responses to disease outbreaks and bioterrorism threats.
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Affiliation(s)
- Yufei Lyu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Dongshu Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Lu Yuan
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Erling Feng
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Li Zhu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Chao Pan
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yan Guo
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Xiankai Liu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hengliang Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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Yudianingtyas DW, Sumiarto B, Susetya H, Salman M, Djatmikowati TF, Haeriah H, Rahman A, Mangidi R. Identification of the molecular characteristics of Bacillus anthracis (1982-2020) isolates in East Indonesia using multilocus variable-number tandem repeat analysis. Vet World 2022; 15:953-961. [PMID: 35698492 PMCID: PMC9178602 DOI: 10.14202/vetworld.2022.953-961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: Anthrax is one of the endemic strategic diseases in East Indonesia, particularly in the provinces of South Sulawesi, West Sulawesi, Gorontalo, East Nusa Tenggara, and West Nusa Tenggara. Anthrax is an important disease due to its zoonotic and economic impact on the livestock industry. This study aimed to identify the molecular characteristics of Bacillus anthracis in East Indonesia using multilocus variable-number tandem repeat (VNTR) analysis (MLVA). Materials and Methods: Isolates were obtained from an investigation of anthrax outbreaks in five provinces of East Indonesia from 1982 to 2020. Conventional polymerase chain reaction for B. anthracis was used to identify MLVA-8. Deoxyribonucleic acid sequencing analysis was based on MLVA-8 primers for VNTR identification of the phylogenetic relationship among 24 isolates of B. anthracis obtained from 17 distinct districts/cities in East Indonesia. Tandem Repeats Finder was used for VNTR identification, and Molecular Evolutionary Genetics Analysis X was used to construct phylogenetic analysis. Results: In this study, 24 isolates were classified as genotype or lineage A. There were four subgroups of B. anthracis circulating in East Indonesia based on eight molecular marker loci sequence results. Conclusion: The findings of this study show that MLVA-8 typing might be useful as a subtyping tool for the epidemiological investigation of identical genotypes and low genetic diversity of B. anthracis. No other lineage of B. anthracis was circulating in East Indonesia. Other molecular methods are needed, such as extended MLVA, whole-genome sequencing, and canonical single-nucleotide polymorphism, for a more precise study of B. anthracis genetic diversity.
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Affiliation(s)
- D. W. Yudianingtyas
- Doctoral Study Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Epidemiology and Veterinary Information, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Indonesia
| | - B. Sumiarto
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - H. Susetya
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mo Salman
- Department of of Clinical Sciences, Animal Population Health Institute, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, United States of America
| | - T. F. Djatmikowati
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - Haeriah Haeriah
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - Abdul Rahman
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - R. Mangidi
- Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Indonesia
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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] [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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Eremenko E, Pechkovskii G, Pisarenko S, Ryazanova A, Kovalev D, Semenova O, Aksenova L, Timchenko L, Golovinskaya T, Bobrisheva O, Shapakov N, Kulichenko A. Phylogenetics of Bacillus anthracis isolates from Russia and bordering countries. INFECTION GENETICS AND EVOLUTION 2021; 92:104890. [PMID: 33962043 DOI: 10.1016/j.meegid.2021.104890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/20/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022]
Abstract
Anthrax is a concern for public health and veterinary medicine in Russia. The available phylogenetic data on isolates from Russia and neighboring CIS countries are clearly not enough to gain a better understanding of their position in the global phylogenetic population structure of this pathogen. In this study, we analyzed the genomes of 66 Bacillus anthracis strains, which were isolated between 1935 and 2019 from different sources in Russia, as well as in Ukraine, Azerbaijan, Georgia, Armenia and Moldova. Whole genome SNP analysis of genomes of 66 strains obtained in this study along with 222 B. anthracis genomes available in the GenBank database revealed 7242 SNPs used to construct a phylogenetic reconstruction with the method of Maximum Likelihood. Studied strains belong to 6 different genetic groups: A.Br.008(A.Br.008/009), A.Br.081(Ames), A.Br.014(A.Br.Aust94), A.Br.082(A.Br.001/002), A.Br.034(A.Br.005/006, Ancient A) and B.Br.002 (B.Br.001/002). Within the group A.Br.014(A.Br.Aust94) a subcluster A.Br.029 of strains isolated in Georgia, Armenia, Azerbaijan, Russia (Republic of Dagestan) and Turkey, named Caucasus-East Anatolia (CEA), was identified. In the subgroup A.Br.105(Tsiankovskii) the cluster A.Br.117 of strains from Russia, Ukraine and Slovakia are assigned, in the subgroup A.Br118 (STI) - cluster A.Br.123 with strains from Russia and Georgia and cluster A.Br.125 with strains from Republic of Dagestan. New subclusters B.Br.017("EUROPE") were identified in the B.Br.002(B.Br.001/002) cluster, represented by strains from the European part of Russia, as well as from South Korea and Finland. For 8 clusters and subclusters, the SNP markers were identified. The study confirmed a significant genetic diversity of the strains isolated in Russia and border countries and clarified their position in the phylogenetic structure of the global B. anthracis population. New genetic clusters A.Br.029 (CEA), A.Br.117, A.Br.123, A.Br.125, and B.Br.017 («EUROPE») were defined. 96 marker SNPs specific for these clusters were identified.
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Affiliation(s)
- Eugene Eremenko
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation.
| | - Grigorii Pechkovskii
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Sergey Pisarenko
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Alla Ryazanova
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Dmitry Kovalev
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Ol'ga Semenova
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Lyudmila Aksenova
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Lyudmila Timchenko
- Federal State Autonomous Educational Institution for Higher Education "North-Caucasus Federal University", 1 Pushkina Str, 355017 Stavropol, Russian Federation
| | - Tatyana Golovinskaya
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Ol'ga Bobrisheva
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Nikolay Shapakov
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
| | - Alexander Kulichenko
- Federal Government Health Institution «Stavropol Plague Control Research Institute» of the Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, 13-15 Sovetskaya Str, 355035 Stavropol, Russian Federation
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Pisarenko SV, Eremenko EI, Kovalev DA, Ryazanova AG, Evchenko AY, Aksenova LY, Dugarzhapova ZF, Kravets EV, Semenova OV, Bobrysheva OV, Balakhonov SV, Kulichenko AN. Molecular genotyping of 15 B. anthracis strains isolated in Eastern Siberia and Far East. Mol Phylogenet Evol 2021; 159:107116. [PMID: 33609703 DOI: 10.1016/j.ympev.2021.107116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/25/2021] [Accepted: 02/08/2021] [Indexed: 11/15/2022]
Abstract
Bacillus anthracis is a pathogenic bacterium, which causes anthrax disease. The ability of this bacterium to form spores, which can be preserved in soil for decades and cause outbreaks later on, makes this pathogen a serious problem for veterinary and health services of many countries. Siberia is one of the most anthrax-influenced regions of Russia. In this research we report on the results of genotyping based on whole genome SNP analysis of 15 strains, isolated on the territory of Eastern Siberia and the Far East in 1956-2018. In this research, we sequenced 15 genomes of B. anthracis strains isolated from infected humans and animals, and from soil samples from the territory of Eastern Siberia and the Far East in the period from 1956 to 2018. We used genomic sequences obtained in this study and 219 B. anthracis genomes available in the international GenBank database to perform a comparative analysis. As a result we detected 6400 chromosomal SNPs which allowed to differentiate the studied strains. We built phylogenetic reconstruction of the global B. anthracis population based on the detected SNPs using the Maximum Likelihood Method and described genetic diversity of the strains isolated on the territory of Eastern Siberia and the Far East. Strains, isolated on this territory from 1956 to 2018 belong to 5 different genetic groups: "Ames", "STI", "Tsiankovskii", "Siberia" and "Asia". The greatest diversity of the strains is registered for two regions of the southern part of Eastern Siberia - Tyva and Buryatia. This research expands current understanding of genetic diversity of B. anthracis strains circulating on the territory of Russia.
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Affiliation(s)
- Sergey V Pisarenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | - Eugene I Eremenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | - Dmitry A Kovalev
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | - Alla G Ryazanova
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | - Anna Yu Evchenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | | | - Zorigma F Dugarzhapova
- Irkutsk Antiplague Research Institute of Siberia and Far East, 664047 Irkutsk, Russian Federation.
| | - Elena V Kravets
- Irkutsk Antiplague Research Institute of Siberia and Far East, 664047 Irkutsk, Russian Federation.
| | - Olga V Semenova
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | - Olga V Bobrysheva
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | - Sergei V Balakhonov
- Irkutsk Antiplague Research Institute of Siberia and Far East, 664047 Irkutsk, Russian Federation.
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Whole Genome Sequencing for Studying Bacillus anthracis from an Outbreak in the Abruzzo Region of Italy. Microorganisms 2020; 8:microorganisms8010087. [PMID: 31936409 PMCID: PMC7022239 DOI: 10.3390/microorganisms8010087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/20/2019] [Accepted: 01/06/2020] [Indexed: 11/17/2022] Open
Abstract
Anthrax is a serious infectious disease caused by the gram-positive and spore-forming bacterium Bacillus anthracis. In Italy, anthrax is an endemic disease with sporadic cases each year and few outbreaks, especially in Southern Italy. However, new foci have been discovered in zones without previous history of anthrax. During summer 2016, an outbreak of anthrax caused the death of four goats in the Abruzzo region, where the disease had not been reported before. In order to investigate the outbreak, we sequenced one strain and compared it to 19 Italian B. anthracis genomes. Furthermore, we downloaded 71 whole genome sequences representing the global distribution of canonical SNP lineages and used them to verify the phylogenetic positioning. To this end, we analyzed and compared the genome sequences using canonical SNPs and the whole genome SNP-based analysis. Our results demonstrate that the outbreak strain belonged to the Trans-Eurasian (TEA) group A.Br.011/009, which is the predominant clade in Central-Southern Italy. In conclusion, the high genomic relatedness of the Italian TEA strains suggests their evolution from a common ancestor, while the spread is supposedly driven by trade as well as human and transhumance activities. Here, we demonstrated the capabilities of whole genome sequencing (WGS), which can be used as a tool for outbreak analyses and surveillance activities.
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Phylogenetic Placement of Isolates Within the Trans-Eurasian Clade A.Br.008/009 of Bacillus anthracis. Microorganisms 2019; 7:microorganisms7120689. [PMID: 31842497 PMCID: PMC6955976 DOI: 10.3390/microorganisms7120689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [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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