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Timofeev V, Bakhteeva I, Khlopova K, Mironova R, Titareva G, Goncharova Y, Solomentsev V, Kravchenko T, Dyatlov I, Vergnaud G. New Research on the Bacillus anthracis Genetic Diversity in Siberia. Pathogens 2023; 12:1257. [PMID: 37887773 PMCID: PMC10610006 DOI: 10.3390/pathogens12101257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
Anthrax is a particularly dangerous infection of humans and ungulates caused by the Gram-positive spore-forming bacterium Bacillus anthracis. The highly monomorphic and clonal species B. anthracis is commonly divided into three main lineages, A, B, and C, which in turn are divided into several canSNP groups. We report here a phylogenetic analysis based on the whole-genome sequence (WGS) data of fifteen strains isolated predominantly in Siberia or Central and Southern Russia. We confirm the wide distribution of the cluster of strains of the B.Br.001/002 group, endemic to the Russian Arctic, which is also present in the steppe zone of Southern Siberia. We characterize additional branches within the major A.Br.001/002 polytomy comprising the A.Br.Ames and A.Br.Sterne lineages, one of which is identified in the Arctic.
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Affiliation(s)
- Vitalii Timofeev
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Irina Bakhteeva
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Kseniya Khlopova
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Raisa Mironova
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Galina Titareva
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Yulia Goncharova
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Viktor Solomentsev
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Tatiana Kravchenko
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Ivan Dyatlov
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
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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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Forde TL, Dennis TPW, Aminu OR, Harvey WT, Hassim A, Kiwelu I, Medvecky M, Mshanga D, Van Heerden H, Vogel A, Zadoks RN, Mmbaga BT, Lembo T, Biek R. Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity. Microb Genom 2022; 8:000759. [PMID: 35188453 PMCID: PMC8942019 DOI: 10.1099/mgen.0.000759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen's evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide SNPs among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over 1 year throughout the Ngorongoro Conservation Area, Tanzania, a region hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes (i.e. SNP profiles) within the study area. However, phylogeographical structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.
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Affiliation(s)
- Taya L. Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Tristan P. W. Dennis
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - O. Rhoda Aminu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - William T. Harvey
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Matej Medvecky
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - Henriette Van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Adeline Vogel
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ruth N. Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Present address: Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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Shevtsov A, Lukhnova L, Izbanova U, Vernadet JP, Kuibagarov M, Amirgazin A, Ramankulov Y, Vergnaud G. Bacillus anthracis Phylogeography: New Clues From Kazakhstan, Central Asia. Front Microbiol 2021; 12:778225. [PMID: 34956141 PMCID: PMC8692834 DOI: 10.3389/fmicb.2021.778225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
This article describes Bacillus anthracis strains isolated in Kazakhstan since the 1950s until year 2016 from sixty-one independent events associated with anthrax in humans and animals. One hundred and fifty-four strains were first genotyped by Multiple Locus VNTR (variable number of tandem repeats) Analysis (MLVA) using 31 VNTR loci. Thirty-five MLVA31 genotypes were resolved, 28 belong to the A1/TEA group, five to A3/Sterne-Ames group, one to A4/Vollum and one to the B clade. This is the first report of the presence of the B-clade in Kazakhstan. The MLVA31 results and epidemiological data were combined to select a subset of seventy-nine representative strains for draft whole genome sequencing (WGS). Strains from Kazakhstan significantly enrich the known phylogeny of the Ames group polytomy, including the description of a new branch closest to the Texas, United States A.Br.Ames sublineage stricto sensu. Three among the seven currently defined branches in the TEA polytomy are present in Kazakhstan, “Tsiankovskii”, “Heroin”, and “Sanitary Technical Institute (STI)”. In particular, strains from the STI lineage are largely predominant in Kazakhstan and introduce numerous deep branching STI sublineages, demonstrating a high geographic correspondence between “STI” and Kazakhstan, Central Asia. This observation is a strong indication that the TEA polytomy emerged after the last political unification of Asian steppes in the fourteenth century of the Common Era. The phylogenetic analysis of the Kazakhstan data and of currently available WGS data of worldwide origin strengthens our understanding of B. anthracis geographic expansions in the past seven centuries.
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Affiliation(s)
| | - Larissa Lukhnova
- National Scientific Center for Especially Dangerous Infections Named by Masgut Aykimbayev, Almaty, Kazakhstan
| | - Uinkul Izbanova
- National Scientific Center for Especially Dangerous Infections Named by Masgut Aykimbayev, Almaty, Kazakhstan
| | - Jean-Philippe Vernadet
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | - Yerlan Ramankulov
- National Center for Biotechnology, Nur Sultan, Kazakhstan.,School of Science and Humanities, Nazarbayev University, Nur Sultan, Kazakhstan
| | - Gilles Vergnaud
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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5
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Sushma B, Shedole S, Suresh KP, Leena G, Patil SS, Srikantha G. An Estimate of Global Anthrax Prevalence in Livestock: A Meta-analysis. Vet World 2021; 14:1263-1271. [PMID: 34220129 PMCID: PMC8243666 DOI: 10.14202/vetworld.2021.1263-1271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/06/2021] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: Anthrax, caused by the soil-borne spore-forming bacteria called Bacillus anthracis, is a zoonotic disease that persists worldwide in livestock and wildlife and infects humans. It is a great hazard to livestock; henceforth, evaluating the global concerns about the disease occurrence in livestock is essential. This study was conducted to estimate the global prevalence of anthrax and predict high-risk regions, which could be an input to veterinarians to take necessary steps to control and avoid the disease. Materials and Methods: A literature review was performed using online databases, namely, PubMed, Google Scholar, Scopus, Biomed Central, and Science Direct, to extract relevant publications worldwide between 1992 and 2020.</AQ9> Initially, 174 articles were selected, and after scrutinizing, 24 articles reporting the prevalence of anthrax were found to be adequate for the final meta-analysis. The statistical study was accompanied by employing fixed effects and random effects models using R. Results: The pooled prevalence of anthrax globally was 28% (95% confidence interval, 26-30%) from 2452 samples through the fixed effects model. Continent-wise subgroup analysis through the random effects model revealed that the pooled prevalence of anthrax was highest in Africa (29%) and least in North America (21%). Conclusion: In these publications, anthrax causes economic loss to farmers and, thus, to the world. Hence, controlling anthrax infections in high-risk regions are essential by implementing appropriate control measures to decrease the effect of the disease, thereby reducing economic loss.
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Affiliation(s)
- Bylaiah Sushma
- Department of Computer Science and Engineering, M S Ramaiah Institute of Technology, Matthikere, Bengaluru, Karnataka, India
| | - Seema Shedole
- Department of Computer Science and Engineering, M S Ramaiah Institute of Technology, Matthikere, Bengaluru, Karnataka, India
| | - Kuralayanapalya Puttahonnappa Suresh
- Spatial Epidemiology Laboratory, Indian Council of Agricultural Research (ICAR) National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Gowda Leena
- Department of Veterinary Public Health and Epidemiology, Veterinary College, Hebbal, Bengaluru, Karnataka, India
| | - Sharanagouda S Patil
- Virology Laboratory, Indian Council of Agricultural Research (ICAR) - National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Gowda Srikantha
- Spatial Epidemiology Laboratory, Indian Council of Agricultural Research (ICAR) National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
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6
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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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7
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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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FINKE ERNSTJÜRGEN, BEYER WOLFGANG, LODERSTÄDT ULRIKE, FRICKMANN HAGEN. Review: The risk of contracting anthrax from spore-contaminated soil - A military medical perspective. Eur J Microbiol Immunol (Bp) 2020; 10:29-63. [PMID: 32590343 PMCID: PMC7391381 DOI: 10.1556/1886.2020.00008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 04/10/2020] [Indexed: 12/31/2022] Open
Abstract
Anthrax is an infectious disease of relevance for military forces. Although spores of Bacillus anthracis obiquitously occur in soil, reports on soil-borne transmission to humans are scarce. In this narrative review, the potential of soil-borne transmission of anthrax to humans is discussed based on pathogen-specific characteristics and reports on anthrax in the course of several centuries of warfare. In theory, anthrax foci can pose a potential risk of infection to animals and humans if sufficient amounts of virulent spores are present in the soil even after an extended period of time. In praxis, however, transmissions are usually due to contacts with animal products and reported events of soil-based transmissions are scarce. In the history of warfare, even in the trenches of World War I, reported anthrax cases due to soil-contaminated wounds are virtually absent. Both the perspectives and the experience of the Western hemisphere and of former Soviet Republics are presented. Based on the accessible data as provided in the review, the transmission risk of anthrax by infections of wounds due to spore-contaminated soil is considered as very low under the most circumstance. Active historic anthrax foci may, however, still pose a risk to the health of deployed soldiers.
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Affiliation(s)
| | - WOLFGANG BEYER
- Department of Infectiology and Animal Hygiene, University of Hohenheim, Institute of Animal Science, Stuttgart, Germany
| | - ULRIKE LODERSTÄDT
- Diagnostic Department, Bernhard-Nocht-Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | - HAGEN FRICKMANN
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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9
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Zhang E, Zhang H, He J, Li W, Wei J. Genetic diversity of Bacillus anthracis Ames lineage strains in China. BMC Infect Dis 2020; 20:140. [PMID: 32059712 PMCID: PMC7023782 DOI: 10.1186/s12879-020-4867-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anthrax is an endemic disease that persists in the rural regions of China. The global genetic population structure of B.anthracis has also been defined by the canonical single-nucleotide polymorphisms (canSNP) and multiple-locus variable-number tandem repeat analysis (MLVA). Five canSNP lineages were found in China, and the A.Br.Ames lineage has been the second predominant group in recent years in China. The objective of this study was to reveal genetic diversity of the Ames lineage strains by MLVA. METHODS Two molecular typing methods, canSNP and MLVA with 15markers were used to study the genetic relationship among the Ames lineage strains. The outbreak information associated with these strains was also collected and investigated. RESULTS From 2007 to 2018, a total of 21 human anthrax infection outbreaks (68 patients) associated with B. anthracis Ames lineage strains were reported in China. Ames lineage strain-associated human anthrax is mainly distributed in the northern part of China, including the provinces of Inner Mongolia, Liaoning, Gansu, and Xinjiang. In the study, a total of 30 Ames lineage strains were included and 10 MLVA15 genotypes were identified. These strains were mainly found in northeast China, Inner Mongolia and Liaoning. In recent years, the Ames lineage strains were isolated in the two provinces every year. The 18 Ames lineage strains isolated from Inner Mongolia were divided into eight MLVA15 genotypes. From 2010 to 2015, there were continuous reports of outbreaks in Keyouzhongqi County, Inner Mongolia, and the strains that were isolated annually in succession belonged to the MLVA15-30 genotype. CONCLUSIONS The Ames lineage strains are widely distributed in northern China. Their genetic diversity can be illustrated by the results of the MLVA. The genetic characteristics of the Ames lineage strains from outbreaks in different provinces varied. In some areas, human anthrax outbreaks occurred annually in succession, and these related strains grouped together. These observations indicate that the local environment was persistently contaminated with B. anthracis spores, vaccination of livestock should become the fundamental control measure in the areas.
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Affiliation(s)
- Enmin Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Huijuan Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Jinrong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Jianchun Wei
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. .,State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China.
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Rondinone V, Serrecchia L, Parisi A, Fasanella A, Manzulli V, Cipolletta D, Galante D. Genetic characterization of Bacillus anthracis strains circulating in Italy from 1972 to 2018. PLoS One 2020; 15:e0227875. [PMID: 31931511 PMCID: PMC6957342 DOI: 10.1371/journal.pone.0227875] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/31/2019] [Indexed: 11/18/2022] Open
Abstract
In Italy anthrax is an endemic disease, with a few outbreaks occurring almost every year. We surveyed 234 B. anthracis strains from animals (n = 196), humans (n = 3) and the environment (n = 35) isolated during Italian outbreaks in the years 1972-2018. Despite the considerable genetic homogeneity of B. anthracis, the strains were effectively differentiated using canonical single nucleotide polymorphisms (CanSNPs) assay and multiple-locus variable-number tandem repeat analysis (MLVA). The phylogenetic identity was determined through the characterization of 14 CanSNPs. In addition, a subsequent 31-loci MLVA assay was also used to further discriminate B. anthracis genotypes into subgroups. The analysis of 14 CanSNPs allowed for the identification of four main lineages: A.Br.011/009, A.Br.008/011 (respectively belonging to A.Br.008/009 sublineage, also known Trans-Eurasian or TEA group), A.Br.005/006 and B.Br.CNEVA. A.Br.011/009, the most common subgroup of lineage A, is the major genotype of B. anthracis in Italy. The MLVA analysis revealed the presence of 55 different genotypes in Italy. Most of the genotypes are genetically very similar, supporting the hypothesis that all strains evolved from a local common ancestral strain, except for two genotypes representing the branch A.Br.005/006 and B.Br.CNEVA. The genotyping analysis applied in this study remains a very valuable tool for studying the diversity, evolution, and molecular epidemiology of B. anthracis.
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Affiliation(s)
- Valeria Rondinone
- Anthrax Reference Institute of Italy, Experimental Zooprophylactic Institute of Apulia and Basilicata Regions, Foggia, Italy
| | - Luigina Serrecchia
- Anthrax Reference Institute of Italy, Experimental Zooprophylactic Institute of Apulia and Basilicata Regions, Foggia, Italy
| | - Antonio Parisi
- Anthrax Reference Institute of Italy, Experimental Zooprophylactic Institute of Apulia and Basilicata Regions, Foggia, Italy
| | - Antonio Fasanella
- Anthrax Reference Institute of Italy, Experimental Zooprophylactic Institute of Apulia and Basilicata Regions, Foggia, Italy
| | - Viviana Manzulli
- Anthrax Reference Institute of Italy, Experimental Zooprophylactic Institute of Apulia and Basilicata Regions, Foggia, Italy
| | - Dora Cipolletta
- Anthrax Reference Institute of Italy, Experimental Zooprophylactic Institute of Apulia and Basilicata Regions, Foggia, Italy
| | - Domenico Galante
- Anthrax Reference Institute of Italy, Experimental Zooprophylactic Institute of Apulia and Basilicata Regions, Foggia, Italy
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11
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Education and training in microbial forensics. MICROBIAL FORENSICS 2020. [PMCID: PMC7153755 DOI: 10.1016/b978-0-12-815379-6.00032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Phylogenomic structure of Bacillus anthracis isolates in the Northern Cape Province, South Africa revealed novel single nucleotide polymorphisms. INFECTION GENETICS AND EVOLUTION 2019; 80:104146. [PMID: 31866402 DOI: 10.1016/j.meegid.2019.104146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 11/21/2022]
Abstract
Bacillus anthracis, the aetiological agent of anthrax, is regarded as a highly monomorphic pathogen that presents a low genetic diversity using standard molecular techniques. Whole genome sequencing and single nucleotide polymorphisms (SNPs) are definitive signatures for subtyping of B. anthracis. Here we employed whole genome single nucleotide polymorphism (wgSNP) analysis to investigate the genetic diversity of B. anthracis in the historically endemic region of Northern Cape Province (NCP), South Africa. Twenty-six isolates from anthrax outbreaks that occurred between 1998 and 2008/9 in NCP as well as from Namibia-South Africa Transfontier Conservation area and Botswana were compared to global B. anthracis genomes. Most NCP B. anthracis strains (n = 22) clustered in the A.Br.003/004 (A.Br.101) branch and are closely related to the Zimbabwe and Mozambique strains (A.Br.102 branch). A total of 4923 parsimony informative-SNPs accurately established the A.Br.003/004 phylogenetic relationships of the NCP isolates into two distinct sub-clades and SNP markers designated as A.Br.172 and A.Br.173 were developed. Other NCP strains (n = 2) grouped in the A.Br.001/002 (Sterne) branch while strains (n = 2) from the Namibia-South Africa Transfontier Conservation area and Botswana clustered in A.Br.005/006 (Ancient A) branch. The sequenced B. anthracis strains (A0094, A0096 and A0097) that clustered in the A.Br.064 (V770) clade were isolated from Vaalbos National Park and similar strains have not been isolated. The B. anthracis A0088 strain cluster with the NCP strains in the A.Br.003/004 (A.Br.172) SNP branch which has been isolated in NCP, South Africa. This study highlights the phylogenetic structure of NCP B. anthracis strains with distinctive SNP branches important for forensic tracing and novel SNP discovery purposes. The sequenced strains will serve as a means to further trace the dissemination of B. anthracis outbreaks in NCP, South Africa, and on the continent, as well as for forensic tracking on a global scale.
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Pisarenko SV, Eremenko EI, Ryazanova AG, Kovalev DA, Buravtseva NP, Aksenova LY, Evchenko AY, Semenova OV, Bobrisheva OV, Kuznetsova IV, Golovinskaya TM, Tchmerenko DK, Kulichenko AN, Morozov VY. Genotyping and phylogenetic location of one clinical isolate of Bacillus anthracis isolated from a human in Russia. BMC Microbiol 2019; 19:165. [PMID: 31315564 PMCID: PMC6637652 DOI: 10.1186/s12866-019-1542-3] [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: 01/18/2019] [Accepted: 07/11/2019] [Indexed: 12/05/2022] Open
Abstract
Background Anthrax is a zoonotic disease caused by the Gram-positive bacterium Bacillus anthracis. In Russia, there are more than 35 thousand anthrax stationary unfavourable sites. At the same time, there is very little published information about the isolates of B. anthracis from the territory of Russia. In this study, we report the use of whole genome sequencing (WGS) and bioinformatics analysis to characterize B. anthracis 81/1 strain isolated in Russia in 1969 from a person during an outbreak of the disease in the Stavropol region. Results We used 232 B. anthracis genomes, which are currently available in the GenBank database, to determine the place of the Russian isolate in the global phylogeny of B. anthracis. The studied strain was characterized by PCR-based genetic methods, such as Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA), canonical single nucleotide polymorphisms (canSNP), as well as the method of full-genomic analysis of nucleotide polymorphisms (wgSNP). The results indicate that the Russian B. anthracis 81/1 strain belongs to Trans-Eurasion (TEA) group, the most representative in the world. Conclusions In this study, the full genomic sequence of virulent B. anthracis strain from Russia was characterized for the first time. As a result of complex phylogenetic analysis, the place of this isolate was determined in the global phylogenetic structure of the B. anthracis population, expanding our knowledge of anthrax phylogeography in Russia. Electronic supplementary material The online version of this article (10.1186/s12866-019-1542-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sergey V Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia.
| | - Eugene I Eremenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Alla G Ryazanova
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Dmitry A Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Nina P Buravtseva
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Lyudmila Yu Aksenova
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Anna Yu Evchenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Olga V Semenova
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Olga V Bobrisheva
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Irina V Kuznetsova
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Tatyana M Golovinskaya
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Dmitriy K Tchmerenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Alexander N Kulichenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, 355035, Russia
| | - Vitaliy Yu Morozov
- Stavropol State Agrarian University, Stavropol, 355017, Russian Federation
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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. INFECTION GENETICS AND EVOLUTION 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] [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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Loss of Bacitracin Resistance Due to a Large Genomic Deletion among Bacillus anthracis Strains. mSystems 2018; 3:mSystems00182-18. [PMID: 30417107 PMCID: PMC6208641 DOI: 10.1128/msystems.00182-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/04/2018] [Indexed: 12/25/2022] Open
Abstract
Anthrax is caused by Bacillus anthracis, an endospore-forming soil bacterium. The genetic diversity of B. anthracis is known to be low compared with that of Bacillus species. In this study, we performed whole-genome sequencing of Zambian isolates of B. anthracis to understand the genetic diversity between closely related strains. Comparison of genomic sequences revealed that closely related strains were separated into three groups based on single nucleotide polymorphisms distributed throughout the genome. A large genomic deletion was detected in the region containing a bacitracin resistance gene cluster flanked by rRNA operons, resulting in the loss of bacitracin resistance. The structure of the deleted region, which was also conserved among species of the Bacillus cereus group, has the potential for both deletion and amplification and thus might be enabling the species to flexibly control the level of bacitracin resistance for adaptive evolution. Bacillus anthracis is a Gram-positive endospore-forming bacterial species that causes anthrax in both humans and animals. In Zambia, anthrax cases are frequently reported in both livestock and wildlife, with occasional transmission to humans, causing serious public health problems in the country. To understand the genetic diversity of B. anthracis strains in Zambia, we sequenced and compared the genomic DNA of B. anthracis strains isolated across the country. Single nucleotide polymorphisms clustered these strains into three groups. Genome sequence comparisons revealed a large deletion in strains belonging to one of the groups, possibly due to unequal crossing over between a pair of rRNA operons. The deleted genomic region included genes conferring resistance to bacitracin, and the strains with the deletion were confirmed with loss of bacitracin resistance. Similar deletions between rRNA operons were also observed in a few B. anthracis strains phylogenetically distant from Zambian strains. The structure of bacitracin resistance genes flanked by rRNA operons was conserved only in members of the Bacillus cereus group. The diversity and genomic characteristics of B. anthracis strains determined in this study would help in the development of genetic markers and treatment of anthrax in Zambia. IMPORTANCE Anthrax is caused by Bacillus anthracis, an endospore-forming soil bacterium. The genetic diversity of B. anthracis is known to be low compared with that of Bacillus species. In this study, we performed whole-genome sequencing of Zambian isolates of B. anthracis to understand the genetic diversity between closely related strains. Comparison of genomic sequences revealed that closely related strains were separated into three groups based on single nucleotide polymorphisms distributed throughout the genome. A large genomic deletion was detected in the region containing a bacitracin resistance gene cluster flanked by rRNA operons, resulting in the loss of bacitracin resistance. The structure of the deleted region, which was also conserved among species of the Bacillus cereus group, has the potential for both deletion and amplification and thus might be enabling the species to flexibly control the level of bacitracin resistance for adaptive evolution.
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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] [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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Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains. mSystems 2018; 3:mSystems00065-18. [PMID: 30116789 PMCID: PMC6093989 DOI: 10.1128/msystems.00065-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/28/2018] [Indexed: 12/31/2022] Open
Abstract
Bacillus anthracis microorganisms are of historical and epidemiological importance and are among the most homogenous bacterial groups known, even though the B. anthracis genome is rich in mobile elements. Mobile elements can trigger the diversification of lineages; therefore, characterizing the extent of genomic variation in a large collection of strains is critical for a complete understanding of the diversity and evolution of the species. Here, we sequenced a large collection of B. anthracis strains (>400) that were recovered from human, animal, and environmental sources around the world. Our results confirmed the remarkable stability of gene content and synteny of the anthrax plasmids and revealed no signal of plasmid exchange between B. anthracis and pathogenic B. cereus isolates but rather predominantly vertical descent. These findings advance our understanding of the biology and pathogenomic evolution of B. anthracis and its plasmids. Bacillus anthracis plasmids pXO1 and pXO2 carry the main virulence factors responsible for anthrax. However, the extent of copy number variation within the species and how the plasmids are related to pXO1/pXO2-like plasmids in other species of the Bacillus cereussensu lato group remain unclear. To gain new insights into these issues, we sequenced 412 B. anthracis strains representing the total phylogenetic and ecological diversity of the species. Our results revealed that B. anthracis genomes carried, on average, 3.86 and 2.29 copies of pXO1 and pXO2, respectively, and also revealed a positive linear correlation between the copy numbers of pXO1 and pXO2. No correlation between the plasmid copy number and the phylogenetic relatedness of the strains was observed. However, genomes of strains isolated from animal tissues generally maintained a higher plasmid copy number than genomes of strains from environmental sources (P < 0.05 [Welch two-sample t test]). Comparisons against B. cereus genomes carrying complete or partial pXO1-like and pXO2-like plasmids showed that the plasmid-based phylogeny recapitulated that of the main chromosome, indicating limited plasmid horizontal transfer between or within these species. Comparisons of gene content revealed a closed pXO1 and pXO2 pangenome; e.g., plasmids encode <8 unique genes, on average, and a single large fragment deletion of pXO1 in one B. anthracis strain (2000031682) was detected. Collectively, our results provide a more complete view of the genomic diversity of B. anthracis plasmids, their copy number variation, and the virulence potential of other Bacillus species carrying pXO1/pXO2-like plasmids. IMPORTANCEBacillus anthracis microorganisms are of historical and epidemiological importance and are among the most homogenous bacterial groups known, even though the B. anthracis genome is rich in mobile elements. Mobile elements can trigger the diversification of lineages; therefore, characterizing the extent of genomic variation in a large collection of strains is critical for a complete understanding of the diversity and evolution of the species. Here, we sequenced a large collection of B. anthracis strains (>400) that were recovered from human, animal, and environmental sources around the world. Our results confirmed the remarkable stability of gene content and synteny of the anthrax plasmids and revealed no signal of plasmid exchange between B. anthracis and pathogenic B. cereus isolates but rather predominantly vertical descent. These findings advance our understanding of the biology and pathogenomic evolution of B. anthracis and its plasmids.
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18
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Lekota KE, Hassim A, Rogers P, Dekker EH, Last R, de Klerk-Lorist L, van Heerden H. The reporting of a Bacillus anthracis B-clade strain in South Africa after more than 20 years. BMC Res Notes 2018; 11:264. [PMID: 29716659 PMCID: PMC5930959 DOI: 10.1186/s13104-018-3366-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Anthrax is a disease with an age old history in Africa caused by the Gram-positive endospore forming soil bacterium Bacillus anthracis. Epizootics of wild ungulates occur annually in the enzootic region of Pafuri, Kruger National Park (KNP) in the Limpopo Province of South Africa. Rigorous routine surveillance and diagnostics in KNP, has not revealed these rare isolates since the 1990s, despite unabated annual outbreaks. In 2011 a cheetah was diagnosed as anthrax positive from a private game reserve in Limpopo Province and reported to State Veterinary Services for further investigation. Isolation, molecular diagnostics, whole genome sequencing and comparative genomics were carried out for B. anthracis KC2011. RESULTS Bacteriological and molecular diagnostics confirmed the isolate as B. anthracis. Subsequent typing and whole genome single nucleotide polymorphisms analysis indicated it clustered alongside B. anthracis SA A0091 in the B.Br.010 SNP branch. Unlike B. anthracis KrugerB strain, KC2011 strain has unique SNPs and represents a new branch in the B-clade. The isolation and genotypic characterisation of KC2011 demonstrates a gap in the reporting of anthrax outbreaks in the greater Limpopo province area. The identification of vulnerable and susceptible cheetah mortalities due to this strain has implications for conservation measures and disease control.
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Affiliation(s)
- K E Lekota
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa. .,College of Agriculture and Environmental Sciences, University of South Africa, Christiaan De Wet/Pioneer Dr., Florida, South Africa.
| | - A Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - P Rogers
- Provet Wildlife Services, Raptors Safari Junction, Main Road, Hoedspruit, South Africa
| | - E H Dekker
- State Veterinary Services, Department of Agriculture, Forestry and Fisheries, Skukuza, South Africa
| | - R Last
- Vetdiagnostix-Veterinary Pathology Services, 257 Boshoff Street, Pietermaritzburg, South Africa
| | - L de Klerk-Lorist
- State Veterinary Services, Department of Agriculture, Forestry and Fisheries, Skukuza, South Africa
| | - H van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
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Yu J, Blom J, Glaeser SP, Jaenicke S, Juhre T, Rupp O, Schwengers O, Spänig S, Goesmann A. A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies. J Biotechnol 2017; 261:2-9. [PMID: 28705636 DOI: 10.1016/j.jbiotec.2017.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 12/12/2022]
Abstract
The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics. In this manuscript, we review the most commonly used platforms and approaches for ortholog group analyses with a focus on their potential for phylogenetic and taxonomic research. Furthermore, we describe the latest improvements of the EDGAR platform for comparative genome analyses and present recent examples of its application for the phylogenomic analysis of different taxa. Finally, we illustrate the role of the EDGAR platform as part of the BiGi Center for Microbial Bioinformatics within the German network on Bioinformatics Infrastructure (de.NBI).
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Affiliation(s)
- J Yu
- Int. Research Training Group 1906 (DiDy), Bielefeld University, Bielefeld, 33501, Germany; Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - J Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany.
| | - S P Glaeser
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - S Jaenicke
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - T Juhre
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - O Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - O Schwengers
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - S Spänig
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - A Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
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Rume FI, Ahsan CR, Biswas PK, Yasmin M, Braun P, Walter MC, Antwerpen M, Grass G, Hanczaruk M. Unexpected genomic relationships between Bacillus anthracis strains from Bangladesh and Central Europe. INFECTION GENETICS AND EVOLUTION 2016; 45:66-74. [PMID: 27543395 DOI: 10.1016/j.meegid.2016.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 12/28/2022]
Abstract
The zoonosis anthrax caused by the bacterium Bacillus anthracis has a broad geographical distribution. Active enzootic areas are typically located away from central and northern Europe where cases of the disease occur only sporadically and in limited numbers. In contrast, a few out of the 64 districts of Bangladesh are hyper-endemic for anthrax and there the disease causes major losses in live-stock. In this study we genotyped eight strains of B. anthracis collected from the districts of Sirajganj and Tangail in 2013. All these strains belonged to canSNP group A.Br.001/002 Sterne differing only in a few of 31 tandem-repeat (MLVA)-markers. Whole genome sequences were obtained from five of these strains and compared with genomic information of B. anthracis strains originating from various geographical locations. Characteristic signatures were detected defining two "Bangladesh" clusters potentially useful for rapid molecular epidemiology. From this data high-resolution PCR assays were developed and subsequently tested on additional isolates from Bangladesh and Central Europe. Remarkably, this comparative genomic analysis focusing on SNP-discovery revealed a close genetic relationship between these strains from Bangladesh and historic strains collected between 1991 and 2008 in The Netherlands and Germany, respectively. Possible explanations for these phylogenetic relationships are discussed.
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Affiliation(s)
- Farzana Islam Rume
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh; Department of Microbiology & Public Health, Patuakhali Science and Technology University, Khanpura, Babugonj, Barisal, Bangladesh
| | | | - Paritosh Kumar Biswas
- Department of Microbiology & Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Mahmuda Yasmin
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Peter Braun
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany.
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Li Z, Hwang S, Bar-Peled M. Discovery of a Unique Extracellular Polysaccharide in Members of the Pathogenic Bacillus That Can Co-form with Spores. J Biol Chem 2016; 291:19051-67. [PMID: 27402849 DOI: 10.1074/jbc.m116.724708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Indexed: 11/06/2022] Open
Abstract
An exopolysaccharide, produced during the late stage of stationary growth phase, was discovered and purified from the culture medium of Bacillus cereus, Bacillus anthracis, and Bacillus thuringiensis when strains were grown in a defined nutrient medium that induces biofilm. Two-dimensional NMR structural characterization of the polysaccharide, named pzX, revealed that it is composed of an unusual three amino-sugar sequence repeat of [-3)XylNAc4OAc(α1-3)GlcNAcA4OAc(α1-3)XylNAc(α1-]n The sugar residue XylNAc had never been described previously in any glycan structure. The XNAC operon that contains the genes for the assembly of pzX is also unique and so far has been identified only in members of the Bacillus cereus sensu lato group. Microscopic and biochemical analyses indicate that pzX co-forms during sporulation, so that upon the release of the spore to the extracellular milieu it becomes surrounded by pzX. The relative amounts of pzX produced can be manipulated by specific nutrients in the medium, but rich medium appears to suppress pzX formation. pzX has the following unique characteristics: a surfactant property that lowers surface tension, a cell/spore antiaggregant, and an adherence property that increases spores binding to surfaces. pzX in Bacillus could represent a trait shared by many spore-producing microorganisms. It suggests pzX is an active player in spore physiology and may provide new insights to the successful survival of the B. cereus species in natural environments or in the hosts.
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Affiliation(s)
- Zi Li
- From the Complex Carbohydrate Research Center and Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Soyoun Hwang
- From the Complex Carbohydrate Research Center and
| | - Maor Bar-Peled
- From the Complex Carbohydrate Research Center and Department of Plant Biology, University of Georgia, Athens, Georgia 30602
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