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Wang S, Suluku R, Jalloh MB, Samba AF, Jiang B, Xie Y, Harding D, Zhang M, Sahr F, Sesay ME, Squire JS, Vandi MA, Kallon MN, Zhang S, Hu R, Zhao Y, Mi Z. Molecular characterization of an outbreak-involved Bacillus anthracis strain confirms the spillover of anthrax from West Africa. Infect Dis Poverty 2024; 13:6. [PMID: 38221635 PMCID: PMC10788998 DOI: 10.1186/s40249-023-01172-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/26/2023] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Anthrax, a zoonotic disease caused by the spore-forming bacterium Bacillus anthracis, remains a major global public health concern, especially in countries with limited resources. Sierra Leone, a West African country historically plagued by anthrax, has almost been out of report on this disease in recent decades. In this study, we described a large-scale anthrax outbreak affecting both animals and humans and attempted to characterize the pathogen using molecular techniques. METHODS The causative agent of the animal outbreak in Port Loko District, Sierra Leone, between March and May 2022 was identified using the nanopore sequencing technique. A nationwide active surveillance was implemented from May 2022 to June 2023 to monitor the occurrence of anthrax-specific symptoms in humans. Suspected cases were subsequently verified using quantitative polymerase chain reaction. Full-genome sequencing was accomplished by combining long-read and short-read sequencing methods. Subsequent phylogenetic analysis was performed based on the full-chromosome single nucleotide polymorphisms. RESULTS The outbreak in Port Loko District, Sierra Leone, led to the death of 233 animals between March 26th and May 16th, 2022. We ruled out the initial suspicion of Anaplasma species and successfully identified B. anthracis as the causative agent of the outbreak. As a result of the government's prompt response, out of the 49 suspected human cases identified during the one-year active surveillance, only 6 human cases tested positive, all within the first month after the official declaration of the outbreak. The phylogenetic analysis indicated that the BaSL2022 isolate responsible for the outbreak was positioned in the A.Br.153 clade within the TransEuroAsian group of B. anthracis. CONCLUSIONS We successfully identified a large-scale anthrax outbreak in Sierra Leone. The causative isolate of B. anthracis, BaSL2022, phylogenetically bridged other lineages in A.Br.153 clade and neighboring genetic groups, A.Br.144 and A.Br.148, eventually confirming the spillover of anthrax from West Africa. Given the wide dissemination of B. anthracis spores, it is highly advisable to effectively monitor the potential reoccurrence of anthrax outbreaks and to launch campaigns to improve public awareness regarding anthrax in Sierra Leone.
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Affiliation(s)
- Shuchao Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Roland Suluku
- Department of Animal Sciences, School of Agriculture and Food Sciences, Njala University, Njala, Sierra Leone.
| | - Mohamed B Jalloh
- Department of Microbiology, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Ahmed F Samba
- Ministry of Agriculture and Food Sciences, Freetown, Sierra Leone
| | - Baogui Jiang
- Beijing Institute of Microbiology and Epidemiology, 20 East Street, Fengtai District, Beijing, China
| | - Yubiao Xie
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Doris Harding
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Foday Sahr
- Department of Microbiology, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Mahmud E Sesay
- Department of Animal Sciences, School of Agriculture and Food Sciences, Njala University, Njala, Sierra Leone
| | - James S Squire
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Moinina N Kallon
- Department of Animal Sciences, School of Agriculture and Food Sciences, Njala University, Njala, Sierra Leone
| | - Shoufeng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Rongliang Hu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuee Zhao
- Beijing Institute of Microbiology and Epidemiology, 20 East Street, Fengtai District, Beijing, China.
| | - Zhiqiang Mi
- Beijing Institute of Microbiology and Epidemiology, 20 East Street, Fengtai District, Beijing, China.
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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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3
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Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
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Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
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4
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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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5
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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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6
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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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Bruce SA, Schiraldi NJ, Kamath PL, Easterday WR, Turner WC. A classification framework for Bacillus anthracis defined by global genomic structure. Evol Appl 2020; 13:935-944. [PMID: 32431744 PMCID: PMC7232756 DOI: 10.1111/eva.12911] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/18/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study, whole-genome sequence analysis of over 350 B. anthracis isolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative and compatible with multiple genomic assays. The data presented in this study shed new light on the diverse global dissemination of this species and indicate that many lineages may be uniquely suited to the geographic regions in which they are found. In addition, we demonstrate that plasmid genomic structure for this species is largely consistent with chromosomal population structure, suggesting vertical inheritance in this bacterium has contributed to its evolutionary persistence. This classification methodology is the first based on population genomic structure for this species and has potential use for local and broader institutions seeking to understand both disease outbreak origins and recent introductions. In addition, we provide access to a newly developed genotyping script as well as the full whole-genome sequence analyses output for this study, allowing future studies to rapidly employ and append their data in the context of this global collection. This framework may act as a powerful tool for public health agencies, wildlife disease laboratories, and researchers seeking to utilize and expand this classification scheme for further investigations into B. anthracis evolution.
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Affiliation(s)
- Spencer A. Bruce
- Department of Biological SciencesUniversity at Albany – State University of New YorkAlbanyNYUSA
| | - Nicholas J. Schiraldi
- Department of Information Technology ServicesUniversity at Albany – State University of New YorkAlbanyNYUSA
| | | | - W. Ryan Easterday
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | - Wendy C. Turner
- Department of Biological SciencesUniversity at Albany – State University of New YorkAlbanyNYUSA
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8
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Braun P, Knüpfer M, Antwerpen M, Triebel D, Grass G. A Rare Glimpse into the Past of the Anthrax Pathogen Bacillus anthracis. Microorganisms 2020; 8:microorganisms8020298. [PMID: 32098212 PMCID: PMC7074940 DOI: 10.3390/microorganisms8020298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 11/16/2022] Open
Abstract
The bacterium Bacillus anthracis is the causative agent of the zoonotic disease anthrax. While genomics of extant B. anthracis isolates established in-depth phylogenomic relationships, there is scarce information on the historic genomics of the pathogen. Here, we characterized the oldest documented B. anthracis specimen. The inactive 142-year-old material originated from a bovine diseased in Chemnitz (Germany) in 1878 and is contemporary with the seminal studies of Robert Koch on B. anthracis. A specifically developed isolation method yielded high-quality DNA from this specimen for genomic sequencing. The bacterial chromosome featuring 242 unique base-characters placed it into a major phylogenetic clade of B. anthracis (B.Branch CNEVA), which is typical for central Europe today. Our results support the notion that the CNEVA-clade represents part of the indigenous genetic lineage of B. anthracis in this part of Europe. This work emphasizes the value of historic specimens as precious resources for reconstructing the past phylogeny of the anthrax pathogen.
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Affiliation(s)
- Peter Braun
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany; (P.B.); (M.K.); (M.A.)
| | - Mandy Knüpfer
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany; (P.B.); (M.K.); (M.A.)
| | - Markus Antwerpen
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany; (P.B.); (M.K.); (M.A.)
| | - Dagmar Triebel
- Bavarian Natural History Collections (SNSB—Botanische Staatssammlung München), 80638 Munich, Germany;
| | - Gregor Grass
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany; (P.B.); (M.K.); (M.A.)
- Correspondence: ; Tel.: +49-992692-3981
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9
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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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Pisarenko SV, Eremenko EI, Ryazanova AG, Kovalev DA, Buravtseva NP, Aksenova LY, Dugarzhapova ZF, Evchenko AY, Kravets EV, Semenova OV, Bobrisheva OV, Kuznetsova IV, Golovinskaya TM, Volynkina AS, Balakhonov SV, Kulichenko AN. Phylogenetic analysis of Bacillus anthracis strains from Western Siberia reveals a new genetic cluster in the global population of the species. BMC Genomics 2019; 20:692. [PMID: 31477029 PMCID: PMC6720099 DOI: 10.1186/s12864-019-6060-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/25/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Anthrax is a zoonotic disease caused by the gram-positive bacterium Bacillus anthracis. The most anthrax-endemic regions of Russia are Siberia and North Caucasus. Previously, genotyping of Russian B.anthracis isolates was carried out using canSNP and MLVA data; these methods yield lower resolution results compared to whole genome SNP analysis (wgSNP). In this research, we have used wgSNP method for genotyping of 10 B.anthracis isolates, obtained during 1961-2016 in Russia on territory of Western Siberia. RESULTS We have analyzed 185 B.anthracis genomes available in GenBank database and genomes of 10 isolates obtained in this study to determine the place of Russian isolates in the global phylogeny of B.anthracis. For the studied genomes we have detected 7203 SNPs, which were used for building a phylogenetic reconstruction with Maximum Likelihood Method. Results of the phylogenetic analysis indicate that Russian strains belong to three different genetic groups. Three strains belong to genetic group "Ames", two strains - to "STI" group. Five strains belong to the main genetic line B, and four of them form a subcluster, described for the first time, which we have named "Siberia". CONCLUSIONS In this study, the data on genetic diversity of B.anthracis strains on the territory of Western Siberia is presented for the first time. As a result of complex phylogenetic analysis, the place of these isolates was determined in the global phylogenetic structure of the B.anthracis population. We describe a new cluster in the main genetic line B for the first time.
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Affiliation(s)
- Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Eugene I. Eremenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Alla G. Ryazanova
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Nina P. Buravtseva
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Lyudmila Yu. Aksenova
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Zorigma F. Dugarzhapova
- Irkutsk Antiplague Research Institute of Siberia and Far East, Irkutsk, Russian Federation , 664047
| | - Anna Yu. Evchenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Elena V. Kravets
- Irkutsk Antiplague Research Institute of Siberia and Far East, Irkutsk, Russian Federation , 664047
| | - Olga V. Semenova
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Olga V. Bobrisheva
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Irina V. Kuznetsova
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Tatyana M. Golovinskaya
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Anna S. Volynkina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya Str, Stavropol, Russian Federation , 355035
| | - Sergei V. Balakhonov
- Irkutsk Antiplague Research Institute of Siberia and Far East, Irkutsk, Russian Federation , 664047
| | - Alexander N. Kulichenko
- Irkutsk Antiplague Research Institute of Siberia and Far East, Irkutsk, Russian Federation , 664047
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Friman M, Kakko L, Constantin C, Simojoki H, Andersson MA, Nagy S, Salonen H, Andersson M. An atypical Bacillus anthracis infection in a bull-A potential occupational health hazard. Reprod Domest Anim 2019; 54:1279-1283. [PMID: 31348839 DOI: 10.1111/rda.13532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/16/2019] [Indexed: 11/28/2022]
Abstract
Bacillus anthracis infecting cattle is usually identified based on the typical symptom: sudden death. Bacillus anthracis causing atypical symptoms may remain undiagnosed and represent a potential occupational health hazard for, that is veterinarians and producers, butchers and tanners. In the year 2004, one case of sudden death in a dairy farm in southern Finland was diagnosed as bovine anthrax. Four years later 2008, an atypical case of anthrax was diagnosed in the same holding. The bull was taken to the Production Animal Hospital of the Faculty of Veterinary Medicine, University of Helsinki because of fever, loss of appetite and a symmetrically swollen scrotal sac. Penicillin treatment cured the fever but not the swollen scrotum. Before the intended therapeutic castration, a punctuate consisting of 10 ml fluid collected into a syringe from the scrotal sac was cultivated on blood agar at 37°C. After 24 hr, an almost pure culture of a completely non-hemolytic Bacillus cereus-like bacteria was obtained. The strain was identified as B. anthracis using Ba-specific primers by the Finnish Food Safety Authority (RUOKAVIRASTO). After the diagnosis, the bull was euthanized and destroyed, the personnel were treated with prophylactic antibiotics and the clinic was disinfected. In this particular case, treatment with water, Virkon S and lime seemed to be effective to eliminate endospores and vegetative cells since no relapses of anthrax have occurred in 10 years. This case is the last reported anthrax case in Finland.
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Affiliation(s)
- Mari Friman
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Leila Kakko
- Department of Civil Engineering, Aalto University, Aalto, Finland.,Tampere University of Applied Sciences, Tampere, Finland
| | | | - Heli Simojoki
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Maria A Andersson
- Department of Civil Engineering, Aalto University, Aalto, Finland.,Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Szabolcs Nagy
- Department of Animal Sciences, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Heidi Salonen
- Department of Civil Engineering, Aalto University, Aalto, Finland
| | - Magnus Andersson
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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Timofeev V, Bahtejeva I, Mironova R, Titareva G, Lev I, Christiany D, Borzilov A, Bogun A, Vergnaud G. Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS One 2019; 14:e0209140. [PMID: 31116737 DOI: 10.1101/486290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/07/2019] [Indexed: 05/28/2023] Open
Abstract
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, and whole genome sequence analysis showed that it is most closely related to the Yamal strains in spite of the remoteness of Yamal from Yakutia. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in the B. anthracis species. The geographic distribution of the strains belonging to A.Br.008/011 is suggesting that the polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
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Affiliation(s)
- Vitalii Timofeev
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Irina Bahtejeva
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Raisa Mironova
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Galina Titareva
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Igor Lev
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - David Christiany
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Alexander Borzilov
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Alexander Bogun
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
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Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS One 2019; 14:e0209140. [PMID: 31116737 PMCID: PMC6530834 DOI: 10.1371/journal.pone.0209140] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/07/2019] [Indexed: 12/24/2022] Open
Abstract
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, and whole genome sequence analysis showed that it is most closely related to the Yamal strains in spite of the remoteness of Yamal from Yakutia. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in the B. anthracis species. The geographic distribution of the strains belonging to A.Br.008/011 is suggesting that the polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
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