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Antwerpen M, Beyer W, Grass G. New Insights into the Phylogeny of the A.Br.161 ("A.Br.Heroin") Clade of Bacillus anthracis. Pathogens 2024; 13:593. [PMID: 39057820 PMCID: PMC11279936 DOI: 10.3390/pathogens13070593] [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: 06/19/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Bacillus anthracis is a rare but highly dangerous zoonotic bacterial pathogen. At the beginning of this century, a new manifestation of the disease, injectional anthrax, emerged as a result of recreational heroin consumption involving contaminated drugs. The organisms associated with this 13-year-lasting outbreak event in European drug consumers were all grouped into the canonical single-nucleotide polymorphism (canSNP) clade A-branch (A.Br.) 161 of B. anthracis. Related clade A.Br.161 strains of B. anthracis not associated with heroin consumption have also been identified from different countries, mostly in Asia. Because of inadvertent spread by anthropogenic activities, other strains of this A.Br.161 lineage were, however, isolated from several countries. Thus, without additional isolates from this clade, its origin of evolution or its autochthonous region remains obscure. Here, we genomically characterized six new A.Br.161 group isolates, some of which were from Iran, with others likely historically introduced into Germany. All the chromosomes of these isolates could be grouped into a distinct sub-clade within the A.Br.161 clade. This sub-clade is separated from the main A.Br.161 lineage by a single SNP. We have developed this SNP into a PCR assay facilitating the future attribution of strains to this group.
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Affiliation(s)
- Markus Antwerpen
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany
| | - Wolfgang Beyer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany
| | - Gregor Grass
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany
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Goossens PL. Bacillus anthracis, "la maladie du charbon", Toxins, and Institut Pasteur. Toxins (Basel) 2024; 16:66. [PMID: 38393144 PMCID: PMC10891547 DOI: 10.3390/toxins16020066] [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: 11/08/2023] [Revised: 12/25/2023] [Accepted: 12/30/2023] [Indexed: 02/25/2024] Open
Abstract
Institut Pasteur and Bacillus anthracis have enjoyed a relationship lasting almost 120 years, starting from its foundation and the pioneering work of Louis Pasteur in the nascent fields of microbiology and vaccination, and blooming after 1986 following the molecular biology/genetic revolution. This contribution will give a historical overview of these two research eras, taking advantage of the archives conserved at Institut Pasteur. The first era mainly focused on the production, characterisation, surveillance and improvement of veterinary anthrax vaccines; the concepts and technologies with which to reach a deep understanding of this research field were not yet available. The second period saw a new era of B. anthracis research at Institut Pasteur, with the anthrax laboratory developing a multi-disciplinary approach, ranging from structural analysis, biochemistry, genetic expression, and regulation to bacterial-host cell interactions, in vivo pathogenicity, and therapy development; this led to the comprehensive unravelling of many facets of this toxi-infection. B. anthracis may exemplify some general points on how science is performed in a given society at a given time and how a scientific research domain evolves. A striking illustration can be seen in the additive layers of regulations that were implemented from the beginning of the 21st century and their impact on B. anthracis research. B. anthracis and anthrax are complex systems that raise many valuable questions regarding basic research. One may hope that B. anthracis research will be re-initiated under favourable circumstances later at Institut Pasteur.
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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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Bassy O, Antwerpen M, Ortega-García MV, Ortega-Sánchez MJ, Bouzada JA, Cabria-Ramos JC, Grass G. Spanish Outbreak Isolates Bridge Phylogenies of European and American Bacillus anthracis. Microorganisms 2023; 11:microorganisms11040889. [PMID: 37110312 PMCID: PMC10146487 DOI: 10.3390/microorganisms11040889] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023] Open
Abstract
The geographical origin of a major present-day phylogenetic group (A branch WNA; A.Br.WNA) of American Bacillus anthracis is controversial. One hypothesis postulated that the anthrax pathogen reached North America via a then-existing land bridge from northeastern Asia thousands of years ago. A competing hypothesis suggested that B. anthracis was introduced to America a couple of hundred years ago, related to European colonization. The latter view is strongly supported by genomic analysis of a group of French B. anthracis isolates that are phylogenetically closely related to the North American strains of the A branch A.Br.WNA clade. In addition, three West African strains also belong to this relationship group. Recently, we have added a Spanish strain to these close relatives of the WNA lineage of American B. anthracis. Nevertheless, the diversity of Spanish B. anthracis remains largely unexplored, and phylogenetic links to European or American relatives are not well resolved. Here, we genome sequenced and characterized 29 new B. anthracis isolates (yielding 18 unique genotypes) from outbreaks in west central and central Spain in 2021. Applying comparative chromosomal analysis, we placed the chromosomes of these isolates within the established phylogeny of the A.Br.008/009 (A.Br.TEA) canonical SNP group. From this analysis, a new sub-clade, named A.Br.11/ESPc, emerged that constitutes a sister group of American A.Br.WNA.
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Affiliation(s)
- Olga Bassy
- Chemical, Biological, Radiological and Nuclear (CBRN) Defence Systems Department, Campus La Marañosa, Instituto Nacional de Técnica Aeroespacial “Esteban Terradas” (INTA), 28330 San Martín de la Vega, Madrid, Spain
| | - Markus Antwerpen
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany
| | - María Victoria Ortega-García
- Chemical, Biological, Radiological and Nuclear (CBRN) Defence Systems Department, Campus La Marañosa, Instituto Nacional de Técnica Aeroespacial “Esteban Terradas” (INTA), 28330 San Martín de la Vega, Madrid, Spain
| | - María Jesús Ortega-Sánchez
- Laboratorio Central de Sanidad Animal (LCSA), Ministerio de Agricultura Pesca y Alimentación (MAPA), 18320 Santa Fe, Granada, Spain
| | - José Antonio Bouzada
- Laboratorio Central de Veterinaria, Ministerio de Agricultura Pesca y Alimentación (MAPA), 28110 Algete, Madrid, Spain
| | - Juan Carlos Cabria-Ramos
- Chemical, Biological, Radiological and Nuclear (CBRN) Defence Systems Department, Campus La Marañosa, Instituto Nacional de Técnica Aeroespacial “Esteban Terradas” (INTA), 28330 San Martín de la Vega, Madrid, Spain
| | - Gregor Grass
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany
- Correspondence: ; Tel.: +49-992692-3981
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Yudianingtyas DW, Sumiarto B, Susetya H, Salman M, Djatmikowati TF, Haeriah H, Rahman A, Mangidi R. Identification of the molecular characteristics of Bacillus anthracis (1982-2020) isolates in East Indonesia using multilocus variable-number tandem repeat analysis. Vet World 2022; 15:953-961. [PMID: 35698492 PMCID: PMC9178602 DOI: 10.14202/vetworld.2022.953-961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: Anthrax is one of the endemic strategic diseases in East Indonesia, particularly in the provinces of South Sulawesi, West Sulawesi, Gorontalo, East Nusa Tenggara, and West Nusa Tenggara. Anthrax is an important disease due to its zoonotic and economic impact on the livestock industry. This study aimed to identify the molecular characteristics of Bacillus anthracis in East Indonesia using multilocus variable-number tandem repeat (VNTR) analysis (MLVA). Materials and Methods: Isolates were obtained from an investigation of anthrax outbreaks in five provinces of East Indonesia from 1982 to 2020. Conventional polymerase chain reaction for B. anthracis was used to identify MLVA-8. Deoxyribonucleic acid sequencing analysis was based on MLVA-8 primers for VNTR identification of the phylogenetic relationship among 24 isolates of B. anthracis obtained from 17 distinct districts/cities in East Indonesia. Tandem Repeats Finder was used for VNTR identification, and Molecular Evolutionary Genetics Analysis X was used to construct phylogenetic analysis. Results: In this study, 24 isolates were classified as genotype or lineage A. There were four subgroups of B. anthracis circulating in East Indonesia based on eight molecular marker loci sequence results. Conclusion: The findings of this study show that MLVA-8 typing might be useful as a subtyping tool for the epidemiological investigation of identical genotypes and low genetic diversity of B. anthracis. No other lineage of B. anthracis was circulating in East Indonesia. Other molecular methods are needed, such as extended MLVA, whole-genome sequencing, and canonical single-nucleotide polymorphism, for a more precise study of B. anthracis genetic diversity.
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Affiliation(s)
- D. W. Yudianingtyas
- Doctoral Study Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Epidemiology and Veterinary Information, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Indonesia
| | - B. Sumiarto
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - H. Susetya
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mo Salman
- Department of of Clinical Sciences, Animal Population Health Institute, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, United States of America
| | - T. F. Djatmikowati
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - Haeriah Haeriah
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - Abdul Rahman
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - R. Mangidi
- Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Indonesia
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Brangsch H, Golovko A, Pinchuk N, Deriabin O, Kyselova T, Linde J, Melzer F, Elschner MC. Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques. Microorganisms 2022; 10:microorganisms10020461. [PMID: 35208915 PMCID: PMC8875922 DOI: 10.3390/microorganisms10020461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining long- and short-read next-generation sequencing techniques, highly accurate genomes were reconstructed, enabling detailed in silico genotyping. Thus, the strains could be assigned to the Tsiankovskii subgroup of the “TransEurAsia” clade, which is commonly found in this region. Their high genetic similarity suggests that the four strains are members of the endemic population whose progenitor was once introduced in the Ukraine and bordering regions. This study provides information on B. anthracis strains from a region where there is little knowledge of the local population, thereby adding to the picture of global B. anthracis genotype distribution. We also emphasize the importance of surveillance and prevention methods regarding anthrax outbreaks, as other studies predicted a higher number of cases in the future due to global warming.
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Affiliation(s)
- Hanka Brangsch
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
- Correspondence:
| | - Anatolii Golovko
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Nataliia Pinchuk
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Oleg Deriabin
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Tetiana Kyselova
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Jörg Linde
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| | - Falk Melzer
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| | - Mandy Carolina Elschner
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
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Ma B, Chen J, Yang X, Bai J, Ouyang S, Mo X, Chen W, Wang CC, Hai X. The Genetic Structure and East-West Population Admixture in Northwest China Inferred From Genome-Wide Array Genotyping. Front Genet 2022; 12:795570. [PMID: 34992635 PMCID: PMC8724515 DOI: 10.3389/fgene.2021.795570] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/06/2021] [Indexed: 01/02/2023] Open
Abstract
Northwest China is a contacting region for East and West Eurasia and an important center for investigating the migration and admixture history of human populations. However, the comprehensive genetic structure and admixture history of the Altaic speaking populations and Hui group in Northwest China were still not fully characterized due to insufficient sampling and the lack of genome-wide data. Thus, We genotyped genome-wide SNPs for 140 individuals from five Chinese Mongolic, Turkic speaking groups including Dongxiang, Bonan, Yugur, and Salar, as well as the Hui group. Analysis based on allele-sharing and haplotype-sharing were used to elucidate the population history of Northwest Chinese populations, including PCA, ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave/qpAdm and ALDER, fineSTRUCTURE and GLOBETROTTER. We observed Dongxiang, Bonan, Yugur, Salar, and Hui people were admixed populations deriving ancestry from both East and West Eurasians, with the proportions of West Eurasian related contributions ranging from 9 to 15%. The genetic admixture was probably driven by male-biased migration- showing a higher frequency of West Eurasian related Y chromosomal lineages than that of mtDNA detected in Northwest China. ALDER-based admixture and haplotype-based GLOBETROTTER showed this observed West Eurasian admixture signal was introduced into East Eurasia approximately 700 ∼1,000 years ago. Generally, our findings provided supporting evidence that the flourish transcontinental communication between East and West Eurasia played a vital role in the genetic formation of northwest Chinese populations.
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Affiliation(s)
- Bin Ma
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, China
| | - Jinwen Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jingya Bai
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, China
| | - Siwei Ouyang
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, China
| | - Xiaodan Mo
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, China
| | - Wangsheng Chen
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiangjun Hai
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, China
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Braun P, Nguyen MDT, Walter MC, Grass G. Ultrasensitive Detection of Bacillus anthracis by Real-Time PCR Targeting a Polymorphism in Multi-Copy 16S rRNA Genes and Their Transcripts. Int J Mol Sci 2021; 22:12224. [PMID: 34830105 PMCID: PMC8618755 DOI: 10.3390/ijms222212224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 02/03/2023] Open
Abstract
The anthrax pathogen Bacillus anthracis poses a significant threat to human health. Identification of B. anthracis is challenging because of the bacterium's close genetic relationship to other Bacillus cereus group species. Thus, molecular detection is founded on species-specific PCR targeting single-copy genes. Here, we validated a previously recognized multi-copy target, a species-specific single nucleotide polymorphism (SNP) present in 2-5 copies in every B. anthracis genome analyzed. For this, a hydrolysis probe-based real-time PCR assay was developed and rigorously tested. The assay was specific as only B. anthracis DNA yielded positive results, was linear over 9 log10 units, and was sensitive with a limit of detection (LoD) of 2.9 copies/reaction. Though not exhibiting a lower LoD than established single-copy PCR targets (dhp61 or PL3), the higher copy number of the B. anthracis-specific 16S rRNA gene alleles afforded ≤2 unit lower threshold (Ct) values. To push the detection limit even further, the assay was adapted for reverse transcription PCR on 16S rRNA transcripts. This RT-PCR assay was also linear over 9 log10 units and was sensitive with an LoD of 6.3 copies/reaction. In a dilution series of experiments, the 16S RT-PCR assay achieved a thousand-fold higher sensitivity than the DNA-targeting assays. For molecular diagnostics, we recommend a real-time RT-PCR assay variant in which both DNA and RNA serve as templates (thus, no requirement for DNase treatment). This can at least provide results equaling the DNA-based implementation if no RNA is present but is superior even at the lowest residual rRNA concentrations.
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Affiliation(s)
| | | | | | - Gregor Grass
- Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany; (P.B.); (M.D.-T.N.); (M.C.W.)
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A Whole-Genome-Based Gene-by-Gene Typing System for Standardized High-Resolution Strain Typing of Bacillus anthracis. J Clin Microbiol 2021; 59:e0288920. [PMID: 33827898 PMCID: PMC8218748 DOI: 10.1128/jcm.02889-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequencing (WGS) has been established for bacterial subtyping and is regularly used to study pathogen transmission, to investigate outbreaks, and to perform routine surveillance. Core-genome multilocus sequence typing (cgMLST) is a bacterial subtyping method that uses WGS data to provide a high-resolution strain characterization. This study aimed at developing a novel cgMLST scheme for Bacillus anthracis, a notorious pathogen that causes anthrax in livestock and humans worldwide. The scheme comprises 3,803 genes that were conserved in 57 B. anthracis genomes spanning the whole phylogeny. The scheme has been evaluated and applied to 584 genomes from 50 countries. On average, 99.5% of the cgMLST targets were detected. The cgMLST results confirmed the classical canonical single-nucleotide-polymorphism (SNP) grouping of B. anthracis into major clades and subclades. Genetic distances calculated based on cgMLST were comparable to distances from whole-genome-based SNP analysis with similar phylogenetic topology and comparable discriminatory power. Additionally, the application of the cgMLST scheme to anthrax outbreaks from Germany and Italy led to a definition of a cutoff threshold of five allele differences to trace epidemiologically linked strains for cluster typing and transmission analysis. Finally, the association of two clusters of B. anthracis with human cases of injectional anthrax in four European countries was confirmed using cgMLST. In summary, this study presents a novel cgMLST scheme that provides high-resolution strain genotyping for B. anthracis. This scheme can be used in parallel with SNP typing methods to facilitate rapid and harmonized interlaboratory comparisons, essential for global surveillance and outbreak analysis. The scheme is publicly available for application by users, including those with little bioinformatics knowledge.
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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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