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Kompes G, Duvnjak S, Reil I, Mihaljević Ž, Habrun B, Benić M, Cvetnić L, Špičić S, Bagarić A. Antimicrobial Resistance Profile, Whole-Genome Sequencing and Core Genome Multilocus Sequence Typing of B. anthracis Isolates in Croatia from 2001 to 2022. Antibiotics (Basel) 2024; 13:639. [PMID: 39061321 PMCID: PMC11274125 DOI: 10.3390/antibiotics13070639] [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: 06/17/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. It is also considered one of the most important pathogens of bioterrorism. Rapid and reliable diagnosis and administration of antimicrobials are essential for effective anthrax treatment. In this study, we determined the in vitro susceptibilities of 40 isolates of B. anthracis isolated in Croatia over the recent two decades to 18 antimicrobials. Whole-genome sequencing was performed, and bioinformatics tools were used to determine virulence factors and antimicrobial resistance genes. Core genome-based multilocus sequence typing was used for isolate comparison and phylogenetic analysis. All isolates were susceptible to all antimicrobials recommended for post-exposure prophylaxis or anthrax therapy. Susceptibility was found to all other tested antimicrobials that are an alternative for primary therapy. We found two beta-lactamase genes, but their expression is not sufficient to confer resistance. In all isolates used in this study, we found 21 virulence genes, 8 of which are responsible for toxin and capsule production. As far as phylogenetic analysis is concerned, the B. anthracis isolates from Croatia are categorised into two clades. The first is clade A, subclade Trans Eurasia, and the other is clade B, subclade B2.
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Affiliation(s)
- Gordan Kompes
- Laboratory for General Bacteriology and Mycology, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (B.H.); (A.B.)
| | - Sanja Duvnjak
- Laboratory for Bacterial Zoonoses and Molecular Diagnostics of Bacterial Diseases, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Irena Reil
- Laboratory for Bacterial Zoonoses and Molecular Diagnostics of Bacterial Diseases, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Željko Mihaljević
- Laboratory for Pathology, Department for Pathology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Boris Habrun
- Laboratory for General Bacteriology and Mycology, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (B.H.); (A.B.)
| | - Miroslav Benić
- Laboratory for Mastitis and Raw Milk Quality, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (M.B.); (L.C.)
| | - Luka Cvetnić
- Laboratory for Mastitis and Raw Milk Quality, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (M.B.); (L.C.)
| | - Silvio Špičić
- Laboratory for Bacterial Zoonoses and Molecular Diagnostics of Bacterial Diseases, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Antonela Bagarić
- Laboratory for General Bacteriology and Mycology, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (B.H.); (A.B.)
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Anisimova EA, Fakhrutdinov NA, Mirgazov DA, Dodonova EA, Elizarova IA, Gorbunova ME, Khammadov NI, Zainullin LI, Osyanin KA. Bacillus anthracis strain differentiation based on SNP and VNTR loci. Vavilovskii Zhurnal Genet Selektsii 2022; 26:560-567. [PMID: 36313827 PMCID: PMC9556301 DOI: 10.18699/vjgb-22-68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 06/16/2023] Open
Abstract
Bacillus anthracis is the anthrax causative agent. For its epidemiology, it is important not only to identify the etiological agent but also to determine the patterns of its evolution and spread. Modern methods of molecular biology make it possible to detect a number of genetic markers suitable for indicating and differentiating the strains of B. anthracis, including the loci arranged as variable number tandem repeats (VNTRs) and SNPs, one nucleotide-sized differences in the DNA sequence of the loci being compared. The objective of the present study was to examine the effectiveness of SNP analysis and PCR amplif ication of VNTR loci combined with the high-resolution amplicon melting analysis for identif ication and differentiation of the anthrax agent strains. In the study, seven strains of B. anthracis obtained from soil samples and animal carcasses were investigated using vaccine strain STI-1 as a reference. For molecular genetic characterization of these bacteria, analysis of 12 SNPs and variability analysis of eight VNTR loci were carried out. To detect the differences between the strains, their PCR product melting points were measured in the presence of the EvaGreen (Sintol, Russia) intercalating dye. For SNP detection, a PCR assay with double TaqMan probes was applied. It was found that the studied virulent strains, except for B. anthracis No. 1 and 3, could not be attributed to any phylogenetic subgroup of the anthrax agents. The proposed method made it possible to differentiate four out of the seven investigated strains. Strains No. 5-7 had identical SNP and HRM prof iles and, as a result, formed a single cluster. Our investigation has conf irmed that the proposed method can be successfully used for preliminary analysis of an epizootic situation in the case of anthrax.
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Affiliation(s)
- E A Anisimova
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - N A Fakhrutdinov
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - D A Mirgazov
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - E A Dodonova
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - I A Elizarova
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - M E Gorbunova
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - N I Khammadov
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - L I Zainullin
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - K A Osyanin
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
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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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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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Pilo P, Frey J. Pathogenicity, population genetics and dissemination of Bacillus anthracis. INFECTION GENETICS AND EVOLUTION 2018; 64:115-125. [PMID: 29935338 DOI: 10.1016/j.meegid.2018.06.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 12/30/2022]
Abstract
Bacillus anthracis, the etiological agent of anthrax, procures its particular virulence by a capsule and two AB type toxins: the lethal factor LF and the edema factor EF. These toxins primarily disable immune cells. Both toxins are translocated to the host cell by the adhesin-internalin subunit called protective antigen PA. PA enables LF to reach intra-luminal vesicles, where it remains active for long periods. Subsequently, LF translocates to non-infected cells, leading to inefficient late therapy of anthrax. B. anthracis undergoes slow evolution because it alternates between vegetative and long spore phases. Full genome sequence analysis of a large number of worldwide strains resulted in a robust evolutionary reconstruction of this bacterium, showing that B. anthracis is split in three main clades: A, B and C. Clade A efficiently disseminated worldwide underpinned by human activities including heavy intercontinental trade of goat and sheep hair. Subclade A.Br.WNA, which is widespread in the Northern American continent, is estimated to have split from clade A reaching the Northern American continent in the late Pleistocene epoch via the former Bering Land Bridge and further spread from Northwest southwards. An alternative hypothesis is that subclade A.Br.WNA. evolved from clade A.Br.TEA tracing it back to strains from Northern France that were assumingly dispatched by European explorers that settled along the St. Lawrence River. Clade B established mostly in Europe along the alpine axis where it evolved in association with local cattle breeds and hence displays specific geographic subclusters. Sequencing technologies are also used for forensic applications to trace unintended or criminal acts of release of B. anthracis. Under natural conditions, B. anthracis generally affects domesticated and wild ruminants in arid ecosystems. The more recently discovered B. cereus biovar anthracis spreads in tropical forests, where it threatens particularly endangered primate populations.
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Affiliation(s)
- Paola Pilo
- Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Bern, Switzerland.
| | - Joachim Frey
- Dean's Office, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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Mehta B, Daniel R, McNevin D. HRM and SNaPshot as alternative forensic SNP genotyping methods. Forensic Sci Med Pathol 2017; 13:293-301. [PMID: 28523436 DOI: 10.1007/s12024-017-9874-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2017] [Indexed: 01/25/2023]
Abstract
Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing. This study compares HRM and SNaPshot®. HRM produced reproducible and concordant genotypes at 500 pg, however, difficulties were encountered when genotyping SNPs with high GC content in flanking regions and differentiating variants of symmetrical SNPs. SNaPshot® was reproducible at 100 pg and is less dependent on SNP choice. HRM has a shorter processing time in comparison to SNaPshot®, avoids post PCR contamination risk and has potential as a screening tool for many forensic applications.
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Affiliation(s)
- Bhavik Mehta
- National Centre for Forensic Studies, Faculty of Education, Science, Technology & Mathematics, University of Canberra, ACT, Bruce, 2617, Australia.
| | - Runa Daniel
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, 31 Forensic Drive, Macleod, VIC, 3085, Australia
| | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of Education, Science, Technology & Mathematics, University of Canberra, ACT, Bruce, 2617, Australia
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Genome Sequence of Historical Bacillus anthracis Strain Tyrol 4675 Isolated from a Bovine Anthrax Case in Austria. GENOME ANNOUNCEMENTS 2017; 5:5/10/e00002-17. [PMID: 28280006 PMCID: PMC5347226 DOI: 10.1128/genomea.00002-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In 1988, an outbreak of anthrax occurred among cattle in the Austrian state of Tyrol. Since then, Austria has been declared anthrax-free. Here, we report the draft genome sequence of one of these last outbreak strains, Bacillus anthracis Tyrol 4675, isolated from a diseased cow.
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Vergnaud G, Girault G, Thierry S, Pourcel C, Madani N, Blouin Y. Comparison of French and Worldwide Bacillus anthracis Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade. PLoS One 2016; 11:e0146216. [PMID: 26901621 PMCID: PMC4763433 DOI: 10.1371/journal.pone.0146216] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
Background Bacillus anthracis, the highly dangerous zoonotic bacterial pathogen species is currently composed of three genetic groups, called A, B and C. Group A is represented worldwide whereas group B is present essentially in Western Europe and Southern Africa. Only three strains from group C have been reported. This knowledge is derived from the genotyping of more than 2000 strains collected worldwide. Strains from both group A and group B are present in France. Previous investigations showed that the majority of sporadic French strains belong to the so-called A.Br.011/009 group A clade and define a very remarkable polytomy with six branches. Here we explore the significance of this polytomy by comparing the French B. anthracis lineages to worldwide lineages. We take advantage of whole genome sequence data previously determined for 122 French strains and 45 strains of various origins. Results A total of 6690 SNPs was identified among the available dataset and used to draw the phylogeny. The phylogeny of the French B group strains which belongs to B.Br.CNEVA indicates an expansion from the south-east part of France (the Alps) towards the south-west (Massif-Central and Pyrenees). The relatively small group A strains belonging to A.Br.001/002 results from at least two independent introductions. Strikingly, the data clearly demonstrates that the currently predominant B. anthracis lineage in North America, called WNA for Western North American, is derived from one branch of the A.Br.011/009 polytomy predominant in France. Conclusions/Significance The present work extends the range of observed substitution rate heterogeneity within B. anthracis, in agreement with its ecology and in contrast with some other pathogens. The population structure of the six branches A.Br.011/009 polytomy identified in France, diversity of branch length, and comparison with the WNA lineage, suggests that WNA is of post-Columbian and west European origin, with France as a likely source. Furthermore, it is tempting to speculate that the polytomy’s most recent common ancestor -MRCA- dates back to the Hundred Years' war between France and England started in the mid-fourteenth century. These events were associated in France with deadly epidemics and major economic and social changes.
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Affiliation(s)
- Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
- * E-mail:
| | - Guillaume Girault
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Simon Thierry
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Nora Madani
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Yann Blouin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
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Derzelle S, Girault G, Kokotovic B, Angen Ø. Whole Genome-Sequencing and Phylogenetic Analysis of a Historical Collection of Bacillus anthracis Strains from Danish Cattle. PLoS One 2015; 10:e0134699. [PMID: 26317972 PMCID: PMC4552859 DOI: 10.1371/journal.pone.0134699] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/13/2015] [Indexed: 11/28/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is known as one of the most genetically monomorphic species. Canonical single-nucleotide polymorphism (SNP) typing and whole-genome sequencing were used to investigate the molecular diversity of eleven B. anthracis strains isolated from cattle in Denmark between 1935 and 1988. Danish strains were assigned into five canSNP groups or lineages, i.e. A.Br.001/002 (n = 4), A.Br.Ames (n = 2), A.Br.008/011 (n = 2), A.Br.005/006 (n = 2) and A.Br.Aust94 (n = 1). The match with the A.Br.Ames lineage is of particular interest as the occurrence of such lineage in Europe is demonstrated for the first time, filling an historical gap within the phylogeography of the lineage. Comparative genome analyses of these strains with 41 isolates from other parts of the world revealed that the two Danish A.Br.008/011 strains were related to the heroin-associated strains responsible for outbreaks of injection anthrax in drug users in Europe. Eight novel diagnostic SNPs that specifically discriminate the different sub-groups of Danish strains were identified and developed into PCR-based genotyping assays.
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Affiliation(s)
- Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Maisons-Alfort, France
| | - Guillaume Girault
- University Paris-Est, Anses, Animal Health Laboratory, Maisons-Alfort, France
| | - Branko Kokotovic
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Øystein Angen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
- * E-mail:
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Zhou W, Sun Y, Zhu L, Zhou B, Liu J, Ji X, Wang X, Wang N, Gu G, Feng S, Qian J, Guo X. Investigation of Anthrax Cases in North-East China, 2010-2014. PLoS One 2015; 10:e0135777. [PMID: 26308449 PMCID: PMC4550413 DOI: 10.1371/journal.pone.0135777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/24/2015] [Indexed: 12/04/2022] Open
Abstract
We determined the genotypes of seven Bacillus anthracis strains that were recovered from nine anthrax outbreaks in North-East China from 2010 to 2014, and two approved vaccine strains that are currently in use in China. The causes of these cases were partly due to local farmers being unaware of the presence of anthrax, and butchers with open wounds having direct contact with anthrax-contaminated meat products. The genotype of five of the seven recovered strains was A.Br.001/002 sub-lineage, which was concordant with previously published research. The remaining two cases belongs to the A.Br.Ames sub-lineage. Both of these strains displayed an identical SNR pattern, which was the first time that this genotype was identified in North-East China. Strengthening education in remote villages of rural China is an important activity aimed at fostering attempts to prevent and control anthrax. The genotype of the vaccine strain Anthrax Spore Vaccine No.II was A.Br.008/009 and A.Br.001/002 for the vaccine strain Anthrax Spore Vaccine Non-capsulated. Further studies of their characteristics are clearly warranted.
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Affiliation(s)
- Wei Zhou
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Yang Sun
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Lingwei Zhu
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Bo Zhou
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Jun Liu
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Xue Ji
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Xiaofeng Wang
- Animal Diseases Control and Prevention Centre of Jilin Province, Jilin, China
| | - Nan Wang
- Animal Diseases Control and Prevention Centre of Jilin Province, Jilin, China
| | - Guibo Gu
- Animal Diseases Control and Prevention Centre of Liaoning Province, Liaoning, China
| | - Shuzhang Feng
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Jun Qian
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Xuejun Guo
- Institute of Military Veterinary, AMMS, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
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11
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Seyed-Mohamadi S, Moradi Bidhendi S, Tadayon K, Ghaderi R. Genetic Characterization of Bacillus anthracis 17 JB strain. IRANIAN JOURNAL OF MICROBIOLOGY 2015; 7:168-72. [PMID: 26668705 PMCID: PMC4676987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND AND OBJECTIVES Bacillus anthracis is one of the most homogenous bacteria ever described. Some level of diversity. Bacillus anthracis 17JB is a laboratory strain It is broadly used as a challenge strain in guinea pigs for potency test of anthrax vaccine. MATERIAL AND METHODS This work describes genetic characterization of B. anthracis 17 JB strain using the SNPs and MLVA genotyping. RESULTS AND CONCLUSION In SNPs typing, the originally French 17JB strain represented the A.Br. 008/009 subgroup. In Levy's genotyping method, 843, 451 and 864 bp long fragments were identified at AA03, AJ03 and AA07 loci, respectively. In the vaccine manufacturer perspective these findings are much valuable on their own account, but similar research is required to extend molecular knowledge of B. anthracis epidemiology in Persia.
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Affiliation(s)
| | - Soheila Moradi Bidhendi
- Department of Microbiology, Razi Institute, Karaj, Iran,Corresponding author: Soheila Moradi Bidhendi, PhD. Tel: +98-26-34502892, E-mail:
| | - Keyvan Tadayon
- Department of Aerobic Veterinary Bacteria, Razi Institute, Karaj, Iran
| | - Rainak Ghaderi
- Department of Aerobic Veterinary Bacteria, Razi Institute, Karaj, Iran
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12
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Derzelle S, Girault G, Roest HIJ, Koene M. Molecular diversity of Bacillus anthracis in the Netherlands: Investigating the relationship to the worldwide population using whole-genome SNP discovery. INFECTION GENETICS AND EVOLUTION 2015; 32:370-6. [DOI: 10.1016/j.meegid.2015.03.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 01/01/2023]
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13
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Draft Genomes of Three Strains Representative of the Bacillus anthracis Diversity Found in France. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00736-14. [PMID: 25081258 PMCID: PMC4118061 DOI: 10.1128/genomea.00736-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genomes of three Bacillus anthracis strains isolated in France: 08-8_20 (A.Br.001/002), 99-100 (A.Br.011/009), and 00-82 (B.Br CNEVA). The total lengths of assemblies are 5,440,708 bp, 5,446,472 bp, and 5,436,014 bp for 08-8_20, 99-100, and 00-82, respectively.
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14
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Derzelle S, Thierry S. Genetic diversity of Bacillus anthracis in Europe: genotyping methods in forensic and epidemiologic investigations. Biosecur Bioterror 2014; 11 Suppl 1:S166-76. [PMID: 23971802 DOI: 10.1089/bsp.2013.0003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacillus anthracis, the etiological agent of anthrax, a zoonosis relatively common throughout the world, can be used as an agent of bioterrorism. In naturally occurring outbreaks and in criminal release of this pathogen, a fast and accurate diagnosis is crucial to an effective response. Microbiological forensics and epidemiologic investigations increasingly rely on molecular markers, such as polymorphisms in DNA sequence, to obtain reliable information regarding the identification or source of a suspicious strain. Over the past decade, significant research efforts have been undertaken to develop genotyping methods with increased power to differentiate B. anthracis strains. A growing number of DNA signatures have been identified and used to survey B. anthracis diversity in nature, leading to rapid advances in our understanding of the global population of this pathogen. This article provides an overview of the different phylogenetic subgroups distributed across the world, with a particular focus on Europe. Updated information on the anthrax situation in Europe is reported. A brief description of some of the work in progress in the work package 5.1 of the AniBioThreat project is also presented, including (1) the development of a robust typing tool based on a suspension array technology and multiplexed single nucleotide polymorphisms scoring and (2) the typing of a collection of DNA from European isolates exchanged between the partners of the project. The know-how acquired will contribute to improving the EU's ability to react rapidly when the identity and real origin of a strain need to be established.
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15
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Thierry S, Tourterel C, Le Flèche P, Derzelle S, Dekhil N, Mendy C, Colaneri C, Vergnaud G, Madani N. Genotyping of French Bacillus anthracis strains based on 31-loci multi locus VNTR analysis: epidemiology, marker evaluation, and update of the internet genotype database. PLoS One 2014; 9:e95131. [PMID: 24901417 PMCID: PMC4046976 DOI: 10.1371/journal.pone.0095131] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 03/24/2014] [Indexed: 12/28/2022] Open
Abstract
Background Bacillus anthracis is known to have low genetic variability. In spite of this lack of diversity, multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) and single nucleotide polymorphisms (SNPs) including the canonical SNPs assay (canSNP) have proved to be highly effective to differentiate strains. Five different MLVA schemes based on a collection of 31 VNTR loci (MLVA8, MLVA15, MLVA20, MLVA25 and MLVA31) with increased resolving power have been described. Results MLVA31 was applied to characterize the French National Reference Laboratory collection. The total collection of 130 strains is resolved in 35 genotypes. The 119 veterinary and environmental strains collection in France were resolved into 26 genotypes belonging to three canSNP lineages and four MLVA clonal complexes (CCs) with particular geographical clustering. A subset of seven loci (MLVA7) is proposed to constitute a first line assay. The loci are compatible with moderate resolution equipment such as agarose gel electrophoresis and show a good congruence value with MLVA31. The associated MLVA and SNP data was imported together with published genotyping data by taking advantage of major enhancements to the MLVAbank software and web site. Conclusions The present report provides a wide coverage of the genetic diversity of naturally occurring B. anthracis strains in France as can be revealed by MLVA. The data obtained suggests that once such coverage is achieved, it becomes possible to devise optimized first-line MLVA assays comprising a sufficiently low number of loci to be typed either in one multiplex PCR or on agarose gels. Such a selection of seven loci is proposed here, and future similar investigations in additional countries will indicate to which extend the same selection can be used worldwide as a common minimum set. It is hoped that this approach will contribute to an efficient and low-cost routine surveillance of important pathogens for biosecurity such as B. anthracis.
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Affiliation(s)
- Simon Thierry
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Christophe Tourterel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Philippe Le Flèche
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Division of Analytical Microbiology, DGA CBRN Defence, Vert le Petit, France
| | - Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Neira Dekhil
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Christiane Mendy
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Cécile Colaneri
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Gilles Vergnaud
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- DGA/MRIS- Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France
| | - Nora Madani
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
- * E-mail:
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16
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Girault G, Blouin Y, Vergnaud G, Derzelle S. High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery. BMC Genomics 2014; 15:288. [PMID: 24734872 PMCID: PMC4023602 DOI: 10.1186/1471-2164-15-288] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/09/2014] [Indexed: 11/10/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) are ideal signatures for subtyping monomorphic pathogens such as Bacillus anthracis. Here we report the use of next-generation sequencing technology to investigate the historical, geographic and genetic diversity of Bacillus anthracis in France. 122 strains isolated over a 60-years period throughout the country were whole-genome sequenced and comparative analyses were carried out with a focus on SNPs discovery to discriminate regional sub-groups of strains. Results A total of 1581 chromosomal SNPs precisely establish the phylogenetic relationships existing between the French strains. Phylogeography patterns within the three canSNP sub-lineages present in France (i.e. B.Br.CNEVA, A.Br.011/009 and A.Br.001/002) were observed. One of the more remarkable findings was the identification of a variety of genotypes within the A.Br.011/009 sub-group that are persisting in the different regions of France. The 560 SNPs defining the A.Br.011/009- affiliated French strains split the Trans-Eurasian sub-group into six distinct branches without any intermediate nodes. Distinct sub-branches, with some geographic clustering, were resolved. The 345 SNPs defining the major B.Br CNEVA sub-lineage clustered three main phylogeographic clades, the Alps, the Pyrenees, and the Massif Central, with a small Saône-et-Loire sub-cluster nested within the latter group. The French strains affiliated to the minor A.Br.001/002 group were characterized by 226 SNPs. All recent isolates collected from the Doubs department were closely related. Identification of SNPs from whole-genome sequences facilitates high-resolution strain tracking and provides the level of discrimination required for outbreak investigations. Eight diagnostic SNPs, representative of the main French-specific phylogeographic clusters, were therefore selected and developed into high-resolution melting SNP discriminative assays. Conclusions This work has established one of the most accurate phylogenetic reconstruction of B. anthracis population structure in a country. An extensive next-generation sequencing (NGS) dataset of 122 French strains have been created that allowed the identification of novel diagnostic SNPs useful to rapidly determine the geographic origin of any strain found in France.
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Affiliation(s)
| | | | | | - Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort 94706, France.
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17
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Girault G, Thierry S, Cherchame E, Derzelle S. Application of High-Throughput Sequencing: Discovery of Informative SNPs to Subtype <i>Bacillus anthracis</i>. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/abb.2014.57079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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A multiplex bead-based suspension array assay for interrogation of phylogenetically informative single nucleotide polymorphisms for Bacillus anthracis. J Microbiol Methods 2013; 95:357-65. [DOI: 10.1016/j.mimet.2013.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 10/06/2013] [Indexed: 11/24/2022]
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Beyer W, Turnbull P. Co-infection of an animal with more than one genotype can occur in anthrax. Lett Appl Microbiol 2013; 57:380-4. [DOI: 10.1111/lam.12140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/09/2013] [Accepted: 07/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- W. Beyer
- University of Hohenheim; Institute of Environmental and Animal Hygiene; Stuttgart Germany
| | - P.C.B. Turnbull
- University of Hohenheim; Institute of Environmental and Animal Hygiene; Stuttgart Germany
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Göransson J, Ke R, Nong RY, Howell WM, Karman A, Grawé J, Stenberg J, Granberg M, Elgh M, Herthnek D, Wikström P, Jarvius J, Nilsson M. Rapid identification of bio-molecules applied for detection of biosecurity agents using rolling circle amplification. PLoS One 2012; 7:e31068. [PMID: 22383994 PMCID: PMC3285169 DOI: 10.1371/journal.pone.0031068] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 01/01/2012] [Indexed: 11/22/2022] Open
Abstract
Detection and identification of pathogens in environmental samples for biosecurity applications are challenging due to the strict requirements on specificity, sensitivity and time. We have developed a concept for quick, specific and sensitive pathogen identification in environmental samples. Target identification is realized by padlock- and proximity probing, and reacted probes are amplified by RCA (rolling-circle amplification). The individual RCA products are labeled by fluorescence and enumerated by an instrument, developed for sensitive and rapid digital analysis. The concept is demonstrated by identification of simili biowarfare agents for bacteria (Escherichia coli and Pantoea agglomerans) and spores (Bacillus atrophaeus) released in field.
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Affiliation(s)
- Jenny Göransson
- the Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
- Q-linea AB, Dag Hammarskjölds, Uppsala, Sweden
| | - Rongqin Ke
- the Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Rachel Yuan Nong
- the Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - W. Mathias Howell
- the Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Anna Karman
- Olink AB, Dag Hammarskjölds väg, Uppsala, Sweden
- Q-linea AB, Dag Hammarskjölds, Uppsala, Sweden
| | - Jan Grawé
- Q-linea AB, Dag Hammarskjölds, Uppsala, Sweden
| | | | | | - Magnus Elgh
- Q-linea AB, Dag Hammarskjölds, Uppsala, Sweden
| | - David Herthnek
- the Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Jonas Jarvius
- the Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
- Q-linea AB, Dag Hammarskjölds, Uppsala, Sweden
| | - Mats Nilsson
- the Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
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