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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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Roonie A, Majumder S, Kingston JJ, Parida M. Molecular characterization of B. anthracis isolates from the anthrax outbreak among cattle in Karnataka, India. BMC Microbiol 2020; 20:232. [PMID: 32736522 PMCID: PMC7394690 DOI: 10.1186/s12866-020-01917-1] [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: 01/05/2020] [Accepted: 07/21/2020] [Indexed: 12/02/2022] Open
Abstract
Background Anthrax, a zoonotic disease is caused by the Gram positive bacterium Bacillus anthracis. During January 2013, an anthrax outbreak among cattle was reported in Gundlupet Taluk, neighboring Bandipur National Park and tiger reserve, India. The present study aims at the molecular identification and characterization of 12 B. anthracis isolates from this outbreak by 16S rRNA gene sequencing, screening B. anthracis specific prophages and chromosomal markers, protective antigen (pag) gene and canonical single nucleotide polymorphism (canSNP) analysis to subtype the isolates into one of the twelve globally identified clonal sub-lineages of B. anthracis. Results These isolates had identical 16S rDNA nucleotide sequences with B. anthracis specific dual peaks showing mixed base pair R (G/A) at position 1139 with visual inspection while the automated basecaller software indicated a G. Alternatively the nucleotide A at 1146 position was indicative of the 16S rDNA type 7. Multiple sequence alignment with additional 170 (16S rDNA) sequences of B. cereus sensu lato group from GenBank database revealed 28 new 16S types in addition to eleven 16S types reported earlier. The twelve B. anthracis isolates were found to harbor the four B. anthracis specific prophages (lambdaBa01, lambdaBa02, lambdaBa03, and lambdaBa04) along with its four specific loci markers (dhp 61.183, dhp 77.002, dhp 73.019, and dhp 73.017). The pag gene sequencing identified the isolates as protective antigen (PA) genotype I with phenylalanine-proline-alanine phenotype (FPA phenotype). However, sequence clustering with additional 34 pag sequences from GenBank revealed two additional missense mutations at nucleotide positions 196 bp and 869 bp of the 2294 bp pag sequence among the 5 B. cereus strains with pXO1 like plasmids. The canSNP analysis showed that the isolates belong to A.Br.Aust94 sub-lineage that is distributed geographically in countries of Asia, Africa, Europe and Australia. Conclusions The analysis of 16S rDNA sequences reiterated the earlier findings that visual inspection of electropherogram for position 1139 having nucleotide R could be used for B. anthracis identification and not the consensus sequence from base caller. The canSNP results indicated that the anthrax outbreak among cattle was caused by B. anthracis of A.Br.Aust94 sub-lineage.
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Affiliation(s)
- Akanxa Roonie
- Microbiology Division, Defence Food Research Laboratory, Siddartha Nagar, Mysore, Karnataka, 570011, India
| | - Saugata Majumder
- Microbiology Division, Defence Food Research Laboratory, Siddartha Nagar, Mysore, Karnataka, 570011, India
| | - Joseph J Kingston
- Microbiology Division, Defence Food Research Laboratory, Siddartha Nagar, Mysore, Karnataka, 570011, India.
| | - Manmohan Parida
- Microbiology Division, Defence Food Research Laboratory, Siddartha Nagar, Mysore, Karnataka, 570011, India
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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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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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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: 44] [Impact Index Per Article: 7.3] [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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Timofeev VS, Bakhteeva IV, Dyatlov IA. Genotyping of Bacillus anthracis and Closely Related Microorganisms. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418010118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
In 1998, it was claimed that an 80-year-old glass tube intentionally filled with Bacillus anthracis and embedded in a sugar lump as a WWI biological weapon still contained viable spores. Today, genome sequencing of three colonies isolated in 1998 and subjected to phylogenetic analysis surprisingly identified a well-known B. anthracis reference strain isolated in the United States in 1981, pointing to accidental laboratory contamination. Next-generation sequencing and subsequent phylogenetic analyses are useful and reliable tools for the classification of recent and historical samples. The reliability of sequences obtained and bioinformatic algorithms has increased in recent years, and research has uncovered the identity of a presumed bioweapon agent as a contaminant.
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Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M, Sun Y, Wang L, Shao Z. Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 2015; 5:14082. [PMID: 26373441 PMCID: PMC4571650 DOI: 10.1038/srep14082] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 08/17/2015] [Indexed: 02/01/2023] Open
Abstract
The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments.
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Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraβe 7B, 38124, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraβe 7B, 38124, Braunschweig, Germany
| | - Meng Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Yamin Sun
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
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Braun P, Grass G, Aceti A, Serrecchia L, Affuso A, Marino L, Grimaldi S, Pagano S, Hanczaruk M, Georgi E, Northoff B, Schöler A, Schloter M, Antwerpen M, Fasanella A. Microevolution of Anthrax from a Young Ancestor (M.A.Y.A.) Suggests a Soil-Borne Life Cycle of Bacillus anthracis. PLoS One 2015; 10:e0135346. [PMID: 26266934 PMCID: PMC4534099 DOI: 10.1371/journal.pone.0135346] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/15/2015] [Indexed: 01/10/2023] Open
Abstract
During an anthrax outbreak at the Pollino National Park (Basilicata, Italy) in 2004, diseased cattle were buried and from these anthrax-foci Bacillus anthracis endospores still diffuse to the surface resulting in local accumulations. Recent data suggest that B. anthracis multiplies in soil outside the animal-host body. This notion is supported by the frequent isolation of B. anthracis from soil lacking one or both virulence plasmids. Such strains represent an evolutionary dead end, as they are likely no longer able to successfully infect new hosts. This loss of virulence plasmids is explained most simply by postulating a soil-borne life cycle of the pathogen. To test this hypothesis we investigated possible microevolution at two natural anthrax foci from the 2004 outbreak. If valid, then genotypes of strains isolated from near the surface at these foci should be on a different evolutionary trajectory from those below residing in deeper-laying horizons close to the carcass. Thus, the genetic diversity of B. anthracis isolates was compared conducting Progressive Hierarchical Resolving Assays using Nucleic Acids (PHRANA) and next generation Whole Genome Sequencing (WGS). PHRANA was not discriminatory enough to resolve the fine genetic relationships between the isolates. Conversely, WGS of nine isolates from near-surface and nine from near-carcass revealed five isolate specific SNPs, four of which were found only in different near-surface isolates. In support of our hypothesis, one surface-isolate lacked plasmid pXO1 and also harbored one of the unique SNPs. Taken together, our results suggest a limited soil-borne life cycle of B. anthracis.
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Affiliation(s)
- Peter Braun
- Bundeswehr Institute of Microbiology, Munich, Germany
- Technische Universität München, Wissenschaftszentrum Weihenstephan, Chair for Soil Ecology, Freising, Germany
| | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Angela Aceti
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Alessia Affuso
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Leonardo Marino
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Stefania Grimaldi
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Stefania Pagano
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | | | - Enrico Georgi
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Bernd Northoff
- Bundeswehr Institute of Microbiology, Munich, Germany
- Ludwig Maximilians Universität München, Institute for Laboratory Medicine, Munich, Germany
| | - Anne Schöler
- German Research Center for Environmental Health, Research Unit for Environmental Genomics, Neuherberg, Germany
| | - Michael Schloter
- Technische Universität München, Wissenschaftszentrum Weihenstephan, Chair for Soil Ecology, Freising, Germany
- German Research Center for Environmental Health, Research Unit for Environmental Genomics, Neuherberg, Germany
| | | | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
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Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+"). PLoS One 2015; 10:e0123298. [PMID: 25856198 PMCID: PMC4391923 DOI: 10.1371/journal.pone.0123298] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/17/2015] [Indexed: 11/19/2022] Open
Abstract
The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.
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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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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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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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Abstract
Bacillus anthracis strains previously isolated from Bulgaria form a unique subcluster within the A1.a cluster that is typical for isolates from southeastern Europe. Here, we report the draft genome sequences of two Bulgarian B. anthracis strains belonging to the A branch (A.Br.)008/009 canonical single nucleotide polymorphism (SNP) group of the major A branch.
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Molecular epidemiology of the Bacillus anthracis isolates collected throughout Turkey from 1983 to 2011. Eur J Clin Microbiol Infect Dis 2012; 31:2783-90. [PMID: 22576652 DOI: 10.1007/s10096-012-1628-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
Abstract
The main perspective of this study was to determine cross-transmissions amongst anthrax cases and provide detailed information regarding the genotypes of Bacillus anthracis isolates circulating in Turkey. A total of 251 B. anthracis isolates were obtained from human (93 isolates), animal (155 isolates), and environmental (three isolates) samples in various provinces of Turkey. All isolates were susceptible to quinolones, vancomycin, tigecycline, and linezolid, but not to ceftriaxone. Excluding human isolates, one of the animal isolates was found to be resistant to penicillin, erythromycin, and doxycycline. Multiple-locus variable-number tandem repeats analysis including 8 loci (MLVA8) revealed 12 genotypes, in which genotype 43 was observed at the highest frequency (41.8 %), followed by genotype 35 (25.5 %) and genotype 27 (10.4 %). Major subtype A3.a was the predominant cluster, including 86.8 % of the isolates. The MLVA25 analysis for the 251 isolates yielded 62 different genotypes, 33 of which had only one isolate, while the remaining 29 genotypes had 2 to 43 isolates, with a total of 218 isolates (86.9 %). These findings indicate very high cross-transmission rates within anthrax cases in Turkey. The genotypes diagnosed in Turkey are populated in the A major cluster. Penicillin prescribed as the first-choice antibiotic for the treatment of anthrax is still effective.
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Derzelle S, Laroche S, Le Flèche P, Hauck Y, Thierry S, Vergnaud G, Madani N. Characterization of genetic diversity of Bacillus anthracis in France by using high-resolution melting assays and multilocus variable-number tandem-repeat analysis. J Clin Microbiol 2011; 49:4286-92. [PMID: 21998431 PMCID: PMC3232934 DOI: 10.1128/jcm.05439-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 10/04/2011] [Indexed: 11/20/2022] Open
Abstract
Using high-resolution melting (HRM) analysis, we developed a cost-effective method to genotype a set of 13 phylogenetically informative single-nucleotide polymorphisms (SNPs) within the genome of Bacillus anthracis. SNP discrimination assays were performed in monoplex or duplex and applied to 100 B. anthracis isolates collected in France from 1953 to 2009 and a few reference strains. HRM provided a reliable and cheap alternative to subtype B. anthracis into one of the 12 major sublineages or subgroups. All strains could be correctly positioned on the canonical SNP (canSNP) phylogenetic tree, except the divergent Pasteur vaccine strain ATCC 4229. We detected the cooccurrence of three canSNP subgroups in France. The dominant B.Br.CNEVA sublineage was found to be prevalent in the Alps, the Pyrenees, the Auvergne region, and the Saône-et-Loire department. Strains affiliated with the A.Br.008/009 subgroup were observed throughout most of the country. The minor A.Br.001/002 subgroup was restricted to northeastern France. Multiple-locus variable-number tandem-repeat analysis using 24 markers further resolved French strains into 60 unique profiles and identified some regional patterns. Diversity found within the A.Br.008/009 and B.Br.CNEVA subgroups suggests that these represent old, ecologically established clades in France. Phylogenetic relationships with strains from other parts of the world are discussed.
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Affiliation(s)
- S Derzelle
- Bacterial Zoonosis Unit, Maisons-Alfort Laboratory for Animal Health, ANSES, 23 Avenue du Général de Gaulle, 94706 Maisons Alfort cedex, France.
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Bacillus anthracis: Molecular taxonomy, population genetics, phylogeny and patho-evolution. INFECTION GENETICS AND EVOLUTION 2011; 11:1218-24. [DOI: 10.1016/j.meegid.2011.05.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 05/18/2011] [Accepted: 05/18/2011] [Indexed: 11/17/2022]
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Garofolo G, Serrecchia L, Corrò M, Fasanella A. Anthrax phylogenetic structure in Northern Italy. BMC Res Notes 2011; 4:273. [PMID: 21801397 PMCID: PMC3163213 DOI: 10.1186/1756-0500-4-273] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 07/29/2011] [Indexed: 12/04/2022] Open
Abstract
Background Anthrax has almost disappeared from mainland Europe, except for the Mediterranean region where cases are still reported. In Central and South Italy, anthrax is enzootic, but in the North there are currently no high risk areas, with only sporadic cases having been registered in the last few decades. Regional genetic and molecular characterizations of anthrax in these regions are still lacking. To investigate the potential molecular diversity of Bacillus anthracis in Northern Italy, canonical Single nucleotide polymorphism (canSNP) and Multilocus variable number tandem repeat analysis (MLVA) genotyping was performed against all isolates from animal outbreaks registered in the last twenty years in the region. Findings Six B. anthracis strains were analyzed. The canSNP analysis indicates the presence of three sublineages/subgroups each of which belong to one of the 12 worldwide CanSNP genotypes: B.Br.CNEVA (3 isolates), A.Br.005/006 (1 isolates) and A.008/009 (2 isolate). The latter is the dominant canSNP genotype in Italy. The 15-loci MLVA analysis revealed five different genotypes among the isolates. Conclusions The major B branch and the A.Br.005/006 were recovered in the Northeast region. The genetic structure of anthrax discovered in this area differs from the rest of the country, suggesting the presence of a separate and independent B. anthracis molecular evolution niche. Although the isolates analyzed in this study are limited in quantity and representation, these results indicate that B. anthracis genetic diversity changes around the Alps.
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Affiliation(s)
- Giuliano Garofolo
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Anthrax Reference Institute of Italy-Foggia, Italy.
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