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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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Railean V, Sobolewski J, Jaśkowski JM. Anthrax in one health in Southern and Southeastern Europe - the effect of climate change? Vet Res Commun 2024; 48:623-632. [PMID: 37863848 PMCID: PMC10998808 DOI: 10.1007/s11259-023-10238-3] [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: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023]
Abstract
Anthrax is a serious infection caused by Bacillus anthracis. The anthracis spores are highly resistant and can persist in the environment for several decades. Therefore, anthrax is considered a global health threat affecting wildlife, livestock, and the general public. The resistance mechanism is influenced not only by the environment or the ecological niche but also by virulence factors. In the last 10 years the Southern and Southeastern Europe have been confronted with this threat. Recently, there have been 8 human anthrax cases reported in Croatia (2022), and 4 cases in Romania (2023). Moreover, this incident and the COVID situation could be a starting point to encourage researchers to raise the alarm. On the other hand, climate change is causing glaciers to melt and land to thaw, and many wetlands and swampy areas are being drained. It should not be forgotten that epidemiological and epizootic threats significantly affect the country's economic development. The Covid-19 epidemic best illustrates these threats.
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Affiliation(s)
- Viorica Railean
- Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, Toruń, 87-100, Poland.
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, Torun, 87-100, Poland.
| | - Jarosław Sobolewski
- Department of Public Health and Animal Welfare, Institute of Veterinary Medicine, Nicolaus Copernicus University, Gagarina 7, Toruń, 87-100, Poland
| | - Jędrzej M Jaśkowski
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University, Gagarina 7, Toruń, 87-100, Poland.
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Eremenko EI, Ryazanova AG, Pisarenko SV, Aksenova LY, Semenova OV, Koteneva EA, Tsygankova OI, Kovalev DA, Golovinskaya TM, Chmerenko DK, Kulichenko AN. Comparative Analysis of Genotyping Methods for Bacillus anthracis. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541901006x] [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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Lekota KE, Bezuidt OKI, Mafofo J, Rees J, Muchadeyi FC, Madoroba E, van Heerden H. Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa. BMC Microbiol 2018; 18:67. [PMID: 29986655 PMCID: PMC6038202 DOI: 10.1186/s12866-018-1205-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 06/20/2018] [Indexed: 11/25/2022] Open
Abstract
Background Bacillus endophyticus is a soil plant-endophytic bacterium, while B. anthracis is the causative agent of anthrax. The virulence factors of B. anthracis are the plasmid encoded tripartite toxins (pXO1) and poly-γ-glutamic acid (PGA) capsule (pXO2). B. endophyticus isolated alongside B. anthracis from animals that died of anthrax in Northern Cape Province (NCP), South Africa, harbored polyglutamate genes. The study compared the characteristics of B. anthracis and B. endophyticus with other Bacillus species with a focus on the presence of the PGA capsule or/and unbound PGA. The morphology and whole genome sequence analysis of B. endophyticus strains and B. anthracis were compared. Results In conventional microbiology, B. endophyticus showed gram-positive round-shaped rods in single/short chains, which were endospore-forming, non-motile, non-haemolytic with white and dry colonies, and γ-phage resistant. B. anthracis was differentiated from B. endophyticus based on the latter’s box-shaped rods in pairs/long chains, white-grey and slimy colonies, encapsulated and γ-phage susceptible. The study identified a PGA polyglutamate synthase operon that consisted of pgsBCA, γ-glutamyltranspeptidase (ggt) and pgsE in B. endophyticus genomes. Conclusions PGA regions of B. anthracis contain capBCADE genes located in the pXO2 required for capsulation formation, while B. endophyticus contain the pgsBCAE genes in the chromosome. Whole genome and microbiology analysis identified B. endophyticus, as a non-capsuled endospore-forming bacterium that consists of PGA required for biosynthesis. B. endophyticus strains do not synthesize surface associated PGA, therefore capsule visualization of B. anthracis is a key diagnostic characteristic. The study highlights the significance of using whole genome shotgun sequencing to identify virulence and other important genes that might be present amongst unknown samples from natural outbreaks. None of the B. anthracis related plasmids or virulence genes were found in the B. endophyticus genomes. Electronic supplementary material The online version of this article (10.1186/s12866-018-1205-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kgaugelo Edward Lekota
- The Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa.,Department of Veterinary Tropical Diseases, University of Pretoria, Private bag X4, Onderstepoort, 0110, South Africa.,Bacteriology section, Agricultural Research Council-Onderstepoort Veterinary Institute, Private Bag X5, Onderstepoort, 0110, South Africa.,College of Agriculture and Environmental Sciences, University of South Africa, Florida Campus, Christiaan De Wet/ Pioneer Dr, P.O. Box X6, Florida, 1710, South Africa
| | | | - Joseph Mafofo
- The Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa
| | - Jasper Rees
- The Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa
| | - Farai Catherine Muchadeyi
- The Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa
| | - Evelyn Madoroba
- Bacteriology section, Agricultural Research Council-Onderstepoort Veterinary Institute, Private Bag X5, Onderstepoort, 0110, South Africa.,College of Agriculture and Environmental Sciences, University of South Africa, Florida Campus, Christiaan De Wet/ Pioneer Dr, P.O. Box X6, Florida, 1710, South Africa.,Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa, 3886, South Africa
| | - Henriette van Heerden
- Department of Veterinary Tropical Diseases, University of Pretoria, Private bag X4, Onderstepoort, 0110, South Africa.
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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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Whole genome SNP analysis of bovine B. anthracis strains from Switzerland reflects strict regional separation of Simmental and Swiss Brown breeds in the past. Vet Microbiol 2016; 196:1-8. [DOI: 10.1016/j.vetmic.2016.10.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/11/2016] [Accepted: 10/09/2016] [Indexed: 11/20/2022]
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Nejman-Faleńczyk B, Bloch S, Januszkiewicz A, Węgrzyn A, Węgrzyn G. A simple and rapid procedure for the detection of genes encoding Shiga toxins and other specific DNA sequences. Toxins (Basel) 2015; 7:4745-57. [PMID: 26580652 PMCID: PMC4663531 DOI: 10.3390/toxins7114745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/26/2015] [Accepted: 11/10/2015] [Indexed: 11/25/2022] Open
Abstract
A novel procedure for the detection of specific DNA sequences has been developed. This procedure is based on the already known method employing PCR with appropriate primers and a sequence-specific DNA probe labeled with the fluorescent agent 6-carboxylfluorescein (FAM) at the 5′ end and the fluorescence quencher BHQ-1 (black hole quencher) at the 3′ end. However, instead of the detection of the fluorescence signal with the use of real-time PCR cyclers, fluorescence/luminescence spectrometers or fluorescence polarization readers, as in all previously-reported procedures, we propose visual observation of the fluorescence under UV light directly in the reaction tube. An example for the specific detection of the Shiga toxin-producing Escherichia coli (STEC) strains, by detecting Shiga toxin genes, is demonstrated. This method appears to be specific, simple, rapid and cost effective. It may be suitable for use in research laboratories, as well as in diagnostic units of medical institutions, even those equipped only with a thermocycler and a UV transilluminator, particularly if rapid identification of a pathogen is required.
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Affiliation(s)
- Bożena Nejman-Faleńczyk
- Depratment of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Sylwia Bloch
- Depratment of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Aleksandra Januszkiewicz
- Department of Bacteriology, National Institute of Public Health-Public Institute of Hygiene, 24 Chocimska Street, 00-791 Warsaw, Poland.
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology (affiliated with the University of Gdansk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Grzegorz Węgrzyn
- Depratment of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
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Blackburn JK, Odugbo MO, Van Ert M, O’Shea B, Mullins J, Perrenten V, Maho A, Hugh-Jones M, Hadfield T. Bacillus anthracis Diversity and Geographic Potential across Nigeria, Cameroon and Chad: Further Support of a Novel West African Lineage. PLoS Negl Trop Dis 2015; 9:e0003931. [PMID: 26291625 PMCID: PMC4546381 DOI: 10.1371/journal.pntd.0003931] [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: 03/13/2015] [Accepted: 06/23/2015] [Indexed: 01/11/2023] Open
Abstract
Zoonoses, diseases affecting both humans and animals, can exert tremendous pressures on human and veterinary health systems, particularly in resource limited countries. Anthrax is one such zoonosis of concern and is a disease requiring greater public health attention in Nigeria. Here we describe the genetic diversity of Bacillus anthracis in Nigeria and compare it to Chad, Cameroon and a broader global dataset based on the multiple locus variable number tandem repeat (MLVA-25) genetic typing system. Nigerian B. anthracis isolates had identical MLVA genotypes and could only be resolved by measuring highly mutable single nucleotide repeats (SNRs). The Nigerian MLVA genotype was identical or highly genetically similar to those in the neighboring countries, confirming the strains belong to this unique West African lineage. Interestingly, sequence data from a Nigerian isolate shares the anthrose deficient genotypes previously described for strains in this region, which may be associated with vaccine evasion. Strains in this study were isolated over six decades, indicating a high level of temporal strain stability regionally. Ecological niche models were used to predict the geographic distribution of the pathogen for all three countries. We describe a west-east habitat corridor through northern Nigeria extending into Chad and Cameroon. Ecological niche models and genetic results show B. anthracis to be ecologically established in Nigeria. These findings expand our understanding of the global B. anthracis population structure and can guide regional anthrax surveillance and control planning. Anthrax, caused by the soil-borne bacterium Bacillus anthracis, is a disease with important public health and national security implications globally. Understanding the global genetic diversity of the pathogen is important for epidemiological and forensic investigations of anthrax events. Toward this, we describe B. anthracis genetic diversity in Nigeria and confirm it belongs to a unique West African genetic group not yet reported beyond neighboring Cameroon and Chad and Mali. This refines the global phylogeny of B. anthracis, allowing the development of more accurate diagnostics. We coupled these efforts with ecological niche modeling to map the geographic distribution of this strain group across the region. Suitable habitat for the pathogen is predicted across central Nigeria from west to east into Cameroon and Chad. Understanding the geography of B. anthracis plays an important role in informing public health by targeting disease control to high risk regions. This is particularly important in resource limited areas where intervention strategies are constrained and zoonotic disease risk is high.
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Affiliation(s)
- Jason K. Blackburn
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Moses Ode Odugbo
- Bacterial Research Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Matthew Van Ert
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Bob O’Shea
- MRI Global, Palm Bay, Florida, United States of America
| | - Jocelyn Mullins
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Vincent Perrenten
- Institute of Veterinary Bacteriology, University of Berne, Berne, Switzerland
| | - Angaya Maho
- Laboratoire de Recherches Vétérinaires et Zootechniques, N’Djaména, Chad
| | - Martin Hugh-Jones
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Ted Hadfield
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- MRI Global, Palm Bay, Florida, United States of America
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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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Jung KH, Kim SH, Kim SK, Cho SY, Chai JC, Lee YS, Kim JC, Kim SJ, Oh HB, Chai YG. Genetic populations of Bacillus anthracis isolates from Korea. J Vet Sci 2013; 13:385-93. [PMID: 23271180 PMCID: PMC3539124 DOI: 10.4142/jvs.2012.13.4.385] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacillus (B.) anthracis is the pathogen that causes fatal anthrax. Strain-specific detection of this bacterium using molecular approaches has enhanced our knowledge of microbial population genetics. In the present study, we employed molecular approaches including multiple-locus variable-number tandem repeat analysis (MLVA) and canonical single-nucleotide polymorphism (canSNP) analysis to perform molecular typing of B. anthracis strains isolated in Korea. According to the MLVA, 17 B. anthracis isolates were classified into A3a, A3b, and B1 clusters. The canSNP analyses subdivided the B. anthracis isolates into two of the three previously recognized major lineages (A and B). B. anthracis isolates from Korea were found to belong to four canSNP sub-groups (B.Br.001/2, A.Br.005/006, A.Br.001/002, and A.Br.Ames). The A.Br.001/002 and A.Br.Ames sub-lineages are closely related genotypes frequently found in central Asia and most isolates were. On the other hand, B. anthracis CH isolates were analyzed that belonged to the B.Br.001/002 sub-group which found in southern Africa, Europe and California (USA). B.Br.001/002 genotype is new lineage of B. anthracis in Korea that was not found before. This discovery will be helpful for the creation of marker systems and might be the result of human activity through the development of agriculture and increased international trade in Korea.
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Affiliation(s)
- Kyoung Hwa Jung
- Institute of Natural Science and Technology, Hanyang University, Ansan 426-791, Korea
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Chikerema SM, Pfukenyi DM, Hang'ombe BM, L'Abee-Lund TM, Matope G. Isolation of Bacillus anthracis from soil in selected high-risk areas of Zimbabwe. J Appl Microbiol 2012; 113:1389-95. [PMID: 22984812 DOI: 10.1111/jam.12006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/27/2012] [Accepted: 08/31/2012] [Indexed: 12/01/2022]
Abstract
AIMS To isolate Bacillus anthracis from cattle carcass burial sites from high-risk districts in Zimbabwe. METHODS AND RESULTS Soil samples were collected from carcass burial sites from seven areas, including two national game parks. Samples were collected from top 5-10 cm, and for spore extraction, 25 g of soil was suspended in sterile distilled water overnight. Supernatants were filtered through 0.45-μm pore cellulose nitrate, deposits suspended in 5 ml phosphate-buffered saline, aliquoted and heated at temperature regimen of 65, 70, 75 and 80 °C for 15 min. Samples were plated onto PLET agar. B. anthracis isolates were identified using growth morphology and PCR detecting pXO1 and pXO2 virulence plasmids. From samples heated at 75 °C for 15 min, B. anthracis were isolated from 9 of 81 (11.1%) soil samples representing five of the seven sampled areas. CONCLUSIONS We isolated B. anthracis from soil collected from carcass burial sites. PCR targeting virulence plasmids provided a rapid confirmation of B. anthracis. SIGNIFICANCE AND IMPACT OF THE STUDY The positive isolation indicated that some carcass burial sites may retain viable spores for at least 12 months after the previous outbreak, which suggests that they may be important sources of B. anthracis and new disease outbreaks.
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Affiliation(s)
- S M Chikerema
- Department of Clinical Veterinary Studies, Faculty of Veterinary Science, University of Zimbabwe, Harare, Zimbabwe
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Eremenko EI, Ryazanova AG, Tsygankova OI, Tsygankova EA, Buravtseva NP, Kulitchenko AN. Genotype diversity of Bacillus anthracis strains isolated from the Caucasus region. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2012. [DOI: 10.3103/s0891416812020024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Steiner I, Račić I, Spičić S, Habrun B. Genotyping of Bacillus anthracis isolated from Croatia and Bosnia and Herzegovina. Zoonoses Public Health 2012; 60:202-8. [PMID: 22726272 DOI: 10.1111/j.1863-2378.2012.01513.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anthrax is a serious disease caused by Bacillus anthracis. Humans can become infected by handling products from infected animals, by breathing spores and rarely by eating undercooked meat from infected animals. The genome of B. anthracis is highly monomorphic and thus shows very low DNA sequence variation. We analysed the molecular characteristics of 12 B. anthracis isolates from outbreaks in Croatia and Bosnia and Herzegovina, which have occurred during the past 10 years along with two vaccine strains. Genotyping system based on variable-number tandem repeat analysis at six loci revealed that six isolates belong to genotype from the A1.a cluster whilst six isolates relate to the B2 cluster, compared to 89 previously described genotypes. The distribution of two evolutionarily distant clusters suggests an introduction of B. anthracis to this area in at least two separate events.
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Affiliation(s)
- I Steiner
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
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16
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Antimicrobial susceptibility and molecular subtyping of 55 Turkish Bacillus anthracis strains using 25-loci multiple-locus VNTR analysis. Comp Immunol Microbiol Infect Dis 2012; 35:355-61. [PMID: 22445310 DOI: 10.1016/j.cimid.2012.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 02/20/2012] [Accepted: 02/29/2012] [Indexed: 11/22/2022]
Abstract
Anthrax, which is caused by the bacterium Bacillus anthracis, is one of the oldest documented infectious diseases in both livestock and humans. The differentiation of B. anthracis strains is difficult because of their highly homogeneous genomes. We used multiple-locus variable-number tandem repeat analysis (MLVA) with 25 markers to genotype 55 B. anthracis isolates from 16 distinct regions of Turkey. The antimicrobial susceptibility of the isolates was investigated using the agar dilution method. An eight-loci MLVA assay revealed six unique genotypes (G(K)13, G(K)27, G(K)35, G(K)43, G(K)44, and G(K)61). However, the 25-loci MLVA was more discriminatory, revealing the presence of ten genotypes instead of six. The additional genotypes resulted from the split of four subtypes: G(K)35 (b and c), G(K)43 (a and f), G(K)44 (d and e), and G(K)61 (i and j). All of the Turkish B. anthracis isolates were susceptible to ciprofloxacin, levofloxacin, tigecycline, linezolid, and vancomycin. One isolate was resistant to penicillin and to doxycycline. A total of 34 isolates were susceptible, 20 isolates were partially susceptible, and one isolate was resistant to erythromycin. None of the isolates exhibited susceptibility to cefotaxime. A total of 53 isolates were susceptible to gentamicin, and two were resistant. The genotypes G(K)35 (n=24), G(K)44 (n=13), and G(K)43 (n=10) were the most prevalent in 10, 6, and 5 regions, respectively, of the total 16 provinces. The B. anthracis isolates collected from these regions implied that the movement of B. anthracis is a result of the increased transportation of livestock and the resultant cross contamination.
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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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18
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Zacharczuk K, Piekarska K, Szych J, Jagielski M, Hidalgo L, San Millán Á, Gutiérrez B, Rastawicki W, González-Zorn B, Gierczyński R. Plasmid-borne 16S rRNA methylase ArmA in aminoglycoside-resistant Klebsiella pneumoniae in Poland. J Med Microbiol 2011; 60:1306-1311. [DOI: 10.1099/jmm.0.024026-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Katarzyna Zacharczuk
- Department of Bacteriology, National Institute of Public Health – National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
| | - Katarzyna Piekarska
- Department of Bacteriology, National Institute of Public Health – National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
| | - Jolanta Szych
- Department of Bacteriology, National Institute of Public Health – National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
| | - Marek Jagielski
- Department of Bacteriology, National Institute of Public Health – National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
| | - Laura Hidalgo
- Departamento de Sanidad Animal, Facultad de Veterinaria and VISAVET (Centro de Vigilancia Sanitaria Veterinaria), Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Álvaro San Millán
- Departamento de Sanidad Animal, Facultad de Veterinaria and VISAVET (Centro de Vigilancia Sanitaria Veterinaria), Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Belén Gutiérrez
- Departamento de Sanidad Animal, Facultad de Veterinaria and VISAVET (Centro de Vigilancia Sanitaria Veterinaria), Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Waldemar Rastawicki
- Department of Bacteriology, National Institute of Public Health – National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
| | - Bruno González-Zorn
- Departamento de Sanidad Animal, Facultad de Veterinaria and VISAVET (Centro de Vigilancia Sanitaria Veterinaria), Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Rafał Gierczyński
- Department of Bacteriology, National Institute of Public Health – National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
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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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Aikembayev AM, Lukhnova L, Temiraliyeva G, Meka-Mechenko T, Pazylov Y, Zakaryan S, Denissov G, Easterday WR, Van Ert MN, Keim P, Francesconi SC, Blackburn JK, Hugh-Jones M, Hadfield T. Historical distribution and molecular diversity of Bacillus anthracis, Kazakhstan. Emerg Infect Dis 2010; 16:789-96. [PMID: 20409368 PMCID: PMC2953997 DOI: 10.3201/eid1605.091427] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
This study provides useful baseline data for guiding future disease control programs. To map the distribution of anthrax outbreaks and strain subtypes in Kazakhstan during 1937–2005, we combined geographic information system technology and genetic analysis by using archived cultures and data. Biochemical and genetic tests confirmed the identity of 93 archived cultures in the Kazakhstan National Culture Collection as Bacillus anthracis. Multilocus variable number tandem repeat analysis genotyping identified 12 genotypes. Cluster analysis comparing these genotypes with previously published genotypes indicated that most (n = 78) isolates belonged to the previously described A1.a genetic cluster, 6 isolates belonged to the A3.b cluster, and 2 belonged to the A4 cluster. Two genotypes in the collection appeared to represent novel genetic sublineages; 1 of these isolates was from Krygystan. Our data provide a description of the historical, geographic, and genetic diversity of B. anthracis in this Central Asian region.
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Affiliation(s)
- Alim M Aikembayev
- Kazakhstan Scientific Center for Quarantine and Zoonotic Diseases, Almaty, Kazakhstan
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21
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Beyer W, Turnbull P. Anthrax in animals. Mol Aspects Med 2009; 30:481-9. [DOI: 10.1016/j.mam.2009.08.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 08/26/2009] [Indexed: 11/26/2022]
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Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases. Nat Rev Microbiol 2009; 7:813-21. [PMID: 19820723 DOI: 10.1038/nrmicro2219] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The development of human civilizations and global commerce has led to the emergence and worldwide circulation of many infectious diseases. Anthrax, plague and tularaemia are three zoonotic diseases that have been intensely studied through genome characterization of the causative species and phylogeographical analyses. A few highly fit genotypes in each species represent the causative agents for most of the observed disease cases. Together, mutational and selective forces create highly adapted pathogens, but this must be coupled with ecological opportunities for global expansion. This Review describes the distributions of the bacteria that cause anthrax, plague and tularaemia and investigates the forces that created clonal structures in these species.
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Keim P, Gruendike JM, Klevytska AM, Schupp JM, Challacombe J, Okinaka R. The genome and variation of Bacillus anthracis. Mol Aspects Med 2009; 30:397-405. [PMID: 19729033 DOI: 10.1016/j.mam.2009.08.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 08/24/2009] [Indexed: 01/01/2023]
Abstract
The Bacillus anthracis genome reflects its close genetic ties to Bacillus cereus and Bacillus thuringiensis but has been shaped by its own unique biology and evolutionary forces. The genome is comprised of a chromosome and two large virulence plasmids, pXO1 and pXO2. The chromosome is mostly co-linear among B. anthracis strains and even with the closest near neighbor strains. An exception to this pattern has been observed in a large inversion in an attenuated strain suggesting that chromosome co-linearity is important to the natural biology of this pathogen. In general, there are few polymorphic nucleotides among B. anthracis strains reflecting the short evolutionary time since its derivation from a B. cereus-like ancestor. The exceptions to this lack of diversity are the variable number tandem repeat (VNTR) loci that exist in genic and non genic regions of the chromosome and both plasmids. Their variation is associated with high mutability that is driven by rapid insertion and deletion of the repeats within an array. A notable example is found in the vrrC locus which is homologous to known DNA translocase genes from other bacteria.
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Affiliation(s)
- Paul Keim
- The Microbial Genetics and Genomics Center, Northern Arizona University, Flagstaff AZ 86011-4073, USA.
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24
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Multiple-locus variable-number tandem-repeat analysis of Salmonella enterica serovar Typhi. J Clin Microbiol 2009; 47:2369-76. [PMID: 19535521 DOI: 10.1128/jcm.00223-09] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus variable-number tandem repeats (VNTRs) are widely used as molecular markers to differentiate isolates of homogenous pathogenic clones. We explored the genomes of Salmonella enterica serovar Typhi strains CT18 and Ty2 for potential VNTRs. Among the 43 potential VNTRs screened, 2 were found to be polymorphic. Together with seven polymorphic VNTRs from previous studies, they were used to type 73 global serovar Typhi isolates. A total of 70 multilocus VNTR analysis (MLVA) profiles were found, distinguishing all except three pairs of isolates into individual profiles. The discriminatory power was 0.999. Phylogenetic analysis showed that the MLVA profiles can be divided into seven clusters. However, except for the closely related isolates, the relationships derived were in conflict with those inferred from single nucleotide polymorphism (SNP) typing using 38 SNPs done previously. We concluded that MLVA can resolve the relationships only among closely related isolates. A combination of SNP typing and MLVA typing offers the best approach for local and global epidemiology and the evolutionary analysis of serovar Typhi. We suggest that seven of the nine most polymorphic VNTRs be used as a standardized typing scheme for epidemiological typing.
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Molecular epidemiology of Bacillus anthracis: determining the correct origin. Appl Environ Microbiol 2008; 74:2928-31. [PMID: 18326672 DOI: 10.1128/aem.02574-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed and compared strains of Bacillus anthracis isolated from husbandry and industrial anthrax cases in Switzerland between 1952 and 1981 with published data using multiple-locus variable-number tandem repeat analysis. Strains isolated from autochthonous cases of anthrax in cattle belong to genotype B2, together with strains from continental Europe, while human B. anthracis strains clustered with genotype A4. These strains could be traced back to outbreaks of human anthrax that occurred between 1978 and 1981 in a factory processing cashmere wool from the Indian subcontinent. We interpret the worldwide occurrence of B. anthracis strains of cluster A4 to be due to the extensive global trade of untreated cashmere wool during the last century.
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Fortini D, Ciammaruconi A, De Santis R, Fasanella A, Battisti A, D'Amelio R, Lista F, Cassone A, Carattoli A. Optimization of High-Resolution Melting Analysis for Low-Cost and Rapid Screening of Allelic Variants of Bacillus anthracis by Multiple-Locus Variable-Number Tandem Repeat Analysis. Clin Chem 2007; 53:1377-80. [PMID: 17525105 DOI: 10.1373/clinchem.2007.085993] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Molecular genotyping of Bacillus anthracis, the etiologic agent of anthrax, is important for differentiating and identifying strains from different geographic areas and for tracing strains deliberately released in a bioterrorism attack. We previously described a multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) based on 25 marker loci. Although the method has great differentiating power and reproducibility, faster genotyping at low cost may be requested to accurately identify B. anthracis strains in the field.
Methods: We used the High Resolution Melter-1 (Idaho Technology) and a saturating dye of double-stranded DNA (LCGreen I) to identify alleles via PCR and melting-curve analysis of the amplicons. We applied high-resolution melting analysis (HRMA) to a collection of 19 B. anthracis strains.
Results: HRMA produced reproducible results for 6 of the 25 B. anthracis loci tested. These easily interpretable and distinguishable melting curve results were consistent with MLVA results obtained for the same alleles. The feasibility of this method was demonstrated in testing of different allelic variants for the 6 selected loci.
Conclusions: The described HRMA application for screening B. anthracis VNTR loci is fast and widely accessible and may prove particularly useful under field conditions.
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Affiliation(s)
- Daniela Fortini
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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Gierczyński R, Golubov A, Neubauer H, Pham JN, Rakin A. Development of multiple-locus variable-number tandem-repeat analysis for Yersinia enterocolitica subsp. palearctica and its application to bioserogroup 4/O3 subtyping. J Clin Microbiol 2007; 45:2508-15. [PMID: 17553973 PMCID: PMC1951228 DOI: 10.1128/jcm.02252-06] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yersinia enterocolitica bioserogroup 4/O3 is the predominant causative agent of yersiniosis in Europe and North America. Multiple-locus variable-number tandem-repeat analysis (MLVA) was developed to improve the resolution power of classical genotyping methods. MLVA based on six loci was able to distinguish 76 genotypes among 91 Y. enterocolitica isolates of worldwide origin and 41 genotypes among 51 nonepidemiologically linked bioserogroup 4/O3 isolates, proving that it has a high resolution power. However, only a slight correlation of the MLVA genotypes and the geographic distribution of the isolates was observed. Although MLVA was also capable of distinguishing strains of Y. enterocolitica subsp. palearctica O9 and O5,27, there was only a minor correlation between the MLVA genotypes and serogroups. MLVA may be a helpful tool for epidemiological investigations of Y. enterocolitica subsp. palearctica outbreaks.
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Affiliation(s)
- Rafał Gierczyński
- Department of Bacteriology, National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland.
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28
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Van Ert MN, Easterday WR, Huynh LY, Okinaka RT, Hugh-Jones ME, Ravel J, Zanecki SR, Pearson T, Simonson TS, U'Ren JM, Kachur SM, Leadem-Dougherty RR, Rhoton SD, Zinser G, Farlow J, Coker PR, Smith KL, Wang B, Kenefic LJ, Fraser-Liggett CM, Wagner DM, Keim P. Global genetic population structure of Bacillus anthracis. PLoS One 2007; 2:e461. [PMID: 17520020 PMCID: PMC1866244 DOI: 10.1371/journal.pone.0000461] [Citation(s) in RCA: 255] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Accepted: 03/20/2007] [Indexed: 11/19/2022] Open
Abstract
Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and its true global population structure has remained largely cryptic. Seven diverse B. anthracis strains were whole-genome sequenced to identify rare single nucleotide polymorphisms (SNPs), followed by phylogenetic reconstruction of these characters onto an evolutionary model. This analysis identified SNPs that define the major clonal lineages within the species. These SNPs, in concert with 15 variable number tandem repeat (VNTR) markers, were used to subtype a collection of 1,033 B. anthracis isolates from 42 countries to create an extensive genotype data set. These analyses subdivided the isolates into three previously recognized major lineages (A, B, and C), with further subdivision into 12 clonal sub-lineages or sub-groups and, finally, 221 unique MLVA15 genotypes. This rare genomic variation was used to document the evolutionary progression of B. anthracis and to establish global patterns of diversity. Isolates in the A lineage are widely dispersed globally, whereas the B and C lineages occur on more restricted spatial scales. Molecular clock models based upon genome-wide synonymous substitutions indicate there was a massive radiation of the A lineage that occurred in the mid-Holocene (3,064-6,127 ybp). On more recent temporal scales, the global population structure of B. anthracis reflects colonial-era importation of specific genotypes from the Old World into the New World, as well as the repeated industrial importation of diverse genotypes into developed countries via spore-contaminated animal products. These findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease. Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated.
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Affiliation(s)
- Matthew N. Van Ert
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - W. Ryan Easterday
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Lynn Y. Huynh
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard T. Okinaka
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
- Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Martin E. Hugh-Jones
- Department of Environmental Studies, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jacques Ravel
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Shaylan R. Zanecki
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Talima Pearson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Tatum S. Simonson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jana M. U'Ren
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Sergey M. Kachur
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Rebecca R. Leadem-Dougherty
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Shane D. Rhoton
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Guenevier Zinser
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason Farlow
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Pamala R. Coker
- Department of Environmental Studies, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Kimothy L. Smith
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Bingxiang Wang
- Lanzhou Institute of Biological Products, Lanzhou, China
| | - Leo J. Kenefic
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - David M. Wagner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
- Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * To whom correspondence should be addressed. E-mail:
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Sue D, Marston CK, Hoffmaster AR, Wilkins PP. Genetic diversity in a Bacillus anthracis historical collection (1954 to 1988). J Clin Microbiol 2007; 45:1777-82. [PMID: 17392445 PMCID: PMC1933066 DOI: 10.1128/jcm.02488-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis, the etiologic agent of anthrax, has been widely described as a genetically monomorphic species. We used both multiple-locus variable-number tandem-repeat analysis (MLVA) and pagA gene sequencing to determine the genetic diversity of a historical collection of B. anthracis isolates collected from the 1950s to the 1980s from various geographic locations and sources. We sequenced the pagA gene of 124 diverse B. anthracis isolates and found all previously identified B. anthracis pagA types except type 4. Sixty-three of the 124 B. anthracis strains were identified as pagA type 6, while 44 were pagA type 5, 12 were pagA type 1, and individual isolates were identified for types 2 and 3, respectively. Two new pagA genotypes were discovered in three environmental isolates within the historical collection. Two isolates had the same new genotype, and an additional isolate produced a second new genotype. MLVA detected 22 previously described genotypes in the historical collection. In addition, 33 new MLVA genotypes were found. For 11 isolates, an MLVA genotype could not be assigned because one or more alleles did not amplify. While only two additional B. anthracis pagA types were identified, in two instances, the use of pagA sequencing discriminated isolates with the same MLVA genotype. MLVA revealed that 39 of the 124 isolates were previously undocumented genotypes and that 1 isolate was found to be in the C cluster when it was subtyped by MLVA.
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Affiliation(s)
- David Sue
- Bacterial Zoonoses Branch, Division of Foodborne, Bacterial and Mycotic Diseases, National Center for Zoonotic, Vector-Borne and Enteric Diseases, Centers for Disease Control and Prevention, NE, Atlanta, Georgia 30333, USA
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30
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Wardak S, Szych J, Zasada AA, Gierczynski R. Antibiotic resistance of Campylobacter jejuni and Campylobacter coli clinical isolates from Poland. Antimicrob Agents Chemother 2007; 51:1123-5. [PMID: 17210776 PMCID: PMC1803138 DOI: 10.1128/aac.01187-06] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We tested 102 Campylobacter jejuni and 6 Campylobacter coli clinical isolates from Poland. All were susceptible to erythromycin. Among the tested C. jejuni isolates 55.9% and 13.7% were resistant to ciprofloxacin and tetracycline, respectively. Replacement of Thr86 with Ile in GyrA and a plasmid-borne tet(O) gene were the main resistance mechanisms for fluoroquinolones and tetracycline, respectively.
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Affiliation(s)
- Sebastian Wardak
- National Institute of Hygiene, Department of Bacteriology, 24 Chocimska Street, 00-791 Warsaw, Poland.
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31
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Zasada AA, Gierczynski R, Raddadi N, Daffonchio D, Jagielski M. Some Bacillus thuringiensis strains share rpoB nucleotide polymorphisms also present in Bacillus anthracis. J Clin Microbiol 2006; 44:1606-7. [PMID: 16597912 PMCID: PMC1448658 DOI: 10.1128/jcm.44.4.1606-1607.2006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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32
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Maho A, Rossano A, Hächler H, Holzer A, Schelling E, Zinsstag J, Hassane MH, Toguebaye BS, Akakpo AJ, Van Ert M, Keim P, Kenefic L, Frey J, Perreten V. Antibiotic susceptibility and molecular diversity of Bacillus anthracis strains in Chad: detection of a new phylogenetic subgroup. J Clin Microbiol 2006; 44:3422-5. [PMID: 16954291 PMCID: PMC1594716 DOI: 10.1128/jcm.01269-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We genotyped 15 Bacillus anthracis isolates from Chad, Africa, using multiple-locus variable-number tandem repeat analysis and three additional direct-repeat markers. We identified two unique genotypes that represent a novel genetic lineage in the A cluster. Chadian isolates were susceptible to 11 antibiotics and free of 94 antibiotic resistance genes.
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Affiliation(s)
- Angaya Maho
- Laboratoire de Recherches Vétérinaires et Zootechniques, BP433 Farcha, N'Djaména, Chad
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Merabishvili M, Natidze M, Rigvava S, Brusetti L, Raddadi N, Borin S, Chanishvili N, Tediashvili M, Sharp R, Barbeschi M, Visca P, Daffonchio D. Diversity of Bacillus anthracis strains in Georgia and of vaccine strains from the former Soviet Union. Appl Environ Microbiol 2006; 72:5631-6. [PMID: 16885320 PMCID: PMC1538727 DOI: 10.1128/aem.00440-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the increased number of anthrax outbreaks in Georgia and the other Caucasian republics of the former Soviet Union, no data are available on the diversity of the Bacillus anthracis strains involved. There is also little data available on strains from the former Soviet Union, including the strains previously used for vaccine preparation. In this study we used eight-locus variable-number tandem repeat analyses to genotype 18 strains isolated from infected animals and humans at different sites across Georgia, where anthrax outbreaks have occurred in the last 10 years, and 5 strains widely used for preparation of human and veterinary vaccines in the former Soviet Union. Three different genotypes affiliated with the A3.a cluster were detected for the Georgian isolates. Two genotypes were previously shown to include Turkish isolates, indicating that there is a regional strain pattern in the South Caucasian-Turkish region. Four of the vaccine strains were polymorphic, exhibiting three different patterns of the cluster A1.a genotype and the cluster A3.b genotype. The genotype of vaccine strain 71/12, which is considered an attenuated strain in spite of the presence of both of the virulence pXO plasmids, appeared to be a novel genotype in the A1.a cluster.
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Affiliation(s)
- Maya Merabishvili
- The G.Eliava Institute of Bacteriophage, Microbiology and Virology, 0160 Tbilisi, Georgia
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Colborn JM, Koita OA, Cissé O, Bagayoko MW, Guthrie EJ, Krogstad DJ. Identifying and quantifying genotypes in polyclonal infections due to single species. Emerg Infect Dis 2006; 12:475-82. [PMID: 16704787 PMCID: PMC3291430 DOI: 10.3201/eid1203.05057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The combination of real-time PCR and capillary electrophoresis permits the rapid identification and quantification of pathogen genotypes. Simultaneous infection with multiple pathogens of the same species occurs with HIV, hepatitis C, Epstein-Barr virus, dengue, tuberculosis, and malaria. However, available methods do not distinguish among or quantify pathogen genotypes in individual patients; they also cannot test for novel insertions and deletions in genetically modified organisms. The strategy reported here accomplishes these goals with real-time polymerase chain reaction (PCR) and capillary electrophoresis. Real-time PCR with allotype-specific primers defines the allotypes (strains) present and the intensity of infection (copy number). Capillary electrophoresis defines the number of genotypes within each allotype and the intensity of infection by genotype. This strategy can be used to study the epidemiology of emerging infectious diseases with simultaneous infection by multiple genotypes, as demonstrated here with malaria. It also permits testing for insertions or deletions in genetically modified organisms that may be used for bioterrorism.
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Affiliation(s)
- James M. Colborn
- Tulane University Health Sciences Center, New Orleans, Louisiana, USA
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Lista F, Faggioni G, Valjevac S, Ciammaruconi A, Vaissaire J, le Doujet C, Gorgé O, De Santis R, Carattoli A, Ciervo A, Fasanella A, Orsini F, D'Amelio R, Pourcel C, Cassone A, Vergnaud G. Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis. BMC Microbiol 2006; 6:33. [PMID: 16600037 PMCID: PMC1479350 DOI: 10.1186/1471-2180-6-33] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 04/06/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR) Analysis (MLVA) assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary. RESULTS Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats. CONCLUSION In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the B branch was described, and two new branches, D and E, are proposed. Owing to the upgrading achieved here, precise genotyping can now be produced either by automated capillary electrophoresis, or by the more accessible but slower and for some markers slightly less accurate agarose gel methodology.
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Affiliation(s)
- Florigio Lista
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
- Cattedra di Allergologia e Immunologia Clinica, II Facoltà di Medicina, Università di Roma "La Sapienza", Roma, Italy
| | - Giovanni Faggioni
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | - Samina Valjevac
- Division of Analytical Microbiology, Centre d'Etudes du Bouchet, BP3, 91710 Vert le Petit, France
- Institut de Génétique et Microbiologie, Université Paris Sud, 91405 Orsay Cedex, France
| | - Andrea Ciammaruconi
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | - Josée Vaissaire
- AFSSA/LERPAZ, LNR/CNR associé Laboratoire du Charbon, 23 avenue du Général de Gaulle, 94700 Maisons-Alfort, France
| | - Claudine le Doujet
- AFSSA/LERPAZ, LNR/CNR associé Laboratoire du Charbon, 23 avenue du Général de Gaulle, 94700 Maisons-Alfort, France
| | - Olivier Gorgé
- Division of Analytical Microbiology, Centre d'Etudes du Bouchet, BP3, 91710 Vert le Petit, France
- Institut de Génétique et Microbiologie, Université Paris Sud, 91405 Orsay Cedex, France
| | - Riccardo De Santis
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | | | - Alessandra Ciervo
- Istituto Superiore di Sanità, Viale Regina Elena 299 00161 Rome, Italy
| | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata – Anthrax Reference Institute of Italy, Foggia 71100, Italy
| | - Francesco Orsini
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | - Raffaele D'Amelio
- Cattedra di Allergologia e Immunologia Clinica, II Facoltà di Medicina, Università di Roma "La Sapienza", Roma, Italy
- Direzione Generale della Sanità Militare, Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | - Christine Pourcel
- Institut de Génétique et Microbiologie, Université Paris Sud, 91405 Orsay Cedex, France
| | - Antonio Cassone
- Istituto Superiore di Sanità, Viale Regina Elena 299 00161 Rome, Italy
| | - Gilles Vergnaud
- Division of Analytical Microbiology, Centre d'Etudes du Bouchet, BP3, 91710 Vert le Petit, France
- Institut de Génétique et Microbiologie, Université Paris Sud, 91405 Orsay Cedex, France
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Lindstedt BA. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005; 26:2567-82. [PMID: 15937984 DOI: 10.1002/elps.200500096] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.
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Affiliation(s)
- Bjørn-Arne Lindstedt
- Norwegian Institute of Public Health, Division for Infectious Diseases Control, Oslo, Norway.
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Fasanella A, Van Ert M, Altamura SA, Garofolo G, Buonavoglia C, Leori G, Huynh L, Zanecki S, Keim P. Molecular diversity of Bacillus anthracis in Italy. J Clin Microbiol 2005; 43:3398-401. [PMID: 16000465 PMCID: PMC1169099 DOI: 10.1128/jcm.43.7.3398-3401.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used multiple-locus variable-number tandem repeat analysis (MLVA) to type 64 Bacillus anthracis isolates from outbreaks that have occurred during the past 40 years in Italy. MLVA of the 64 isolates revealed 10 unique genotypes; 9 of these genotypes and the majority of isolates (63/64) belonged to the previously described genetic cluster A1.a. Within the A1.a isolates, two previously described genotypes (G1 and G3), which differ by a single mutation in the pX01 locus, account for the majority of isolates in the country (53/63). The low diversity of B. anthracis genotypes in Italy suggests a single, dominant historical introduction, followed by limited localized differentiation.
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Affiliation(s)
- Antonio Fasanella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata-Anthrax Reference Institute of Italy, Foggia 71100, Italy.
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