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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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Li S, Ma Q, Chen H, Liu Y, Yao G, Tang G, Wang D. Epidemiological Investigation and Etiological Analysis of a Cutaneous Anthrax Epidemic Caused by Butchering Sick Cattle in Guizhou, China. Front Public Health 2020; 8:65. [PMID: 32269982 PMCID: PMC7109284 DOI: 10.3389/fpubh.2020.00065] [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: 07/05/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Abstract
A suspected human cutaneous anthrax epidemic caused by butchering sick cattle occurred in Zhijin County of Guizhou Province, Southwest of China, in 2016. Epidemiological investigation and etiological analysis were performed to provide a scientific basis for the source tracking of the epidemic. The epidemic was epidemiologically investigated, and skin blister samples collected from patients and soil samples collected from the butchering spots were used for Bacillus anthracis isolation. The suspicious B. anthracis isolates were identified using conventional methods and PCR, followed by genotyping using multiple-locus variable-number tandem repeats (VNTRs) analysis (MLVA-15) and canonical single-nucleotide polymorphism (canSNP). The genetic relationship of epidemic strains and isolates collected from other regions was analyzed. Epidemiological investigation results showed that the patients may be infected by B. anthracis during butchering sick cattle. Two suspected B. anthracis strains were isolated from blood samples and blister fluids, respectively. Conventional methods identified the two suspected isolates as B. anthracis, while PCR results showed that anti-protective antigen (PA) and capsule (CAP) gene were positive in the two isolates. MLVA-15 showed that the MLVA profiles of the two isolates were 9-20-12-53-16-2-8-8-8-4-4-4-4-10-4, which is different from the MLVA profiles of representative strains from other regions. CanSNP analysis showed that the two strains belonged to cluster A.Br.001/002. Clustering analysis and minimum spanning tree (MST) demonstrated that the two isolates were clustered with strains previously isolated from Guizhou Province. The results indicated that B. anthracis was the pathogen for this epidemic, and the patients were infected during butchering the sick. The genetic characteristics and the relationship of the B. anthracis isolates to strains from other regions indicated that the epidemic was a local occurrence.
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Affiliation(s)
- Shijun Li
- Laboratory of Bacterial Disease, Experiment Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Qing Ma
- Laboratory of Bacterial Disease, Experiment Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Hong Chen
- Guiyang Centre for Animal Disease Control and Prevention, Guiyang, China
| | - Ying Liu
- Laboratory of Bacterial Disease, Experiment Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Guanghai Yao
- Guizhou Provincial Center for Disease Control and Prevention, Institute for Communicable Disease Control and Prevention, Guiyang, China
| | - Guangpeng Tang
- Guizhou Provincial Center for Disease Control and Prevention, Institute for Communicable Disease Control and Prevention, Guiyang, China
| | - Dingming Wang
- Guizhou Provincial Center for Disease Control and Prevention, Institute for Communicable Disease Control and Prevention, Guiyang, China
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3
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Zasada AA. Detection and Identification of Bacillus anthracis: From Conventional to Molecular Microbiology Methods. Microorganisms 2020; 8:E125. [PMID: 31963339 PMCID: PMC7023132 DOI: 10.3390/microorganisms8010125] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
Rapid and reliable identification of Bacillus anthracis is of great importance, especially in the event of suspected deliberate release of anthrax spores. However, the identification of B. anthracis is challenging due to its high similarity to closely related species. Since Amerithrax in 2001, a lot of effort has been made to develop rapid methods for detection and identification of this microorganism with special focus on easy-to-perform rapid tests for first-line responders. This article presents an overview of the evolution of B. anthracis identification methods from the time of the first description of the microorganism until the present day.
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Affiliation(s)
- Aleksandra A Zasada
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
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4
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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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5
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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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Zheng F, Niu C, Tang D, Liu C, Li Y, Wang J, Li Q. Monitoring the Microbial Conditions in Breweries in Yangtze River Delta Region, China. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1080/03610470.2017.1398509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Dongjian Tang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yongxian Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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7
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El-Sayed A, El-Shannat S, Kamel M, Castañeda-Vazquez MA, Castañeda-Vazquez H. Molecular Epidemiology of Mycobacterium bovis in Humans and Cattle. Zoonoses Public Health 2015; 63:251-64. [PMID: 26684712 DOI: 10.1111/zph.12242] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/29/2022]
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), is a serious re-emerging disease in both animals and humans. The evolution of the Multi- and Extensively drug-resistant M. bovis strains (MDR-TB and XDR-TB) represents a global threat to public health. Worldwide, the disease is responsible for great economic losses in the veterinary field, serious threat to the ecosystem, and about 3.1% of human TB cases, up to 16% in Tanzania. Only thorough investigation to understand the pathogen's epidemiology can help in controlling the disease and minimizing its threat. For this purpose, various tools have been developed for use in advanced molecular epidemiological studies of bTB, either alone or in combination with standard conventional epidemiological approaches. These techniques enable the analysis of the intra- and inter-species transmission dynamics of bTB. The delivered data can reveal detailed insights into the source of infection, correlations among human and bovine isolates, strain diversity and evolution, spread, geographical localization, host preference, tracing of certain virulence factors such as antibiotic resistance genes, and finally the risk factors for the maintenance and spread of M. bovis. They also allow for the determination of epidemic and endemic strains. This, in turn, has a significant diagnostic impact and helps in vaccine development for bTB eradication programs. The present review discusses many topics including the aetiology, epidemiology and importance of M. bovis, the prevalence of bTB in humans and animals in various countries, the molecular epidemiology of M. bovis, and finally applied molecular epidemiological techniques.
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Affiliation(s)
- A El-Sayed
- Laboratory of Molecular Epidemiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - S El-Shannat
- Laboratory of Molecular Epidemiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - M Kamel
- Laboratory of Molecular Epidemiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt.,Faculty of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - M A Castañeda-Vazquez
- Laboratory of Mastitis and Molecular Diagnostic, Department of Veterinary Medicine, Division of Veterinary Sciences, University of Guadalajara, Guadalajara, Mexico
| | - H Castañeda-Vazquez
- Laboratory of Mastitis and Molecular Diagnostic, Department of Veterinary Medicine, Division of Veterinary Sciences, University of Guadalajara, Guadalajara, Mexico
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Ryu C, Lee K, Yoo C, Seong WK, Oh HB. Sensitive and Rapid Quantitative Detection of Anthrax Spores Isolated from Soil Samples by Real-Time PCR. Microbiol Immunol 2013; 47:693-9. [PMID: 14605435 DOI: 10.1111/j.1348-0421.2003.tb03434.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitative analysis of anthrax spores from environmental samples is essential for accurate detection and risk assessment since Bacillus anthracis spores have been shown to be one of the most effective biological weapons. Using TaqMan real-time PCR, specific primers and probes were designed for the identification of pathogenic B. anthracis strains from pag gene and cap gene on two plasmids, pXO1 and pXO2, as well as a sap gene encoded on the S-layer. To select the appropriate lysis method of anthrax spore from environmental samples, several heat treatments and germination methods were evaluated with multiplex-PCR. Among them, heat treatment of samples suspended with sucrose plus non-ionic detergent was considered an effective spore disruption method because it detected up to 10(5) spores/g soil by multiplex-PCR. Serial dilutions of B. anthracis DNA and spore were detected up to a level of 0.1 ng/ microliters and 10 spores/ml, respectively, at the correlation coefficient of 0.99 by real-time PCR. Quantitative analysis of anthrax spore could be obtained from the comparison between C(T) value and serial dilutions of soil sample at the correlation coefficient of 0.99. Additionally, spores added to soil samples were detected up to 10(4) spores/g soil within 3 hr by real-time PCR. As a consequence, we established a rapid and accurate detection system for environmental anthrax spores using real-time PCR, avoiding time and labor-consuming preparation steps such as enrichment culturing and DNA preparation.
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Affiliation(s)
- Chunsun Ryu
- Research Center for Pathogen Control, National Institute of Health, 5-rokbun-dong, Eunpyung-gu, Seoul 122-701, Korea
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Abhyankar W, Hossain AH, Djajasaputra A, Permpoonpattana P, Ter Beek A, Dekker HL, Cutting SM, Brul S, de Koning LJ, de Koster CG. In Pursuit of Protein Targets: Proteomic Characterization of Bacterial Spore Outer Layers. J Proteome Res 2013; 12:4507-21. [DOI: 10.1021/pr4005629] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Patima Permpoonpattana
- School
of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom
| | | | | | - Simon M. Cutting
- School
of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom
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Ågren J, Hamidjaja RA, Hansen T, Ruuls R, Thierry S, Vigre H, Janse I, Sundström A, Segerman B, Koene M, Löfström C, Van Rotterdam B, Derzelle S. In silico and in vitro evaluation of PCR-based assays for the detection of Bacillus anthracis chromosomal signature sequences. Virulence 2013; 4:671-85. [PMID: 24005110 DOI: 10.4161/viru.26288] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is a zoonotic pathogen that is relatively common throughout the world and may cause life threatening diseases in animals and humans. There are many PCR-based assays in use for the detection of B. anthracis. While most of the developed assays rely on unique markers present on virulence plasmids pXO1 and pXO2, relatively few assays incorporate chromosomal DNA markers due to the close relatedness of B. anthracis to the B. cereus group strains. For the detection of chromosomal DNA, different genes have been used, such as BA813, rpoB, gyrA, plcR, S-layer, and prophage-lambda. Following a review of the literature, an in silico analysis of all signature sequences reported for identification of B. anthracis was conducted. Published primer and probe sequences were compared for specificity against 134 available Bacillus spp. genomes. Although many of the chromosomal targets evaluated are claimed to be specific to B. anthracis, cross-reactions with closely related B. cereus and B. thuringiensis strains were often observed. Of the 35 investigated PCR assays, only 4 were 100% specific for the B. anthracis chromosome. An interlaboratory ring trial among five European laboratories was then performed to evaluate six assays, including the WHO recommended procedures, using a collection of 90 Bacillus strains. Three assays performed adequately, yielding no false positive or negative results. All three assays target chromosomal markers located within the lambdaBa03 prophage region (PL3, BA5345, and BA5357). Detection limit was further assessed for one of these highly specific assays.
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Affiliation(s)
- Joakim Ågren
- National Veterinary Institute; Department of Bacteriology; Uppsala, Sweden; Department of Biomedical Sciences and Veterinary Public Health; Swedish University of Agricultural Sciences (SLU); Uppsala, Sweden
| | - Raditijo A Hamidjaja
- National Institute for Public Health and the Environment; Centre for Infectious Disease Control; Laboratory for Zoonoses and Environmental Microbiology; Bilthoven, the Netherlands
| | - Trine Hansen
- National Food Institute; Technical University of Denmark; Søborg, Denmark
| | - Robin Ruuls
- Central Veterinary Institute of Wageningen University and Research Centre; Lelystad, the Netherlands
| | - Simon Thierry
- University Paris-Est Anses; Animal Health Laboratory; Maisons-Alfort, France
| | - Håkan Vigre
- National Food Institute; Technical University of Denmark; Søborg, Denmark
| | - Ingmar Janse
- National Institute for Public Health and the Environment; Centre for Infectious Disease Control; Laboratory for Zoonoses and Environmental Microbiology; Bilthoven, the Netherlands
| | - Anders Sundström
- National Veterinary Institute; Department of Bacteriology; Uppsala, Sweden
| | - Bo Segerman
- National Veterinary Institute; Department of Bacteriology; Uppsala, Sweden
| | - Miriam Koene
- Central Veterinary Institute of Wageningen University and Research Centre; Lelystad, the Netherlands
| | - Charlotta Löfström
- National Food Institute; Technical University of Denmark; Søborg, Denmark
| | - Bart Van Rotterdam
- National Institute for Public Health and the Environment; Centre for Infectious Disease Control; Laboratory for Zoonoses and Environmental Microbiology; Bilthoven, the Netherlands
| | - Sylviane Derzelle
- University Paris-Est Anses; Animal Health Laboratory; Maisons-Alfort, France
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11
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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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12
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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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13
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Bishop AH. Pasteuria penetrans and Its Parasitic Interaction with Plant Parasitic Nematodes. SOIL BIOLOGY 2011. [DOI: 10.1007/978-3-642-19577-8_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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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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15
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Klee SR, Brzuszkiewicz EB, Nattermann H, Brüggemann H, Dupke S, Wollherr A, Franz T, Pauli G, Appel B, Liebl W, Couacy-Hymann E, Boesch C, Meyer FD, Leendertz FH, Ellerbrok H, Gottschalk G, Grunow R, Liesegang H. The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids. PLoS One 2010; 5:e10986. [PMID: 20634886 PMCID: PMC2901330 DOI: 10.1371/journal.pone.0010986] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 05/05/2010] [Indexed: 11/18/2022] Open
Abstract
Anthrax is a fatal disease caused by strains of Bacillus anthracis. Members of this monophyletic species are non motile and are all characterized by the presence of four prophages and a nonsense mutation in the plcR regulator gene. Here we report the complete genome sequence of a Bacillus strain isolated from a chimpanzee that had died with clinical symptoms of anthrax. Unlike classic B. anthracis, this strain was motile and lacked the four prohages and the nonsense mutation. Four replicons were identified, a chromosome and three plasmids. Comparative genome analysis revealed that the chromosome resembles those of non-B. anthracis members of the Bacillus cereus group, whereas two plasmids were identical to the anthrax virulence plasmids pXO1 and pXO2. The function of the newly discovered third plasmid with a length of 14 kbp is unknown. A detailed comparison of genomic loci encoding key features confirmed a higher similarity to B. thuringiensis serovar konkukian strain 97-27 and B. cereus E33L than to B. anthracis strains. For the first time we describe the sequence of an anthrax causing bacterium possessing both anthrax plasmids that apparently does not belong to the monophyletic group of all so far known B. anthracis strains and that differs in important diagnostic features. The data suggest that this bacterium has evolved from a B. cereus strain independently from the classic B. anthracis strains and established a B. anthracis lifestyle. Therefore we suggest to designate this isolate as "B. cereus variety (var.) anthracis".
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Affiliation(s)
- Silke R Klee
- Centre for Biological Security (ZBS), Robert Koch-Institut, Berlin, Germany.
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Detection technologies for Bacillus anthracis: Prospects and challenges. J Microbiol Methods 2010; 82:1-10. [DOI: 10.1016/j.mimet.2010.04.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 04/09/2010] [Accepted: 04/12/2010] [Indexed: 01/20/2023]
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Prevalence of Bacillus anthracis-like organisms and bacteriophages in the intestinal tract of the earthworm Eisenia fetida. Appl Environ Microbiol 2010; 76:2286-94. [PMID: 20118353 DOI: 10.1128/aem.02518-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Stable infection of Bacillus anthracis laboratory strains with environmental bacteriophages confers survival phenotypes in soil and earthworm intestinal niches (R. Schuch and V. A. Fischetti, PLoS One 4:e6532, 2009). Here, the natural occurrence of two such B. anthracis-infective bacteriophages, Wip1 and Wip4, was examined in the intestines of Eisenia fetida earthworms as part of a 6-year longitudinal study at a Pennsylvania forest site. The Wip1 tectivirus was initially dominant before being supplanted by the Wip4 siphovirus, which was then dominant for the next 3 years. In a host range analysis of a wide-ranging group of Bacillus species and related organisms, Wip1 and Wip4 were both infective only toward B. anthracis and certain B. cereus strains. The natural host of Wip4 remained constant for 3 years and was a B. cereus strain that expressed a B. anthracis-like surface polysaccharide at septal positions on the cell surface. Next, a novel metagenomic approach was used to determine the extent to which such B. cereus- and B. anthracis-like strains are found in worms from two geographical locations. Three different enrichment strategies were used for metagenomic DNA isolation, based either on the ability of B. cereus sensu lato to form heat-resistant spores, the sensitivity of B. anthracis to the PlyG lysin, or the selective amplification of environmental phages cocultured with B. anthracis. Findings from this work indicate that B. cereus sensu lato and its phages are common inhabitants of earthworm intestines.
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18
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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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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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Felder KM, Hoelzle K, Wittenbrink MM, Zeder M, Ehricht R, Hoelzle LE. A DNA microarray facilitates the diagnosis of Bacillus anthracis in environmental samples. Lett Appl Microbiol 2009; 49:324-31. [PMID: 19552771 DOI: 10.1111/j.1472-765x.2009.02664.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS In order to improve the diagnosis of Bacillus anthracis in environmental samples, we established a DNA microarray based on the ArrayTube technology of Clondiag. METHODS AND RESULTS Total DNA of a bacterial colony is randomly biotinylated and hybridized to the array. The probes on the array target the virulence genes, the genomic marker gene rpoB, as well as the selective 16S rDNA sequence regions of B. anthracis, of the Bacillus cereus group and of Bacillus subtilis. Eight B. anthracis reference strains were tested and correctly identified. Among the analysed environmental Bacillus isolates, no virulent B. anthracis strain was detected. CONCLUSIONS This array clearly differentiates B. anthracis from members of the B. cereus group and other Bacillus species in environmental samples by chromosomal (rpoB) and plasmid markers. Additionally, recognition of B. cereus strains harbouring the toxin genes or atypical B. anthracis strains that have lost the virulence plasmids is feasible. SIGNIFICANCE AND IMPACT OF THE STUDY The array is applicable to the complex diagnostics for B. anthracis detection in environmental samples. Because of low costs, high security and easy handling, the microarray is applicable to routine diagnostics.
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Affiliation(s)
- K M Felder
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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21
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Multiple-locus variable-number tandem-repeat analysis for clonal identification of Vibrio parahaemolyticus isolates by using capillary electrophoresis. Appl Environ Microbiol 2009; 75:4079-88. [PMID: 19376898 DOI: 10.1128/aem.02729-08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epidemics of Vibrio parahaemolyticus in Chile have occurred since 1998. Direct genome restriction enzyme analysis (DGREA) using conventional gel electrophoresis permitted discrimination of different V. parahaemolyticus isolates obtained from these outbreaks and showed that this species consists of a highly diverse population. A multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) approach was developed and applied to 22 clinical and 91 environmental V. parahaemolyticus isolates from Chile to understand their clonal structures. To this end, an advanced molecular technique was developed by applying multiplex PCR, fluorescent primers, and capillary electrophoresis, resulting in a high-resolution and high-throughput (HRHT) genotyping method. The genomic basis of this HRHT method was eight VNTR loci described previously by Kimura et al. (J. Microbiol. Methods 72:313-320, 2008) and two new loci which were identified by a detailed molecular study of 24 potential VNTR loci on both chromosomes. The isolates of V. parahaemolyticus belonging to the same DGREA pattern were distinguishable by the size variations in the indicative 10 VNTRs. This assay showed that these 10 VNTR loci were useful for distinguishing isolates of V. parahaemolyticus that had different DGREA patterns and also isolates that belong to the same group. Isolates that differed in their DGREA patterns showed polymorphism in their VNTR profiles. A total of 81 isolates was associated with 59 MLVA groups, providing fine-scale differentiation, even among very closely related isolates. The developed approach enables rapid and high-resolution analysis of V. parahaemolyticus with pandemic potential and provides a new surveillance tool for food-borne pathogens.
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Kim W, Kim JY, Cho SL, Nam SW, Shin JW, Kim YS, Shin HS. Glycosyltransferase: a specific marker for the discrimination of Bacillus anthracis from the Bacillus cereus group. J Med Microbiol 2008; 57:279-286. [PMID: 18287289 DOI: 10.1099/jmm.0.47642-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacillus anthracis, the aetiological agent of anthrax, has been taxonomically classified with the Bacillus cereus group, which comprises B. cereus, Bacillus thuringiensis, Bacillus mycoides, Bacillus pseudomycoides and Bacillus weihenstephanensis. Although the pathogenesis and ecological manifestations may be different, B. anthracis shares a high degree of DNA sequence similarity with its group member species. As a result, the discrimination of B. anthracis from its close relatives in the B. cereus group is still quite difficult. Suppression subtractive hybridization (SSH) was performed to search for genomic differences between a B. anthracis Korean isolate CR and the most closely related B. cereus type strain KCTC 3624(T). Two-hundred and five B. anthracis CR clones obtained by SSH underwent Southern hybridization, and comparative sequences were analysed using the blast program from the National Center for Biotechnology Information (NCBI). Subsequently, primer sets based on the glycosyltransferase group 1 family protein gene specific to B. anthracis were designed from the sequences of subtracted clones, and their specificities were evaluated using eight B. anthracis, 33 B. cereus, 10 B. thuringiensis, six B. mycoides, one B. pseudomycoides, one B. weihenstephanensis and 19 strains from 11 other representative Bacillus species. PCR primers specific for the glycosyltransferase group 1 family protein gene did not amplify the desired products from any of the Bacillus strains under examination, except B. anthracis alone. These findings may be useful in the future development of efficient diagnostic tools for the rapid identification of B. anthracis from other members of the B. cereus group.
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Affiliation(s)
- Wonyong Kim
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, Seoul, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Sung-Lim Cho
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, Seoul, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Sun-Woo Nam
- Korea Health Industry Development Institute, Seoul, Republic of Korea
| | - Jong-Wook Shin
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Yang-Soo Kim
- Department of Radiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
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Mouton L, Nong G, Preston JF, Ebert D. Variable-number tandem repeats as molecular markers for biotypes of Pasteuria ramosa in Daphnia spp. Appl Environ Microbiol 2007; 73:3715-8. [PMID: 17400766 PMCID: PMC1932705 DOI: 10.1128/aem.02398-06] [Citation(s) in RCA: 18] [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
Variable-number tandem repeats (VNTRs) have been identified in populations of Pasteuria ramosa, a castrating endobacterium of Daphnia species. The allelic polymorphisms at 14 loci in laboratory and geographically diverse soil samples showed that VNTRs may serve as biomarkers for the genetic characterization of P. ramosa isolates.
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Affiliation(s)
- Laurence Mouton
- Zoologisches Institut der Universität Basel, Evolutionsbiologie, Vesalgasse 1, 4051 Basel, Switzerland.
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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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Dorfman A, Kumar N, Hahm JI. Highly sensitive biomolecular fluorescence detection using nanoscale ZnO platforms. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:4890-5. [PMID: 16700567 DOI: 10.1021/la053270+] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Fluorescence detection is currently one of the most widely used methods in the areas of basic biological research, biotechnology, cellular imaging, medical testing, and drug discovery. Using model protein and nucleic acid systems, we demonstrate that engineered nanoscale zinc oxide structures can significantly enhance the detection capability of biomolecular fluorescence. Without any chemical or biological amplification processes, nanoscale zinc oxide platforms enabled increased fluorescence detection of these biomolecules when compared to other commonly used substrates such as glass, quartz, polymer, and silicon. The use of zinc oxide nanorods as fluorescence enhancing substrates in our biomolecular detection permitted sub-picomolar and attomolar detection sensitivity of proteins and DNA, respectively, when using a conventional fluorescence microscope. This ultrasensitive detection was due to the presence of ZnO nanomaterials which contributed greatly to the increased signal-to-noise ratio of biomolecular fluorescence. We also demonstrate the easy integration potential of zinc oxide nanorods into periodically patterned nanoplatforms which, in turn, will promote the assembly and fabrication of these materials into multiplexed, high-throughput, optical sensor arrays. These zinc oxide nanoplatforms will be extremely beneficial in accomplishing highly sensitive and specific detection of biological samples involving nucleic acids, proteins and cells, particularly under detection environments involving extremely small sample volumes of ultratrace-level concentrations.
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Affiliation(s)
- Adam Dorfman
- Department of Chemical Engineering, The Pennsylvania State University, 160 Fenske Laboratory, University Park, Pennsylvania 16802, USA
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Almeida JL, Wang L, Morrow JB, Cole KD. Requirements for the Development of Bacillus Anthracis Spore Reference Materials Used to Test Detection Systems. JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY 2006; 111:205-217. [PMID: 27274929 PMCID: PMC4659448 DOI: 10.6028/jres.111.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/20/2006] [Indexed: 06/06/2023]
Abstract
Bacillus anthracis spores have been used as biological weapons and the possibility of their further use requires surveillance systems that can accurately and reliably detect their presence in the environment. These systems must collect samples from a variety of matrices, process the samples, and detect the spores. The processing of the sample may include removal of inhibitors, concentration of the target, and extraction of the target in a form suitable for detection. Suitable reference materials will allow the testing of each of these steps to determine the sensitivity and specificity of the detection systems. The development of uniform and well-characterized reference materials will allow the comparison of different devices and technologies as well as assure the continued performance of detection systems. This paper discusses the special requirements of reference materials for Bacillus anthracis spores that could be used for testing detection systems. The detection of Bacillus anthracis spores is based on recognition of specific characteristics (markers) on either the spore surface or in the nucleic acids (DNA). We have reviewed the specific markers and their relevance to characterization of reference materials. We have also included the approach for the characterization of candidate reference materials that we are developing at the NIST laboratories. Additional applications of spore reference materials would include testing sporicidal treatments, techniques for sampling the environment, and remediation of spore-contaminated environments.
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27
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Wintzingerode F, Rainey FA, Kroppenstedt RM, Stackebrandt E. Identification of environmental strains of Bacillus mycoides by fatty acid analysis and species-specific 16S rDNA oligonucleotide probe. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00437.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Sjöstedt A, Eriksson U, Ramisse V, Garrigue H. Detection of Bacillus anthracis spores in soil by PCR. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00399.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Valjevac S, Hilaire V, Lisanti O, Ramisse F, Hernandez E, Cavallo JD, Pourcel C, Vergnaud G. Comparison of minisatellite polymorphisms in the Bacillus cereus complex: a simple assay for large-scale screening and identification of strains most closely related to Bacillus anthracis. Appl Environ Microbiol 2005; 71:6613-23. [PMID: 16269689 PMCID: PMC1287610 DOI: 10.1128/aem.71.11.6613-6623.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polymorphism of five tandem repeats that are monomorphic in Bacillus anthracis was investigated in 230 isolates of the B. cereus group and in 5 sequenced B. cereus genomes in search for markers allowing identification of B. cereus and B. thuringiensis strains most closely related to B. anthracis. Using this multiple-locus variable number of tandem repeat analysis (MLVA), a cluster of 30 strains was selected for further characterization. Eventually, six of these were characterized by multilocus sequence type analysis. One of the strains is only six point mutations (of almost 3,000 bp) away from B. anthracis and was also proposed to be closest to B. anthracis by MLVA analysis. However, this strain remains separated from B. anthracis by a number of significant genetic events observed in B. anthracis, including the loss of the hemolysin activity, the presence of four prophages, and the presence of the two virulence plasmids, pXO1 and pXO2. One particular minisatellite marker provides an efficient assay to identify the subset of B. cereus and B. thuringiensis strains closely related to B. anthracis. Based on these results, a very simple assay is proposed that allows the screening of hundreds of strains from the B. cereus complex, with modest equipment and at a low cost, to eventually fill the gap with B. anthracis and better understand the origin and making of this dangerous pathogen.
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Affiliation(s)
- Samina Valjevac
- Institut de Génétique et Microbiologie, Université Paris XI, Orsay, France
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Perez A, Hohn C, Higgins J. Filtration methods for recovery of Bacillus anthracis spores spiked into source and finished water. WATER RESEARCH 2005; 39:5199-211. [PMID: 16290183 DOI: 10.1016/j.watres.2005.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 10/03/2005] [Accepted: 10/04/2005] [Indexed: 05/05/2023]
Abstract
Spores of Bacillus anthracis Sterne strain were recovered from 100ml and 1L volumes of tap and source waters using filtration through a 0.45um filter, followed by overnight culture on agar plates. In a set of experiments comparing sheep red blood cell (SRBC) plates with a chromogenic agar formulation designed by R & F Laboratories, with a spiking dose of 47 plate-enumerated spores in 100 ml tap water, the mean spore recoveries were 34.0 and 30.8 spores, respectively. When a spiking dose of 100 fluorescence activated cell sorter(FACS)-enumerated spores was used in 100 ml potable water, the average recovery with SRBC plates was 48 spores. Detection efforts with spiking doses of 35 and 10 spores in 1 L tap water were successful, but recovery efforts from spiked 1 L volumes of source water were problematic due to the concomitant growth of normal spore-forming flora. Recoveries were also attempted on 10 L volumes of tap water. For a spiking dose of 100 spores, mean recovery from six replicates was 11 spores (+/- 6.8, range 2-20), and for a spiking dose of 10 spores, mean recovery from six replicates was 2.3 spores (+/- 3.5, range 0-9). Efforts were also made to "direct detect" spores via polymerase chain reaction (PCR) on washes from filters. When spiking 534 spores in 100 ml, 9/9 replicates of spiked tap water, 6/6 source water replicates, and 0/3 unspiked controls were positive by lef PCR. When 534 spores were spiked into 1 L tap water, the lef PCR was unsuccessful; however, using the nested vrrA PCR resulted in 4/9 spiked samples, and 0/3 unspiked controls, testing positive. Our results indicate that an inexpensive and user-friendly method, utilizing filtration apparatus commonly present in many water quality testing labs, can readily be adapted for use in detecting this potential threat agent.
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Affiliation(s)
- Abril Perez
- City of Phoenix Water Services Laboratory, 2474 South 22nd Avenue, Phoenix, AZ 85009, USA
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Zahner V, Cabral DA, Régua-Mangia AH, Rabinovitch L, Moreau G, McIntosh D. Distribution of genes encoding putative virulence factors and fragment length polymorphisms in the vrrA gene among Brazilian isolates of Bacillus cereus and Bacillus thuringiensis. Appl Environ Microbiol 2005; 71:8107-14. [PMID: 16332792 PMCID: PMC1317458 DOI: 10.1128/aem.71.12.8107-8114.2005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Accepted: 09/02/2005] [Indexed: 11/20/2022] Open
Abstract
One hundred twenty-one strains of the Bacillus cereus complex, of which 80 were isolated from a variety of sources in Brazil, were screened by PCR for the presence of sequences (bceT, hblA, nheBC, plc, sph, and vip3A) encoding putative virulence factors and for polymorphisms in variable-number tandem repeats (VNTR), using a variable region of the vrrA open reading frame as the target. Amplicons were generated from isolates of B. cereus and Bacillus thuringiensis for each of the sequences encoding factors suggested to play a role in infections of mammals. Intriguingly, the majority of these sequences were detected more frequently in Bacillus thuringiensis than in B. cereus. The vip3A sequence, which encodes an insecticidal toxin, was detected exclusively in B. thuringiensis. VNTR analysis demonstrated the presence of five different fragment length categories in both species, with two of these being widely distributed throughout both taxa. In common with data generated from previous studies examining European, Asian, or North American populations, our investigation of Brazilian isolates supports the notion that B. cereus and B. thuringiensis should be considered to represent a single species.
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Affiliation(s)
- Viviane Zahner
- Laboratory of Systematic Biochemistry, Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute-FIOCRUZ, Manguinhos CEP 21045-900 Rio de Janeiro, RJ, Brazil.
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Edwards KA, Clancy HA, Baeumner AJ. Bacillus anthracis: toxicology, epidemiology and current rapid-detection methods. Anal Bioanal Chem 2005; 384:73-84. [PMID: 16283259 DOI: 10.1007/s00216-005-0090-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 08/18/2005] [Accepted: 08/18/2005] [Indexed: 01/27/2023]
Abstract
B. anthracis, the causative agent for anthrax, has been well studied for over 150 years. Due to the genetic similarities among various Bacillus species, as well as its existence in both a spore form and a vegetative state, the detection and specific identification of B. anthracis have been proven to require complex techniques and/or laborious methods. With the heightened interest in the organism as a potential biological threat agent, a large number of interesting detection technologies have recently been developed, including methods involving immunological and nucleic acid-based assay formats. The technologies range from culture-based methods to portable Total Analysis Systems based on real-time PCR. This review with 170 references provides a brief background on the toxicology and epidemiology of B. anthracis, discusses challenges associated with its detection related to genetic similarities to other species, and reviews immunological and, with greater emphasis, nucleic acid-based detection systems.
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Affiliation(s)
- Katie A Edwards
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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Ryu C, Lee K, Hawng HJ, Yoo CK, Seong WK, Oh HB. Molecular characterization of Korean Bacillus anthracis isolates by amplified fragment length polymorphism analysis and multilocus variable-number tandem repeat analysis. Appl Environ Microbiol 2005; 71:4664-71. [PMID: 16085861 PMCID: PMC1183344 DOI: 10.1128/aem.71.8.4664-4671.2005] [Citation(s) in RCA: 34] [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 analyzed the genetic relationships and molecular characteristics of 34 Bacillus anthracis isolates from soil and clinical samples in various regions of Korea and 17 related Bacillus species, using the amplified fragment length polymorphism (AFLP) and multilocus variable-number tandem repeat (MLVA) approaches. Triplicate AFLP profiles of these strains showed high reproducibility and identified 376 polymorphisms. AFLP phylogenetic analysis of B. anthracis isolates showed a high level of similarity, 0.93, and this monomorphic fragment profile proved to be useful to differentiate B. anthracis strains from other Bacillus species. The B. cereus group was separated from other Bacillus species at a level of similarity of 0.68. Among them, some B. cereus strains showed genetic interspersion with B. thuringiensis strains. The evolutionary pattern of nucleotide differences among B. anthracis strains with the eight MLVA markers showed nine MLVA types. Three MLVA types, M1 to M3, were pathogenic B. anthracis isolates and were assigned as new genotypes belonging to the A4 and B3 clusters, compared with 89 genotypes deduced from previous data. This indicates that differences in cluster prevalence and distribution may be influenced more by MLVA markers on two plasmids loci and human activity. Consequently, we suggest that the novel MLVA type may represent significant evidence for historic adaptation to environmental conditions of the Asian continent, particularly Korea. Therefore, MLVA techniques may be available for molecular monitoring on anthrax-release-related bioterrorism and further study is required for the continuous epidemiological study of variable anthrax collections.
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Affiliation(s)
- Chunsun Ryu
- Department of Bacteriology, National Institute of Health, 5-Nokbeon-dong, Eunpyeong-gu, Seoul 122-701, South Korea
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Kudva IT, Griffin RW, Garren JM, Calderwood SB, John M. Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation. Infect Immun 2005; 73:5685-96. [PMID: 16113286 PMCID: PMC1231109 DOI: 10.1128/iai.73.9.5685-5696.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified spore targets of Anthrax Vaccine Adsorbed (AVA)-induced immunity in humans by screening recombinant clones of a previously generated, limited genomic Bacillus anthracis Sterne (pXO1(+), pXO2(-)) expression library of putative spore surface (spore-associated [SA]) proteins with pooled sera from human adults immunized with AVA (immune sera), the anthrax vaccine currently approved for use by humans in the United States. We identified 69 clones that reacted specifically with pooled immune sera but not with pooled sera obtained from the same individuals prior to immunization. Positive clones expressed proteins previously identified as localized on the anthrax spore surface, proteins highly expressed during spore germination, orthologs of proteins of diverse pathogens under investigation as drug targets, and orthologs of proteins contributing to the virulence of both gram-positive and gram-negative pathogens. Among the reactive clones identified by this immunological screen was one expressing a 15.2-kDa hypothetical protein encoded by a gene with no significant homology to sequences contained in databases. Further studies are required to define the subset of SA proteins identified in this study that contribute to the virulence of this pathogen. We hypothesize that optimal delivery of a subset of SA proteins identified by such studies to the immune system in combination with protective antigen (PA), the principal immunogen in AVA, might facilitate the development of defined, nonreactogenic, more-efficacious PA-based anthrax vaccines. Future studies might also facilitate the identification of SA proteins with potential to serve as targets for drug design, spore inactivation, or spore detection strategies.
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Affiliation(s)
- Indira T Kudva
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
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35
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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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36
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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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37
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Kim K, Seo J, Wheeler K, Park C, Kim D, Park S, Kim W, Chung SI, Leighton T. Rapid genotypic detection of Bacillus anthracis and the Bacillus cereus group by multiplex real-time PCR melting curve analysis. ACTA ACUST UNITED AC 2005; 43:301-10. [PMID: 15681162 DOI: 10.1016/j.femsim.2004.10.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2004] [Revised: 10/10/2004] [Accepted: 10/18/2004] [Indexed: 11/27/2022]
Abstract
Bacillus anthracis has four plasmid possible virulence genotypes: pXO1+/pXO2+, pXO1+/pXO2-, pXO1-/pXO2+ or pXO1-/pXO2-. Due to the lack of a specific chromosomal marker for B. anthracis, differentiation of the pXO1-/pXO2- form of B. anthracis from closely related Bacillus cereus group species is difficult. In this study, we evaluate the ability of sspE, pXO1 and pXO2 primers to discriminate individual B. anthracis and the B. cereus group genotypes using multiplex real-time PCR and melting curve analysis. Optimal conditions for successful multiplex assays have been established. Purified DNAs from 38 bacterial strains including 11 strains of B. anthracis and 18 B. cereus group strains were analyzed. Nine of the B. cereus group near-neighbor strains were shown by multilocus sequence typing to be phylogenetically proximate to the B. anthracis clade. We have demonstrated that the four plasmid genotypes of B. anthracis and B. cereus group near-neighbors were differentially and simultaneously discriminated by this assay.
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Affiliation(s)
- Kijeong Kim
- Department of Microbiology, College of Medicine, Chung-Ang Univerisity, 221, Heuksuk-dong, Dongjak-gu, Seoul 156-756, South Korea.
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38
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Castanha ER, Swiger RR, Senior B, Fox A, Waller LN, Fox KF. Strain discrimination among B. anthracis and related organisms by characterization of bclA polymorphisms using PCR coupled with agarose gel or microchannel fluidics electrophoresis. J Microbiol Methods 2005; 64:27-45. [PMID: 15992950 DOI: 10.1016/j.mimet.2005.04.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Revised: 04/08/2005] [Accepted: 04/09/2005] [Indexed: 11/16/2022]
Abstract
The bclA gene codes for the protein backbone of the exosporium glycoprotein BclA of B. anthracis. BclA has a central collagen-like region formed by polymorphic GXX repeats and conserved amino- and carboxy-termini. It is noted here that the bclA gene is also present in the genome of Bacillus cereus and Bacillus thuringiensis. There is considerable size heterogeneity among the BclA proteins, both for species and strains, due to different numbers of GPT repeats and [GPT]5GDTGTT repeats (BclA repeats). PCR products that included the entire variable region were analyzed by conventional agarose gel electrophoresis and by micro-channel fluidics (MCF) LabChip to assess differences in molecular weight (MW). Both methods provided discrimination at the strain level for B. cereus group organisms. Results obtained by MCF electrophoresis were superior to conventional agarose gel analysis demonstrating improved reproducibility and much faster analysis time. The expression of a carbohydrate-rich exosporium (corresponding to BclA) in other members of the B. cereus group, in addition to B. anthracis, was also demonstrated ultra-structurally. Analysis of sequence variability within the bclA gene CLR revealed even greater potential for strain and species identification.
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Affiliation(s)
- Elisangela R Castanha
- Department of Pathology and Microbiology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
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39
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Levy H, Fisher M, Ariel N, Altboum Z, Kobiler D. Identification of strain specific markers in Bacillus anthracis by random amplification of polymorphic DNA. FEMS Microbiol Lett 2005; 244:199-205. [PMID: 15727841 DOI: 10.1016/j.femsle.2005.01.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 01/24/2005] [Accepted: 01/24/2005] [Indexed: 11/17/2022] Open
Abstract
Classification and differentiation of Bacillus anthracis isolates by genetic markers play an important role in anthrax research. We used a PCR based method--Random Amplification of Polymorphic DNA (RAPD)--to identify genetic markers in B. anthracis strains. Twenty-five differential genetic markers were identified which divided the strains into five different groups. Three selected RAPD-markers were cloned and sequenced. The five RAPD-derived genotypes could be defined by integration of these three markers. This system offers a simple non-expensive method to classify B. anthracis strains in laboratories involved in the research of this bacterium.
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Affiliation(s)
- Haim Levy
- Department of Infectious Diseases, Israel Institute for Biological Research, PO Box 19, Ness-Ziona, Israel.
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40
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Van Ert MN, Hofstadler SA, Jiang Y, Busch JD, Wagner DM, Drader JJ, Ecker DJ, Hannis JC, Huynh LY, Schupp JM, Simonson TS, Keim P. Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis. Biotechniques 2005; 37:642-4, 646, 648 passim. [PMID: 15517976 DOI: 10.2144/04374rr01] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Epidemiological and forensic analyses of bioterrorism events involving Bacillus anthracis could be improved if both variable number tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs) could be combined on a single analysis platform. Here we present the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) to characterize 24 alleles from 6 VNTR loci and 11 alleles from 7 SNP loci in B. anthracis. The results obtained with ESI-FTICR-MS were consistent with independent results obtained from traditional approaches using electrophoretic detection of fluorescent products. However, ESI-FTICR-MS improves on the traditional approaches because it does not require fluorescent labeling of PCR products, minimizes post-PCR processing, obviates electrophoresis, and provides unambiguous base composition of both SNP and VNTR PCR products. In addition, ESI-FTICR-MS allows both marker types to be examined simultaneously and at a rate of approximately 1 sample per min. This technology represents a significant advance in our ability to rapidly characterize B. anthracis isolates using VNTR and SNP loci.
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41
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Bode E, Hurtle W, Norwood D. Real-time PCR assay for a unique chromosomal sequence of Bacillus anthracis. J Clin Microbiol 2005; 42:5825-31. [PMID: 15583318 PMCID: PMC535252 DOI: 10.1128/jcm.42.12.5825-5831.2004] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time PCR has become an important method for the rapid identification of Bacillus anthracis since the 2001 anthrax mailings. Most real-time PCR assays for B. anthracis have been developed to detect virulence genes located on the pXO1 and pXO2 plasmids. In contrast, only two published chromosomal targets exist, the rpoB gene and the gyrA gene. In the present study, subtraction-hybridization with a plasmid-cured B. anthracis tester strain and a Bacillus cereus driver was used to find a unique chromosomal sequence. By targeting this region, a real-time assay was developed with the Ruggedized Advanced Pathogen Identification Device. Further testing has revealed that the assay has 100% sensitivity and 100% specificity, with a limit of detection of 50 fg of DNA. The results of a search for sequences with homology with the BLAST program demonstrated significant alignment to the recently published B. anthracis Ames strain, while an inquiry for protein sequence similarities indicated homology with an abhydrolase from B. anthracis strain A2012. The importance of this chromosomal assay will be to verify the presence of B. anthracis independently of plasmid occurrence.
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Affiliation(s)
- Elizabeth Bode
- United States Army Medical Research Institute of Infectious Diseases, Diagnostic Systems Division, 1425 Porter St., Fort Detrick, MD 21702, USA
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42
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Zwick ME, Mcafee F, Cutler DJ, Read TD, Ravel J, Bowman GR, Galloway DR, Mateczun A. Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biol 2004; 6:R10. [PMID: 15642093 PMCID: PMC549062 DOI: 10.1186/gb-2004-6-1-r10] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Revised: 10/18/2004] [Accepted: 11/19/2004] [Indexed: 11/15/2022] Open
Abstract
Custom-designed resequencing arrays were used to generate 3.1 Mb of genomic sequence from a panel of 56 Bacillus anthracis strains. Sequence quality was shown to be very high by replication and by comparison to independently generated shotgun sequence We used custom-designed resequencing arrays to generate 3.1 Mb of genomic sequence from a panel of 56 Bacillus anthracis strains. Sequence quality was shown to be very high by replication (discrepancy rate of 7.4 × 10-7) and by comparison to independently generated shotgun sequence (discrepancy rate < 2.5 × 10-6). Population genomics studies of microbial pathogens using rapid resequencing technologies such as resequencing arrays are critical for recognizing newly emerging or genetically engineered strains.
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Affiliation(s)
- Michael E Zwick
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Farrell Mcafee
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - David J Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Timothy D Read
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Jacques Ravel
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Gregory R Bowman
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Darrell R Galloway
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Alfred Mateczun
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
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43
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Gierczyński R, Kałuzewski S, Rakin A, Jagielski M, Zasada A, Jakubczak A, Borkowska-Opacka B, Rastawicki W. Intriguing diversity ofBacillus anthracisin eastern Poland â the molecular echoes of the past outbreaks. FEMS Microbiol Lett 2004; 239:235-40. [PMID: 15476971 DOI: 10.1016/j.femsle.2004.08.038] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Revised: 08/23/2004] [Accepted: 08/25/2004] [Indexed: 11/21/2022] Open
Abstract
The multiple locus VNTRs analysis (MLVA) revealed the presence of five genotypes in a group of 10 Bacillus anthracis isolates from epidemiologically unrelated cases of bovine-anthrax in eastern Poland. Eight tested isolates possessed the pagA and capB genes indicating the presence of both virulence plasmids, while two isolates revealed only pagA and lacked pXO2. The MLVA and DNA sequence analysis indicated that seven tested isolates represent four novel genotypes. Five tested strains revealed a unique 144 bp vrrB2 variant as well as 220 bp variant of vrrB1, implying the relatedness to the lineage B2. Consequently, we propose establishing of novel B2 strains sub-lineage. Multiple anthrax outbreaks, which took place in Poland several decades ago were proposed as a cause of intriguing diversity of B. anthracis observed in this study.
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Affiliation(s)
- Rafał Gierczyński
- Department of Bacteriology, National Institute of Hygiene, Chocimska Street 24, 00-791 Warsaw, Poland.
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44
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Bavykin SG, Lysov YP, Zakhariev V, Kelly JJ, Jackman J, Stahl DA, Cherni A. Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. J Clin Microbiol 2004; 42:3711-30. [PMID: 15297521 PMCID: PMC497648 DOI: 10.1128/jcm.42.8.3711-3730.2004] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to determine if variations in rRNA sequence could be used for discrimination of the members of the Bacillus cereus group, we analyzed 183 16S rRNA and 74 23S rRNA sequences for all species in the B. cereus group. We also analyzed 30 gyrB sequences for B. cereus group strains with published 16S rRNA sequences. Our findings indicated that the three most common species of the B. cereus group, B. cereus, Bacillus thuringiensis, and Bacillus mycoides, were each heterogeneous in all three gene sequences, while all analyzed strains of Bacillus anthracis were found to be homogeneous. Based on analysis of 16S and 23S rRNA sequence variations, the microorganisms within the B. cereus group were divided into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, and these seven subgroups were further organized into two distinct clusters. This classification of the B. cereus group conflicts with current taxonomic groupings, which are based on phenotypic traits. The presence of B. cereus strains in six of the seven subgroups and the presence of B. thuringiensis strains in three of the subgroups do not support the proposed unification of B. cereus and B. thuringiensis into one species. Analysis of the available phenotypic data for the strains included in this study revealed phenotypic traits that may be characteristic of several of the subgroups. Finally, our results demonstrated that rRNA and gyrB sequences may be used for discriminating B. anthracis from other microorganisms in the B. cereus group.
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Affiliation(s)
- Sergei G Bavykin
- BioChip Technology Center, Argonne National Laboratory, Argonne, IL 60439, USA.
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45
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Leendertz FH, Ellerbrok H, Boesch C, Couacy-Hymann E, Mätz-Rensing K, Hakenbeck R, Bergmann C, Abaza P, Junglen S, Moebius Y, Vigilant L, Formenty P, Pauli G. Anthrax kills wild chimpanzees in a tropical rainforest. Nature 2004; 430:451-2. [PMID: 15269768 DOI: 10.1038/nature02722] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2004] [Accepted: 06/07/2004] [Indexed: 11/09/2022]
Abstract
Infectious disease has joined habitat loss and hunting as threats to the survival of the remaining wild populations of great apes. Nevertheless, relatively little is known about the causative agents. We investigated an unusually high number of sudden deaths observed over nine months in three communities of wild chimpanzees (Pan troglodytes verus) in the Taï National Park, Ivory Coast. Here we report combined pathological, cytological and molecular investigations that identified Bacillus anthracis as the cause of death for at least six individuals. We show that anthrax can be found in wild non-human primates living in a tropical rainforest, a habitat not previously known to harbour B. anthracis. Anthrax is an acute disease that infects ruminants, but other mammals, including humans, can be infected through contacting or inhaling high doses of spores or by consuming meat from infected animals. Respiratory and gastrointestinal anthrax are characterized by rapid onset, fever, septicaemia and a high fatality rate without early antibiotic treatment. Our results suggest that epidemic diseases represent substantial threats to wild ape populations, and through bushmeat consumption also pose a hazard to human health.
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Affiliation(s)
- Fabian H Leendertz
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
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46
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Volokhov D, Pomerantsev A, Kivovich V, Rasooly A, Chizhikov V. Identification of Bacillus anthracis by multiprobe microarray hybridization. Diagn Microbiol Infect Dis 2004; 49:163-71. [PMID: 15246505 DOI: 10.1016/j.diagmicrobio.2004.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Accepted: 03/22/2004] [Indexed: 11/19/2022]
Abstract
We have developed a rapid assay based on microarray analysis of amplified genetic markers for reliable identification of Bacillus anthracis and its discrimination from other closely related bacterial species of the Bacillus cereus group. By combining polymerase chain reaction (PCR) amplification of six B. anthracis-specific genes (plasmid-associated genes encoding virulence factors (cyaA, pagA, lef, and capA, capB, capC) and one chromosomal marker BA-5449) with analysis of amplicons by microarray hybridization, we were able to unambiguously identify and discriminate B. anthracis among other closely related species. Bacillus identification relied on hybridization with multiple individual microarray oligonucleotide probes (oligoprobes) specific to each target B. anthracis gene. Evaluation of the assay was conducted using several B. anthracis strains (with or without pXO1 and pXO2 plasmids) as well as over 50 other species phylogenetically related to B. anthracis, including B. cereus, B. thuringiensis, B. mycoides, and B. subtilis. The developed microarray analysis of amplified genetic markers protocol provides an efficient method for (i) unambiguous identification and discrimination of B. anthracis from other Bacillus species and (ii) distinguishing between plasmid-containing and plasmid-free Bacillus anthracis strains.
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Affiliation(s)
- Dmitriy Volokhov
- Center for Biologics Evaluation and Research, Food and Drug Administration, Kensington, MD 20895, USA
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47
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Lindstedt BA, Heir E, Gjernes E, Vardund T, Kapperud G. DNA fingerprinting of Shiga-toxin producing Escherichia coli O157 based on Multiple-Locus Variable-Number Tandem-Repeats Analysis (MLVA). Ann Clin Microbiol Antimicrob 2003; 2:12. [PMID: 14664722 PMCID: PMC317353 DOI: 10.1186/1476-0711-2-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2003] [Accepted: 12/10/2003] [Indexed: 12/03/2022] Open
Abstract
Background The ability to react early to possible outbreaks of Escherichia coli O157:H7 and to trace possible sources relies on the availability of highly discriminatory and reliable techniques. The development of methods that are fast and has the potential for complete automation is needed for this important pathogen. Methods In all 73 isolates of shiga-toxin producing E. coli O157 (STEC) were used in this study. The two available fully sequenced STEC genomes were scanned for tandem repeated stretches of DNA, which were evaluated as polymorphic markers for isolate identification. Results The 73 E. coli isolates displayed 47 distinct patterns and the MLVA assay was capable of high discrimination between the E. coli O157 strains. The assay was fast and all the steps can be automated. Conclusion The findings demonstrate a novel high discriminatory molecular typing method for the important pathogen E. coli O157 that is fast, robust and offers many advantages compared to current methods.
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Affiliation(s)
- Bjørn-Arne Lindstedt
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
| | - Even Heir
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
| | - Elisabet Gjernes
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
| | - Traute Vardund
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
| | - Georg Kapperud
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
- Department of Pharmacology, Microbiology and Food Hygiene, Norwegian School of Veterinary Sciences, Oslo, Norway
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48
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Perdue ML, Karns J, Higgins J, Van Kessel JA. Detection and fate of Bacillus anthracis (Sterne) vegetative cells and spores added to bulk tank milk. J Food Prot 2003; 66:2349-54. [PMID: 14672236 DOI: 10.4315/0362-028x-66.12.2349] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A preparation of Bacillus anthracis (Sterne strain) spores was used to evaluate commercially available reagents and portable equipment for detecting anthrax contamination by using real-time PCR and was used to assess the fate of spores added directly to bulk tank milk. The Ruggedized Advanced Pathogen Identification Device (RAPID) was employed to detect spores in raw milk down to a concentration of 2,500 spores per ml. Commercially available primers and probes developed to detect either the protective antigen gene or the lethal factor gene both provided easily read positive signals with the RAPID following extraction from milk with a commercially available DNA extraction kit. Nucleotide sequence analysis of the vrrA gene with the use of DNA extracted from spiked milk provided molecular data that readily identified the spores as B. anthracis with a 100% BLAST match to the Sterne and Ames strains and easily distinguished them from B. cereus. Physical-fate and thermal-stability studies demonstrated that spores and vegetative cells have a strong affinity for the cream fraction of whole milk. A single treatment at standard pasteurization temperatures, while 100% lethal to vegetative cells, had no effect on spore viability even 14 days after the treatment. Twenty-four hours after the first treatment, a second treatment at 72 degrees C for 15 s reduced the viability of the population by ca. 99% but still did not kill all of the spores. From these studies, we conclude that standard pasteurization techniques for milk would have little effect on the viability of B. anthracis spores and that raw or pasteurized milk poses no obstacles to the rapid detection of the spores by molecular techniques.
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Affiliation(s)
- Michael L Perdue
- Environmental Microbial Safety Laboratory, Animal and Natural Resources Institute, USDA Agricultural Research Service, Building 173, Room 102, BARC-East, Beltsville, Maryland 20705, USA.
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Liu Y, Lee MA, Ooi EE, Mavis Y, Tan AL, Quek HH. Molecular typing of Salmonella enterica serovar typhi isolates from various countries in Asia by a multiplex PCR assay on variable-number tandem repeats. J Clin Microbiol 2003; 41:4388-94. [PMID: 12958274 PMCID: PMC193819 DOI: 10.1128/jcm.41.9.4388-4394.2003] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex PCR method incorporating primers flanking three variable-number tandem repeat (VNTR) loci (arbitrarily labeled TR1, TR2, and TR3) in the CT18 strain of Salmonella enterica serovar Typhi has been developed for molecular typing of S. enterica serovar Typhi clinical isolates from several Asian countries, including Singapore, Indonesia, India, Bangladesh, Malaysia, and Nepal. We have demonstrated that the multiplex PCR could be performed on crude cell lysates and that the VNTR banding profiles produced could be easily analyzed by visual inspection after conventional agarose gel electrophoresis. The assay was highly discriminative in identifying 49 distinct VNTR profiles among 59 individual isolates. A high level of VNTR profile heterogeneity was observed in isolates from within the same country and among countries. These VNTR profiles remained stable after the strains were passaged extensively under routine laboratory culture conditions. In contrast to the S. enterica serovar Typhi isolates, an absence of TR3 amplicons and a lack of length polymorphisms in TR1 and TR2 amplicons were observed for other S. enterica serovars, such as Salmonella enterica serovar Typhimurium, Salmonella enterica serovar Enteritidis, and Salmonella enterica serovar Paratyphi A, B, and C. DNA sequencing of the amplified VNTR regions substantiated these results, suggesting the high stability of the multiplex PCR assay. The multiplex-PCR-based VNTR profiling developed in this study provides a simple, rapid, reproducible, and high-resolution molecular tool for the epidemiological analysis of S. enterica serovar Typhi strains.
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Affiliation(s)
- Yichun Liu
- Biomedical Science Laboratory, Defence Medical Research Institute, Defence Science and Technology Agency, Singapore
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Chang YH, Shangkuan YH, Lin HC, Liu HW. PCR assay of the groEL gene for detection and differentiation of Bacillus cereus group cells. Appl Environ Microbiol 2003; 69:4502-10. [PMID: 12902235 PMCID: PMC169126 DOI: 10.1128/aem.69.8.4502-4510.2003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2002] [Accepted: 05/08/2003] [Indexed: 11/20/2022] Open
Abstract
Strains of species in the Bacillus cereus group are potentially enterotoxic. Thus, the detection of all B. cereus group strains is important. As 16S ribosomal DNA sequence analysis cannot adequately differentiate species of the B. cereus group, we explored the potential of the groEL gene as a phylogenetic marker. A phylogenetic analysis of the groEL sequences of 78 B. cereus group strains revealed that the B. cereus group strains were split into two major clusters, one including six B. mycoides and one B. pseudomycoides (cluster II) and the other including two B. mycoides and the rest of the B. cereus group strains (cluster I). Cluster I was further differentiated into two subclusters, Ia and Ib. The sodA gene sequences of representative strains from different clusters were also compared. The phylogenetic tree constructed from the sodA sequences showed substantial similarity to the tree constructed from the groEL sequences. Based on the groEL sequences, a PCR assay for detection and identification of B. cereus group strains was developed. Subsequent restriction fragment length polymorphism (RFLP) analysis verified the PCR amplicons and the differentiation of the B. cereus group strains. RFLP with MboI was identical for all the B. cereus group strains analyzed, while RFLP with MfeI or PstI classified all B. cereus and B. thuringiensis strains into two groups. All cluster II B. mycoides and B. pseudomycoides strains could be discriminated from other B. cereus group bacteria by restriction analysis with TspRI.
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Affiliation(s)
- Yu-Hsiu Chang
- Division of Bacteriology, Institute of Preventive Medicine, National Defense Medical Center, Sanhsia, Taipei, Taiwan 237, Republic of China
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