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Distribution and Molecular Evolution of Bacillus anthracis Genotypes in Namibia

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      Abstract

      The recent development of genetic markers for Bacillus anthracis has made it possible to monitor the spread and distribution of this pathogen during and between anthrax outbreaks. In Namibia, anthrax outbreaks occur annually in the Etosha National Park (ENP) and on private game and livestock farms. We genotyped 384 B. anthracis isolates collected between 1983–2010 to identify the possible epidemiological correlations of anthrax outbreaks within and outside the ENP and to analyze genetic relationships between isolates from domestic and wild animals. The isolates came from 20 animal species and from the environment and were genotyped using a 31-marker multi-locus-VNTR-analysis (MLVA) and, in part, by twelve single nucleotide polymorphism (SNP) markers and four single nucleotide repeat (SNR) markers. A total of 37 genotypes (GT) were identified by MLVA, belonging to four SNP-groups. All GTs belonged to the A-branch in the cluster- and SNP-analyses. Thirteen GTs were found only outside the ENP, 18 only within the ENP and 6 both inside and outside. Genetic distances between isolates increased with increasing time between isolations. However, genetic distance between isolates at the beginning and end of the study period was relatively small, indicating that while the majority of GTs were only found sporadically, three genetically close GTs, accounting for more than four fifths of all the ENP isolates, appeared dominant throughout the study period. Genetic distances among isolates were significantly greater for isolates from different host species, but this effect was small, suggesting that while species-specific ecological factors may affect exposure processes, transmission cycles in different host species are still highly interrelated. The MLVA data were further used to establish a model of the probable evolution of GTs within the endemic region of the ENP. SNR-analysis was helpful in correlating an isolate with its source but did not elucidate epidemiological relationships.

      Author Summary

      Anthrax, the disease caused by Bacillus anthracis, is a neglected zoonotic diseases in the context of its impact on poor rural and periurban communities in Africa and other less developed areas of the world. Several regions of Namibia, the Etosha National Park in particular, are well known as being endemic areas for anthrax and, together, provide a good model for the investigation of the genetic diversity of B. anthracis circulating in livestock, wildlife and humans, and surrounding environments. The application of modern molecular strain typing techniques to the analysis of genotypic diversity, as it relates to the spatial and temporal distribution of B. anthracis strains in Namibia, is described in this paper. In particular, we demonstrate how it is possible to distinguish outbreaks of the disease caused by different strains from those caused by the spread of a single strain, to trace an outbreak strain back to its possible origin, and to track the routes of transmission of an outbreak strain within and between animal populations. The data described are relevant to all those concerned with monitoring, surveillance and prevention of the spread of anthrax in endemic areas.

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      Most cited references 41

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      Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis.

      Bacillus anthracis is one of the most genetically homogeneous pathogens described, making strain discrimination particularly difficult. In this paper, we present a novel molecular typing system based on rapidly evolving variable-number tandem repeat (VNTR) loci. Multiple-locus VNTR analysis (MLVA) uses the combined power of multiple alleles at several marker loci. In our system, fluorescently labeled PCR primers are used to produce PCR amplification products from eight VNTR regions in the B. anthracis genome. These are detected and their sizes are determined using an ABI377 automated DNA sequencer. Five of these eight loci were discovered by sequence characterization of molecular markers (vrrC(1), vrrC(2), vrrB(1), vrrB(2), and CG3), two were discovered by searching complete plasmid nucleotide sequences (pXO1-aat and pXO2-at), and one was known previously (vrrA). MLVA characterization of 426 B. anthracis isolates identified 89 distinct genotypes. VNTR markers frequently identified multiple alleles (from two to nine), with Nei's diversity values between 0.3 and 0.8. Unweighted pair-group method arithmetic average cluster analysis identified six genetically distinct groups that appear to be derived from clones. Some of these clones show worldwide distribution, while others are restricted to particular geographic regions. Human commerce doubtlessly has contributed to the dispersal of particular clones in ancient and modern times.
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        Global Genetic Population Structure of Bacillus anthracis

        Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and its true global population structure has remained largely cryptic. Seven diverse B. anthracis strains were whole-genome sequenced to identify rare single nucleotide polymorphisms (SNPs), followed by phylogenetic reconstruction of these characters onto an evolutionary model. This analysis identified SNPs that define the major clonal lineages within the species. These SNPs, in concert with 15 variable number tandem repeat (VNTR) markers, were used to subtype a collection of 1,033 B. anthracis isolates from 42 countries to create an extensive genotype data set. These analyses subdivided the isolates into three previously recognized major lineages (A, B, and C), with further subdivision into 12 clonal sub-lineages or sub-groups and, finally, 221 unique MLVA15 genotypes. This rare genomic variation was used to document the evolutionary progression of B. anthracis and to establish global patterns of diversity. Isolates in the A lineage are widely dispersed globally, whereas the B and C lineages occur on more restricted spatial scales. Molecular clock models based upon genome-wide synonymous substitutions indicate there was a massive radiation of the A lineage that occurred in the mid-Holocene (3,064–6,127 ybp). On more recent temporal scales, the global population structure of B. anthracis reflects colonial-era importation of specific genotypes from the Old World into the New World, as well as the repeated industrial importation of diverse genotypes into developed countries via spore-contaminated animal products. These findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease. Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated.
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          Multiple regression on distance matrices: a multivariate spatial analysis tool

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            Author and article information

            Affiliations
            [1 ]University of Hohenheim, Institute of Environmental and Animal Hygiene, Stuttgart, Germany
            [2 ]Department Environmental Science Policy and Management, University of California, Berkeley, California, United States of America
            [3 ]Central Veterinary Laboratory, Ministry of Agriculture, Water and Forestry, Windhoek, Namibia
            [4 ]School of Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
            [5 ]Etosha Ecological Institute, Ministry of Environment and Tourism, Okaukuejo, Namibia
            [6 ]Salisbury, United Kingdom
            Yale School of Public Health, United States of America
            Author notes

            Conceived and designed the experiments: WB GE WK JL PCBT. Performed the experiments: WB GE RH KAH JL PCBT. Analyzed the data: WB SB HHG WMG RH KAH JL WCT PCBT. Contributed reagents/materials/analysis tools: WB SB GE HHG WMG RH KAH WK JL WCT PCBT. Wrote the paper: WB SB HHG WMG WCT PCBT.

            Contributors
            Role: Editor
            Journal
            PLoS Negl Trop Dis
            plos
            plosntds
            PLoS Neglected Tropical Diseases
            Public Library of Science (San Francisco, USA )
            1935-2727
            1935-2735
            March 2012
            6 March 2012
            : 6
            : 3
            3295808
            22413024
            PNTD-D-11-00614
            10.1371/journal.pntd.0001534
            (Editor)
            Beyer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
            Counts
            Pages: 12
            Categories
            Research Article
            Biology
            Microbiology
            Bacteriology
            Veterinary Science
            Veterinary Diseases
            Veterinary Epidemiology
            Veterinary Medicine
            Veterinary Microbiology

            Infectious disease & Microbiology

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