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. 2004 Mar;186(5):1518-30.
doi: 10.1128/JB.186.5.1518-1530.2004.

eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data

Edward J Feil  1 , Bao C Li, David M Aanensen, William P Hanage, Brian G Spratt
Affiliations

eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data

Edward J Feil et al. J Bacteriol. 2004 Mar.

Abstract

The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain(23F)-1 clonal complex of Streptococcus pneumoniae, "population snapshots" of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.

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Figures

FIG. 1.
FIG. 1.
Analysis of the ST81 clonal complex of S. pneumoniae. The relatedness between isolates in the pneumococcal MLST database that shared alleles at four or more loci with the allelic profile of ST81 (Spain23F-1 clone) is displayed as a dendrogram. The entire pneumococcal MLST database was analyzed by eBURST with the stringent (default) group definition; the group that included ST81 is displayed as an eBURST diagram (inset). Numbers in the eBURST diagram correspond to ST numbers. The STs in the eBURST diagram included all of those arising from the node on the dendrogram marked by an asterisk. One DLV of ST81 (arrow) was not included in the eBURST group when the stringent group definition was used. The area of each circle in the eBURST diagram corresponds to the abundance of the isolates of the ST in the input data; ST81 is the predicted founder of the group (bootstrap confidence value of 100%).
FIG. 2.
FIG. 2.
Population snapshot of S. pneumoniae. Clusters of related STs and individual unlinked STs within the entire pneumococcal MLST database are displayed as a single eBURST diagram by setting the group definition to zero of seven shared alleles. Clusters of linked isolates correspond to clonal complexes. Primary founders (blue) are positioned centrally in the cluster, and subgroup founders are shown in yellow. Only the ST81 cluster shown in Fig. 1 is labeled; the other ST labels have been removed for clarity.
FIG. 3.
FIG. 3.
Population snapshot of S. aureus. The entire S. aureus MLST database is displayed as a single eBURST diagram as described in the legend to Fig. 2. The major STs within the ST30 and ST239 clonal complexes are marked by arrows; the patterns of descent within these complexes are discussed in the text. For clarity, ST labels have been removed.
FIG. 4.
FIG. 4.
Relationships of isolates of the C. jejuni ST21 clonal complex. STs that shared alleles at ≥3 of the 7 MLST loci with ST21 were obtained from the C. jejuni MLST website, and a dendrogram was constructed by using UPGMA. The node that defines the ST21 clonal complex is labeled on the dendrogram. Only one example of each ST is shown.
FIG. 5.
FIG. 5.
Analysis of the ST21 complex of C. jejuni. The 2,001 isolates in the entire C. jejuni public MLST database were analyzed by eBURST with the stringent (default) group definition; the group that included ST21 is displayed as an eBURST diagram. The predicted primary founder, ST21 (bootstrap confidence value of 99%), is labeled.
FIG. 6.
FIG. 6.
Analysis of the ST32 clonal complex of N. meningitidis. eBURST groups were obtained from the entire meningococcal public MLST database with the stringent (default) group definition; the eBURST group that included ST32 is displayed. The primary founder, ST32 (bootstrap confidence value of 100%), and a major subgroup founder, ST33, are labeled.
FIG. 7.
FIG. 7.
Relatedness of STs of the ST8 and ST11 clonal complexes. STs that shared alleles at ≥3 of the 7 MLST loci with ST8 or ST11 were obtained from the Neisseria MLST website, and a dendrogram was constructed. The clusters of STs corresponding to the ST8 (A4) and ST11 (ET-37) complexes are shown. Only one example of each ST was used in the analysis.
FIG. 8.
FIG. 8.
Analysis of the ST8 and ST11 clonal complexes of N. meningitidis. eBURST groups were obtained from the entire N. meningitidis MLST database with the group definition of five of seven shared alleles. With this group definition, ST8 and ST11 were placed in a single group, which is displayed as an eBURST diagram. ST8 and ST11 are the primary founders of two clonal complexes (bootstrap confidence value of 100%), and most other isolates are SLVs of either ST8 or ST11; there are also two pairs of linked STs and a number of individual unlinked STs.
FIG. 9.
FIG. 9.
Relatedness of STs of lineage 3 displayed as a dendrogram. STs that shared alleles at ≥3 of the 7 MLST loci with ST41 or ST44 were obtained from the Neisseria MLST website, and a dendrogram was constructed. STs assigned to lineage 3 descended from the node marked by an arrow. A major subdivision of lineage 3 into a cluster of STs that included ST41 and another that included ST44 is shown. Only one example of each ST was used in the analysis.
FIG. 10.
FIG. 10.
Analysis of lineage 3 of N. meningitidis. The entire N. meningitidis MLST database was analyzed with the stringent (default) group definition; the group that included ST41 and ST44 is displayed as an eBURST diagram. The two main subgroups and the linking ST303 subgroup are shown. Bootstrap support values for ST41 and ST44 as the primary founders were 79 and 57%, respectively.
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References

    1. Achtman, M., K. Zurth, G. Morelli, G. Torrea, A. Guiyoule, and E. Carniel. 1999. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96:14043-14048. - PMC - PubMed
    1. Bougnoux, M. E., S. Morand, and C. d'Enfert. 2002. Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J. Clin. Microbiol. 40:1290-1297. - PMC - PubMed
    1. Caugant, D. A., L. F. Mocca, C. E. Frasch, L. O. Froholm, W. D. Zollinger, and R. K. Selander. 1987. Genetic structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern. J. Bacteriol. 169:2781-2792. - PMC - PubMed
    1. Caugant, D. A. 1998. Population genetics and molecular epidemiology of Neisseria meningitidis. APMIS 106:505-525. - PubMed
    1. Claus, H., H. Weinand, M. Frosch, and U. Vogel. 2003. Identification of the hypervirulent lineages of Neisseria meningitidis, the ST-8 and ST-11 complexes, by using monoclonal antibodies specific to NmeDI. J. Clin. Microbiol. 41:3873-3876. - PMC - PubMed

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