EBURST: Inferring Patterns of Evolutionary Descent Among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data

Overview

Journal J Bacteriol

Publisher American Society for Microbiology

Specialty Microbiology

Date 2004 Feb 20

PMID 14973027

Citations 899

Authors

Edward J Feil

Bao C Li

David M Aanensen

William P Hanage

Brian G Spratt

Affiliations

Soon will be listed here.

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.

Citing Articles

Serovar and multilocus sequence typing analysis of Pasteurella multocida from diseased pigs in Taiwan.

Wu C, Liao C, Chou C, Wang C, Huang S, Kuo H BMC Vet Res. 2025; 21(1):117.

PMID: 40011950 PMC: 11866582. DOI: 10.1186/s12917-025-04595-1.

Genetic Diversity and Genotype Distribution of Erwinia amylovora in Korea.

Ham H, Lee S, Lee Y Plant Pathol J. 2025; 41(1):88-99.

PMID: 39916418 PMC: 11834498. DOI: 10.5423/PPJ.OA.09.2024.0151.

Epidemiological and genomic analysis of strains from retailed raw meat.

Hamze L, Garcia-Fierro R, Drapeau A, Francois P, Endimiani A, Madec J Heliyon. 2025; 11(1):e41487.

PMID: 39831164 PMC: 11742621. DOI: 10.1016/j.heliyon.2024.e41487.

Genomic Investigation and Comparative Analysis of European High-Risk Clone of ST2.

Hummel D, Juhasz J, Kamotsay K, Kristof K, Xavier B, Koster S Microorganisms. 2025; 12(12.

PMID: 39770677 PMC: 11728346. DOI: 10.3390/microorganisms12122474.

Organic vs. Conventional Milk: Uncovering the Link to Antibiotic Resistance in sensu lato.

Bartoszewicz M, Czyzewska U, Zambrzycka M, Swiecicka I Int J Mol Sci. 2025; 25(24.

PMID: 39769288 PMC: 11677985. DOI: 10.3390/ijms252413528.

References

Jones N, Bohnsack J, Takahashi S, Oliver K, Chan M, Kunst F . Multilocus sequence typing system for group B streptococcus. J Clin Microbiol. 2003; 41(6):2530-6. PMC: 156480. DOI: 10.1128/JCM.41.6.2530-2536.2003. View

Spratt B . Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet. Curr Opin Microbiol. 1999; 2(3):312-6. DOI: 10.1016/S1369-5274(99)80054-X. View

Claus H, Weinand H, Frosch M, Vogel U . 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. 2003; 41(8):3873-6. PMC: 179822. DOI: 10.1128/JCM.41.8.3873-3876.2003. View

Caugant D, Mocca L, Frasch C, Froholm L, Zollinger W, Selander R . Genetic structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern. J Bacteriol. 1987; 169(6):2781-92. PMC: 212185. DOI: 10.1128/jb.169.6.2781-2792.1987. View

Feil E, Maiden M, Achtman M, Spratt B . The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol Biol Evol. 1999; 16(11):1496-502. DOI: 10.1093/oxfordjournals.molbev.a026061. View

Achtman M, Zurth K, Morelli G, Torrea G, Guiyoule A, Carniel E . Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A. 1999; 96(24):14043-8. PMC: 24187. DOI: 10.1073/pnas.96.24.14043. View

Zhou J, Enright M, Spratt B . Identification of the major Spanish clones of penicillin-resistant pneumococci via the Internet using multilocus sequence typing. J Clin Microbiol. 2000; 38(3):977-86. PMC: 86318. DOI: 10.1128/JCM.38.3.977-986.2000. View

Enright M, Day N, Davies C, Peacock S, Spratt B . Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol. 2000; 38(3):1008-15. PMC: 86325. DOI: 10.1128/JCM.38.3.1008-1015.2000. View

Reid S, Herbelin C, Bumbaugh A, Selander R, Whittam T . Parallel evolution of virulence in pathogenic Escherichia coli. Nature. 2000; 406(6791):64-7. DOI: 10.1038/35017546. View

10.

Jolley K, Kalmusova J, Feil E, Gupta S, Musilek M, Kriz P . Carried meningococci in the Czech Republic: a diverse recombining population. J Clin Microbiol. 2000; 38(12):4492-8. PMC: 87626. DOI: 10.1128/JCM.38.12.4492-4498.2000. View

11.

Dingle K, Colles F, Wareing D, Ure R, Fox A, Bolton F . Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol. 2001; 39(1):14-23. PMC: 87672. DOI: 10.1128/JCM.39.1.14-23.2001. View

12.

Feil E, Holmes E, Bessen D, Chan M, Day N, Enright M . Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci U S A. 2001; 98(1):182-7. PMC: 14565. DOI: 10.1073/pnas.98.1.182. View

13.

Enright M, Spratt B, Kalia A, Cross J, Bessen D . Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone. Infect Immun. 2001; 69(4):2416-27. PMC: 98174. DOI: 10.1128/IAI.69.4.2416-2427.2001. View

14.

McGee L, McDougal L, Zhou J, Spratt B, Tenover F, George R . Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network. J Clin Microbiol. 2001; 39(7):2565-71. PMC: 88185. DOI: 10.1128/JCM.39.7.2565-2571.2001. View

15.

Crisostomo M, Westh H, Tomasz A, Chung M, Oliveira D, de Lencastre H . The evolution of methicillin resistance in Staphylococcus aureus: similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones. Proc Natl Acad Sci U S A. 2001; 98(17):9865-70. PMC: 55544. DOI: 10.1073/pnas.161272898. View

16.

Feil E, Spratt B . Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol. 2001; 55:561-90. DOI: 10.1146/annurev.micro.55.1.561. View

17.

Bougnoux M, Morand S, dEnfert C . Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J Clin Microbiol. 2002; 40(4):1290-7. PMC: 140389. DOI: 10.1128/JCM.40.4.1290-1297.2002. View

18.

Enright M, Robinson D, Randle G, Feil E, Grundmann H, Spratt B . The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc Natl Acad Sci U S A. 2002; 99(11):7687-92. PMC: 124322. DOI: 10.1073/pnas.122108599. View

19.

Homan W, Tribe D, Poznanski S, Li M, Hogg G, Spalburg E . Multilocus sequence typing scheme for Enterococcus faecium. J Clin Microbiol. 2002; 40(6):1963-71. PMC: 130786. DOI: 10.1128/JCM.40.6.1963-1971.2002. View

20.

Schouls L, Reulen S, Duim B, Wagenaar J, Willems R, Dingle K . Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J Clin Microbiol. 2003; 41(1):15-26. PMC: 149617. DOI: 10.1128/JCM.41.1.15-26.2003. View