Population structure and evolution of the Bacillus cereus group

Abstract

Representative strains of the Bacillus cereus group of bacteria, including Bacillus anthracis (11 isolates), B. cereus (38 isolates), Bacillus mycoides (1 isolate), Bacillus thuringiensis (53 isolates from 17 serovars), and Bacillus weihenstephanensis (2 isolates) were assigned to 59 sequence types (STs) derived from the nucleotide sequences of seven alleles, glpF, gmk, ilvD, pta, pur, pycA, and tpi. Comparisons of the maximum likelihood (ML) tree of the concatenated sequences with individual gene trees showed more congruence than expected by chance, indicating a generally clonal structure to the population. The STs followed two major lines of descent. Clade 1 comprised B. anthracis strains, numerous B. cereus strains, and rare B. thuringiensis strains, while clade 2 included the majority of the B. thuringiensis strains together with some B. cereus strains. Other species were allocated to a third, heterogeneous clade. The ML trees and split decomposition analysis were used to assign STs to eight lineages within clades 1 and 2. These lineages were defined by bootstrap analysis and by a preponderance of fixed differences over shared polymorphisms among the STs. Lineages were named with reference to existing designations: Anthracis, Cereus I, Cereus II, Cereus III, Kurstaki, Sotto, Thuringiensis, and Tolworthi. Strains from some B. thuringiensis serovars were wholly or largely assigned to a single ST, for example, serovar aizawai isolates were assigned to ST-15, serovar kenyae isolates were assigned to ST-13, and serovar tolworthi isolates were assigned to ST-23, while other serovars, such as serovar canadensis, were genetically heterogeneous. We suggest a revision of the nomenclature in which the lineage and clone are recognized through name and ST designations in accordance with the clonal structure of the population.

FIG. 1.

ML phylogenetic tree for the concatenated gene sequences for the 59 STs included in the study. Strain identifications: , B. anthracis; ○, B. cereus; ▵, B. thuringiensis; ▪, B. mycoides; □, B. weihenstephanensis. All horizontal branch lengths were drawn to a scale of substitutions per site, and the tree was rooted at the midpoint for the purpose of clarity only. All bootstrap support values of >80% are shown next to the appropriate nodes. The 85% bootstrap value associated with clade 2 excludes the highly divergent ST-9 type.

FIG. 2.

Maximum likelihood phylogenetic trees obtained for the concatenated sequence and the seven loci. ST designations are given in Table 1. All horizontal branch lengths were drawn to scale.

FIG. 2.

Maximum likelihood phylogenetic trees obtained for the concatenated sequence and the seven loci. ST designations are given in Table 1. All horizontal branch lengths were drawn to scale.

FIG. 3.

Maximum likelihood analysis of phylogenetic congruence in the B. cereus group. An ML tree that was reconstructed from the data for the concatenated loci and each of the seven loci was compared to each of the eight ML trees, with the branch lengths optimized for each analysis. The differences in likelihood (Δ−ln L) are shown for each tree (open symbols) and for 200 random trees (closed symbols).