Population structure of the Bacillus cereus group

Abstract

The Bacillus cereus group of bacteria comprises B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis and B. weihenstephanensis. Species status has been allocated to these taxa largely according to pathogenic properties. B. anthracis is the causative agent of anthrax in ungulates and humans. B. thuringiensis is primarily an insect pathogen and B. cereus is associated with food poisoning and occasionally soft tissue infections in humans. One hundred and forty-six strains of the B. cereus group were examined by multilocus sequence typing (MLST) in which partial sequences for seven housekeeping genes (glpF, gmk, ilvD, pta, pur, pycA and tpi) were generated to provide a definitive sequence type (ST) for each strain. Statistical analyses of the data using pairwise comparisons between groups for (i) Fst (gene flow), (ii) shared mutations and (iii) fixed differences confirmed that the present designation of separate species status for members of the B. cereus group was inappropriate. Comparison of neighbour joining (NJ) trees derived from the concatenated sequence data with trees constructed for each allele individually indicated limited recombination between strains and a largely clonal structure to the group. Three major clades were recovered: clade 1 was made up of B. anthracis, B. cereus and rare B. ringiensis strains; clade 2 comprised a heterogeneous mixture of B. thuringiensis and B. cereus strains while clade 3 was composed of strains of B. cereus, B. mycoides and B. weihenstephanensis. Two B. pseudomycoides strains were distant outliers from the main tree. Four lineages were recognised in both clades 1 and 2 based on shared mutations within the lineages and fixed differences between them. B. anthracis strains and the emetic toxin-producing strains of B. cereus formed two clones within clade 1. A clonal group of entomopathogenic B. thuringiensis strains was identified in clade 2 and named the ‘Sotto’ lineage (after the predicted founder group). Strains of B. cereus that had been isolated from human wound infections and septicaemia, on the other hand, were distributed over clades 1 and 2, and were not restricted to a particular clonal group. Similarly, some serotypes of B. thuringiensis were found to have a clonal structure while others were heterogeneous. Representative strains from several serotypes of B. thuringiensis were examined by the RAPD (random amplified polymorphic DNA) method. Serovars israelensis and thuringiensis were strongly clonal, morrisoni and tolworthi were partially clonal while darmstadiensis and canadensis were heterogeneous. Serotype, MLST profile and RAPD did not always correlate with delta-endotoxin cry gene content. This may be due to the cry genes being located on plasmids and subject to transfer between strains. MLST does not support the separate species status of B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis and B. weihenstephanensis and an alternative classification based on DNA sequence data is proposed based on three main clades with nine distinct lineages. The proposed lineages were named to be consistent with current nomenclature, as far as possible.