Ecological origin rather than phylogeny shapes antimicrobial resistance in Bacillus cereus sensu lato

Bacillus cereus sensu lato comprises phylogenetically closely related but ecologically and phenotypically highly diverse bacteria inhabiting natural environments and food. The aim of this study was to determine whether antimicrobial resistance in these microorganisms is more strongly associated with their ecological origin than with their phylogenetic affiliation and toxigenic potential.

The results obtained for 370 B. cereus s.l. isolates originating from soil, freshwater, and organic and conventional food were compiled and analysed. Genetic diversity (MLST, 16S rRNA gene sequencing), toxigenic potential (immunochromatographic assays, dPCR), antimicrobial resistance (MIC values), and psychrotolerance (PCR, growth assays at different temperatures) were assessed. In addition, the population structure of milk-derived isolates (geoBURST) was compared with their phenotypic characteristics.

Food-derived isolates more frequently exhibited multidrug resistance and higher MIC values than strains originating from natural environments with limited direct selective pressure associated with antibiotic use. The highest frequency of resistance was observed for β-lactams, whereas susceptibility to macrolides, tetracyclines, and aminoglycosides varied among isolates. MLST and goeBURST analyses demonstrated that antimicrobial resistance profiles did not strictly correspond to phylogenetic structure or clonal complex affiliation. Enterotoxigenic potential also showed considerable variation within the analysed populations, whereas psychrotolerance was associated with specific phylogenetic lineages.

The results indicate that B. cereus s.l. represents a useful model for investigating relationships among genetic diversity, environmental adaptation, and anthropogenic selective pressure. Among the traits analysed, antimicrobial resistance in particular was more strongly associated with the ecological origin of the isolates than with their phylogenetic relatedness.