Diagnostic challenges within the Bacillus cereus-group: finding the beast without teeth

Abstract

The <i>Bacillus cereus</i>-group (<i>B. cereus sensu lato</i>) includes common, usually avirulent species, often considered contaminants of patient samples in routine microbiological diagnostics, as well as the highly virulent <i>B. anthracis</i>. Here we describe 16 isolates from 15 patients, identified as <i>B. cereus</i>-group using a MALDI-TOF MS standard database. Whole genome sequencing (WGS) analysis identified five of the isolates as <i>B. anthracis</i> species not carrying the typical virulence plasmids pXO1 and pXO2, four isolates as <i>B. paranthracis,</i> three as <i>B. cereus sensu stricto</i>, two as <i>B. thuringiensis</i>, one as <i>B. mobilis</i>, and one isolate represents a previously undefined species of <i>Bacillus</i> (<i>B. basilensis</i> sp. nov.). More detailed analysis using alternative MALDI-TOF MS databases, biochemical phenotyping, and diagnostic PCRs, gave further conflicting species results. These cases highlight the difficulties in identifying avirulent <i>B. anthracis</i> within the <i>B. cereus</i>-group using standard methods. WGS and alternative MALDI-TOF MS databases offer more accurate species identification, but so far are not routinely applied. We discuss the diagnostic resolution and discrepancies of various identification methods.