Genomic determinants of Bacillus cereus and outcomes of infection in preterm neonates: a multicentre retrospective study

Objectives: Bacillus cereus sensu lato (s.l.) or B. cereus group increasingly causes severe infections in preterm neonates. However, species-level identification and virulence characterization remain limited. This study aimed to identify B. cereus group species responsible for invasive infections in preterm neonates and to correlate genomic virulence profiles with clinical outcomes. Methods: We conducted a retrospective, multicentre study across 13 French hospitals (2010-21), including 40 B. cereus group isolates from blood or cerebrospinal fluid of preterm neonates with invasive infections. Clinical data were extracted from patient records. Whole-genome sequencing (Illumina and Oxford Nanopore) with hybrid assemblies enabled species identification using digital DNA-DNA hybridisation and average nucleotide identity. Virulence genes were screened against a curated database of 65 virulence genes, and associations with clinical outcomes were analysed. Results: Forty isolates were analyzed, 42.5% (17/40) of patients developed septic shock, and 37.5% (15/40), died, usually following rapid clinical deterioration. WGS identified seven species, predominantly Bacillus paranthracis (47.5%, 19/40) and B. cereus sensu stricto (20%, 8/40). Virulence gene content varied by species. The presence of hblCDAB (60%, 9/15), nprB (46.5%, 7/15), asbABCDEF (80%, 12/15), and essC-cereus/esxA (66.7%, 10/15) genes correlated with mortality (p=0.00015, 0.002, 0.0027, and 0.02, respectively). B. cereus sensu stricto carried more virulence determinants and was associated with higher mortality than B. paranthracis and other species, at day 7 (p=0.05) and at day 28 (p=0.0065). The cesH gene (60%, 15/25) is significantly associated with survival (p=0.007), particularly with B. paranthacis, the predominant species in our cohort. Conclusions: Invasive B. cereus group infections in preterm neonates are associated with high mortality, particularly in cases due to B. cereus sensu stricto. WGS enables precise species identification and virulence profiling, which are essential insights for diagnostic refinement, outbreak control, and risk stratification in neonatal intensive care settings.