Genomic mining of Bacillus safensis and Enterococcus lactis from food sources

Abstract The growing complexity of food-safety systems and the increasing emergence of multidrug-resistant (MDR) foodborne pathogens demonstrate the importance of enhanced genomic surveillance. This study employed whole genome sequencing (WGS) to characterise the genomes of Bacillus safensis NWU MK_WT, Enterococcus lactis ENT7_CNKT_NWU, and ENT3_CNKT_NWU, isolated from food sources. Phenotypic antibiotic susceptibility testing revealed that all strains displayed MDR phenotypes, with resistance to erythromycin, ampicillin, and meropenem. Genome assemblies ranged from 2.6 to 3.7 Mb, exhibiting high completeness (100%) and diverse functional gene profiles. Furthermore, antibiotic resistance genes (ARGs), including vanT and aac(6′), mediating antibiotic inactivation, efflux, and target modification, were identified. Virulence factors, including adhesion, invasion, and biofilm formation, were detected across genomes, indicating pathogenic potential. Mobile genetic element profiling revealed the presence of insertion sequences, plasmids, and an intact prophage in B. safensis NWU MK_WT, demonstrating genomic plasticity and the potential for horizontal gene transfer (HGT). Phylogenomic comparison showed close relatedness between the isolates and strains from Asia, suggesting possible transboundary movement of genetic material. These findings highlight the growing relevance of WGS for monitoring opportunistic foodborne bacteria that harbour and disseminate resistance and virulence determinants, provide foundational data for improving food safety surveillance, and support antimicrobial resistance mitigation strategies.