Genomic Characterization of Bacillus spp. from Fresh Lettuce in Traditional and Modern Markets

Abstract

Bacillus spp., particularly members of the Bacillus cereus sensu lato group, are widely distributed in the environment. Their frequent detection in fresh vegetables raises food safety concerns due to their potential pathogenicity. This study aimed to characterize Bacillus paranthracis isolates obtained from fresh lettuce collected from traditional (RTJ) and modern market (RSF). Whole-genome sequencing (WGS) was performed using the GenoLab M high-throughput sequencing platform to analyze genomic characteristics, antimicrobial resistance, and virulence potential of the isolates. Genome-based identification confirmed that both isolates were B. paranthracis and represented distinct strains. The genome sizes of RTJ and RSF were 4.91 Mb and 5.36 Mb, with GC contents of 35.42% and 35.22%. Comparative genomic analysis revealed notable differences in gene content, indicating genomic heterogeneity within the species. Antimicrobial resistance profiling identified 11 resistance genes associated with antibiotic inactivation, target protection, target alteration, and efflux mechanisms. Virulence analysis detected the presence of inhA and the complete nheABC enterotoxin gene cluster in both isolates. No plasmid sequences were identified indicating that resistance and virulence determinants are chromosomally encoded. This study provides genomic insights into B. paranthracis contamination in fresh produce and highlights potential food safety risks associated with lettuce marketed in retail environments.