Genomic diversity of Cronobacter sakazakii across the food system to consumers at the global scale

Abstract

Understanding how foodborne pathogens adapt to changing environments is essential for improving food safety monitoring and control. Cronobacter sakazakii, a persistent opportunistic pathogen associated with powdered infant formula outbreaks, poses critical health risks to neonates and other vulnerable populations. This study tested the hypothesis that genetic variation in C. sakazakii correlates with specific isolation sources and geographic origins across the global food system. We conducted a pangenomics meta-analysis of C. sakazakii derived from food, environmental, and clinical sources spanning North America, Asia, and Europe. A robust fine-tuned Generative Pre-trained Transformer (GPT) model was developed to standardize the categorization of isolate metadata descriptors. C. sakazakii genome assemblies (n = 748) were used to build and annotate the pangenome, and genome size and accessory gene profiles were found to be significantly associated with source type and continent of origin. Isolates from powdered foods, compared to those sourced from alternative foods, had larger genomes and were enriched in functions annotated to Clusters of Orthologous Genes (COG) category L for DNA replication, recombination and repair (e.g., transposase, integrase), among other features. Random forest models using both accessory genes and the subset of virulence factor homologs accurately predicted source attributions, identifying type VI secretion system and heavy metal response genes as key indicators of isolate origins. Several antimicrobial resistance genes associated with efflux (i.e., arlR, facT, oprZ) also exhibited patterns for biogeography. Overall, this study uncovered the distribution of key accessory genetic elements of C. sakazakii throughout the food system, revealing putative adaptations for its persistence and transmission. Our reproducible and automated workflow has potential applications in molecular surveillance for emerging food safety concerns.