Genome-scale metabolic reconstruction of Cronobacter sakazakii reveals essential metabolic pathways linked to pathogenicity and biofilm formation

Cronobacter sakazakii is an opportunistic foodborne pathogen associated with life-threatening infections in neonates fed with contaminated powdered infant formula. Here, I present iMN1443, a curated genome-scale metabolic model (GEM) for C. sakazakii ATCC BAA-894 for the purpose of understanding its metabolic versatility, biofilm persistence, or virulence-associated metabolism. The model was reconstructed from its annotated genome using CarveMe and iteratively refined through manual curation, gap-filling, and flux balance analysis (FBA). The final model comprises 2,902 reactions, 1,849 metabolites, and 1,443 genes (73.2% gene-protein-reaction coverage), a growth rate of 0.893 h⁻¹ on glucose minimal medium, and a MEMOTE score of 93%. iMN1443 correctly reproduced utilization of fourteen carbon sources characteristic of dairy and infant-formula environments. When calibrated against empirical Cronobacter growth trajectories across two temperatures and two culture volumes, the GEM captured 91.8%–98.4% of the experimental variance. Flux analysis revealed a highly active, fully oxidative central carbon metabolism supporting substantial ATP synthase flux. Comparison of standard and parsimonious FBA highlighted extensive pathway redundancy. Simulating six host- and biofilm-associated microenvironments further revealed a pronounced growth-virulence trade-off: growth declined up to 14-fold from laboratory medium to the biofilm interior while the macrophage phagolysosome triggered a 308-fold upregulation of reactive oxygen species defense pathways alongside collapse of oxidative energy metabolism. Simulated biofilm depth stratification showed a similar growth decline (up to 88%) accompanied by maintained biofilm-associated pathway flux. This is consistent with a persister-like survival strategy in nutrient- and oxygen-depleted zones. Genome-wide single-gene deletion analysis identified 107 essential genes that are predominantly involved in amino acid, nucleotide, and cell-envelope biosynthesis. These represent candidate antimicrobial targets. iMN1443 provides a metabolic modeling framework for C. sakazakii and a foundation for rational antimicrobial target discovery and food-safety risk assessment.