Integrated multi-omics reveals coordinated Staphylococcus aureus metabolic, iron transport, and stress responses to human serum

ABSTRACT Bloodstream infections caused by Staphylococcus aureus remain a leading cause of mortality worldwide. Our understanding of S. aureus survival and persistence in human serum, a cell-free fraction of blood hostile for bacteria, is still limited. Here, we applied multivariate data integration methods and network analysis to a multi-omic data set generated from five clinically prevalent S. aureus genotypes exposed to human serum. We observed, and then confirmed using isogenic mutants the significant roles of gapdhB , sucA , sirA , sstD , and perR in bacterial survival in serum. These data show that metabolic versatility in carbon source usage, iron transport, and resistance to oxidative stress is interlinked and central to S. aureus fitness in serum, representing potential S. aureus vulnerabilities that could be exploited therapeutically. IMPORTANCE Bloodstream infections caused by Staphylococcus aureus are associated with mortality rates of up to 30%. However, the molecular mechanisms that enable this pathogen to survive in human serum—a nutrient-limited and immunologically hostile environment—remain poorly understood. By integrating multi-omic data from five clinically relevant S. aureus genotypes and validating key signatures using mutants, we identified conserved genetic determinants critical for bacterial survival in serum. Our findings highlight the interconnected roles of carbohydrate metabolic flexibility, iron acquisition, and oxidative stress resistance in shaping S. aureus adaptation to serum. This work advances our understanding of microbial strategies to survive in the bloodstream and demonstrates the potential of multi-omic integration to uncover therapeutic vulnerabilities in bacterial pathogens.