Microbial contamination of platelet concentrates (PC) remains a persistent challenge in transfusion medicine, necessitating robust preventive measures prior to product release. Differentially expressed gene (DEG) analysis of microbe inoculated PC offers a promising approach to identifying potential biomarkers for contamination detection. Within PC, each (ATCC 29213) and (ATCC 12228) was inoculated in a 10 CFU/mL concentration. Total RNA was extracted from the samples at predetermined time points (0-, 1-, 3-, and 6-hours post-inoculation), followed by high-throughput RNA sequencing. DEG, gene enrichment, and pathway analysis were conducted. Diagnostic potential was evaluated through the calculation of area under the curve (AUC) values and the assessment of additional performance metrics. DEG identified 5884 and 974 DEGs in and samples, respectively. Pathway analysis revealed distinct biological responses: -inoculated samples showed prominent enrichment in ribosomal and spliceosome pathways, while -inoculated samples demonstrated significant activation of mitogen-activated protein kinase (MAPK) signaling pathways and natural killer (NK) cell-mediated cytotoxicity pathways. ROC analysis of the commonly differentially expressed genes in both and -inoculated samples demonstrated significant diagnostic potential. The genes , , , and exhibited statistically significant adjusted -values and AUC values exceeding 0.8, with the exception of the gene in , suggesting their utility as potential biomarkers for staphylococcal contamination detection. Interaction between PC and microbial contaminants resulted in DEG and genes could be analyzed for microbial contamination of PC. However, to establish the robustness and broader applicability of these findings, further studies encompassing a more diverse range of microbial species are necessary.