Leveraging whole-genome sequencing for microbial contamination tracking and risk assessment in pharmaceutical manufacturing

Background: Pharmaceutical cleanrooms remain vulnerable to microbial contamination introduced through environmental and personnel-associated pathways, yet the genomic characteristics and transmission dynamics of these contaminants are not well defined. Methods: In this study, whole-genome sequencing (WGS) was applied to characterize microbial populations across a sterile vaccine production line. We adopted an integrated strategy that combined routine environmental monitoring with targeted genomic investigation, mapping the overall distribution of microorganisms and prioritizing isolates showing abnormal or recurrent detection for sequencing. By integrating SNP-based phylogeny, sampling location metadata, and ARG/virulence profiling. we identified five dominant opportunistic species, each displaying distinct genomic signatures indicative of different introduction pathways. Results: , suggesting elevated persistence potential under disinfectant pressure. Conclusion: These findings demonstrate that WGS enables precise source attribution and transmission-route reconstruction beyond the capability of conventional typing methods, thereby supporting real-time contamination control and evidence-based microbial-risk management in pharmaceutical manufacturing.