Spatial ecology meets quality control: a GIS-integrated strategy for visualizing and managing microbial contamination in sterile pharmaceutical cleanrooms

ABSTRACT To enhance contamination source identification in sterile drug manufacturing, this study innovatively developed an integrated strategy combining geographic information system (GIS) spatial visualization with microbial contamination control. Between 2022 and 2025, researchers collected 1,117 environmental microbial isolates from sterile preparation workshops, analyzing their population structure, distribution patterns, and potential risks through 16S rRNA/ITS sequencing. GIS technology was employed to associate strain data with workshop spatial information, thereby providing a visual representation of microbial quantity, species composition, and distribution patterns. Results showed that Staphylococcus and Micrococcus dominated in clean areas, with microbial diversity highest in Controlled Not Classified (CNC) environments and lowest in A-grade areas. The microbial community structure in A-grade areas significantly differed from that in CNC/C/B-grade areas, while CNC/C/B-grade areas exhibited relative similarity. In the case study, the environmental microbial distribution maps clearly demonstrated regional variations and aggregation patterns. By identifying critical control areas and transmission pathways through contamination risk analysis, targeted interventions were designed and implemented, reducing the microbial contamination rate in target C-grade areas from 4.3% to 2.2%, thereby validating the strategy’s effectiveness. This study targets the deficiency of “spatial visualization analysis” in clean area environmental monitoring. The proposed comprehensive strategy effectively fills the methodology gap in spatial analysis and contamination control for current clean area microbial monitoring. It provides a feasible framework for transforming environmental monitoring in the pharmaceutical industry from a passive surveillance system to an active early-warning system, assisting in enhancing the sterility assurance level of pharmaceutical production. IMPORTANCE Analyzing the spatial distribution characteristics of microorganisms is crucial for developing effective pollution control strategies. However, existing environmental monitoring methods have limitations in revealing these spatial distribution patterns. This paper proposes an innovative strategy that integrates geographic information system (GIS) spatial analysis with microbial ecology research to enhance the accuracy and scientific rigor of pollution source identification and risk control. This approach enables the visualization of environmental microbial quantities, types, and spatial distribution, providing a quantitative tool for analyzing microbial contamination patterns and tracing transmission pathways. The developed “GIS-integrated strategy” methodology promotes a paradigm shift from merely confirming “microbial presence” to systematically analyzing the multidimensional relationships among “microorganism-environment-control.” This study not only provides a scientific basis for formulating pollution control protocols in the pharmaceutical industry, contributing to improved sterility assurance, but also serves as a practical example of interdisciplinary integration between microbial ecology and spatial information science, demonstrating significant theoretical value and industry application prospects.