Bacterial community structure and dominant species in pharmaceutical manufacturing water revealed by high-throughput sequencing

Control of the microbiological quality of water for pharmaceutical manufacturing is essential to ensure the safety of pharmaceutical products. A major issue in the quality control of pharmaceutical manufacturing water is the time required to identify microbial contaminants, which can be as long as several days using traditional culture methods. Here, we demonstrate the use of high-throughput sequencing of samples taken from a pharmaceutical water production system, using the Oxford Nanopore Technologies MinION sequencing platform. We successfully revealed the bacterial community structure and dominant species in stagnation sampling ports of the pharmaceutical water supply system. Dynamic changes in dominant bacteria were detected across different treatment stages: Phreatobacter in the city water, Methylobacterium in the reverse osmosis-treated water (>95 % of the bacterial abundance) and Ralstonia in the ultrafiltration-treated water (>93 % of the bacterial abundance). Compared with traditional culture methods, the MinION sequencing approach enabled rapid characterization of bacterial composition and prompt identification of dominant species. This cost-effective, molecular-based approach will usher in a new era of bioburden monitoring and identification in pharmaceutical water systems, in line with regulatory recommendations to implement rapid microbiological methods. Our findings demonstrate the practical application of high-throughput sequencing for comprehensive bacterial analysis in the pharmaceutical industry.