Customer Challenge
A biopharmaceutical client preparing an E. coli cell bank for GMP manufacturing detected lytic and/or lysogenic bacteriophages during routine microbiological testing. These viral contaminants posed a significant risk to cell culture stability, production yields, and regulatory compliance. To trace the contamination source and evaluate potential impact, the client required a rapid and accurate method to identify the specific phages present.
Avance Biosciences’ Solution
A phage identification assay was designed and executed using next-generation sequencing (NGS), involving:
- Direct isolating of phage material from contaminated plates with visible plaques
- Enzymatic treatment and filtration to enrich phage DNA and remove residual host ( coli) DNA
- DNA extraction and fragmentation using validated methods optimized for
- Library construction and quantification, followed by paired-end sequencing on the Illumina MiSeq platform
- Bioinformatic analysis using a custom pipeline, including:
- De novo contig assembly
- Host ( coli) sequence filtering
- BLAST-based identification of non-host sequences to determine phage species present
Results
Within four weeks, Avance delivered a complete data package identifying multiple phage species within the cell bank. The results enabled the client to trace contamination sources, assess risk, and make informed decisions about remediation strategies and future banking procedures.
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