Situation
The research team at a large global pharmaceutical company (“our Client”) needed to perform strain-level bacterial taxonomic classification in their bacterial stock used for manufacturing purposes. While the taxonomic classification was an essential component for regulatory approval of their new immunotherapy product, our Client lacked the specific in-house resources to conduct whole genome sequencing (WGS) data analysis, so they turned to us for help.
Strategy & Process
Fortunately, BI had the necessary bioinformatics expertise to analyze our Client’s WGS data from a large cohort of bacterial colonies. We utilized well-established pipelines for bacterial strain level characterization which included:
- Assembly: Reference-guided assembly of colony genomes was performed using AMOScmp and MetaCompass pipelines, resulting in high-quality contiguous colony-specific genomes.
- Variant Calling: Variant calling was performed on the assembled colony-specific genomes to identify single nucleotide polymorphisms (SNPs) markers that could be used for downstream clustering. Variant calling was performed using BCF tools.
- Clustering & Phylogenetic Analysis: The colonies were clustered based on their SNP profiles to determine the number of unique strains.
- Strain Abundance Analysis: Pathoscope was then utilized to estimate the abundance of each strain.
Results
We successfully, rapidly, and accurately identified the presence of a single predominant bacterial strain within our client’s bacterial stock, thereby speeding up our Client’s product development timeline.
Our Client used our report to confirm bacterial strain identity with the Food and Drug Administration, which was a crucial step for regulatory approval.
Conclusion
This case study demonstrates Bridge Informatics’ (BI) expertise in whole genome metagenomic sequencing analysis and its application to strain-level taxonomic characterization in a pharmaceutical setting. BI’s efficient workflow, coupled with close collaboration with the client, allowed for accurate and timely results, ultimately contributing to a smooth regulatory approval process.
Interested in partnering with Bridge Informatics? Contact us to learn more about our team of bioinformaticians with experience at the bench whose core specialty is understanding and analyzing biological data.
Jessica Corrado, Head of Business Development & Commercial Operations, Bridge Informatics
As the Head of Business Development & Commercial Operations, Jessica is responsible for driving strategic growth initiatives and overseeing the company’s commercial activities. She has both a keen understanding of the life sciences industry and a strong track record in building successful partnerships.
Prior to joining Bridge, Jessica held a number of leadership roles across sales, marketing, and communications. Outside of work, Jessica is responsible for the majority of marketing and event planning for Shore Saves, a non-profit animal rescue. She enjoys reading and is often reading at least two books of various genres at a time. If you’re interested in reaching out, please email [email protected].
