Advanced Microbial Strain Typing Using Whole Genome Sequencing

Microbial identification and strain typing are critical in pharmaceutical microbiology for ensuring product safety, controlling contaminants, and meeting regulatory requirements. Traditional strain typing methods like pulsed-field gel electrophoresis and multi-locus sequence typing have their limitations in scalability and resolution. Increased use of next-generation sequencing (NGS) techniques for microbial identification and characterization, coupled with the availability of bacterial whole genomes, advanced sequence analysis approaches such as single nucleotide polymorphisms (SNPs), core and pan-genome analysis, is opening the door for more modern approaches to microbial strain typing. However, several of these approaches are species-specific and require optimization per species or project. In this study, we analyzed conserved genes from several bacterial species to analyze the possibility of using these genes as a set of universal genes for prokaryotic strain typing. We compared the strain typing results using these universal genes to results from species-specific housekeeping genes and with species with no established strain typing methods. Our data demonstrated that these conserved genes successfully distinguished bacterial strains when compared to the results from established species-specific strain typing schemes, providing a path forward in the development of a rapid, universal strain typing solution using bacterial genomes that is not limited to a single species.