Methods for strain comparison and differentiation of environmental isolates

Identification of environmental isolates is a regular requirement in pharmaceutical manufacturing, and strain differentiation can be valuable in a variety of circumstances. There have been huge advances in the technology available for sequencing bacterial genomes, which has fed through to the analyses that are available to pharmaceutical microbiologists. NCIMB’s Identification Services Manager, Vikki Warren, looks at how this has changed her approach to strain comparison, the role of whole genome sequencing in pharmaceutical microbiology and its benefits in terms of costs and accuracy.

NCIMB Ltd provides microbial identification services and curates The National Collection of Industrial, Food and Marine Bacteria – one of the culture collections that makes up the UK Biological Resource Centre Network. This culture collection dates back to 19501 and, given this history, it is no surprise that we occasionally find that a strain within it has been reclassified. The tools available to microbiologists have changed dramatically since the 1950s – and especially since Carl Woese pioneered the use of the 16S ribosomal RNA (rRNA) gene to delineate taxonomic lineage in 1977.2 Today, 16S sequencing is not only used in research projects, but is a routine analytical method commonly used to identify environmental isolates, and we use it to check the identity of strains within our culture collection.

Benefits of genotypic identification

While phylogenetic or proteolytic approaches to the identification of isolates are popular, identification based on 16S sequencing is fast, unambiguous and a huge amount of sequence data is available that can be used to identify samples. Matches to sequence data can be made at species or sometimes even the subspecies level, enabling phylogenetic trees to be generated.

Another advantage of the 16S approach is that in the event that no species-level match is made using a validated database, the sequence data is available for comparison to future isolates. This can be valuable in pharmaceutical manufacturing environments when investigating incursions or process contaminants, as the sequences of isolates can be compared to determine whether they are the same species.