5.4.4 PCR-based bacterial identification

As you learned in Section 5.2, bacterial genera may comprise species that share overlapping phenotypes, and it may be necessary to apply PCR-based genotypic methods for their differentiation.

Two main PCR-based genotyping strategies are used for species identification:

1. Sequence analysis of 16S rRNA (16S ribosomal RNA) gene regions is often used for bacterial species identification as this gene regularly displays greater variation between than within species. Hence, comparative analysis of 16S rRNA sequence data may allow the identification of the species where phenotypic tests alone fail to do so.
2. PCR amplification of species-specific gene fragments. Many bacterial species contain genes that are not present in the genomes of related bacteria. Detection of such genes can be used to confirm or rule out a species. Identification of some Campylobacter species, and even S. aureus can be achieved using this method.