Targeted mutagenesis methods may be beneficial if a virulence island has been identified in the pathogen’s genome. Using a highly specific method, such as Crispr, individual genes can be disrupted / knocked out to determine their phenotypic effect.
Random mutagenesis, which includes techniques using radiation and chemicals, could be used where a group of genes has been identified for virulence. This could be a novel pathogen with no homologues in other species (which could be identified with a search tool like Blast). Random techniques introduce SNPs in random locations in the genome, which can then be assayed to determine the impact on virulence factor production.
Both of these methods can be used for improving the understanding of the function of specific genes in the pathogen of interest.