The Effect of Phage Genetic Diversity on Bacterial Resistance Evolution

Bacterial CRISPR-Cas adaptive immune systems insert phage-derived sequences into CRISPR loci on the host genome to provide sequence specific immunological memory against re-infection. Under laboratory conditions the bacterium Pseudomonas aeruginosa readily evolves high levels of CRISPR-based resistance against clonal populations of its phage DMS3vir, which in turn causes rapid extinction of the phage. However, in nature phage populations are likely to be more genetically diverse, which could theoretically impact the evolution of CRISPR resistance and its effects on phage persistence. Here we experimentally test these ideas and find that a smaller proportion of infected bacterial populations evolve CRISPR-based resistance against genetically diverse phage populations, but those that do acquire greater numbers of CRISPR memory sequences in order to resist a wider range of phage genotypes, resulting in a similar rate of phage extinction as observed in the context of clonal phage populations. These data help to understand the drivers of CRISPR-mediated resistance and their consequences for bacteria-phage coexistence.