An investigation into the effects of phage diversity on the evolution of bacterial resistance mechanisms

Abstract

Bacteria possess multiple resistance mechanisms, but little is known why one mechanism can be favoured over others. With a focus on two resistance mechanisms of the pathogenic bacteria Pseudomonas aeruginosa, I expand on present knowledge by looking at ecological and genetic selection pressures that drive the adaptive resistance mechanism of the CRISPR-Cas (Clustered Regular Interspaced Short Palindromic Repeats – CRISPR associated) system compared with general resistance through cell surface modification. Specifically, I show that 1) the evolution of CRISPR-Cas immunity is not general across all phage species. 2) I examine how adaptive evolution is affected when a phage species, known to elicit CRISPR-Cas evolution, is mixed with novel phage species and demonstrate that the resistance mechanism is switched in combination with multiple phages, to surface modification. 3) I show how priming is important for continued resistance when phage have escaped the CRISPR-Cas system. However, significant detection of priming may vary between different host-phage interactions. 4) I then show how primed bacterial strains fail to evolve CRISPR-Cas resistance when infected with phage mixtures, even though prior spacer acquisition exists. 5) Finally, the benefit of the CRISPR-Cas system in generating genetic diversity is shown to rapidly clear phage from the environment. Combined, these results show that, even though there are substantial fitness benefits associated with CRISPR-Cas immunity, P. aeruginosa will develop resistance by means of surface modification in the face of phage diversity.