Evolution of the CRISPR-Cas9 defence system following a bacterial host shift

CRISPR-Cas systems are rapidly evolving bacterial defences targeting phages and mobile genetic elements. How these defences evolve in novel host environments remains, however, unknown. We address this question usingMycoplasma gallisepticum, a bacterial pathogen of poultry that jumped into a novel host ∼30 yrs ago. In the 12 yrs following the jump, both active and inactive forms of MgCas9 were found in circulation, after which all isolates displayed inactive forms only. Isolates with active CRISPR-Cas harboured new sets of spacers, and a MgCas9 PI domain targeting a new protospacer adjacent motif (PAM), consistent with a change in the community of phages and mobile elements encountered within the novel host. The striking concordance in time between the rise of inactivated forms of CRISPR-Cas and the evolution of widespread host resistance, suggests that inactivation was subsequently necessary for adaptive bacterial responses. We highlight the need to consider both host and pathogen selection pressures on bacteria for understanding CRISPR systems evolution.