Evolutionary sweeps of subviral parasites and their phage host bring unique parasite variants and disappearance of a phage CRISPR-Cas system

Vibrio cholerae is a significant threat to global public health in part due to its propensity for large-scale evolutionary sweeps where lineages emerge and are replaced. These sweeps may originate from the Bay of Bengal where bacteriophage predation and the evolution of anti-phage counter defenses is a recurring theme. The bacteriophage ICP1 is a key predator of epidemic V. cholerae and is notable for acquiring a CRISPR-Cas system to combat PLE, a defensive subviral parasite encoded by its V. cholerae host. Here we describe the discovery of five previously unknown PLE variants, including one found during recent surveillance of patient samples in Bangladesh. We also observed a lineage sweep of PLE negative V. cholerae occurring within a patient population in under a year which coincided with a loss of ICP1s CRISPR-Cas system. These findings reinforce the importance of surveillance to better understand the selective pressures that drive pandemic cholera.