Background:
The M1 serotype of Streptococcus pyogenes was the first classified by Lancefield during the 1900’s, and since that time it has been the most prevalent serotype responsible for worldwide streptococcal disease throughout history; the nature of the stability of M1 in the population is unknown. The discovery and characterization of CRISPR-Cas9 from S. pyogenes has led to the development of groundbreaking genome-editing technologies. However, despite its vast biotechnological potential, the role of CRISPR-Cas immunity in the biology and evolution of S. pyogenes and its temperate bacteriophages is currently unclear.
Methods:
To study the co-evolution of the CRISPR-Cas systems and the prophages in S. pyogenes, we analyzed the sequences of 520 diverse M1 strain genomes, sampled over a century (1918 - 2020), including clinical isolates from the Rebecca Lancefield Collection at the Rockefeller University. We then characterized signature evolutionary markers of phage/host interactions across the dataset.
Results:
Despite a surprisingly low rate of spacer acquisition over 100 years, we found that differences in the prophage repertoire of specific M1 sub-lineages strongly correlate with single-spacer variations in their CRISPR arrays. Furthermore, we obtained both genetic and experimental proof of evasion of CRISPR immunity by prophages, such as deletion of protospacer regions, recombination events, CRISPR inactivation by in loco integration or anti-CRISPR proteins.
Conclusions:
Our study reveals that CRISPR-Cas9 facilitates the maintenance of lineage-specific diversity in the accessory genome by exerting strong selective pressure on lysogenic phages that contribute to the remarkable recurring pathogenic plasticity of the M1 serotype.