Diversity of CRISPR systems in strains of Streptococcus thermophilus utilized in Argentina

Abstract

Study the presence of CRISPR1 and CRISPR3 systems in Streptococcus thermophilus strains used in Argentina and perform the analysis of their spacers. Perform a comparative analysis of CRISPR1 and CRISPR3 systems in local strains, and identify “new” spacers (not found in database sequences). Detect the presence of spacers (as protospacers) in phage genomes, both previously reported in databases and from local phages sequenced at our institute. Most of the spacers found in CRISPR systems of our regional strains already existed in databases. We found a greater quantity, prevalence and diversity of spacers in the CRISPR3 systems of our strains, unlike what has been reported in other countries where CRISPR1 systems seem to be more relevant.Although more CRISPR3 spacers were identified in total, the percentages of spacers found in local phage genomes was similar (~18%) between CRISPR1 and CRISPR3. Among the spacers found in 2 or more local phage genomes, a clear general correspondence of them to a given phage genetic group (cos, pac or 5093) was observed; however, a few spacers were found in 2 (or even all 3) different genetic groups; observation valid for both CRISPR1 and CRISPR3). Notable differences were observed between spacers corresponding to phages isolated from different matrices (cheese whey vs. yogurt). Even numerous spacers corresponded only to phages of a certain origin. Advancing the knowledge of the CRISPR systems of S. thermophilus strains circulating in our country will allow the design of strategies to reduce the impact of phages in the regional dairy industry.