Prevalence and genomic insights into type III-A CRISPR-Cas system acquisition in global strains.

INTRODUCTION

The CRISPR-Cas system serves as a defense mechanism in bacteria and archaea, protecting them against the invasion of mobile genetic elements. , a Gram-positive bacterium that diverged from , is characterized by the rare presence of the CRISPR-Cas system in only a few isolates.

METHODS

In this study, we analyzed the prevalence of the type III-A CRISPR-Cas system in 368 genome sequences from animals, food sources, and humans across 26 countries, available in public database.

RESULTS

Our findings revealed that 44.0% of these strains carry this immune system, with 98.1% of them belonging to the sequence type 2250 (ST2250). Genomic localization analysis indicated that the CRISPR-Cas is closely associated with () or Insertion sequence (IS) transposase. Further analysis identified a common IS target inverted repeats (IR) sequence in ST2250 strains, providing insights into why these strains are more likely to acquire the CRISPR-Cas system. CRISPR typing identified 41 sequences types, classifying these strains into two clusters, with Cluster II being the predominant one. Homology analysis of spacers revealed that all the identified 15 spacers exhibited homology to sequences from plasmids, lytic phages, or prophages.

CONCLUSION

This study suggests that the acquisition of the CRISPR-Cas system in enhances its resistance to phage attacks and plasmid invasions in environmental settings, potentially posing significant challenges for clinical treatment of infections caused by these strains and hindering efforts to control their spread in food products using phage-based interventions.