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

Abstract

Introduction: The CRISPR-Cas system serves as a defense mechanism in bacteria and archaea, protecting them against the invasion of mobile genetic elements. Staphylococcus argenteus, a Gram-positive bacterium that diverged from Staphylococcus aureus, 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 S. argenteus 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 SCCmec (mecA-ΔmecR1-IS1272-ccrB2-ccrA2) or Insertion sequence 1272 (IS1272) transposase. Further analysis identified a common IS1272 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 S. argenteus 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.

Keywords: CRISPR-Cas; IS1272; SCCmec; Staphylococcus argenteus; poultry.

Figure 1

Distribution, Sources, and Characteristics of Global S. argenteus isolates. (A) Geographic locations and MLST types of S. argenteus isolates. (B) Number of S. argenteus isolates obtained from different hosts. (C). Number of S. argenteus with different MLST types. (D) Distribution of CRISPR-Cas-positive S. argenteus isolates from different hosts. (E) Distribution of methicillin-sensitive S. argenteus (MSSA) and methicillin-sensitive S. argenteus (MRSA) isolates carrying the CRISPR-Cas system across different countries.

Figure 2

CRISPR typing of CRISPR-Cas-positive S. argenteus isolates. (A) Phylogenetic tree of CRISPR-Cas-positive S. argenteus isolates based on 41 distinct CRISPR types. The spacer arrangements in the CRISPR 1 and CRISPR 2 loci were used to define CRISPR types. The number of strains corresponding to each CRISPR type and their associated MLST types are indicated in the right columns. (B). Distribution of strains with CRISPR 1 or CRISPR 2 types, with spacer arrangements shown for each type.

Figure 3

Genetic relationship and characteristics of CRISPR-Cas-positive S. argenteus isolates. The Minimum spanning tree of CRISPR-Cas-positive S. argenteus isolates were constructed using BioNumerics 7.5 software based on CRISPR types. Each circle represents the strains sharing a single CRISPR type. The presence of mecA and IS1272 is indicated in each circle, while “-” indicates strains lacking both mecA and IS1272.

Figure 4

Genetic location of CRISPR-Cas system in the S. argenteus chromosome. The arrangement and chromosomal location of the CRISPR-Cas system are illustrated in MSSA and MRSA strains with two distinct MLST types. The conserved IS1272 target IR sequences are also highlighted in these strains.