Purpose: To explore the use of the CRISPR-cas system to discriminate between S. Bareilly isolates, and to study the association between epidemiological characteristics and CRISPR in S. Bareilly.
Methods: Because the genome assemblies often break inside the CRISPR array, this region was amplified and Sanger sequenced for 50 S. Bareilly strains, comprising different PFGE patterns. Two new primers were designed for this experiment. Repeats were extracted using CRISPRdb, and the individual spacers and array organization were compared and described across strains. Phylogenetic trees (4) were reconstructed from concatenated genes mined from WGS data: cas genes, housekeeping genes (MLST), and leader sequences 1 and 2. Additionally, strains were tested for antimicrobial susceptibility.
Results: S. Bareilly displayed 1 type of CRISPR1 and 2 types of divergent CRISPR2 arrays. Leader1 sequences were conserved across strains, but phylogenetic trees of cas genes, housekeeping genes, and leader2 sequences grouped strains in 2 clusters, similarly to CRISPR2. Overall, strains with similar CRISPR2 arrays also clustered together for the other genomic elements (cas genes, leader2 sequence and MLST genes). Clustering by CRISPR array content or phylogenetic trees did not correlate with geographical origin of the isolate or food vehicle. All strains displayed susceptibility to every antimicrobial tested, and a correlation between antimicrobial resistance and CRISPR elements was not established.
Significance: Although CRISPR arrays could differentiate strains in two groups, they lacked the discriminatory power suitable for outbreak investigations.