Occurrence of CRISPR-Cas genes and lack of association with antibiotic resistance in Shigella isolates collected from patients with diarrhea in Ahvaz, southwest Iran

So far, few studies have examined the association between CRISPR-Cas and antibiotic resistance in Shigella isolates. Hence, this study sought to address this issue in Shigella species isolated from stool samples of patients with diarrhea in Ahvaz, southwest Iran. In this cross-sectional study, stool samples were collected from 103 children (3–14 years) with diarrhea admitted to Abuzar Hospital affiliated to the Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. All samples were cultured on the xylose lysine desoxycholate agar and hektoen enteric agar and incubated at 37 °C for 24 h. Primary identification of the Shigella species was performed by biochemical tests and polymerase chain reaction (PCR). Antibiotic resistance rates were evaluated by the Kirby-Bauer disc diffusion. The prevalence of 12 CRISPR-Cas genes was investigated by PCR. Overall, 83 Shigella isolates were identified by standard biochemical tests. Finally, 72 Shigella isolates including 45 S. flexneri (46.8%) and 27 (53.2%) S. sonnei were confirmed by PCR. The most effective antibiotics were trimethoprim/sulfamethoxazole (n = 48, 66.7%), imipenem (n = 46, 63.9%), and ceftazidime (n = 43, 59.7%), respectively. All isolates harbored at least one of the CRISPR-Cas genes. Occurrence of CRISPR-Cas genes was as follows: CRa (100.0%), CRb (100.0%), CRc (100.0%), CSe2 (100.0%), CRf (95.8%), CSe1_Cas3 (87.5%), Cas2_Cas (84.7%), Cas (81.9%), CRd (80.6%), Cas7 (76.4%), Cas6e_Cas5 (72.2%), and CRe (48.6%). There was no significant association between the occurrence of CRISPR-Cas elements and resistance to any antibiotic in Shigella isolates (P-value ≥ 0.9999), except for Cas gene with ceftriaxone and cefepime. This study revealed high resistance rates of various antibiotics in Shigella isolates. However, there was no significant association between the existences of CRISPR-Cas genes with antibiotic resistance. Further investigation with higher sample size is needed to confirm this observation.