Genomic approach to studying the relationship between the CRISPR/Cas system and multidrug resistance in clinical isolates of Klebsiella pneumoniae

Background: Gene editing techniques have been identified as potential tools to combat antimicrobial resistance (AMR). Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated sequences (Cas) can be key players in this process. Their presence in bacteria can impact the success of this technology in combating AMR. The aim of this study is to investigate whether CRISPR loci are associated by multidrug, extensive drug, or pan-drug resistance in Klebsiella pneumoniae from Iraq. Methods: Antibiotic susceptibility testing was performed for 100 isolates to detect patterns of resistance. PCR was used to investigate CRISPR/Cas systems. Whole genome sequencing (WGS) was performed on relevant isolates using a DNA nanoball sequencing platform. Results: Out of 81 K. pneumoniae isolates, 81% were resistant to antibiotics, with 71% producing ESBLs and 21% producing carbapenemases. Additionally, 53% were MDR, 19% XDR, and 9% PDR. Complete CRISPR/Cas systems were found in 38% of isolates, while 78% had incomplete systems. Furthermore, intact CRISPR-1, CRISPR2, and CRISPR3 types were found in 27.0%, 34%, and 18.0% of the isolates, respectively. An inverse correlation was found between antibiotic resistance levels and the presence of CRISPR/Cas systems. Two carbapenemase-producing K. pneumoniae (XDR and PDR) isolates were characterized by WGS. They were found to be carrying blaNDM-5 and blaOXA-181 genes with additional resistance genes against various antibiotic classes, in addition to CRISPR/Cas systems. Phylogenetic analysis indicated relationships with United Kingdom and Chinese strains. Furthermore, the entire genome revealed the presence of unique virulence and antibiotic resistance genes in Klebsiella pneumoniae. Conclusion: An inverse relationship was found between CRISPR/Cas systems and antimicrobial resistance in K. pneumoniae. The discovery of blaNDM-5 and blaOXA-181 genes in Iraqi strains is alarming as this can increase the risk of nosocomial outbreaks. This study elucidates the importance of monitoring CRISPR/Cas systems and antimicrobial resistance for more efficient control and prevention of infection in healthcare settings.