Investigation into the presence of CRISPR-Cas- and R-M systems in Klebsiella pneumoniae and correlation with antibiotic resistance, virulence and plasmids

Abstract

The aims were to perform a bioinformatic-statistical analysis of CRISPR-Cas- and R-M systems in a diverse whole genome sequenced K. pneumoniae population, and their correlations to virulence score and AMR -/ plasmid content. The strains (n=999) consisted of Norwegian fecal carrier (n=484) and clinical (NORM; ESBL and non-ESBL producing) (n=414), and national-international clinical ST307 strains (n=101). Structural complete CRISPR-Cas systems were found in 26% of the strains; carrier (30%), NORM non-ESBL (26%), NORM-ESBL (29%), and ST307 (0%). R-M systems were found in 48% of the strains; carrier (43%), NORM (44%) and ST307 (90%). The presence of CRISPR-cas- and R-M systems seems to be equally distributed between carrier and clinical strains. The systems distributions had ST-specific profiles as illustrated with the ST307 strains. Some significant cross-population correlations were observed between the presence/absence of CRISPR-Cas-/R-M systems in terms of MGE acquisition, represented by virulence score, AMR - and plasmid content. CRISPR-Cas systems strains were associated with a higher virulence score and a lower AMR-/plasmid load. The R-M systems strains were associated with lower virulence score and a higher AMR-/plasmid load. Future studies should include analysis of CRISPR spacer content and specificity, overall phage content and utilize more advanced comparisons and statistical analyses.