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bioRxiv · 10.64898/2025.12.03.692015

Genomic characterization of type I-E* CRISPR-Cas systems in Klebsiella pneumoniae: association of spacer diversity and antimicrobial resistance

Rao, A.·Kazi, T. A.·Naha, S.·Roy, D.·Mukherjee, S.·Ghosh, D.·Basu, S.
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Abstract

BackgroundKlebsiella pneumoniae, known to acquire antimicrobial resistance genes (ARGs) through horizontal gene transfer, possess type I CRISPR-Cas systems. This study investigated the association of multidrug resistance (MDR) and CRISPR-Cas in septicemic K. pneumoniae, along with comparative analysis of CRISPR-positive global K. pneumoniae. MethodsArchived K. pneumoniae from septicemic neonates (2008-2020) were assessed for CRISPR-Cas system, cas gene expression and correlation with ARG carriage. Whole-genome sequencing was performed and diversity of spacers, protospacers adjacent motifs (PAMs), targeted plasmids, were evaluated. Comparative analyses were performed for CRISPR-positive global K. pneumoniae. ResultsTwenty-five percent of study K. pneumoniae possessed complete type I-E* CRISPR-Cas comparable to 22% of global K. pneumoniae, which were distributed equally to type I-E & I-E*. CRISPR-positive study strains (83%) were MDR, and exhibited no significant association of CRISPR-Cas with MDR phenotype. Spacers noted in non-MDRs were diverse, showed increased average count and identified more diverse PAMs compared to spacers from MDR strains. Plasmids harboring ARGs such as blaNDM, blaCTX-M, qnrS1, mcr-8, etc. were frequently targeted by spacers from non-MDRs. Presence of CRISPR-Cas system in epidemic MDR clones such as ST14/15/23 in I-E* (local, global) and ST147 in I-E (global), indicated a lineage-specific association with CRISPR-Cas subtypes. ConclusionThis study demonstrated the co-existence of CRISPR-Cas systems within both MDR and non-MDR K. pneumoniae, with no significant correlation with either group. However, presence of diverse spacers in non-MDR strains that identified more PAMs and targeted ARG-bearing plasmid implied role of CRISPR-Cas system in limiting ARG acquisition.

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Rao, A., Kazi, T. A., Naha, S., Roy, D., Mukherjee, S., Ghosh, D., Basu, S.. 2025-12-03. Genomic characterization of type I-E* CRISPR-Cas systems in Klebsiella pneumoniae: association of spacer diversity and antimicrobial resistance. https://doi.org/10.64898/2025.12.03.692015

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