Genomic and transcriptomic characteristics of type VI secretion system in Klebsiella pneumoniae

Abstract

The Type VI secretion system (T6SS) serves as a crucial molecular weapon in interbacterial competition and significantly influences cell-cell interactions. Various bacterial species utilize their T6SSs to execute a multitude of functions, dictated by their ecological niche. However, the characteristics of T6SS in clinical Klebsiella pneumoniae, a common opportunistic nosocomial pathogen, have not been fully elucidated. Here, we conducted a genomic analysis of 65 clinical K. pneumoniae isolates obtained from patients with varying infections. Genes encoding a T6SS cluster were present in all analyzed strains of K. pneumoniae. Strains of identical sequence type (ST) carried structurally and numerically identical T6SS. Our study also highlights the importance of selecting conserved regions in key T6SS genes for effective primer design in PCR identification. We then utilized the predominant ST11 K. pneumoniae HS11286 to investigate the effect of knocking out T6SS marker genes hcp or vgrG. Transcriptome analysis identified a total of 1,298 co-upregulated and 1,752 co-downregulated differentially expressed genes. Additionally, the absence of hcp or vgrG gene suppressed the expression of other T6SS-related genes within the locus I cluster. Pathway analysis showed that the {Delta}hcp mutant exhibited alterations in transport, establishment of localization, localization and cell processes. Furthermore, interbacterial competition experiments showed that hcp and vgrG are essential for competitive ability of ST11 K. pneumoniae HS11286. This study furthers our understanding of the genomic characteristics of T6SS in K. pneumoniae and suggested that the involvement of multiple genes in T6SS of strain HS11286. ImportanceGram-negative bacteria use T6SS to deliver effectors that interact with neighboring cells for niche advantage. K. pneumoniae is an opportunistic nosocomial pathogen that often carriers multiple T6SS loci, the function of which has not yet been elucidated. We performed a genomic analysis of 65 clinical K. pneumoniae strains isolated from various sources, confirming that all strains contained T6SS. We then used transcriptomics to further study changes in gene expression and effect upon interbacterial competition following knockout of key T6SS genes in ST11 K. pneumoniae HS11286. Our findings revealed the distribution and genomic characteristics of T6SS in clinical K. pneumoniae. This study also described the overall transcriptional changes in the predominant Chinese ST11 strain HS11286 upon deletion of crucial T6SS genes. Additionally, this work provides a reference for future research on the identification of T6SS in bacteria.