The Clustered Regularly Interspaced Short Palindromic Repeats-Associated System and Its Relationship With Mobile Genetic Elements in Klebsiella.

Yuqiao Zhou,Daofeng Qu,Jinchang Yan,Ping Jiang,Xiner Zheng,Dingting Xu,Shuaizhou Zong,Jinzhi Zhou,Jianzhong Han,Wei Zhou,Shiyi Tian

doi:10.3389/fmicb.2021.790673

Abstract

Microorganisms have developed many strategies in the process of long-term defense against external attacks, one of which is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) bacterial immunological system. In this study, the whole genome of 300 strains of Klebsiella was collected, the CRISPR-Cas system in the strains was statistically analyzed, and the types and structures of CRISPR system in Klebsiella were explored, as well as the correlation between CRISPR and mobile genetic elements (MGEs). Through principal component analysis (PCA), we found that Cas gene, plasmids, integron, IS1, IS609, and enzymes of DNA metabolism were closely related to CRISPR-Cas. Compared the structural characteristics of plasmids, the DinG family helicases, Cas6, Csf2, and IS5 were observed near the CRISPR loci in plasmid, which is also confirmed by the results of PCA that they may be important factors affecting the plasmid with CRISPR.

Highlights

The genus Klebsiella, a member of the family Enterobacteriaceae, encompasses a huge diversity in terms of phylogenetic lineages, genomic content, pathogenic properties, and ecological distribution (Bridel et al, 2020)
Diversity of the Clustered Regularly Interspaced Short Palindromic Repeats-Associated Proteins System in Klebsiella In April 2020, all 300 Klebsiella strains from April 2018 to March 2020 were downloaded from the National Center for Biotechnology information (NCBI) database (Supplementary Table 1)
The in-depth sequence analysis of the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) system was implemented for genome sequences of 300 Klebsiella in the NCBI database

Summary

Introduction

The genus Klebsiella, a member of the family Enterobacteriaceae, encompasses a huge diversity in terms of phylogenetic lineages, genomic content, pathogenic properties, and ecological distribution (Bridel et al, 2020). The occurrence of infectious antibiotic resistance in Klebsiella is a major problem worldwide. Klebsiella pneumoniae has a huge antibiotic resistance gene pool, which are shared with other Enterobacteriaceae mainly through self-transferring plasmids (NavonVenezia et al, 2017). In genus Klebsiella, almost all modern antibiotic resistance (to carbapenems, cephalosporins, aminoglycosides, and even colistin) are encoded in large (40–200 Kb) low-copy (16 per cell) conjugated plasmids (Samson et al, 2015). CRISPR-Cas is an adaptive immune system which stores memories of encounters with foreign DNA which are mostly mobile genetic elements (MGEs) in unique spacing sequences extracted from the MGEs and inserted into the CRISPR array (Samson et al, 2015).

Methods

Results

Discussion

Conclusion