摘要
      CRISPR系统通常由许多原核生物编码，作为对移动遗传元件（MGE）的适应性防御，但一些MGE也会募集CRISPR成分来执行额外的生物功能。在克雷伯菌质粒中鉴定出IV-A型系统，但这些携带CRISPR系统的质粒在整个克雷伯杆菌属中的分布、特征和作用尚不清楚。在这里，我们使用公开的质粒基因组对这些质粒进行了大规模的比较分析。携带CRISPR的质粒主要分布在肺炎克雷伯菌中（9.09%），覆盖19.23%的序列类型，但在肺炎克雷伯菌以外的克雷伯杆菌中很少（3.92%）。质粒基因组比较重申，这些质粒通常携带IncFIB和IncHI1B复制子的共整合物，偶尔与其他复制子连接，如IncFIA、IncFII、IncR、IncQ和IncU。比较基因组分析表明，携带CRISPR的克雷伯菌质粒共享一个保守的pNDM-MAR样结合模块作为其主链，并作为抗生素抗性基因（ARGs）甚至毒力基因（VGs）积累的重要载体。此外，与CRISPR阴性IncFIB/IncHIB质粒相比，CRISPR阳性IncFIB/IncHIB质粒在ARGs、VGs、GC含量、质粒长度和主链结构方面表现出高度差异，表明它们的进化路径不同。网络分析显示，CRISPR阳性质粒与其他质粒类型，特别是偶联质粒产生了激烈的竞争，从而影响了质粒的传播动力学。总的来说，我们的研究为CRISPR阳性质粒在克雷伯菌属ARGs和VGs传播中的作用提供了有价值的见解。
ABSTRACT
CRISPR systems are often encoded by many prokaryotes as adaptive defense against mobile genetic elements (MGEs), but several MGEs also recruit CRISPR components to perform additional biological functions. Type IV-A systems are identified in Klebsiella plasmids, yet the distribution, characterization, and role of these plasmids carrying CRISPR systems in the whole Klebsiella genus remain unclear. Here, we performed large-scale comparative analysis of these plasmids using publicly available plasmid genomes. CRISPR-harboring plasmids were mainly distributed in Klebsiella pneumoniae (9.09%), covering 19.23% of sequence types, but sparse in Klebsiella species outside Klebsiella pneumoniae (3.92%). Plasmid genome comparison reiterated that these plasmids often carried the cointegrates of IncFIB and IncHI1B replicons, occasionally linked to other replicons, such as IncFIA, IncFII, IncR, IncQ, and IncU. Comparative genome analysis showed that CRISPR-carrying Klebsiella plasmids shared a conserved pNDM-MAR-like conjugation module as their backbones and served as an important vector for the accretion of antibiotic resistance genes (ARGs) and even virulence genes (VGs). Moreover, compared with CRISPR-negative IncFIB/IncHIB plasmids, CRISPR-positive IncFIB/IncHIB plasmids displayed high divergences in terms of ARGs, VGs, GC content, plasmid length, and backbone structures, suggesting their divergent evolutionary paths. The network analysis revealed that CRISPR-positive plasmids yielded fierce competitions with other plasmid types, especially conjugative plasmids, thereby affecting the dynamics of plasmid transmission. Overall, our study provides valuable insights into the role of CRISPR-positive plasmids in the spread of ARGs and VGs in Klebsiella genus.

https://journals.asm.org/doi/abs/10.1128/aac.01189-22