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Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola
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  • Yanyan Xi,
  • Jiaxue Zhao,
  • Jiangfeng Zhang,
  • Yuefei Jin,
  • Haiyan Yang,
  • Guangcai Duan,
  • Shuaiyin Chen,
  • Jinzhao Long
Jiaxue Zhao
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Jiangfeng Zhang
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Yuefei Jin
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Haiyan Yang
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Guangcai Duan
Zhengzhou Univ
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Shuaiyin Chen
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Jinzhao Long

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Klebsiella variicola (K. variicola) is an emerging human pathogen, which poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver for the emergence of multiple antibiotic-resistant K. variicola. The clustered regularly interspersed short palindromic repeats coupled with the CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, which provide acquired immunity against HGT. However, the information about CRISPR/Cas system in K. variicola is still limited. In this study, a total of 487 genomes from NCBI database were used to analyze the characterization of CRISPR/Cas systems. 105 of the 487 genomes harbored at least one confirmed CRISPR array. Three types of CRISPR/Cas system, including types I-E, I-E*, and Ⅳ-A systems, were identified among 105 strains. The distribution of type I system was strongly associated with MLST, whereas type IV system was randomly distributed. Approximately one-third of spacer origins were homologous with plasmids or phages, indicating the role of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tended to target mobile genetic elements (MGEs) from Klebsiella pneumoniae, which provides new evidence for their interaction during evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.