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.

Multidrug-resistant (MDR) Enterobacteriaceae critically threaten duck farming and public health. The phenotypes, genotypes, and associated mobile genetic elements (MGEs) of MDR Enterobacteriaceae isolated from six duck farms in Zhejiang province, China, were investigated. A total of 215 isolates were identified as Escherichia coli (64.65%), Klebsiella pneumoniae (12.09%), Proteus mirabilis (10.23%), Salmonella (8.84%), and Enterobacter cloacae (4.19%). Meanwhile, all isolates were resistant to at least two antibiotics. Most isolates carried tet(A) (85.12%), bla TEM (78.60%) and sul1 (67.44%) resistance genes. Gene co-occurrence analysis showed that the resistance genes were associated with IS26 and integrons. A conjugative IncFII plasmid pSDM004 containing all the above MGEs was detected in Proteus mirabilis isolate SDM004. This isolate was resistant to 18 antibiotics and carried the bla NDM-5 gene. MGEs, especially plasmids, are the primary antibiotic resistance gene (ARG) transmission route in duck farms. These findings provide a theoretical basis for the rational use of antibiotics in farms which are substantial for evaluating public health and food safety.