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Abstract Carbapenem-resistant Enterobacteriaceae strains as a new serious threat for the public health have been increasingly reported worldwide. In this study, one multi-resistant Escherichia coli strain Z SH6 which co-carried bla KPC-2 , bla NDM-5 and bla CTX-M , was isolated from human blood sample. By using plasmid conjugation experiments, ZSH6 was found to harbor three plasmids carrying the bla NDM-5 gene, the bla KPC-2 and bla CTX-M gene, respectively. Whole-genome sequencing of Z SH6 yielded 122 scaffolds of chromosomal DNA and three circular plasmids including pZSH6- bla KPC-2 (46,319 bp), pZSH6- bla NDM-5 (46,161bp) and pZSH6- bla CTX-M (184,723). The isolate was classified to Sequence Type 2 and to the O89: H10 serotype. The results of genome analyses revealed that Z SH6 carried three virulence factors (capU , gad and iss) and twenty resistance genes [ bla KPC-2 bla NDM-5 , bla CTX-M-3 , bla CTX-M-65 , bla TEM-1 , floR , tet(A) , tet(B) , dfrA17 , aadA5 , sul1 , mdf(A) , mph(A) , erm(B) , aph(3′)-Ia , aph(3′)-Ib , aph(4)-Ia , aph(6)-Id , aac(3)-Iva , aac(3)-IId ]. Therefore, the co-existence of such a large number of resistance genes in multiple plasmids making Z SH6 highly resistant to almost all kinds of commonly used antibiotics, and brings a serious challenge for resistance control and clinical treatment of infections caused by this bacterium. Highlights • O89: H10 E.coli Z SH6 strain co-carried a large number resistance genes. • E.coli Z SH6 strain co-carried three plasmids. • Three plasmids were pZSH6- bla KPC-2 , pZSH6- bla NDM-5 and pZSH6- bla CTX-M. [ABSTRACT FROM AUTHOR]