Characterization of a carbapenem- and colistin-resistant Enterobacter cloacae carrying Tn6901 in blaNDM-1 genomic context

Tam-Duong Le-Ha,1 Lien Le,1 Hong-Ngoc Le-Vo,1 Mizue Anda,2 Daisuke Motooka,3 Shota Nakamura,3 Linh Khanh Tran,1 Phuong Thi-Bich Tran,1 Tetsuya Iida,2 Van Cao11Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam; 2Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan; 3Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, JapanAbstract: We report a clinical strain of Enterobacter cloacae, PIMB10EC27, isolated in Vietnam in 2010 that was resistant to 21 of 26 tested antibiotics, including carbapenems (MICs >64 μg/mL) and colistin (MIC >128 μg/mL). The complete genome of strain PIMB10EC27 was sequenced by PacBio RSII and the Illumina Miseq system. Whole-genome analysis revealed that PIMB10EC27 contains a chromosome of the ST513 group (PIMBEC27, length 5,272,177 bp) and two plasmids, pEC27-1 of the IncX3 group (length 62,470 bp) and pEC27-2 of the IncHI1 group (length 84,602 bp). It also revealed that strain PIMB10EC27 carries 15 genes that confer resistance to at least 10 antibiotic groups. Particularly, the insertion of ISKpn19 and Tn6901 into the genomic context of blaNDM-1 was first identified and described. In another context, amino acid mutations G273D in PmrB and F515S in PmrC were first identified on the chromosome of PIMB10EC27, which may confer resistance to colistin in this strain.Keywords: blaNDM-1, colistin, Enterobacter cloacae, multidrug-resistance, Tn690