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In this study, we characterized the first clinical Klebsiella pneumoniae strain co- harboring mcr-1 and blaNDM-4 genes in Vietnam, which was recovered from a patient admitted to hospital in 2015. This strain demonstrated nonsusceptible to all tested antibiotics, including last-line antibiotics such as carbapenems (MICs ≥128 μg/mL) and colistin (MIC =32 μg/mL), except tigecycline (MIC =1 μg/mL). Whole-genome analysis using both MinION and MiSeq data revealed that the strain carried 29 resistance genes. Particularly, mcr-1 and blaNDM-4 genes were carried by different self-conjugative plasmids and able to be transferred to a recipient by conjugation. The colistin resistance of this strain was conferred by mcr-1 and additional chromosomal resistance determinants. Eight amino acid substitutions found in PmrA, PmrB, PmrC, PmrI, and PmrJ, all proteins that are involved in lipopolysaccharide modifications, may be associated with chromosomal colistin resistance. The accumulation of multiple antibiotic resistance mechanisms in this clinical isolate raises alarm on potential spread of extensively drug-resistant K. pneumoniae in healthcare settings. [ABSTRACT FROM AUTHOR]

The co-production of MCR and carbapenemase in Enterobacteriaceae has been previously reported. Here, we describe a clinical strain of Escherichia coli from Vietnam carrying both mcr-1 and bla NDM–1. Whole-genome sequencing showed that the genome of this strain consists of a 4,975,832-bp chromosome and four plasmids. The mcr-1 and bla NDM–1 genes are located on IncI2 and IncA/C2-type plasmids, respectively. Genetic analysis revealed the presence of a multidrug-resistant region with the structure of a novel complex class 1 integron including a class 1 integron region bearing two 5′ conserved segments and one 3′ conserved segment and two complete structures of IS CR1. The complex integron contains aminoglycoside resistance genes aadA2 , aadB , strA , strB , and aphA6 , quinolone resistance gene qnrA1 , extended-spectrum β-lactamase gene bla OXA–4, and a Tn 125 -like transposon bearing bla NDM–1. In addition, the dfrA12 - gcuF - aadA2 - cmlA1 - aadA1-qacH gene cassette array belonging to the sul3 -type integron was also identified, but the region found downstream of the gene cassette array is the IS 440 - tet(M) -IS 26 element instead of the sul3 gene. The results further support that Enterobacteriaceae isolates co-harboring mcr and bla NDM are widely being distributed. The structural characteristics of the complex integron reveal that IS CR1 elements play an important role in the mobilization of bla NDM–1 and the development of multidrug-resistant regions. [ABSTRACT FROM AUTHOR]

The co-production of MCR and carbapenemase in Enterobacteriaceae has been previously reported. Here, we describe a clinical strain of Escherichia coli from Vietnam carrying both mcr-1 and bla NDM-1 . Whole-genome sequencing showed that the genome of this strain consists of a 4,975,832-bp chromosome and four plasmids. The mcr-1 and bla NDM-1 genes are located on IncI2 and IncA/C2-type plasmids, respectively. Genetic analysis revealed the presence of a multidrug-resistant region with the structure of a novel complex class 1 integron including a class 1 integron region bearing two 5' conserved segments and one 3' conserved segment and two complete structures of IS CR1 . The complex integron contains aminoglycoside resistance genes aadA2 , aadB , strA , strB , and aphA6 , quinolone resistance gene qnrA1 , extended-spectrum β-lactamase gene bla OXA- 4 , and a Tn 125 -like transposon bearing bla NDM-1 . In addition, the dfrA12 - gcuF - aadA2 - cmlA1 - aadA1-qacH gene cassette array belonging to the sul3 -type integron was also identified, but the region found downstream of the gene cassette array is the IS 440 - tet(M) -IS 26 element instead of the sul3 gene. The results further support that Enterobacteriaceae isolates co-harboring mcr and bla NDM are widely being distributed. The structural characteristics of the complex integron reveal that IS CR1 elements play an important role in the mobilization of bla NDM-1 and the development of multidrug-resistant regions., (Copyright © 2019 Le-Vo, Tran, Le, Matsumoto, Motooka, Nakamura, Jones, Iida and Cao.)

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 IS Kpn19 and Tn 6901 into the genomic context of bla NDM-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., Competing Interests: Dr Tam-Duong Le-Ha reports grants from the US Armed Forces Research Institute of Medical Sciences (AFRIMS), grants from the National Institute of Health (NIH), and grants from the Research Institute for Microbial Diseases, Osaka University, during the conduct of the study. Ms Lien Le reports grants from the US Armed Forces Research Institute of Medical Sciences (AFRIMS), grants from the National Institute of Health (NIH), and grants from the Research Institute for Microbial Diseases, Osaka University, during the conduct of the study. Miss Hong-Ngoc Le-Vo reports grants from US Armed Forces Research Institute of Medical Sciences, grants from National Institute of Health, and grants from Grant for Joint Research Project of the Research Institute for Microbial Diseases, Osaka University, during the conduct of the study. Dr Mizue Anda has nothing to disclose. Dr Daisuke Motooka has nothing to disclose. Dr Shota Nakamura has nothing to disclose. Dr Linh Khanh Tran reports grants from the US Armed Forces Research Institute of Medical Sciences (AFRIMS), grants from the National Institute of Health (NIH), and grants from the Grant for Joint Research Project of the Research Institute for Microbial Diseases, Osaka University, during the conduct of the study. Dr Phuong Thi-Bich Tran reports grants from The US Armed Forces Research Institute of Medical Sciences (AFRIMS), grants from The National Institute of Health (NIH), and grants from The Research Institute for Microbial Diseases, Osaka University, during the conduct of the study. Dr Tetsuya Iida has nothing to disclose. Dr Van Cao reports grants from the US Armed Forces Research Institute of Medical Sciences (AFRIMS), grants from the National Institute of Health (NIH), and grants from the Research Institute for Microbial Diseases, Osaka University, during the conduct of the study.