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 blaNDM–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 blaNDM–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 ISCR1. The complex integron contains aminoglycoside resistance genes aadA2, aadB, strA, strB, and aphA6, quinolone resistance gene qnrA1, extended-spectrum β-lactamase gene blaOXA–4, and a Tn125-like transposon bearing blaNDM–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 IS440-tet(M)-IS26 element instead of the sul3 gene. The results further support that Enterobacteriaceae isolates co-harboring mcr and blaNDM are widely being distributed. The structural characteristics of the complex integron reveal that ISCR1 elements play an important role in the mobilization of blaNDM–1 and the development of multidrug-resistant regions.

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.

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.

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Klebsiella pneumoniae is an important opportunistic pathogen that causes urinary tract infections, intraabdominal infections and pneumonia in immunocompromised individuals. The prevalence of multiple antibiotic resistant isolates has been increasing worldwide. Fifty one clinical strains obtained from tracheal aspirates, urine, blood, and swabs of patients from various public hospitals in Malaysia were analyzed by antimicrobial susceptibility test and DNA fingerprinting techniques. PCR detection of several resistance genes was also carried out. Using disk diffusion, the rates of resistance among the isolates were as follows: ampicillin 96%, piperacillin 61%, aztreonam 45%, ceftazidime 41%, cefriaxone 35%, gentamicin 27%, tetracycline 16%, amoxicillin, clavulanate and ciprofloxacin, 10% each, and cefepime 8%. Among them, 31 isolates were multi-drug resistant (MDR; resistant to 2 or more classes of antimicrobial agents). Most MDR isolates were resistant to cefriaxone and aztreonam compared to non-MDR isolates. Using PCR, bla SHV , bla CTX-M , bla TEM and bla OXA genes encoding for extended spectrumˇ-lactamases (ESBL) were detected in 46, 19, 4 and 5 isolates, respectively. 41% of the strains produced 2 or more ESBLs. Pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) were used to subtype these microorganisms to determine their genetic diversity. The clinical K. pneumoniae strains obtained from sporadic cases of infections were very diverse as determined by 2 DNA fingerprinting techniques. PFGE and RAPD-PCR generated 47 PFGE profiles (F = 0.53-1.0) and 49 PCR patterns (F = 0.30-1.0). Only two of the K. pneumoniae strains were indistinguishable by DNA fingerprinting. There were no correlation between the occurence of MDR and their DNA fingerprints. Imipenem seems to be the most active agent against Klebsiellae. In conclusion, 61% of the K. pneumoniae were MDR and the DNA fingerprinting indicated that the strains were very heterogeneous.