Complex Class 1 Integron in a Clinical Escherichia coli Strain From Vietnam Carrying Both mcr-1 and blaNDM–1

Abstract

The co-production of MCR and carbapenemase in <i>Enterobacteriaceae</i> has been previously reported. Here, we describe a clinical strain of <i>Escherichia coli</i> from Vietnam carrying both <i>mcr-1</i> and <i>bla</i> _NDM-1. Whole-genome sequencing showed that the genome of this strain consists of a 4,975,832-bp chromosome and four plasmids. The <i>mcr-1</i> and <i>bla</i> _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<i>CR1</i>. The complex integron contains aminoglycoside resistance genes <i>aadA2</i>, <i>aadB</i>, <i>strA</i>, <i>strB</i>, and <i>aphA6</i>, quinolone resistance gene <i>qnrA1</i>, extended-spectrum β-lactamase gene <i>bla</i> _OXA- ₄, and a Tn<i>125</i>-like transposon bearing <i>bla</i> _NDM-1. In addition, the <i>dfrA12</i>-<i>gcuF</i>-<i>aadA2</i>-<i>cmlA1</i>-<i>aadA1-qacH</i> gene cassette array belonging to the <i>sul3</i>-type integron was also identified, but the region found downstream of the gene cassette array is the IS<i>440</i>-<i>tet(M)</i>-IS<i>26</i> element instead of the <i>sul3</i> gene. The results further support that <i>Enterobacteriaceae</i> isolates co-harboring <i>mcr</i> and <i>bla</i> _NDM are widely being distributed. The structural characteristics of the complex integron reveal that IS<i>CR1</i> elements play an important role in the mobilization of <i>bla</i> _NDM-1 and the development of multidrug-resistant regions.