Genomic Characterization of Two Escherichia fergusonii Isolates Harboring mcr-1 Gene From Farm Environment

Abstract

The prevalence and transmission of mobile colistin resistance (<i>mcr</i>) genes have led to a severe threat to humans and animals. <i>Escherichia fergusonii</i> is an emerging pathogen which is closely related to a variety of diseases. However, the report of <i>mcr</i> genes harboring <i>E. fergusonii</i> is still rare. One study in Brazil reported the <i>E. fergusonii</i> isolates with IncHI2-type plasmids harboring <i>mcr-1</i>. A Chinese study reported two strains carrying <i>mcr-1</i> gene with the same plasmid type IncI2. Here, we identified two strains of <i>E. fergusonii</i> carrying <i>mcr-1</i> gene from farm environments with IncX4-type and IncI2-type plasmids, respectively. To our best knowledge, this is the first report about <i>mcr-1</i> gene located on IncX4-type plasmid in <i>E. fergusonii</i>. We investigate the resistance mechanism of colistin-resistant <i>Escherichia fergusonii</i> strains 6S41-1 and 5ZF15-2-1 and elucidate the genetic context of plasmids carrying <i>mcr-1</i> genes. In addition, we also investigated chromosomal mutations mediated colistin resistance in these two strains. Species identification was performed using MALDI-TOF MS and 16S rRNA gene sequencing. The detection of <i>mcr-1</i> gene was determined by PCR and Sanger sequencing. S1-pulsed-field gel electrophoresis (PFGE), Southern blotting, antimicrobial susceptibility testing, conjugation experiments, complete genome sequencing, and core genome analysis were conducted to investigate the characteristics of isolates harboring <i>mcr-1</i>. The <i>mcr-1</i> genes on two strains were both plasmids encoded and the typical IS<i>26</i>-<i>parA</i>-<i>mcr-1</i>-<i>pap2</i> cassette was identified in p6S41-1 while a <i>nikA</i>-<i>nikB</i>-<i>mcr-1</i> locus sites on the conjugative plasmid p5ZF15-2-1. In addition, Core genome analysis reveals that <i>E. fergusonii</i> 6S41-1 and 5ZF15-2-1 have close genetic relationships. The <i>mcr-1</i> gene is located on conjugative IncI2-type plasmid p5ZF15-2-1, which provides support for its further transmission. In addition, there's the possibility of <i>mcr-1</i> spreading to humans through farm environments and thereby threatening public health. Therefore, continuous monitoring and investigations of <i>mcr-1</i> among <i>Enterobacteriaceae</i> in farm environments are necessary to control the spread.