Genetic Features of Plasmid- and Chromosome-Mediated mcr-1 in Escherichia coli Isolates From Animal Organs With Lesions

Abstract

The genomic context of the <i>mcr-1</i> gene in <i>Escherichia coli</i> from animal feces has been widely reported. However, less is known about the <i>mcr-1</i>-carrying plasmid characteristics and other functional regions of <i>Escherichia coli</i> isolates from animal organs with lesions. The present study investigated the antimicrobial resistance, population structure, and genetic features of <i>mcr-1</i>-positive <i>Escherichia coli</i> strains isolated from animal organs with lesions. The antimicrobial susceptibility testing indicated that 24 <i>mcr-1</i>-positive <i>Escherichia coli</i> isolates were resistant to at least three or all antimicrobial categories. MLST analysis suggested that the dominant clone complexes (CC) were mainly CC156, CC448, and CC10. In addition, ST10596, a newly discovered sequence type in swine, failed to be classified. Meanwhile, the <i>mcr-1</i> gene located on the different plasmids was successfully transferred to the recipients, and whole-genome sequencing indicated the <i>mcr-1</i> gene was embedded in <i>mcr-1-pap2</i> cassette but not flanked by IS<i>Apl1</i>. The <i>mcr-1</i> gene is located on the chromosome and embedded in Tn<i>6330</i>. Furthermore, <i>NDM-5</i> was found on the IncX3-type plasmid of J-8. The <i>virB6</i> and <i>traI</i> gene of type IV secretion system (T4SS) were truncated by IS<i>2</i> and IS<i>100</i> and located on the IncX4- and the IncHI2/HI2A/N-type plasmids, respectively. The multidrug-resistant (MDR) region of IncHI2/HI2A/N-type plasmids contained two class 1 integrons (In<i>0</i>, In<i>640</i>) and four composite transposons (Tn<i>4352</i>, Tn<i>6010</i>, cn_4692_IS<i>26</i>, cn_6354_IS<i>26</i>). Overall, 24 <i>mcr-1</i>-positive <i>Escherichia coli</i> isolates in our study showed MDR, or even extensively drug resistant (XDR), and exhibited population diversity. The T4SS gene truncation by the insertion sequence may affect the efficiency of plasmid conjugative transfer. Furthermore, the class 1 integrons and composite transposons in the MDR region of IncHI2/HI2A/n-type plasmid contributed to the multireplicon plasmid formation, the acquisition, and transfer of antimicrobial resistance genes (ARGs).