Characteristics of a colistin-resistant Escherichia coli ST695 harboring the chromosomally-encoded mcr-1 gene

Enterobacteriaceae having chromosomally-encoded mcr-1 is rarely reported.

In this study, we recovered a chromosomal mcr-1 carrying Escherichia coli, designated HeN100, from the feces of a diarrheal pig in China. Antimicrobial susceptibility testing showed that HeN100 was resistant to three aminoglycosides, twelve β-lactams including three carbapenems, one phenicol, two tetracyclines, two fluoroquinolones, nitrofurantoin, and colistin.

Oxford Nanopore MinION sequencing revealed that the complete genomes of the multidrug resistant (MDR) HeN100 consisted of a single circular chromosome and five circular plasmids. Bioinformatical analysis determined HeN100 as ST695 and it contained many acquired resistance genes responsible for its MDR phenotypes, including colistin resistance mcr-1 and carbapenem resistance blaNDM-1 genes, and most of these genes were located on plasmids. However, mcr-1 was found on the chromosome, and it was located between an IS30-like element ISApl1 and a PAP2-like encoding gene. These three genes consisted of an “ISApl1-mcr-1-orf” segment and were inserted in high AT-rich regions.

Finally, we found that blaNDM-1 was carried on an IncFII type conjugative plasmid. The conjugation frequency of this plasmid was 7.61 ±2.11 x 10−5 per recipient, and its conjugation conferred resistance to carbapenems and other β-lactams, as well as aminoglycosides.

The spread of this mcr-1/blaNDM-1-carrying E. coli ST695 represents a great concern to public health.

Authors: Zhong Peng, Zizhe Hu, Zugang Li, Xiaosong Li, Chaoying Jia, Xiaoxue Zhang, Bin Wu, Huanchun Chen, Xiangru Wang