Characteristics of a Colistin-Resistant Escherichia coli ST695 Harboring the Chromosomally-Encoded mcr-1 Gene

Abstract

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 tested. 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 the carbapenem resistance blaNDM-1, and most of these genes were located on plasmids. However, the 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 inserted in high AT-rich regions. Finally, we found the blaNDM-1 was carried on an IncFII type conjugative plasmid. The conjugation frequency of this plasmid was 7.61 ± 2.11 × 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 of public health.

Plasmid Dynamics of mcr-1-Positive Salmonella spp. in a General Hospital in China

“…Our bioinformatic analysis showed that the mcr-1 gene on the chromosome in strain S530 was flanked by IS Apl1 . Our finding corroborates the hypothesis that the insertion of the mcr-1 gene into the bacterial chromosome is mediated by IS Apl1 ( Peng et al, 2019 ). However, in our case, the chromosomal mcr-1 gene was found to be of plasmid origin.…”

“…The genetic arrangement of chromosome-borne mcr-1 in S530 was investigated. The chromosomal mcr-1 was adjacent to IS Apl1 and the pap2 gene, and they consisted of a “IS Apl1 - mcr-1 - pap2 ” structure, which is commonly presented in chromosome-borne mcr-1 harbored strains ( Peng et al, 2019 ). However, to our surprise, the IncN/IncQ1 replicon and repA gene were identified as a sequence surrounding the mcr-1 gene, indicating a plasmid origin.…”

“…Interestingly, we found one chromosome-encoded mcr-1 in strain S530, which was, however, disrupted by IS Vsa5 . So far, a chromosome-embedded mcr-1 in Enterobacteriaceae has been rarely reported ( Falgenhauer et al, 2016 ; Peng et al, 2019 ). Our bioinformatic analysis showed that the mcr-1 gene on the chromosome in strain S530 was flanked by IS Apl1 .…”

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“…Our bioinformatic analysis showed that the mcr-1 gene on the chromosome in strain S530 was flanked by ISApl1. Our finding corroborates the hypothesis that the insertion of the mcr-1 gene into the bacterial chromosome is mediated by ISApl1 (Peng et al, 2019). However, in our case, the chromosomal mcr-1 gene was found to be of plasmid origin.…”

“…Interestingly, we found one chromosome-encoded mcr-1 in strain S530, which was, however, disrupted by ISVsa5. So far, a chromosome-embedded mcr-1 in Enterobacteriaceae has been rarely reported (Falgenhauer et al, 2016;Peng et al, 2019). Our bioinformatic analysis showed that the mcr-1 gene on the chromosome in strain S530 was flanked by ISApl1.…”