Draft Genome Sequence of Escherichia coli S51, a Chicken Isolate Harboring a Chromosomally Encoded mcr-1 Gene

Abstract

We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum β-lactamase-producing strain isolated in 2015 from raw chicken meat imported from Germany. Assembly and annotation of this draft genome resulted in a 4,994,918-bp chromosome and revealed a chromosomally encoded mcr-1 gene responsible for the colistin resistance of the strain.

GENOME ANNOUNCEMENT

The recent description of the plasmid-mediated colistin resistance gene, mcr-1, in strains isolated from food animals, food, and humans in China was a signal for an avalanche of retrospective studies investigating the presence of this specific gene (1). The mcr-1 gene has been identified almost all over the world now, and the earliest evidence for its presence dates back to the 1980s (2). The wide spread of mcr-1 and the finding that this resistance marker is often associated with multidrug resistant Enterobacteriaceae, e.g., extended-spectrum β-lactamase (ESBL)-producers or carbapenemase-producers, is of great concern (3). The mcr-1 gene was so far associated with different plasmid replicon types such as IncI2, IncHI2, IncP, IncFIP, and IncX4 (1, 4–8).

In a recent study, we isolated an ESBL-producing E. coli (new MLST sequence type: allelic profile: 6-4-5-16-24-1-14) harboring the mcr-1 gene from raw chicken meat imported from Germany (9). Despite repeated attempts, the mcr-1 gene from this isolate could not be transferred by conjugation. Plasmid DNA from S51 was extracted and used in electroporation experiments. Again the transfer of the colistin resistance determinant was also not successful. Further hybridization experiments probing with an mcr-1 fragment indicated the possible chromosomal integration of the mcr-1 gene (data not shown). Therefore, genomic DNA was isolated from S51 and subjected to sequencing using Pacific Biosciences SMRT technology at the ChunLab at Seoul National University. The S51 genome was assembled de novo using the SMRT Analysis 2.3.0 software to a single chromosome of 4,994,918 bp in size with a G+C content of 50.7% and two unclosed plasmid sequences of approx. 93 kb and approx. 98 kb in size, respectively. Gene prediction was carried out using Glimmer 3.0.2 (10). Annotation was conducted based on homology searches against COG, SEED, and KEGG databases (11–13) and using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/).

The mcr-1 gene in S51 is located at the right-hand extremity of an ISApl1 element, together with an 813-bp orf encoding a hypothetical protein with similarities to a PAP2 superfamily protein. This combination of the ISApl1 and the mcr-1 cassette has been often described on mcr-1-harboring plasmids of diverse replicon types (14). The “ISAspl1-mcr-1-cassette” was found to be located in the S51 chromosome between the gene encoding for the outer membrane protein E and for a glutamate-5-kinase, respectively. This ISAspl1-mcr-1-cassette association on a chromosome further supports the hypothesis that ISAspl1 might be involved in mcr-1 acquisition.

Accession number(s).

Sequence and annotation data of the draft genome of E. coli strain S51 and two plasmids were deposited in the GenBank database with the accession numbers CP015995, CP015996, and CP015997.