Draft Genome Sequence of a High-Level Colistin-Resistant Clinical Strain of the Enterobacter cloacae Complex

ABSTRACT

Strain WCHECl-C4 of the Enterobacter cloacae complex, recovered from the blood of a patient with peritonitis, was high-level resistant to colistin. Here, we report its 5.1-Mb draft genome sequence, comprising 92 contigs with an average 55.74% G+C content. The genome contained 4,783 coding sequences and 68 tRNA genes.

GENOME ANNOUNCEMENT

The Enterobacter cloacae complex comprises bacterial species such as E. asburiae, E. cancerogenus, and E. cloacae, which are common pathogens of human infections (1). Strain WCHECl-C4 was recovered from the blood of a 52-year-old female patient with peritonitis at West China Hospital, Chengdu, China, in February 2015. Strain WCHECl-C4 was identified as E. cloacae by Vitek II (bioMérieux, Lyon, France) and is highly resistant to colistin (MIC, >128 μg/mL) but is susceptible to imipenem (MIC, 0.125 μg/mL), as determined using the microdilution broth method (2). Strain WCHECl-C4 did not have the plasmid-borne colistin resistance genes mcr-1 and mcr-2, which were screened by PCR (3, 4).

Whole-genome sequencing of strain WCHECl-C4 was performed using the HiSeq 2500 Sequencer (Illumina, San Diego, CA, USA) with the 150-bp paired-end protocol and 200× coverage, which generated 1.28 Gb of clean bases and 4,265,547 reads. Using SPAdes (5), 92 contigs (69 contigs ≥ 1,000 bp in length; N₅₀, 157,468 bp) with a 55.74% G+C content were assembled. Prokka (6) was used to annotate the genome, which was about 5.1 Mb and had 4,783 coding sequences and 68 tRNA genes. Strain WCHECl-C4 belonged to ST414 (dnaA, fusA, gyrB, leuS, pyrG, rplB, and rpoB; 136-99-153-160-140-12-92), which was determined using the multilocus sequence typing tool of the Center for Genomic Epidemiology (http://genomicepidemiology.org).

Antimicrobial resistance genes were predicted using ResFinder from the Center for Genomic Epidemiology, and only three antimicrobial resistance genes, bla_ACT (encoding an AmpC β-lactamase conferring resistance to cephalosporins), qnrS1 (conferring low-level resistance to quinolones), and fosA (conferring fosfomycin resistance) were identified in strain WCHECl-C4. The bla_ACT gene of strain WCHECl-C4 is chromosomally located and encodes an ACT enzyme that has not been assigned a number yet. The mechanism of colistin resistance in strain WCHECl-C4 remains unclear and warrants further investigation. PlasmidFinder from the Center for Genomic Epidemiology predicted that strain WCHECl-C4 had no plasmid replicons known to the Enterobacteriaceae.

To further determine the species of WCHECl-C4, the JSpecies web program (http://imedea.uib-csic.es/jspecies) with default settings (7) was used to determine the pairwise average nucleotide identities (ANIs) between strain WCHECl-C4 and the type or reference (if the genome of type strain was not available) strain of each species of the E. cloacae complex. The type or reference strains used were E. asburiae JCM 6051^T (GenBank accession no. BBED00000000), E. mori LMG 25706^T, (AEXB00000000), E. cloacae subsp. cloacae ATCC 13047, (CP0019180), E. ludwigii EN-119^T (CP017279), E. hormaechei ATCC 49162 (AFHR00000000), E. xiangfangensis LMG27195^T (CP017183), E. cancerogenus ATCC 35316 (ABWM00000000), and E. soli ATCC BAA-2102^T (LXES00000000). The genome of strain WCHECl-C4 shared only 82.25% to 92.56% ANIs with the type and reference strains of the E. cloacae complex, which were below the ≥95% ANI cutoff to define a bacterial species (8), suggesting that strain WCHECl-C4 is likely to belong to a new species of the E. cloacae complex.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number MTSO00000000. The version described in this paper is the first version, MTSO01000000.