Draft genome sequence data of a tigecycline-resistant Enterobacter cloacae ST93 clinical strain isolated from bloodstream infection

Here we report data on the draft genome sequence of a tigecycline-resistant Enterobacter cloacae ST93 clinical isolate TREC1 producing KPC-2 carbapenemase from China. The draft genome sequence of E. cloacae TREC1 consisted of 74 contigs that comprised 5,322,835 bp, and the overall GC content of this strain amounted to 54.63%. In total, 57 tRNA genes, 5 rRNA operons and 5108 protein-coding sequences were identified in the genome. TREC1 belongs to sequence type ST93. Nineteen antimicrobial resistance genes were confirmed. Antimicrobial susceptibility testing revealed that besides colistin this isolate is resistant to all antibiotics including tigecycline. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number PJZE00000000. (http://www.ncbi.nlm.nih.gov/nuccore/PJZE00000000).


a b s t r a c t
Here we report data on the draft genome sequence of a tigecycline-resistant Enterobacter cloacae ST93 clinical isolate TREC1 producing KPC-2 carbapenemase from China. The draft genome sequence of E. cloacae TREC1 consisted of 74 contigs that comprised 5,322,835 bp, and the overall GC content of this strain amounted to 54.63%. In total, 57 tRNA genes, 5 rRNA operons and 5108 protein-coding sequences were identified in the genome. TREC1 belongs to sequence type ST93. Nineteen antimicrobial resistance genes were confirmed. Antimicrobial susceptibility testing revealed that besides colistin this isolate is resistant to all antibiotics including tigecycline. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number PJZE00000000. (http://www.ncbi.nlm.nih.gov/ nuccore/PJZE00000000

Value of the data
This data may help us to understand the genomic feature and molecular characteristic of this bacterial pathogen.
This data may help us to understand the resistance gene diversity of this bacterial pathogen. The genome sequence of Enterobacter cloacae TREC1 can be used as a reference sequence for comparative analysis of tigecycline-resistant E. cloacae aimed to reveal the mechanism of tigecycline-resistance in CRE.

Data
The draft genome sequence of Enterobacter cloacae TREC1 consisted of 74 contigs that comprised 5,322,835 bp, and the overall GC content of this strain amounted to 54.63%. In total, 57 tRNA genes, 5 rRNA operons and 5108 protein-coding sequences were identified by the RAST server, respectively. According to the MLST scheme of E. cloacae, TREC1 belongs to sequence type ST93. The genome also contains one intact and one incomplete prophage sequences, three CRISPR sequences and several IS elements: the majority belonging to the IS3 and IS5 families. The resistance genes present in the genome of the isolate are presented in Table 1. We identified the aminoglycoside resistance genes armA, aadA5, strA and aph(6)-Id; the beta-lactam resistance genes bla CTX-M-14 , bla ACT-7 , bla KPC-2 , and bla CTX-M-3 ; the fluoroquinolone resistance genes qnrS1 and qnrA1; the fosfomycin resistance gene fosA; the macrolide, Lincosamide and Streptogramin B resistance genes msr(E) and mph(E); the phenicol resistance gene catA2; the sulphonamide resistance genes sul1 and sul2; the trimethoprim resistance genes dfrA1 and dfrA14; and the tetracycline resistance gene tetA. Ceftazidime, cefepime, imipenem, meropenem, piperacillin/tazobactam, cefoperazone/sulbactam, fosfomycin, amikacin, ciprofloxacin, trimethoprim/sulfamethoxazole, minocycline, tigecycline and colistin were used in the susceptibility testing. The isolate was resistant to all antimicrobials above except colistin. The MIC values are presented in Table 2. Isolate E. cloacae TREC1 not only produce KPC-2 carbapenemase, but are also resistant to tigecycline bringing a great challenge to clinical treatment. The relative expression level of efflux pump genes (acrA, acrB, oqxA and oqxB) in the tigecycline-resistant isolate TREC1 were examined by qRT-PCR. Relative expression of each target gene was calibrated against the corresponding expression of a tigecycline-susceptible isolate E. cloacae TSEC (expression ¼ 1), which was served as the control. According to the results (Table 3), the expression level of efflux pump AcrAB was increased 2-3 fold relative to the susceptible isolate. The expression level of efflux pump OqxAB between TREC1 and TSEC was not significant. Tetracycline resistant gene tetA was found in TREC1, but no mutation was detected.

Experimental design, materials and methods
Isolate E. cloacae TREC1 was recovered from a blood sample of a male hospitalised patient in Hangzhou, Zhejiang province, China, in 2017. The isolate was preliminarily identified using the VITEK 2 system (bioMérieux, France) and was further confirmed by 16S rRNA gene sequencing. Antimicrobial susceptibility testing was performed according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). The MICs of tigecycline and colistin were determined using standard broth microdilution tests with fresh (o 12 h) Mueller-Hinton broth (Cation-adjusted, Oxoid LTD, Basingstoke, Hampshire, England). The MICs of other antimicrobial agents were determined using the agar dilution method and Etest method. Whole genome sequencing has increasingly being applied to clinical practice server [1]. The genome of E. cloacae TREC1 was sequenced using the Illumina HiSeq TM 4000 platform (Illumina Inc., San Diego, CA, USA) following the paired-end 2 Â 150 bp protocol. The whole genome sequence was assembled using CLC Genomics Workbench 10.0 software (Qiagen, Valencia, CA) and annotated by the Rapid Annotation System Technology (RAST) server [2]. The pie chart demonstrated the counts for each subsystem feature and the subsystem coverage (Fig. 1). In silico Multilocus sequence typing (MLST) analysis was performed using the PubMLST database. Resistance-related genes were analysed using ResFinder 3.0 [3]. Further bioinformatics analysis, such as identification of insertion elements (IS), prophage sequences and clustered  regularly interspaced short palindromic repeat (CRISPR) sequences were predicted by application of ISfinder, PHASTER and CRISPRFinder, respectively [4][5][6].

Funding
This study was supported by grants from the National Natural Science Foundation of China (81702042) and the Zhejiang Provincial Medical and Health Science and Technology plan (2018KY344).

Transparency document. Supporting information
Transparency data associated with this article can be found in the online version at https://doi.org/ 10.1016/j.dib.2018.10.004.