Draft genome sequence of an NDM-5, CTX-M-15 and OXA-1 co-producing Escherichia coli ST167 clinical strain isolated from a urine sample.

Escherichia coli is the leading cause of urinary tract infections worldwide. Carbapenemase-producing clinical isolates leave few therapeutic options. Here we report the draft genome sequence of an NDM-5, CTX-M-15, and OXA-1 co-producing E. coli sequence type 167 (ST167) multidrug-resistant clinical strain (ECWJ1) isolated from a urine sample of a hospitalised male patient diagnosed with intracranial injury from a road traffic accident. The genome of E. coli ECWJ1 was sequenced using an Illumina HiSeq™ 4000 platform. The generated sequence reads were assembled using CLC Genomics Workbench. The draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server, and further bioinformatics analysis was performed. Escherichia coli ECWJ1 belongs to ST167. The total genome length of the isolate is 4992753bp, with 4890 protein-coding sequences. The presence of blaNDM-5, blaCTX-M-15 and blaOXA-1 genes was detected in addition to other antimicrobial resistance genes conferring resistance to aminoglycosides, fluoroquinolones, sulphonamides, trimethoprim and tetracyclines. Antimicrobial susceptibility testing revealed, that besides tigecycline and colistin, this isolate is resistant to all antimicrobials tested. To our knowledge, this is the first report of an E. coli ST167 strain co-producing NDM-5, CTX-M-15 and OXA-1 isolated from urine sample in China. It may help us to understand the genomic features, molecular characteristics and resistance gene diversity of this bacterial pathogen. The genome sequence of E. coli ECWJ1 can be used as a reference sequence for comparative analysis of NDM-5-producing E. coli, aiming to reveal the mechanism of NDM-5 dissemination in this pathogen.

Sun L ，Xu J ，He F 《-》

Whole-genome analysis of EC129, an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli ST167 strain isolated from Japan.

The emergence and spread of carbapenemase-producing Enterobacteriaceae is a worldwide concern. This study reports the whole genome sequence of an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli sequence type 167 (ST167) multidrug-resistant clinical strain (EC129) isolated from a sputum sample of a hospitalised patient diagnosed with pneumonia. The genome of E. coli EC129 was subjected to next-generation sequencing and reads were assembled. The draft genome was annotated using DDBJ Read Annotation Pipeline DFAST server, followed by subsequent in silico analysis. The genome of E. coli ST167 strain EC129 is 5319159 bp in length and contains 5022 protein-coding sequences. The blaNDM-5, blaCTX-M-14, blaOXA-10 and mcr-1 genes were detected along with other antimicrobial resistance genes conferring resistance to aminoglycosides, fluoroquinolones, sulfonamides, trimethoprim and tetracyclines. Antimicrobial susceptibility testing revealed that the isolate was resistant to all antimicrobial agents except colistin. To our knowledge, this study is the first to report anE. coli ST167 strain co-producing NDM-5, CTX-M-14, OXA-10 and MCR-1 isolated from a sputum sample of an individual with pneumonia in Japan, thus elucidating the molecular characteristics and resistance gene diversity of this strain.

Nukui Y ，Ayibieke A ，Taniguchi M ，Aiso Y ，Shibuya Y ，Sonobe K ，Nakajima J ，Kanehira S ，Hadano Y ，Tohda S ，Koike R ，Saito R ... -  《-》

Whole genome sequence of an Escherichia coli ST410 isolate co-harbouring bla(NDM-5), bla(OXA-1), bla(CTX-M-15), bla(CMY-2), aac(3)-IIa and aac(6')-Ib-cr genes isolated from a patient with bloodstream infection in China.

Mortality associated with carbapenemase-producing Enterobacteriaceae is high as there are few therapeutic options. Escherichia coli sequence type 410 (ST410) is currently an international high-risk clone and is responsible for a large number of clinical infections. Here we report the draft genome sequence of a ST410 clinical E. coli isolate (ECS9) co-harbouring blaNDM-5, blaOXA-1, blaCTX-M-15, blaCMY-2, aac(3)-IIa and aac(6')-Ib-cr genes, obtained from a patient with bloodstream infection in China. The genome of E. coli ECS9 was sequenced using an Illumina HiSeqTM 4000 instrument with a 150-bp paired-end approach. Generated sequence reads were assembled using Velvet 1.2.10. Contigs were annotated using Rapid Annotation using Subsystem Technology (RAST), and further whole-genome sequence data analyses were performed. Escherichia coli ECS9 belongs to multilocus sequence typing (MLST) ST410. The total number of assembled bases was 4 935 145 bp, with 5077 protein-coding sequences. The presence of the blaNDM-5, blaOXA-1, blaCTX-M-15 and blaCMY-2 genes was detected in addition to other antimicrobial resistance genes conferring resistance to fluoroquinolones, aminoglycosides, trimethoprim, sulfonamides and tetracyclines. To our knowledge, this is the first report of anE. coli ST410 strain co-harbouring blaNDM-5, blaOXA-1, blaCTX-M-15, blaCMY-2, aac(3)-IIa and aac(6')-Ib-cr, obtained from a bloodstream infection in China. The presented genome sequence of carbapenemase-producing E. coli strain ST410 could provide further insight into the acquisition of multiple resistance genes by this successful lineage.

Huang J ，Ma S ，Yu Q ，Fu M ，Shao L ，Shan X ，Li X ... -  《-》

Genomic analysis of two bacterial strains co-isolated from a urinary tract infection: NDM-1-producing Enterobacter cloacae accompanied by extended-spectrum β-lactamase-producing Escherichia coli.

Escherichia coli and Enterobacter cloacae are two major pathogens causing urinary tract infection (UTI). Here we characterised the genome of an NDM-1-producing E. cloacae strain and an extended-spectrum β-lactamase (ESBL)-producing E. coli strain that were co-isolated from a UTI. The genomes of E. cloacae strain EC32 and E. coli strain EC33 were sequenced using an Illumina HiSeqTM platform. The whole genome sequences were assembled using CLC Genomics Workbench and were annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server. Genomic analysis was further performed. The draft genome sequences of E. cloacae EC32 (ST66) and E. coli EC33 (ST1139) consisted of 89 contigs comprising 5 178 393 bp and 62 contigs comprising 5 057 666 bp, respectively. Including the blaNDM-1 gene, in total 13 resistance genes were identified in E. cloacae EC32 conferring resistance to β-lactams, rifampicin, phenicols, fosfomycin, macrolides, quinolones, sulfonamides and tetracycline. Nine resistance genes were identified in E. coli EC33 including the ESBL-encoding gene blaCTX-M-27. To our knowledge, this is the first report of genomic characterisation of NDM-1-producing E. cloacae and ESBL-producing E. coli co-isolated from a UTI in China. The two strains inhabiting in the same environment may allow the possibility of horizontal transfer of blaNDM-1 and blaCTX-M-27, making clinical treatment even difficult. This report also sheds light on geographically distinct Enterobacteriaceae strains from China enabling a comparative analysis of NDM-1- or ESBL-producing strains.

Xu J ，He F 《-》

Draft genome sequence of Escherichia coli ST977: A clinical multidrug-resistant strain harbouring bla(NDM-3) isolated from a bloodstream infection.

The emergence of carbapenem-resistant Escherichia coli has become a serious challenge to manage in the clinic because of multidrug resistance. Here we report the draft genome sequence of NDM-3-producing E. coli strain NT1 isolated from a bloodstream infection in China. Whole genomic DNA of E. coli strain NT1 was extracted and was sequenced using an Illumina HiSeq™ X Ten platform. The generated sequence reads were assembled using CLC Genomics Workbench. The draft genome was annotated using Rapid Annotation using Subsystem Technology (RAST). Bioinformatics analysis was further performed. The genome size was calculated at 5,353 620bp, with 5297 protein-coding sequences and the presence of genes conferring resistance to aminoglycosides, β-lactams, quinolones, macrolides, phenicols, sulphonamides, tetracycline and trimethoprim. In addition, genes encoding virulence factors were also identified. To our knowledge, this is the first report of an E. coli strain producing NDM-3 isolated from a human bloodstream infection. The genome sequence will provide valuable information to understand antibiotic resistance mechanisms and pathogenic mechanisms in this strain. Close surveillance is urgently needed to monitor the spread of NDM-3-producing isolates.

Li X ，Sun L ，Zhu Y ，Shen M ，Tu Y ... -  《-》