Draft Genome Sequence of NDM-5-Producing Escherichia coli Sequence Type 648 and Genetic Context of blaNDM-5 in Australia.

We report here the draft genome sequence of uropathogenic Escherichia coli sequence type 648 (ST648) possessing blaNDM-5 from a 55-year-old female in Australia with a history of travel to India. The plasmid-mediated blaNDM-5 was in a genetic context nearly identical to that of the GenBank entry of an IncX3 blaNDM-5 plasmid previously reported from India (Klebsiella pneumoniae MGR-K194).

GENOME ANNOUNCEMENT

The Indian subcontinent has been reported as a geographical reservoir for the acquisition of NDM-producing Enterobacteriaceae (1). A 55-year-old female with chronic diarrhea had carbapenem-resistant Escherichia coli isolated from a urine sample in January 2014. She traveled to India in late 2013 and developed diarrhea but was not admitted to a medical facility. Upon her return to Australia, ongoing diarrhea prompted multiple hospital admissions. She was diagnosed with Crohn’s disease. During admission, a midstream urine sample was collected, from which the carbapenem-resistant E. coli CR694 was identified.

Whole-genomic DNA of E. coli CR694 was prepared using the Nextera XT DNA sample preparation kit (Illumina, USA) and sequenced using the Illumina HiSeq 2000 (Illumina) at the Australian Genome Research Facility. De novo assembly was performed using CLC Genomics Workbench version 7.5 (CLC bio, Denmark). The draft genome consists of 5,523,407 bp. The contigs were initially annotated using RAST (http://rast.nmpdr.org/). A BLAST analysis and manual annotation utilized previously reannotated reference sequences and IS Finder (https://www-is.biotoul.fr/). The MLST, ResFinder, and PlasmidFinder (http://www.genomicepidemiology.org/) databases were used to characterize sequence typing (ST), antibiotic resistance mechanisms, and the plasmid Inc types, respectively, of E. coli CR694. ST648, plasmid Inc types of IncFII, IncFIB, IncX3, IncI1, and IncX4, and the genes blaNDM-5, blaCMY-42, aac-6-Ib-cr, aadA5, erm(B), mph(A), sul1, tet(B), and dfrA17 were identified.

Additionally, the annotation through RAST identified the type 1 fimbriae genes fimABCDEFGHI, virulence determinants relevant for urinary tract adhesion (2). Further, five other types of fimbriae were identified as a membrane transport type VII protein secretion system, namely the (i) htrE fimbriae cluster, (ii) stf fimbriae cluster, (iii) alpha-fimbriae, (iv) colonization factor antigen I fimbriae (CFA/I fimbriae), and (v) sfm fimbrial cluster. A cluster responsible for curli production or type VIII secretion was identified. Siderophore enterobactin, aerobactin, and other hemin transport systems for iron acquisition were identified. In addition, type IV pilus and an IncF conjugal transfer system were identified. A gene for serum survival (iss) was also identified. The identified virulence determinants may have contributed to the infection and or colonization of CR694 in the urinary tract (2).

The contig pCR694-EC-NDM-5 carried the blaNDM-5 genetic context. blaNDM has been reported to reside within a 10,099-bp transposon known as Tn125 (3). blaNDM-5 on pCR694-EC-NDM-5 was found to be located within a truncated 3,167 bp Tn125 structure, flanked by an IS5 upstream and an IS26 downstream. pCR694-EC-NDM-5 was identical to an NDM-5 IncX3 plasmid, pNDM-MGR194 (as a direct submission, with GenBank accession no. KF220657) (4). Both blaNDM-5 genetic contexts did not possess the Tn125-associated genes groES, groEL, and ISCR27. Both pCR694-EC-NDM-5 and pNDM-MGR194 are also highly similar to NDM-1 IncX plasmid pKPN5047 (GenBank accession no. NC_020811), containing a longer Tn125 structure in which groES, groEL, and ISCR27 are present.

The blaNDM-5 genetic context of pCR694-EC-NDM-5 has not been reported within E. coli or within Australia. NDM-5-producing Enterobacteriaceae have been reported in Japan, Algeria, the United Kingdom, and India, of which an E. coli ST648 harbored blaNDM-5 in both the aforementioned United Kingdom and Japan reports (5–8). This case of an NDM-5-producing typical uropathogenic E. coli isolate highlights the further intercontinental acquisition of carbapenemase-producing Enterobacteriaceae through travel to geographical reservoirs.

This work was approved by the Royal Brisbane and Women's Human Research Ethics Committee (HREC/13/QRBW/391>: Epidemiology, clinical significance, treatment and outcome of infections by carbapenem-resistant Enterobacteriaceae and Acinetobacter spp. in Queensland).

Nucleotide sequence accession numbers.

This project is registered as BioProject PRJNA268254 and BioSample SAMN03217331. The blaNDM-5 genetic context pCR694-EC-NDM-5 was submitted to the GenBank database and assigned the accession no. KP178355. The draft genome sequence of NDM-5-producing E. coli ST648 has been deposited in GenBank under accession no. JTGI00000000.