Whole genome sequence of EC16, a blaNDM-5-, blaCTX-M-55-, and fosA3-coproducing Escherichia coli ST167 clinical isolate from China

Abstract

ABSTRACT: Objectives: Escherichia coli sequence type 167 (ST167) is an international multiresistant high-risk clone associated with New Delhi metallo-beta-lactamase (NDM) carbapenemase. Here, we report the whole genome sequence of an ST167 clinical isolate (EC16), obtained from a patient with abdominal infection in China, coharbouring the blaNDM-5, blaCTX-M-55, fosA3, aac(3)-IV, and qnrS1 genes. Methods: E. coli strain EC16 was subjected to antimicrobial susceptibility testing by the broth microdilution method. Whole-genome sequencing of E. coli EC16 was performed using both Oxford Nanopore PromethION and Illumina NovaSeq 6000 platforms. De novo hybrid assembly of short Illumina reads and long PromethION reads was performed using Unicycler. Genome annotation was performed using Prokka 1.14.6, and further whole-genome sequence data analyses were performed. Easyfig 2.2.3 was used to analyse the genetic surroundings of blaNDM-5 and the homologous regions of the blaNDM-5-carrying plasmid pEC16-NDM-5 in E. coli EC16. Results: The complete genome sequence of E. coli EC16 consists of six contigs comprising 5 317 797 bp, including one chromosome and five plasmids. Whole-genome sequencing and further bioinformatics analysis revealed that E. coli EC16 belonged to serotype O101:H9, fumC11 type, and ST167.blaNDM-5 was carried by a novel 145,550-bp IncFII-type plasmid pEC16-NDM-5 within a Tn2-IS26-ISAba125- blaNDM-5- bleMBL-trpF-dsbD-IS91 cassette. Conclusion: In this study, we report a clinical E. coli ST167 strain carrying a novel IncFII-type blaNDM-5 plasmid obtained from abdominal infection in China. The presented genome sequences of the blaNDM-5-producing E. coli strain ST167 could provide further insight into the acquisition of multiple resistance genes by this successful lineage.

Keywords

• Whole genome sequence
• Escherichia coli ST167
• NDM-5
• fosA3
• High-risk clones
• IncFII plasmid