Genomic and phylogenetic analysis of a community-acquired extended-spectrum β-lactamase-producing Escherichia coli ST429 strain recovered from a urinary tract infection.

Abstract Objectives Escherichia coli is one of the most prevalent bacterial pathogens causing urinary tract infections (UTIs). The increasing dissemination of Extended Spectrum β-Lactamases (ESBLs) producing E.coli strains in the community renders clinical treatment difficult. Here, we report the complete genome sequence of a blaCTX-M-15 carrying E.coli strain isolated from a urine sample of a female outpatient with UTI. Methods The whole genome sequence of the strain was determined using both MinION Sequencer and Illumina NovaSeq 6000. The de novo hybrid assembly of both short Illumina reads and long MinION reads was performed using Unicycler. Multilocus sequence typing (MLST), antimicrobial resistance genes (ARGs), plasmid replicons and phylogenetic relationship were analysed by a bacterial whole genome sequence typing and source tracking database (BacWGSTdb). Results The genome sequence of E. coli strain EC28 consists of six contigs that comprised 5,260,133 bp, including one chromosome and five plasmids. According to the MLST analysis, EC28 belongs to ST429. Six ARGs were identified, including blaCTX-M-15 that located in an IncI2-type plasmid with 63,295 bp. Twenty-three phylogenetically related E.coli ST429 strains were identified in the NCBI GenBank database. None of them recovered from China. The closest relative was an isolate recovered from Japan in 2009 that differed by 146 cgMLST loci. Conclusions In summary, we report the first complete genome sequence of an ESBL-producing E.coli ST429 strain isolated from community in China. The genome sequence of EC28 can be used as a reference sequence for comparative analysis, including acquisition and mobilization of blaCTX-M genes in community-acquired strains.