Complete genome sequence of an antibiotic-resistant and virulent Escherichia marmotae isolate recovered from a urinary tract infection.

OBJECTIVES: We aimed at analyzing the whole genome of the antibiotic-resistant Escherichia marmotae isolate 23-MO01035-0, which was obtained from a urinary tract infection of a male patient in Germany. The study focused on the characterization of mobile genetic elements and genetic factors that contribute to antibiotic resistance and pathogenicity. METHODS: Phenotypic antimicrobial susceptibility testing was performed and genomic DNA was sequenced using Illumina NextSeq (2 × 151 bp) and a MinION Mk1C device followed by de novo hybrid assembly using Unicycler v0.4.8. Resistance genes, virulence factors, plasmids, and mobile elements were identified with the bakcharak pipeline and PathogenFinder. RESULTS: The isolate belonged to sequence type ST133 and the 5,041,084 bp whole genome, consisting of one chromosome and five plasmids with an average GC content of 50.4%, revealed resistance genes for various antibiotic classes on an IncFII plasmid that had not yet been described. The isolate was predicted to be a potential human pathogen due to the presence of multiple virulence genes. CONCLUSION: Here, we report one of the first detailed genomic characterization of an antibiotic-resistant and virulent E. marmotae isolate from Germany. Considering that this bacterium was isolated from the urinary tract and possibly belonged to the faecal microbiota of the patient at that time, E. marmotae might contribute to the spread of antibiotic resistance in humans. This underscores the importance of genomic surveillance of E. marmotae, which causes human infections, but may be misidentified as E. coli.