Genomic characterization of a multidrug-resistant TEM-52b extended-spectrum β-lactamase-positive Escherichia coli ST219 isolated from a cat in France

Abstract Objectives TEM-52 extended-spectrum β-lactamases (ESBLs) have been detected in members of the family Enterobacteriaceae isolated from human and non-human reservoirs, mainly in European countries. We hereby report the first draft genome of a multidrug-resistant TEM-52b-positive Escherichia coli isolated from a companion animal in France. Methods Whole genomic DNA from E. coli 39590 was extracted and sequenced using an Illumina NextSeq platform. De novo genome assembly was performed using Velvet version 1.2.10 and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline version 3.2. Genomic analyses were performed through bioinformatics tools from the Center of Genomic Epidemiology. Results The genome size was calculated as 5 362 108-bp, with 5268 protein-coding sequences and GC content of 50.5%. The E. coli strain 39590 belonged to sequence type ST219, serotype O4:H34, and phylogroup E. Antimicrobial resistome consisted of genes encoding resistance to beta-lactams (blaTEM52b), aminoglycosides [aph(3'')-Ib, aph(6)-Id, aadA2, aadA24], phenicols (catA1), sulphonamides (sul1 and sul2), trimethoprim (dfrA1 and dfrA14), lincosamide (lnuG), tetracycline (tetA); and mutations in gyrA (Ser83Leu, Asp87Asn) and parC (Ser80Ile) genes, conferring resistance to quinolones. Virulome revealed iss, astA and eilA genes, whereas IncQ1, IncX4, IncX1, IncFIB, and IncFIC plasmid incompatibility groups were identified. Conclusion This draft genome can be used as a reference sequence for comparative studies using human and non-human E. coli isolates, in order to identify genetic events that have contributed to pathogenicity and adaptation of TEM-52-producing E. coli clones at the human-animal interface, as well as to elucidate dynamics of the spread of blaTEM-52 ESBL genes.