Escherichia coli novel sequence type 11873 harbors a new CTX-M-15-carrying multidrug resistance type 1/2 hybrid IncC plasmid

Abstract

ObjectivesThe aim of the current study was to determine the genomic map of resistance genes of two CTX-M-15-carrying Escherichia coli strains belonging to a novel sequence type (ST) 11873. Complete, closed genome sequences of the E. coli strains were obtained by applying a combination of short-read Illumina and long-read Oxford Nanopore-based sequencing. MethodsIsolation of E. coli was performed, using ECC CHROMagar™, and antibiotic sensitivity patterns were determined, using Sensititre™ EUVSEC plates. Whole-genome sequencing was performed for two E. coli strains (3-338 and 5-325), using Illumina MiSeq- and Oxford Nanopore MinION-based sequencing. ResultsThe complete genome of strain 3-338 (GenBank accession no.: CP130007-17) was assembled into a circular chromosome of 4.65 Mb and ten plasmids (between 2 kb and 148 kb). Strain 5-325 (CP130018-27) exhibited a circular chromosome of 4.7 Mb and nine plasmids (between 2 kb and 148 kb). Both strains carried an identical type 1/2 hybrid IncC plasmid (∼148 kb) harboring multiple antibiotic resistance genes (ARGs), including blaCTX-M-15,blaOXA-1, blaTEM-1, qnrS1, sul2, aphA1, aacC2, mph(A) and floR. This plasmid also carried heavy metal resistance genes, such as chrA and arsR. Strain 5-325 carried an additional IncFIB plasmid (∼78 kb) harboring additional ARGs, including blaTEM-1,qnrS1, tet(A), dfrA14, sul2, strA and strB. ConclusionsOur study shows the emergence of a CTX-M-15-carrying type 1/2 hybrid IncC plasmid in a novel E. coli ST11873. These findings emphasize the need for population-based sewage surveillance for understanding the prevalence of antibiotic resistance in pathogens, in order to mitigate further spread of such resistance factors.