First report of OXA-484 carbapenemase harbouring clinical isolate of Escherichia coli ST2099 in India: Genome characterization using whole genome sequencing

The global spread of carbapenemase-producing Escherichia coli , particularly OXA-48-like variants, poses serious public health concern due to their low-level carbapenem hydrolytic activity and phenotypic detection challenges. Among OXA-48-like variants, OXA-484 is rarely reported, differing from common variants ( bla OXA-181,232 ) by a single amino acid substitution (214G), resulting in reduced carbapenem hydrolysis. This is probably the first report of OXA-484-producing E. coli (ST2099) from India with genomic characterization of the strain. Identification, antibiotic susceptibility and whole-genome sequencing were carried out. Transmissibility and replicon types of bla OXA-484 -harbouring plasmid were determined. The isolate was multidrug-resistant, showing resistance to β-lactams, aminoglycosides, fluoroquinolones, sulfonamides, macrolides while remaining susceptible to carbapenems. WGS revealed a 6,025,542 bp genome with multiple plasmids. The bla OXA-484 gene co-localized with qnrS1 on a non-conjugative 15,326 bp ColKP3 plasmid, flanked upstream by △ ISEcp1 and downstream by truncated lysR , ereA and repA . Additional ARGs, efflux pump genes and fluoroquinolone resistance mutations were found on other plasmids and chromosome. Numerous virulence genes were also detected. SNP-based phylogeny showed lowest genomic proximity of studied genome to E. coli ST101 and ST448 from USA. Transformation confirmed plasmid-mediated transfer of bla OXA-484 with low carbapenem MICs (0.5 mg/L), consistent with OXA-484's reduced hydrolytic activity. This report highlights the first identification of OXA-484 in E. coli ST2099 from India, a ST where OXA-484 has not been detected globally. Given the challenges in phenotypic detection of OXA-48-like carbapenemases, as their presence is often associated with lower carbapenem MICs, genomic surveillance is indispensable for detecting emerging resistance determinants and effective infection management. • First report of OXA-484-producing multidrug-resistant E. coli ST2099 from India. • OXA-484 has not been detected before in ST2099 globally. • The strain belonged to phylogroup D, fumC4 & fimH24 and O153:H25. • WGS detected OXA-484 on a 15,326 bp nonconjugative ColKP3 plasmid with qnrS1 . • Transfer via electroporation confirmed plasmid-borne OXA-484. • WGS revealed multiple plasmids, different ARGs along with virulence determinants.