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.