OXA48typer

OXA48typer is a bioinformatics tool designed to detect and classify blaOXA-48-like carbapenemase genes from sequencing data. It targets OXA-48-like enzymes, a subset of class D beta-lactamases that contribute to carbapenem resistance in Enterobacterales.

OXA-48-type carbapenemases were first described in Enterobacteriaceae and are now found worldwide in species such as Klebsiella pneumoniae, Escherichia coli, and others. The family includes variants such as OXA-48, OXA-181, OXA-232, and OXA-244, among others.

The tool typically relies on a curated reference database of blaOXA-48-like sequences and uses sequence alignment or k-mer matching to determine the presence of a blaOXA-48-like gene and to assign a probable variant. Output may include variant designation, coverage, and confidence.

OXA48typer can be integrated into whole-genome sequencing pipelines or used with targeted sequencing data to support clinical surveillance, outbreak investigation, and antimicrobial stewardship by providing rapid genotype information for carbapenemase producers.

Limitations include dependence on data quality and the reference database; novel or highly divergent variants may be missed or misclassified, and the tool does not substitute for phenotypic antimicrobial susceptibility testing. Proper validation and context are required.

See also: OXA-48-like carbapenemases; blaOXA-48; antimicrobial resistance.