qualibact v2 methods

Achromobacter xylosoxidans

The ESGEM-AMR-v1 QC scheme for Achromobacter xylosoxidans represents a refinement of the original qualibact-v1 thresholds and incorporates a broader and more up-to-date genome set. In total, 441 additional A. xylosoxidans genomes were included that were not part of qualibact-v1. These comprise 171 genomes from BioProject PRJNA1234112 and 76 from PRJNA1148967, both from 2025 and not yet present in the AllTheBacteria dataset. A further 108 genomes are not yet publicly released, and 69 assemblies were retrieved directly from NCBI.

Genome assemblies were filtered following the same principles as qualibact-v1, with species-specific thresholds defined for assembly length, N50, number of contigs, and completeness/contamination based on CheckM analysis. See the Methods page for those details.