Supplementary data for: Stabilising evolution of carbapenem resistance through core–accessory genome co-adaptation in Acinetobacter baumannii

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical global health threat, yet the evolutionary mechanisms that stabilise resistance within high-risk lineages remain poorly defined. Using genomic, phenotypic, and phylogenetic analysis of 1,872 A. baumannii genomes, including a 16-year clinical collection from Eastern Europe, we show that carbapenem resistance evolves through two convergent pathways driven by core–accessory genome co-adaptation. Genome-wide association analysis reveals that acquisition of plasmid-borne blaOXA-72 is repeatedly accompanied by a lineage-specific core SNP that enhances resistance expression, while a second pathway involves chromosomal integration of blaOXA-23 and transcriptional activation via ISAba1 insertion. Machine learning models demonstrate that carbapenem MICs cannot be predicted from gene presence alone, highlighting the contribution of epistatic and regulatory variation. Time-resolved phylogenies show that both resistance mechanisms have independently emerged and expanded in multiple international clones, including a recently diverged lineage originating in Belarus. Together, these findings reveal how the interplay between chromosomal background and mobile genetic elements enables the long-term persistence and repeated emergence of carbapenem resistance. By resolving the genomic basis of resistance stabilisation, this work provides a mechanistic framework for anticipating AMR evolution and identifying emerging high-risk clones.