Genomic signatures of dominant clones and evolutionary divergence of Acinetobacter baumannii in Thailand.

The global dissemination of carbapenem-resistant Acinetobacter baumannii (CRAB) is primarily driven by the expansion of two major international clones, IC1 and IC2, which have achieved widespread geographic distribution. Their success is further facilitated by the acquisition and dissemination of resistance determinants in healthcare settings. However, the evolutionary dynamics and genomic features of dominant clones in endemic settings such as Thailand remain insufficiently characterized. In this study, comparative genomic analyses were conducted on 650 A. baumannii genomes, including 38 newly sequenced CRAB isolates from tertiary hospitals across Thailand and 612 publicly available genomes, to examine lineage structure, resistome architecture and evolutionary trajectories. The dataset was dominated by ST2 (61.08%), followed by the emerging ST164 lineage (8.62%). Lineage-resolved analyses identified associations between STs and intrinsic resistance determinants, including enrichment of the AdeABC efflux component adeC and characteristic blaADC/blaOXA-51-like allelic combinations within dominant clones. Acquired resistance genes were widespread, with blaOXA-23-like carbapenemases predominating across lineages. Phylogenomic reconstruction showed that ST164 [international clone 11 (IC11)] occupies a distinct evolutionary position relative to established epidemic clones. Bayesian phylodynamic inference estimated a recent emergence of ST164 in Thailand around 2013-2014, with rapid initial clonal expansion followed by a period of relative population stability. Overall, this study reveals lineage-associated resistome features and distinct evolutionary trajectories among dominant and emerging A. baumannii lineages in Thailand, providing the value of genome-scale surveillance and lineage-resolved analyses for monitoring high-risk clones in endemic settings.