Genomic Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolated from Patients Admitted to Intensive Care Units in Network Hospitals in Southern Thailand

Abstract

Background/Objectives: Carbapenem-resistant Acinetobacter baumannii (CRAB) is classified as an urgent-threat pathogen because of its resistance to nearly all available antibiotics, resulting in high morbidity and mortality rates. However, data on the molecular epidemiology of CRAB isolates in southern Thailand are limited. This study aimed to investigate the genomic epidemiology of CRAB isolates within a hospital network in lower southern Thailand. Methods: Whole-genome sequencing data of CRAB clinical isolates (n = 224) were obtained from a previous study. Additional isolates (n = 70) were included, for which genomic DNA was extracted and sequenced. In total, 294 isolates were collected from patients across seven hospitals in southern Thailand between 2019 and 2020. Their genomes were analyzed using several bioinformatic tools. Results: A high proportion of isolates were obtained from sputum samples of patients with CRAB infection or colonization. Sequence type (ST) 2 was the most frequent ST and was classified in the quadrant with high resistance and virulence. The Sankey diagram showed that ST2 was the dominant and most versatile CRAB lineage circulating across major hospitals, commonly associated with pneumonia, and that diverse resistance genes and plasmid combinations were dominated by bla<inf>OXA-23</inf>. The core single-nucleotide polymorphism (SNP)-based phylogenetic tree revealed clades A1 (ST215), A2 (multiple STs), and B (ST2). Bloodstream, skin, and soft tissue infections were predominantly observed in clade B. Conclusions: Our analysis revealed widespread circulation of a high-risk ST2 CRAB lineage with enhanced resistance and virulence across hospital networks in the studied region, highlighting the importance of genomics-informed surveillance for controlling CRAB dissemination.