Whole-genome analysis of extensively drug-resistant Acinetobacter baumannii isolates from a Peruvian tertiary hospital reveals the emergence of OXA-23-producing ST79 and ST1079 clones

Acinetobacter baumannii is a leading cause of extensively drug-resistant (XDR) infections in intensive care units (ICUs), with global concern due to its resistance to nearly all antimicrobials. In 2024, the WHO reaffirmed carbapenem-resistant A. baumannii as a critical-priority pathogen. In Peru, over 97% of clinical A. baumannii isolates are carbapenem non-susceptible, yet the genomic features of local strains remain poorly characterized. We performed whole-genome sequencing of 19 XDR A. baumannii isolates collected from ICU patients at Hospital Nacional Dos de Mayo (Lima, Peru) between May 2023 and September 2024. Genomes were analyzed for sequence types (ST), capsular (KL) and lipooligosaccharide (OCL) loci, virulence and resistance genes, and phylogenetic relatedness. All isolates were XDR but remained susceptible to colistin. Fourteen isolates belonged to ST2, forming two closely related subgroups carrying KL2 or KL9 and OCL1, with low SNP distances, suggesting recent clonal expansion. These ST2 genomes lacked bla OXA-23 but carried bla OXA-72 . Two isolates were assigned to ST79, harboring KL13/OCL10 and bla OXA-23 , representing the first report of this resistance gene in Peruvian ST79 strains. Three isolates belonged to ST1079, forming a tight Peruvian clade genetically distant from public ST1079 genomes; all carried KL107/OCL3 and bla OXA-23 , indicating possible local emergence. Our study revealed the emergence in Peru of XDR A. baumannii lineages ST79 and ST1079 harboring bla OXA-23 and the spread of high-risk ST2 clones carrying bla OXA-72 , underscoring the need for enhanced genomic surveillance and targeted infection-control measures. IMPORTANCE A. baumannii is one of the most problematic hospital pathogens worldwide, often resistant to nearly all available antibiotics. In Peru, the proportion of carbapenem-resistant isolates is among the highest reported globally, yet their genetic background has remained largely unknown. This study provides the first genomic and phylogenomic insight into XDR A. baumannii from a major Peruvian hospital, revealing the spread of high-risk clones belonging to sequence type 2 carrying the OXA-72 carbapenemase, and the emergence of two additional lineages, sequence type 79 and sequence type 1079, both producing OXA-23. These findings demonstrate that multiple resistant lineages are established in Peru, highlighting the urgent need to implement genomic surveillance and infection control measures. Understanding the diversity and dynamics of these lineages is critical to limit their further spread and to guide public health responses in South America.