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

Pariona J.G.M.; Barrón-Pastor H.; Tinedo del Aguila J.E.; Santos-Lázaro D.; Huerta-Canales D.; Monteghirfo-Gomero M.; Cucho-Espinoza C.; Huaroto-Valdivia L.; de Barrón Y.L.M. · Microbiology Spectrum (2026) · DOI: 10.1128/spectrum.03415-25

Resumen

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 blaOXA-23 but carried blaOXA-72. Two isolates were assigned to ST79, harboring KL13/OCL10 and blaOXA-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 blaOXA-23, indicating possible local emergence. Our study revealed the emergence in Peru of XDR A. baumannii lineages ST79 and ST1079 harboring blaOXA-23 and the spread of high-risk ST2 clones carrying blaOXA-72, underscoring the need for enhanced genomic surveillance and targeted infection-control measures.

Instituciones: Universidad Nacional Mayor de San Marcos