Genomic epidemiology of carbapenem resistance in Acinetobacter baumannii in Chile

Carbapenem-resistant Acinetobacter baumannii (CRAb) is a World Health Organization (WHO) critical priority pathogen, yet genomic data from Chile are scarce. Here, we investigated the genetic diversity of Chilean isolates, focusing on molecular epidemiology, carbapenemase genes, and mobile genetic elements.

We analysed 83 A. baumannii genomes (42 newly sequenced, 41 public). Newly sequenced isolates underwent antimicrobial susceptibility testing, and whole-genome sequencing was performed using Illumina, with hybrid assemblies for two CRAb strains. Genomes were assembled and analysed for STs, KL/OCL loci, resistance genes, plasmids and mobile elements, supported by phylogenomics.

MLST revealed a diverse population structure dominated by ST15/IC4 (n = 26) and ST318/IC4 (n = 13), followed by ST109/singleton (n = 14), ST162/singleton (n = 13), ST1/IC1 (n = 9), ST79/IC5 (n = 5), and three additional singletons. Four isolates were carbapenem-susceptible, including three ST109 from the 1990s and one ST15 from 2016. Overall, 79/83 isolates were classified as carbapenem-non-susceptible based on phenotypic data and/or genomic determinants. Among these, bla _OXA-58 (n = 24) and bla _OXA-23 (n = 21) predominated, while bla _NDM-1 was detected in a single isolate. Additionally, 33 genomes harboured the ISAba1-bla _OXA-51-like arrangement, with the OXA-219 variant strongly associated with ST15 and ST318.

This three-decade genomic analysis shows sustained circulation of IC4 (ST15/ST318) in Chile. Carbapenem resistance was mainly driven by bla _OXA-23 on conjugative Rp-T1 plasmids, bla _OXA-58 on mobilizable R3-T14 plasmids, and frequent ISAba1-bla _OXA-51-like arrangements, especially OXA-219. The persistence of plasmids and mobile elements highlights ongoing horizontal gene transfer and the importance of genomic surveillance for infection control in Chile.