Changing landscape of 16 S-RMTase-mediated aminoglycoside resistance in clinical Klebsiella pneumoniae isolates from Chile between 1997 and 2023

The emergence of 16S rRNA methyltransferase (16S-RMTases) poses a major therapeutic challenge, as they confer high-level resistance to all clinically relevant aminoglycosides. In Chile, data on these enzymes remain scarce. This study investigated the epidemiological distribution and genetic relatedness of Klebsiella pneumoniae strains carrying 16S-RMTase genes. Antibiotic susceptibility was assessed using the Kirby-Bauer method and complementary techniques. Gene detection was performed via conventional PCR, and genotyping via ERIC-PCR. Among 1,200 K. pneumoniae clinical strains collected between 1997 and 2023; 233 (19.4%) exhibited high-level resistance to both amikacin and gentamicin, suggesting 16S-RMTase gene carriage. All presumptive strains carried 16S-RMTase genes, with rmtG being the most prevalent (n = 174), followed by armA (n = 30), rmtC (n = 24), and rmtD (n = 5). Genotyping revealed 19 distinct clusters. The rmtG gene was widely distributed, whereas rmtC displayed regional clustering, particularly in Concepción, and was associated with broader resistance profiles, including resistance to carbapenems. In contrast, rmtG-positive strains retained partial susceptibility to these agents. Fisher's exact test revealed associations (p < 0.05) between specific 16S-RMTase genes and non-susceptibility antibiotic profiles. The spread of 16S-RMTase genes since 2007, from Iquique to Puerto Montt, highlights their growing clinical relevance. The recent rise of armA and rmtC suggests a shift in dominant resistance mechanisms.