Deciphering acquired resistance to amikacin in Mycobacterium abscessus clinical isolates selected from patients with pulmonary disease (MAB-PD) treated with aminoglycoside: a 2012-2025 retrospective cohort study.

OBJECTIVES: Amikacin (AMK) is one of the most active antimicrobials for treating Mycobacterium abscessus pulmonary disease (MAB-PD). Acquired AMK resistance (AMK-R) was described with an A1408G mutation in rrs encoding the 16S ribosomal RNA. Clinical frequency of other mutations remains unknown. This study aims to decipher AMK-R mechanisms and selection in patients with MAB-PD. METHODS: From 2012 to 2025, we included all MAB isolates sent to our reference centre from patients with MAB-PD and selected the patients for whom at least one AMK-R isolate was obtained (MIC determined by broth microdilution > 64 mg/L according to EUCAST epidemiological cut-off value). We collected patient data, including aminoglycoside intake. Whole genome sequencing was performed on sequential AMK-R and AMK-S isolates. RESULTS: Among 893 MAB isolates from 727 patients, 113 from 30 patients were included in this study (73 AMK-R and 40 AMK-S). Most isolates were from cystic fibrosis patients (28/30) who had received amikacin and/or tobramycin, intravenous and/or inhaled, and/or amikacin liposomal inhaled suspension (29/30). The A1408G rrs mutation was found in 24/30 patients. Other rrs mutations were also found, like C1409T (one patient), G1491T (two patients) and a novel C1496T in two patients. A deletion upstream whiB7, a gene associated with multidrug resistance, was also identified for one patient. Longitudinal follow-up of 16 patients with AMK-S/R couples highlighted the emergence of AMK-R, regardless of the aminoglycoside molecule or the administration route. AMK-R isolates remained in 13/16 patients independently of aminoglycoside discontinuation. Intra-patient AMK-S/AMK-R couples differed only by a median [IQR] of 5 [3-11] SNPs, confirming the in vivo selection of AMK-R mutants from the AMK-S population. CONCLUSIONS: In patients with MAB-PD, AMK resistance can be selected under aminoglycoside treatment, mainly through an A1408G rrs mutation, but also with mutations at other rrs loci or in other genes, requiring a genomic investigation.