Genomic Analysis Highlights the Misinterpretation of Acquired Aminoglycoside Resistance Genes in Deinococcus radiodurans

Aminoglycoside resistance is commonly mediated by enzymatic modification, target alteration, or efflux mechanisms; however, acquired resistance has not been characterized in radiation-resistant Deinococcus species. Here, we investigated the occurrence and genomic context of acquired aminoglycoside resistance genes in all publicly available Deinococcus radiodurans genomes. A total of 19 genomes were screened using ResFinder and CARD, followed by comparative genomic analyses. The aadA1 gene was identified in two genomes, being located on the plasmid pSP1 in strain R1 dM1, a known shuttle vector used for genetic manipulation. In contrast, aadA1 was found on a chromosomal contig in strain DRR11, suggesting a possible assembly artifact. Additionally, the aph(3')-Ia gene was detected in three genomes within a conserved chromosomal region that lacks this gene in reference strains. Sequence similarity analyses indicated that aph(3')-Ia is associated with laboratory vectors, being consistent with a potential non-natural origin. Considering the high recombination capacity and genomic plasticity of D. radiodurans, these findings suggest that the detected aminoglycoside resistance genes may be derived from laboratory constructs, potentially combined with assembly inconsistencies or chromosomal integration events. Therefore, this study highlights the importance of integrating genomic context with molecular and evolutionary plausibility to avoid misinterpretation of antimicrobial resistance in extremophiles and model organisms, and underscores the importance of complementary raw-read analyses to distinguish natural acquisition from technical or laboratory-derived origins.