Nocardia amikacinitolerans sp. nov., an amikacin-resistant human pathogen.
ABSTRACT Five isolates from clinical human sources were evaluated. Analysis of the near full length 16S rRNA gene showed 99.9-100 % similarity among the strains. The results of a comparative phylogenetic analysis of the 16S rRNA gene sequences indicated that the isolates belonged to the genus Nocardia. Phenotypic and molecular analyses were performed on the clinical isolates. Traditional phenotypic analyses included morphologic, biochemical/physiological, chemotaxonomic and antimicrobial susceptibility profiling. Molecular studies included 1441-bp 16S rRNA and 1246-bp gyrB gene sequence analyses, as well as DNA-DNA hybridizations. Biochemical analysis failed to differentiate the putative novel species from its phylogenetic neighbors; however, molecular studies were able to distinguish the patient strains and confirm them as a single species. Based on 16S rRNA gene sequence analysis, similarity between the isolates and their closest relatives (Nocardia araoensis, Nocardia arthritidis, Nocardia beijingensis and Nocardia niwae) were less than or equal to 99.3 %. Partial gyrB gene sequence analysis showed 98-99.7 % relatedness among the isolates. Nocardia lijiangensis and Nocardia xishanensis were the isolates' closest related species based on gyrB gene sequence analysis and showed 95.7 and 95.3 % similarity, respectively. Resistance to amikacin and molecular analyses, including DNA-DNA hybridization, distinguished the five patient strains from their phylogenetic neighbors, and the results of this polyphasic study indicated a novel species of Nocardia for which we propose the name Nocardia amikacinitolerans sp. nov., with strain W9988T (=DSM 45539 T = CCUG 59655T) as the type strain.