Nocardia amikacinitolerans sp. nov., an amikacin-resistant human pathogen

Abstract

Five nocardioform isolates from human clinical sources were evaluated. Analysis of the nearly 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 morphological, 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 neighbours; however, molecular studies were able to distinguish the patient strains and confirm them as members of a single species. Based on 16S rRNA gene sequence analysis, similarity between the isolates and their closest relatives (type strains of Nocardia araoensis, N. arthritidis, N. beijingensis and N. niwae) was ≤99.3 %. Analysis of partial gyrB gene sequences showed 98-99.7 % relatedness among the isolates. Nocardia lijiangensis and N. xishanensis were the closest related species to the isolates based on gyrB gene sequence analysis, and their type strains showed 95.7 and 95.3 % similarity, respectively, to strain W9988(T). Resistance to amikacin and molecular analyses, including DNA-DNA hybridization, distinguished the five patient strains from their phylogenetic neighbours, and the results of this polyphasic study indicated the existence of a novel species of Nocardia, for which we propose the name Nocardia amikacinitolerans sp. nov., with strain W9988(T) ( = DSM 45539(T) = CCUG 59655(T)) as the type strain.