Phylogeny of the Genus Nocardia Based on Reassessed 16S rRNA Gene Sequences Reveals Underspeciation and Division of Strains Classified as Nocardia asteroides into Three Established Species and Two Unnamed Taxons

Abstract

Conventional identification of Nocardia in the routine laboratory remains problematic due to a paucity of reliable phenotypic tests and due to the yet-unresolved taxonomy of strains classified as belonging to the species Nocardia asteroides, which comprises the type strain and isolates with drug pattern types II and VI. The 16S rRNA gene of 74 representative strains of the genus Nocardia, encompassing 25 established species, was sequenced in order to provide a molecular basis for accurate species identification and with the aim of reassessing the phylogeny of taxons assigned to the species N. asteroides. The result of this phylogenetic analysis confirms that the interspecies heterogeneity of closely related nocardial species can be considerably low (a sequence divergence of only 0.5% was found between N. paucivorans and N. brevicatena). We observed a sequence microheterogeneity (sequence divergence of fewer than five bases) in 8 of 11 species of which more than one strain in the species was studied. At least 10 taxons were found that merit description as new species. Strains previously classified as N. asteroides fell into five distinct phylogenetic groups: the type strain cluster (N. asteroides sensu strictu), N. abscessus, N. cyriacigeorgica, and two clusters closely related to N. carnea or N. flavorosea. The strains within the latter two groups probably represent new species, pending further genetic and phenotypic evaluation. Restricted phenotypic data revealed that N. abscessus, N. cyriacigeorgica, and the two Nocardia species taxons are equivalent to drug patterns I, VI, and II, respectively. In the future, these data will help in finding species-specific markers after adoption of a more precise nomenclature for isolates closely related to N. asteroides and unravel confusing phenotypic data obtained in the past for unresolved groups of strains that definitely belong to separate taxons from a phylogenetic point of view.The genus Nocardia forms a group of 30 validly described species. Many of these can cause clinical diseases in humans and animals, including pulmonary, central nervous system, and cutaneous infections that are all diagnosed by culture and identification of the organisms (1, 10, 11). Identification to the genus level is well established based on chemotaxonomic characteristics, mainly on the presence of a major amount of mesodiaminopimelic acid, arabinose, galactose, and mycolic acids with 46 to 60 carbons in cell walls (13,14). A variety of phenotypic characteristics for each Nocardia species can be found in the literature, but those of recently published species, such as N. abscessus and N. cyriacigeorgica (25, 26), have not been analyzed in collaborative numerical phenetic studies systematically in order to obtain a proposal of selected tests for routine identification of all medically relevant species (9,13,17,19,21). Studies of antimicrobial susceptibility revealed distinct drug pattern types within strains identified as N. asteroides, notably drug patterns I through VI (20). A few years la...

Nocardiosis: an overview and additional report of 28 cases in cattle and dogs

“…Classically, N. asteroides is recognized as the more important pathogenic specie for human 2 and animal nocardiosis 26,37 . Nowadays, Nocardia was reclassified in various pathogenic and saprophytic species 10,17,40 . Atypical clinical manifestations of nocardiosis in domestic animals and patients lead frequently to misdiagnose of the disease.…”

“…Microorganisms are usually recovered in pure culture and colonies are smooth or rough, pigmented (white, cream, orange, red tonalities), with characteristic powdery surface, like fungal organisms. However, confirmation of diagnosis and species characterization depend of biochemical characterization, based on hydrolysis of various carbohydrates and other substrates 10,28,36 , and more recently, by use of molecular techniques 17,40 .…”

“…In recent years, according the biochemical characteristics, antimicrobial susceptibility and molecular methods 17,40 , the classification of genera was re-defined. The more important pathogenic species for disease in humans and animals were classified as: Nocardia asteroides (N. asteroides) complex, Nocardia brasiliensis (N. brasiliensis), Nocardia pseudobrasiliensis, Nocardia transvalensis and Nocardia otitidiscaviarum (N. otitidiscaviarum).…”

Nocardia harenae, an uncommon causative organism of mycetoma: report on two patients

“…Nowadays, the development of specific molecular techniques makes it possible to accurately identify species capable of infecting humans and, combined with conventional methods, these tools proved useful in obtaining an accurate Nocardia diagnosis (Brown-Elliott et al, 2006;Roth et al, 2003;Conville et al, 2010). 16S rRNA gene sequencing has been used for identification at the species level, resulting in a considerable reclassification of members of the genus Nocardia, and, due to their distinctive and unique sequence arrangements, it is considered the gold standard for identification of these organisms (Roth et al, 2003;Conville et al, 2010).…”

Nodular non-necrotising anterior scleritis due to Nocardia nova infection

“…nova was identified by sequence analysis of the 16S rRNA gene, an established technique for this organism. 7 Once the organism was identified as N. nova, the patient was changed to oral amoxicillin (500 mg t.i.d.) and clarithromycin (500 mg b.i.d.).…”