No abstract

A severe outbreak of highly virulent and multi-resistant dermatophytosis by species in the Trichophyton mentagrophytes/T. interdigitale complex is ongoing in India. The correct identity of the etiologic agent is a much-debated issue. In order to define species limits, a taxonomic study was undertaken combining molecular, morphological, and physiological characteristics as evidence of classification. Molecular characteristics show that T. mentagrophytes s. str. and T. interdigitale s. str. can be distinguished with difficulty from each other, but are unambiguously different from the Indian genotype, T. indotineae by sequences of the HMG gene. The entities were confirmed by multilocus analysis using tanglegrams. Phenotypic characters of morphology and physiology are not diagnostic, but statistically significant differences are observed between the molecular siblings. These properties may be drivers of separate evolutionary trends. Trichophyton mentagrophytes represents the ancestral, homothallic cloud of genotypes with a probable geophilic lifestyle, while T. indotineae and T. interdigitale behave as anthropophilic, clonal offshoots. The origin of T. indotineae, which currently causes a significant public health problem, is zoonotic, and its emergence is likely due to widespread misuse of antifungals.

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Chaetothyriales is an ascomycetous order within Eurotiomycetes. The order is particularly known through the black yeasts and filamentous relatives that cause opportunistic infections in humans. All species in the order are consistently melanized. Ecology and habitats of species are highly diverse, and often rather extreme in terms of exposition and toxicity. Families are defined on the basis of evolutionary history, which is reconstructed by time of divergence and concepts of comparative biology using stochastical character mapping and a multi-rate Brownian motion model to reconstruct ecological ancestral character states. Ancestry is hypothesized to be with a rock-inhabiting life style. Ecological disparity increased significantly in late Jurassic, probably due to expansion of cytochromes followed by colonization of vacant ecospaces. Dramatic diversification took place subsequently, but at a low level of innovation resulting in strong niche conservatism for extant taxa. Families are ecologically different in degrees of specialization. One of the clades has adapted ant domatia, which are rich in hydrocarbons. In derived families, similar processes have enabled survival in domesticated environments rich in creosote and toxic hydrocarbons, and this ability might also explain the pronounced infectious ability of vertebrate hosts observed in these families. Conventional systems of morphological classification poorly correspond with recent phylogenetic data. Species are hypothesized to have low competitive ability against neighboring microbes, which interferes with their laboratory isolation on routine media. The dataset is unbalanced in that a large part of the extant biodiversity has not been analyzed by molecular methods, novel taxonomic entities being introduced at a regular pace. Our study comprises all available species sequenced to date for LSU and ITS, and a nomenclatural overview is provided. A limited number of species could not be assigned to any extant family.

Phylogenetic analyses of 56 type species of Nocardia were conducted using the partial nucleotide sequences of the gyrase B-encoding gene (gyrB). The interspecies similarities of the gyrB gene for the 56 type species were 82.4-99.9 %, which corresponded to 270-2 nt differences in the partial gene sequences of approximately 1200 nt. In comparison with phylogenetic relationships, gyrB gene sequence information was generally consistent with that of 16S rRNA gene sequences with minor exceptions. However, the degree of divergence of the gyrB gene sequences was approximately 3.6 times greater than those of the 16S rRNA gene, suggesting a higher discriminative power of gyrB sequence information compared with 16S rRNA gene sequences for Nocardia species. The Nocardia type species were clustered based on gyrB sequence similarity values of 93.5 % and above. Among the 56 type species, 38 were distributed in 13 clusters, each comprising 2 to 7 species. The remaining 18 species were classified into an independent cluster, in which the similarity between each species and the other 55 Nocardia species was less than 93.5 %. Among the eight mycolic acid-containing actinomycete genera in the suborder Corynebacterineae, Nocardia was clearly differentiated from the other genera, such as Rhodococcus, by gyrB gene analyses (similarity values of gyrB sequences for Nocardia and Rhodococcus were 75-85 %), indicating that the gyrB gene is a useful alternative to the 16S rRNA gene for the determination of phylogenetic relationships between the genus Nocardia and the seven other actinomycete genera.

In vitro susceptibilities of ten clinical isolates, including five strains of Cryptococcus neoformans var. grubii and five strains of Aspergillus fumigatus, were determined against nine sulfa drugs using a microdilution method. Among the five tested media, minimum inhibitory concentration MIC values were observed only in YNB medium: no detectable level MIC value of less than 125 g/ml was observed in the four remaining media against Cryptococcus species. Of the nine sulfa drugs, of which sulfaphenazole showed the highest antifungal activity, the MIC values for A. fumigatus and C. neoformans var. grubii were, respectively, 64 g/ml and 4-8 g/ml, suggesting high susceptibility of C. neoformans to sulfa drugs.

During 1998-2008, there were 31 strains of Gordonia species isolated from clinical specimens in our laboratory. Our identification of the 31 strains of Gordonia species showed that major pathogenic Gordonia species in Japan were classifiable, respectively into 14 and 13 strains of Gordonia sputi and Gordonia bronchialis. The four remaining strains were identified as three Gordonia species: G. aichiensis (2 strains), and G. terrae (1 strain), and G. otitidis (1 strain). Results of drug susceptibility tests for these 31 strains of Gordonia isolates are reported herein.

Phylogenetic relations within the genus Gordonia were analyzed using partial gyrB and secA1 gene sequences of 23 type species in comparison with those of 16S rRNA gene. The gyrB and secA1 phylogenies showed agreement with that constructed using 16S rRNA gene sequences. The degrees of divergence of the gyrB and secA1 genes were approximately 3.4 and 1.7 times greater, respectively, than that of 16S rRNA gene. The gyrB gene showed more discriminatory power than either the secA1 or 16S rRNA gene, facilitating clear differentiation of any two Gordonia species using gyrB gene analysis. Our data indicate that gyrB and secA1 gene sequences are useful as markers for phylogenetic study and identification at the species level of the genus Gordonia.