The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach

Abstract

The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex.

Trichophyton mentagrophytes ITS genotype VIII and Trichophyton indotineae: A terminological maze, or is it?

“…Taxonomy and terms change and evolve rapidly in the field of mycology. [21][22][23][24] Trichophyton indotineae/Trichophyton mentagrophytes ITS genotype VIII, notwithstanding the terminological confusion, is no longer restricted to the Indian subcontinent. Its presence as early as between 2004 and 2013 has been documented in India, Australia, Iran and Oman.…”

Insights into Changing Dermatophyte Spectrum in India Through Analysis of Cumulative 161,245 Cases Between 1939 and 2021

“…6 a and S5). All the three members of Tr_cluster_2 have recently been identified as T. megninii [ 43 ] and explains the separate cluster formed by these three isolates. The SNP-based phylogenetic tree also shows one major and one minor branch consisting of the same members as the ANI-tree (Fig.…”

Clinical Manifestations of Human Exposure to Fungi

“…This group includes the genera Trichophyton , Microsporum , Epidermophyton , Lophophyton , Paraphyton , Nannizzia , and Arthroderma . Most infections are caused by the three initial genera, which present different geographic distributions: Trichophyton rubrum presents a worldwide distribution, being significantly prevalent in developed countries from North America, Europe, Australia, and East Asia; Microsporum canis and Trichophyton tonsurans can be found in most European countries; Trichophyton violaceum is the most prevalent species in Middle Eastern countries, East Africa, and South China; Microsporum audouinii and Trichophyton soudanense are endemic to West African countries [ 152 , 153 ].…”