Species complex and nomenclature
In one of our previous blogs (number 1) we explained the use of species complexes that consist of a cluster of molecular siblings. The species complex is the umbrella of clones which each may have separate names. The idea behind the Species complex concept was, that if precise determination of the name of the molecular sibling at hand is irrelevant from a routine clinical perspective, identification at the complex level would be sufficient and might save hospital budget and energy.
But what if we face the opposite situation: sequencing reveals the name of an unknown molecular sibling, rather than that of the classical overarching species? A solution in both directions is now available in the Atlas. You are already familiar with the indications on many Atlas pages: a species name followed by “member of XXX complex”. From today onwards, at the front page of all species recommended to belonging to a species complex, you can find a header “Species complex”. The following example is from Trichophyton:
Clinically relevant members of the T. benhaemiae complex: T. benhamiae, T. concentricum, T. europaeum, T. japonicum, T. persicum and T. spiraliforme.
All species names are interlinked so that relevant information on the species complex members in the Atlas can easily be found. Note that only the clinically relevant siblings, i.e. those with a description in the Atlas, are mentioned. Several opportunistic, environmental fungi have been decomposed into a large number of molecular siblings. See for example Cladosporium cladosporioides, where Sandoval-Denis et al. (2016) distinguished 54 siblings using ITS, tef1 and actA, and Wang et al. (2022) reporting 74 siblings in the Fusarium fujikuroi complex with tef1, rpb1 and rpb2.
It should be realized that the Species complex is a practical recommendation rather than a solid scientific conclusion. The complex should be phylogenetically coherent as a single clade, but some clones have more practical importance than others. For example, one of the clones in the Trichophyton mentagrophytes clade is clinically relevant because of its virulence for adult patients and high degree of terbinafine resistance (Kong et al. 2021), and is therefore recommended for targeted identification; therefore the Atlas now excluded it from the T. mentagrophytes complex. A similar situation is observed with Aspergillus lentulus, the most important sibling next to A. fumigatus.
How to report your identification? In view of nomenclatural stability and recognizability, we recommend to use the species complex name at all times. When a particular molecular sibling has been identified, its name can be added in brackets. As an example, with rDNA ITS, the identification is “Trichophyton benhamiae complex”. Sequencing of gapdh, tubb or tef1 may directly lead to the name of the molecular sibling (Čmoková et al. 2020), and then the report would be: “Trichophyton benhamiae complex (T. japonicum).
- Čmoková A, Kolařík M, Dobiáš D, et al. (2020) Resolving the taxonomy of emerging zoonotic pathogens in the Trichophyton benhamiae complex. Fung. Div. 104: 333-387.
- Sandoval-Denis M, Gené J, Sutton DA, et al. (2016) New species of Cladosporium associated with human and animal infections. Persoonia 36: 281-298.
- Wang MM, Crous PW, Sandoval-Denis M, et al. (2022) Fusarium and allied genera from China: species diversity and distribution. Persoonia 48: 1-53.
- Kong X, Tang C, Singh A, et al. Antifungal susceptibility and mutations in the squalene epoxidase gene in dermatophytes of the Trichophyton mentagrophytes species complex. Antimicrob Agents Chemother 65(8): e00056-21.