Over the years, many papers have attempted to prise open the secrets surrounding A. fumigatus population structure, with most papers falling upon an alternative conclusion. Probably the most notable, Pringle et al (2005), used five loci to identify genetic isolation between two well supported clades and concluded that A. fumigatus actually consists of two cryptic species, Aspergillus "fumigatus" fumigatus and Aspergillus "occultum" fumigatus. Pringle's observation were determined according to the phylogenetic species concept (PSC*), as opposed to the more commonly applied biological species concept or ecological species concept.
At the same time, Rydholm et al (2005) investigated a collection of environmental A. fumigatus isolates at three intergenic loci for insights into population structure. In their paper, a comparison was made with closely related Neosartorya spp, N. fischeri and N. spinosa (Neosartorya spp. are the sexual teleomorphic stage of Aspergillus spp.). In accordance with a previous study, which used restriction fragment length polymorphism (Debeaupuis et al. 1997), Rydholm detected no evidence for population differentiation or sub-structure and concluded that lack of population structure could be mediated by large scale gene flow across continents, mostly due to the long distance dispersal of airborne A. fumigatus conidia.
In recent years there has been renewed interest in determining population structure in A. fumigatus, motivated primarily by the emergence of global azole resistance in immunocompromised aspergillosis patients. Klassen et al (2012) and Ashu et al (2017), used microsatellites (a well established genetic marker often used in molecular ecology) to make conclusions on the genetic structure of both environmental and clinical A. fumigatus isolates, with and without azole resistance.
Klassen investigated 255 isolates collected from the Netherlands, 25 of which had the azole resistant allele TR34/L98H (see previous post). Using two well established tools for determining genetic clustering (STRUCTURE** and DAPC), five genetically different, predominantly asexual populations were identified, with the azole resistance allele (TR34/L98H) found in just one of the five populations. Klassen concludes that confinement to a single asexual population suggests that sexual reproduction is not facilitating the emergence or spread of azole resistance, and that reproductive mode and genetic differentiation contribute to the structure of A. fumigatus populations in the Netherlands.
Most recently, Ashu investigated a collection of 2026 globally distributed isolates. They found that their collection fit into eight genetic clusters, with limited but statistically significant geographic or ecological differentiation; somewhat confirming previous observations of ubiquity and long distant dispersion. Notably on this occasion, they found signatures of both asexual and sexual reproduction, with the TR34/L98H resistance allele found in more than just one population.
Although fairly informative, microsatellite markers paint just part of the picture, encompassing a fraction of the genome. Our goal, as a genomics lab, is to unsurprisingly, analyse genomes. We are revisiting the story; firstly, by using information gleaned from the large collection of global A. fumigatus isolates genotyped by microsatellite markers, we have selected spatially and temporally important isolates for whole genome sequence analysis. We will then use the detailed information provided by genome sequencing and multiple sequence alignments to investigate genetic diversity, population structure, azole resistance evolution and mutation rates, to name but a few. Keep checking back for more updates and information regarding the labs progress and/or more information on the evolution of azole resistance in Aspergillus fumigatus.
* Speciation under the PSC can be defined as a group of organisms whose members are all more closely related to each other then they are to other organism outside of the groups. Membership is determined by nucleic acid variation and often visualised using multi-locus phylogenetic trees. It has been tremendously important in the identification of microbial species that are unculturable - especially fungi.
N.B. blog post structure similar to our review - Untangling Aspergillus fumigatus population structure - Sewell et al (in writing)
Pringle, A., Baker, D. M., Platt, J. L., Wares, J. P., Latge, J. P., & Taylor, J. W. (2005). Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution, 59(9), 1886-1899.
Rydholm, C., Szakacs, G. and Lutzoni, F., (2006). Low genetic variation and no detectable population structure in Aspergillus fumigatus compared to closely related Neosartorya species. Eukaryotic cell, 5(4), pp.650-657.
Debeaupuis, J.P., Sarfati, J., Chazalet, V. and Latge, J.P., 1997. Genetic diversity among clinical and environmental isolates of Aspergillus fumigatus. Infection and Immunity, 65(8), pp.3080-3085.
Klaassen, C.H., Gibbons, J.G., Fedorova, N.D., Meis, J.F. and Rokas, A., (2012). Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus. Molecular ecology, 21(1), pp.57-70.
Ashu, E. E., Hagen, F., Chowdhary, A., Meis, J. F., & Xu, J. (2017). Global Population Genetic Analysis of Aspergillus fumigatus. MSphere, 2(1), e00019-17.