Paracoccidioides brasiliensis Isolated from Nine-Banded Armadillos (Dasypus novemcinctus) Reveal Population Structure and Admixture in the Amazon Basin

Abstract

Paracoccidioidomycosis is an endemic fungal disease to Latin America caused by at least five species-level genotypes of Paracoccidioides, named P. lutzii, P. brasiliensis (S1a and S1b populations), P. americana, P. restrepiensis, and P. venezuelensis. In this manuscript, we report on Paracoccidioides sp. sampling efforts in armadillos from two different areas in Brazil. We sequenced the genomes of seven Paracoccidioides isolates and used phylogenomics and populations genetics for genotyping. We found that P. brasiliensis and P. lutzii are both present in the Amazon region. Additionally, we identified two Paracoccidioides isolates that seem to be the result of admixture between divergent populations within P. brasiliensis sensu stricto. Both of these isolates were recovered from armadillos in a P. lutzii endemic area in Midwestern Brazil. Additionally, two isolates from human patients also show evidence of resulting from admixture. Our results suggest that the populations of P. brasiliensis sensu stricto exchange genes in nature. More generally, they suggest that population structure and admixture within species is an important source of variation for pathogenic fungi.

Keywords: Amazon; Paracoccidioides; admixture; armadillos; paracoccidioidomycosis.

Figure 1

Genetic background of Paracoccidioides brasiliensis isolated from nine-banded armadillos in the Amazon basin. (A) Specimen collected, macroscopic characteristics of the fungal growth on tissue, and microscopic characteristics of yeast cells isolated from the tissue. (B) Genome-level maximum likelihood tree of 70 Paracoccidioides spp. genomes, indicating the placement of the Amazonian isolates T19F33 and T20B15 as a monophyletic group sister to P. brasiliensis S1a cluster. (C) Principal Component Analysis (PCA) reveals that P. brasiliensis S1a and S1b are populations separated along the PC1 axis corresponding to 63.68% of the total variation. (D) ADMIXTURE analysis of P. brasiliensis revealed admixed (*) S1a genotypes (T19F33 and T20B15) and S1b genotypes (Pb113 and Pb18). The proportion of admixture of each isolate is represented by height and colors of each of the two populations.

Figure 2

Whole-genome genetic distances between the isolates T17LM2 and T17LM3. Absolute genetic distance (dXY) between the isolates T17LM2 and T17LM3 were calculated by using 5 kb sliding window blocks and plotted across 13 largest scaffolds of the P. brasiliensis Pb18 reference genome.