Describing the Genomic Context of Azole-Resistance Mutations in Aspergillus fumigatus using Whole-Genome Sequencing

A rapid and global emergence of azole resistance has been observed in the pathogenic fungus Aspergillus fumigatus over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves mutations in the cyp51A gene, which encodes a protein targeted by triazole antifungal drugs. Whole-genome sequencing (WGS) was performed for high-resolution SNP analysis of 24 A. fumigatus isolates, including azole-resistant and susceptible clinical and environmental strains obtained from India, The Netherlands and United Kingdom, in order to assess the utility of WGS for characterising the alleles causing resistance. WGS analysis confirmed that TR34/L98H is the predominant mechanism of azole resistance among isolates tested. However, we also showed that some isolates contained no known mutations despite surviving exposure to high concentrations of azoles, confirming that other loci are important in determining resistance. Population genomic analysis confirmed that A. fumigatus is panmictic with as much genetic diversity found within a country as is found between continents. A striking exception to this was shown in India, where all isolates are highly related despite being isolated from both clinical and environmental sources across 1,000 km; this suggests a recent origin and spread of a single highly-fit azole-resistant clonal genotype. Our data shows the multiple origins of azole resistance across the worldwide spectrum of A. fumigatus genotypes, and delineates the fundamental population genetic parameters that are needed to enable the use of genome-wide association studies to identify the contribution of SNP-diversity to the generation of azole resistance in this medically important fungus.