Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus

Abstract

The emergence of azole resistance in the pathogenic fungus Aspergillus fumigatus has continued to increase, with the dominant resistance mechanisms, consisting of a 34-nucleotide tandem repeat (TR34)/L98H and TR46/Y121F/T289A, now showing a structured global distribution. Using hierarchical clustering and multivariate analysis of 4,049 A. fumigatus isolates collected worldwide and genotyped at nine microsatellite loci using analysis of short tandem repeats of A. fumigatus (STRAf), we show that A. fumigatus can be subdivided into two broad clades and that cyp51A alleles TR34/L98H and TR46/Y121F/T289A are unevenly distributed across these two populations. Diversity indices show that azole-resistant isolates are genetically depauperate compared to their wild-type counterparts, compatible with selective sweeps accompanying the selection of beneficial mutations. Strikingly, we found that azole-resistant clones with identical microsatellite profiles were globally distributed and sourced from both clinical and environmental locations, confirming that azole resistance is an international public health concern. Our work provides a framework for the analysis of A. fumigatus isolates based on their microsatellite profile, which we have incorporated into a freely available, user-friendly R Shiny application (AfumID) that provides clinicians and researchers with a method for the fast, automated characterization of A. fumigatus genetic relatedness. Our study highlights the effect that azole drug resistance is having on the genetic diversity of A. fumigatus and emphasizes its global importance upon this medically important pathogenic fungus. IMPORTANCE Azole drug resistance in the human-pathogenic fungus Aspergillus fumigatus continues to emerge, potentially leading to untreatable aspergillosis in immunosuppressed hosts. Two dominant, environmentally associated resistance mechanisms, which are thought to have evolved through selection by the agricultural application of azole fungicides, are now distributed globally. Understanding the effect that azole resistance is having on the genetic diversity and global population of A. fumigatus will help mitigate drug-resistant aspergillosis and maintain the azole class of fungicides for future use in both medicine and crop protection.

First azole‐resistant Aspergillus fumigatus isolates with the environmental TR46/Y121F/T289A mutation in Iran

“…Azole resistance in A fumigatus due to TR 34 /L98H and more recent TR 46 /Y121F/T289A mutations in cyp 51A has been described from wide geographical areas among both clinical and environmental isolates . This is linked to the widespread use of azole fungicides in agriculture rather than the clinical use of antifungal drugs .…”

Detecting Azole-Antifungal Resistance in Aspergillus fumigatus by Pyrosequencing

“…Annual surveys in five academic hospitals in the Netherlands showed that azole resistance in A. fumigatus has doubled from 2014 to 2018 [23,24]. Similar data have been reported worldwide [25][26][27][28][29][30][31][32][33][34][35], and an international resistance surveillance group has been set up by ISHAM/ECMM to capture more information on azole resistance worldwide [36,37].…”

A Low‐Cost Tebuconazole‐Based Screening Test for Azole‐Resistant Aspergillus fumigatus

“…Aspergillus fumigatus is an opportunistic fungal pathogen with an ecological niche of soil and composting vegetation, where it plays a vital role in ecosystem processes including decomposition and nutrient recycling (Rhodes, 2006;Tekaia & Latgé, 2005;Van De Veerdonk, Gresnigt, Romani, Netea, & Latgé, 2017). The fungus has a vast geographical range, facilitated by the rapid dispersion of airborne conidia that are able to tolerate a broad range of biotic stresses (Pringle et al, 2005;Sewell, Zhu, et al, 2019).…”

“…However, continual exposure to these compounds exerts selective pressures that can facilitate the evolution of azole-resistant A. fumigatus (ARAf). The recent emergence of two ARAf-associated cyp51A alleles, TR 34 /L98H and TR 46 /Y121F/T289A, has raised concern due to their environmental association and increasing prevalence in azole-naive patients (Abdolrasouli et al, 2018;Chowdhary, Kathuria, Xu, & Meis, 2013;Mellado et al, 2007;Sewell, Zhu, et al, 2019;Snelders, Camps, et al, 2012;Stensvold, Jorgensen, & Arendrup, 2012;Van Der Linden et al, 2013;Zhang et al, 2017).…”