Biology subjects

Kortenbosch, H. H.

Publications and source records attributed to Kortenbosch, H. H..

3 recordsLinked to original sources

bioRxiv2026

Non-triazole agricultural fungicides indirectly select for triazole resistance in the human pathogen Aspergillus fumigatus

The intensification of agriculture relies on chemical fungicides to manage crop disease1,2, leading to the evolution of resistance in plant pathogens.3 Fungicides have long half-lives, allowing them to remain active well beyond their intended targets and affect downstream ecosystems and agricultural practices. The saprophytic fungus Aspergillus fumigatus is an airborne ubiquitous fungus and an important human pathogen causing severe life-threatening invasive fungal disease.4 Selection pressure from agricultural triazoles, demethylase inhibitors (DMIs), has led to cross-resistance to clinical triazoles, as they share the same target gene, cyp51A.5,6 In the Netherlands7,8, most triazole resistance arises from two cyp51A haplotypes, the TR34 and TR46.9,10 Genomic surveys of A. fumigatus have shown that these triazole-resistance alleles often co-occur with resistance alleles to non-DMI classes, these include some of the dominant fungicide classes used in Europe such as quinone outside inhibitors (QoIs), and succinate dehydrogenase inhibitors (SDHIs).11 Hypothesizing that agricultural environments with non-DMI fungicides can indirectly select for triazole resistance, we used grass mesocosms to compete A. fumigatus isolates. We found that already at low concentrations, commonly found in agricultural residues, DMI, SDHI, and QoI fungicides can each independently increase the proportions of triazole resistant alleles. We show that the resistance alleles for each class are not intrinsically cross-resistant, indicating that their co-occurrences in allelic combinations produce this multi-resistance selection. Consistent with our mesocosms results, environmental samples contained high phenotypic (>20%) triazole resistance in heaps with only non-DMI fungicides. This work provides the first experimental and field evidence of selection for triazole resistance by non-triazole fungicides via genomic hitch-hiking. We thus predict that when novel fungicides are used in the same selective environment, novel resistance alleles will most likely be selected in isolates that have already accumulated resistance alleles to other fungicide classes. Because of linked resistance alleles, tackling selection and spread of environmental triazole resistance will require consideration of all fungicide classes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/728463v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@259848org.highwire.dtl.DTLVardef@30bfdeorg.highwire.dtl.DTLVardef@84bb35org.highwire.dtl.DTLVardef@1eb39d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITriazole-resistance alleles often co-occur with resistance alleles to non-DMI fungicide classes such as SDHI and QoI. C_LIO_LIDMI, SDHI, and QoI all independently increase the proportions of triazole resistant alleles at low concentrations (0.1 mg/kg) commonly found in agricultural residues. C_LIO_LIThe DMI resistance allele TR46 has a high fitness only under fungicide selective conditions, whereas TR34 maintains its fitness also under fungicide free conditions. C_LIO_LIBeneficial alleles for one fungicide class increase in frequency and hitch-hike with resistance alleles to other fungicide classes. C_LIO_LIResistance alleles to novel fungicide classes will more likely be selected in isolates that already accumulated other fungicide resistance alleles. C_LI

microbiology↗

bioRxiv2024

Widely dispersed clonal expansion of multi-fungicide-resistant Aspergillus fumigatus limits genomic epidemiology prospects

BackgroundAspergillus fumigatus is a ubiquitous fungus that causes a range of diseases in animals, including humans. The most lethal manifestation is invasive aspergillosis for which treatment relies on triazoles. Triazole-resistant A. fumigatus can be recovered from decaying plant material and so-called hotspots containing triazole fungicide residues. Although observations have shown clonal isolates between the environment and clinical samples, a direct link between a specific environment and cases of triazole-resistant invasive aspergillus disease in an individual patient has not yet been demonstrated. MethodsTo understand where patients acquire A. fumigatus isolates causing disease, we used a genomic epidemiology approach with 157 Dutch A. fumigatus isolates, based on whole genome sequencing. Isolates were from three well-characterized environmental hotspots and two hospitals between 2016 and 2019. FindingsIn the Dutch dataset, A. fumigatus isolates from six patients showed near-identical genomes compared to five environmental isolates. One environmental isolate matched three probable cases of triazole-resistant invasive aspergillosis, including one fatal case. Patient isolates were recovered up to 34 months later than near-identical environmental isolates. Comparison to over 1{middle dot}2K global publicly available A. fumigatus genomes showed hundreds of clonal groups spread across three continents. In addition, finding variants associated with resistance to non-triazole fungicides such as benzimidazole, succinate dehydrogenase inhibitor and quinone outside inhibitor classes, strongly suggests an exposure history to multiple agricultural fungicides in these environmental hotspots. InterpretationEnvironmental hotspots represent highly selective habitats for multi-fungicide-resistant A. fumigatus, which we can now directly link to probable cases of aspergillus disease, including a triazole-resistant case. However, geographically widely dispersed clonal expansion limits the utility of genomic epidemiology to identify the source of a particular patients isolate. Furthermore, reducing a single class of fungicides in agriculture may not effectively reduce resistance selection when other classes are still in use. FundingNWO.Groen2019.002 Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTriazole fungicides that exhibit activity against Aspergillus fumigatus have been shown to be a major source of resistant aspergillus disease in humans. However, the route of transmission from environmental hotspot to human remains poorly understood. Isolates of A. fumigatus can be recovered from both environmental samples and clinical specimens that harbour the same resistance signature haplotypes, e.g., TR34/L98H and TR46/Y121F/T289A, in the cyp51A-gene. We searched the literature for evidence using high resolution whole genome sequencing (WGS) to link environmental isolates to human infection. We searched PubMed for articles using the search terms Aspergillus fumigatus AND azole resistance AND whole genome sequencing on 15 April 2024. This search retrieved 32 articles describing different evolutionary routes to select for triazole-resistant A. fumigatus or population structure of whole-genome sequenced isolates. Twenty-six articles used whole-genome sequencing, but none focused on identifying clonal groups to identify direct cases of transmission between the environment and clinical cases of aspergillus disease. By using the additional search term transmission, no other records were retrieved. Added value of this studyOur study links triazole-resistant A. fumigatus isolates cultured from three environmental hotspots to cases of aspergillus disease in two hospitals in the Netherlands. Genome comparisons of isolates from environmental hotspots and patients showed multiple near-identical linked genotypes, consistent with a route of transmission from the environment to patients. Although a naive expectation may be a higher probability of matches of the hotspots located in the northwest of the Netherlands with the hospital located in the west of the country, in fact, more patient isolates from the far southeast were linked to the hotspots. Integrating the Dutch data set into a global data set showed 205 clonal groups spread across the Netherlands, Germany, the United Kingdom (UK), the United States of America (USA) and Japan. Our demonstration of a large number of geographically dispersed clonal groups suggests that current sampling is insufficient to definitively identify the source of an individual patients infection. A genetically highly diverse population combined with a wide global distribution of clones can make it impossible to definitively identify the source of an individual patients infection even with much more sampling. Implications of all the available evidenceOur study provides evidence that triazole-resistant A. fumigatus isolates with multi-fungicide resistance profiles cause aspergillus disease in at-risk patients and may contribute to treatment failure and mortality. The risk of infection due to these triazole-resistant isolates is not confined to the geographic vicinity of the environmental hotspot since clonal spread can be detected across great distances. The finding of linked cases without clear transmission routes limits epidemiological studies and underscores the need to better understand the ecology and environmental niches of this fungus. As it is highly unlikely that each patient visited the rural agricultural areas where a hotspot was located, research should address the complex and long-distance transmission routes of resistant isolates, which involves airborne dispersal of conidia or habitats of this fungus outside the agricultural environment. Furthermore, because of the multi-fungicide resistance phenotype of the triazole-resistant A. fumigatus, involving several classes of fungicides, reducing one class of fungicides in the environment may not effectively reduce resistance selection. Effective interventions should instead aim to reduce the burden of environmental resistance by modifying environments that currently favour the massive outgrowth of fungicide-resistant A. fumigatus to limit the escape of aerial spores from these environmental hotspots.

microbiology↗

bioRxiv2022

Catching more air: An effective and simple-to-use air sampling approach to assess aerial resistance fractions in Aspergillus fumigatus

Airborne triazole-resistant spores of the human fungal pathogen Aspergillus fumigatus are a significant human health problem as the agricultural use of triazoles has selected for cross-resistance to life-saving clinical triazoles. However, how to measure the health risk posed by these inhaled spores remains unclear. Here, we describe a method for cost-effective wide-scale outdoor air sampling to measure both spore abundance as well as antifungal resistance fractions. We show that prolonged outdoor exposure of sticky seals placed in delta traps, when combined with a two-layered cultivation approach, can consistently yield sufficient colony-forming units (CFUs) for the quantitative assessment of aerial resistance levels at a spatial scale that was up to now unfeasible. When testing our method in a European pilot sampling of 12 regions, we demonstrate that the triazole-resistant fraction of airborne spores is widespread and varies between 0 and 0.1 for itraconazole ([~]4 mg/L) and voriconazole ([~]2 mg/L). This method facilitates the assessment of health risks by pinpointing potential hot- and coldspots of environmental resistance selection. This efficient and accessible air sampling protocol opens up extensive options for fine-spatial sampling and surveillance studies. IMPORTANCEAspergillus fumigatus is an opportunistic fungal pathogen which humans and other animals are primarily exposed to through inhalation. Due to the limited availability of antifungals, resistance to the first choice class of antifungals, the triazoles, in A. fumigatus can make infections by this fungus untreatable and uncurable. Here we describe and validate a method that allows for the quantification of airborne resistance fractions and quick genotyping of A. fumigatus TR-types. Our pilot study provides proof of concept of the suitability of the method for use by citizen scientists for large-scale spatial air sampling. Spatial air sampling opens up extensive options for surveillance, health-risk assessment, and studying the ecology of A. fumigatus and the development of triazole resistance.

microbiology↗