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Triazole-resistant Aspergillus fumigatus in the Netherlands between 1994 and 2022: a genomic and phenotypic study
Yinggai Song1, Jochem B Buil2, Johanna Rhodes2
1Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China; Department of Medical Microbiology and Radboudumc-CWZ Center of Expertise for Mycology, Radboud University Medical Center, Nijmegen, Netherlands; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Research Center for Medical Mycology, Peking University, Beijing, China.
Background:
Aspergillus fumigatus is the main cause of invasive aspergillosis and triazole antifungals are the primary treatment option. The effectiveness of triazole therapy is hampered by the emergence of resistance, mainly caused by mutations in the cyp51A gene and a tandem repeat (TR) of 34 bases (TR34/Leu98His) and 46 bases (TR46/Tyr121Phe/Thr289Ala) in the promoter region, which correspond with signature triazole resistance phenotypes. We aimed to investigate the occurrence of triazole phenotype and genotype variation over a 29-year period in the Netherlands.
Methods:
In this genomic and phenotypic study, we screened all clinical A fumigatus isolates from Dutch hospitals collected between Jan 6, 1994, and Dec 31, 2022, for resistance to triazole using agar-based methods, and characterised them by sequencing the cyp51A gene and in vitro susceptibility testing using the European Committee on Antimicrobial Susceptibility Testing reference method. Whole-genome sequencing was performed on selected isolates, including those harboring TR34 variants, high-frequency single-nucleotide polymorphisms, and wild-type strains. Clinical information such as age, underlying disease, diagnosis, therapy, and outcomes was collected for patients who had isolates cultured at the Radboud University Medical Centre, Nijmegen, Netherlands, between Jan 1, 2017, and Dec 31, 2022.
Findings:
1979 (15·6%) of the screened 12 679 A fumigatus isolates harboured cyp51A triazole resistance mutations, predominately TR34/Leu98His sensu stricto in 1338 (67·6%) resistant isolates and TR46/Tyr121Phe/Thr289Ala sensu stricto in 332 (16·8%) resistant isolates. Phenotype and genotype variations were observed in 325 (17·2%) triazole resistant isolates harbouring a TR-resistance mechanism, including 12 cyp51A genotype variants. Whole-genome sequencing showed that isolates with combinations of TR34-based and TR46-based polymorphisms seemed to be derived from separate populations, but there was some overlap. 59 cases of proven or probable invasive aspergillosis were identified, including 13 triazole-resistant cases, of which three were caused by genotype variants. Mixed genotype infection was observed in 11 (84·6%) of 13 triazole-resistant patients and the number of antifungal treatment switches was higher compared with triazole-susceptible disease (p<0·0001).
Interpretation:
Our study showed variation in triazole genotypes and phenotypes in clinical A fumigatus isolates with cyp51A-mediated resistance, some of which were cultured from triazole-resistant invasive aspergillosis cases. Triazole resistance variation and mixed A fumigatus genotypes represent a major challenge in clinical management of Aspergillus diseases because current molecular diagnostic tools will increasingly fail to predict the resistance phenotype, underscoring the need for improved detection methods.
Funding:
National Key Research and Development Program of China, National Natural Science Foundation of China, and Wellcome Trust.
Insights
Triazole resistance in Aspergillus fumigatus is increasing, driven by cyp51A gene mutations. This variation challenges effective treatment of invasive aspergillosis, necessitating improved diagnostic methods.
Area of Science:
- Medical Mycology
- Antimicrobial Resistance
- Genomics
Background:
- Aspergillus fumigatus is a primary cause of invasive aspergillosis.
- Triazole antifungals are the main treatment, but resistance is emerging.
- Key resistance mechanisms involve cyp51A gene mutations and promoter tandem repeats (TR34/Leu98His, TR46/Tyr121Phe/Thr289Ala).
Purpose of the Study:
- To investigate the prevalence and variation of triazole resistance phenotypes and genotypes in clinical Aspergillus fumigatus isolates in the Netherlands over 29 years.
Main Methods:
- Screened 12,679 A. fumigatus isolates for triazole resistance using agar-based methods.
- Characterized resistant isolates by sequencing the cyp51A gene and performing in vitro susceptibility testing.
- Conducted whole-genome sequencing on selected isolates and collected clinical data for patients with available isolates.
Main Results:
- 15.6% of isolates (1979/12,679) showed cyp51A-mediated triazole resistance, predominantly TR34/Leu98His (67.6%) and TR46/Tyr121Phe/Thr289Ala (16.8%).
- Observed 12 cyp51A genotype variants among resistant isolates, with 17.2% exhibiting phenotype and genotype variation.
- Identified 13 triazole-resistant invasive aspergillosis cases, three with genotype variants, and noted mixed genotype infections in 84.6% of these patients.
Conclusions:
- Significant variation exists in triazole resistance genotypes and phenotypes in clinical A. fumigatus isolates, impacting invasive aspergillosis treatment.
- Emerging resistance patterns and mixed genotypes pose challenges for current diagnostic tools in predicting resistance.
- Improved detection methods are crucial for effective clinical management of Aspergillus diseases.
