Algorithm to assess the presence of Aspergillus fumigatus resistant strains: The case of Norwegian sawmills

Detection of pan-azole resistant Aspergillus fumigatus in horticulture and a composting facility in Belgium

Azole resistance in Aspergillus fumigatus (ARAf) is becoming a worldwide health threat due to increasing occurrence in the environment. However, environmental surveillance programs are not commonly in place and are lacking in Belgium. Since no data on the occurrence of ARAf and the presence of hotspots for the selection of azole resistance is available in Belgium, a first study on the prevalence of ARAf in the environment was conducted. A total of 232 air and compost or soil samples were taken from two composting facilities, and from horticultural and agricultural crops. The azole susceptibility pattern was determined using the EUCAST method (E. Def. 9.4), and the cyp51A gene and its promotor region were sequenced in A. fumigatus isolates with phenotypic azole resistance. Six pan-azole-resistant A. fumigatus isolates were identified, originating from compost and horticultural crops. Four isolates carried the TR34/L98H mutation, and one isolate carried the TR46/Y121F/T289A mutation. However, we did not observe any ARAf isolates from agricultural crops. In conclusion, this study reported the first TR34/L98H and TR46/Y121F/T289A mutation isolated from a composting facility and horticulture in Belgium. The implementation of standardization in environmental surveillance of A. fumigatus on a European level would be beneficial in order to identify hotspots.

Exposure to resistant fungi across working environments and time

Antifungal resistance has emerged as a significant health concern with increasing reports of resistant variants in previously susceptible species. At present, little is known about occupational exposure to antifungal-resistant fungi. This study aimed to investigate Danish workers' occupational exposure to airborne fungi resistant to first-line treatment drugs. A retrospective study was performed on a unique collection of personal exposure samples gathered over a twenty-year period from Danish working environments, in sectors including agriculture, animal handling, waste management, and healthcare. A total of 669 samples were cultivated at 37 °C and fungal colonies were identified using MALDI-TOF MS. Subsequently, identification was confirmed by amplicon sequencing the genes of calmodulin and beta-tubulin to unveil potential cryptic species. Infectious fungi (495 isolates from 23 species) were tested for resistance against Itraconazole, Voriconazole, Posaconazole, and Amphotericin B. Working environments were highly variable in the overall fungal exposure, and showed vastly different species compositions. Resistance was found in 30 isolates of the species Aspergillus fumigatus (4 of 251 isolates), A. nidulans (2 of 13), A. niger complex (19 of 131), A. versicolor (3 of 18), and A. lentulus (2 of 2). Sequence analysis revealed several cryptic species within the A. niger complex including A. tubingensis, A. luchuensis, and A. phoenicis. Among the resistant A. fumigatus isolates, two contained the well-described TR34/L98H mutation in the cyp51A gene and promoter region, while the remainder harbored silent mutations. The results indicate that the working environment significantly contributes to exposure to resistant fungi, with particularly biofuel plant workers experiencing high exposure. Differences in the prevalence of resistance across working environments may be linked to the underlying species composition.

Prevalence of Azole-Resistant Aspergillus Section Fumigati Strains Isolated from Romanian Vineyard Soil Samples

The relationship between fungal species and their resistance patterns in vineyard soils has important implications for agriculture and medicine. This study explored the prevalence of Aspergillus section Fumigati species and their resistance to azole compounds in Romanian vineyard soils.

METHODS

A total of 265 soil samples from various Romanian vineyards were screened for fungi resistant to azoles.

RESULTS

Aspergillus section Fumigati isolates exhibited significant resistance to itraconazole and voriconazole, but no azole-resistant Aspergillus fumigatus strains were detected. Six percent of the samples were positive for Aspergillus section Fumigati strains, all of which were azole-resistant. The strains were mainly Aspergillus udagawae (93.75%) and Aspergillus lentulus (6.25%). The predominant azole-resistant Aspergillus species were Aspergillus section Nigri strains, which were found in 75 soil samples.

CONCLUSIONS

This study highlights the importance of understanding fungal resistance in vineyard soils for both the agricultural and clinical sectors. The presence of resistant strains may affect vine health and wine production while also constituting a challenge in the selection of effective treatments against severe and potentially fatal fungal infections in humans, stressing the importance of species-specific antifungal resistance knowledge.

Microbial Contamination of Bedding Material: One Health in Poultry Production

In poultry farms, the mixture of bedding material, chicken excrement, and feathers seems to play an important role in pathogen development which may contribute to a potential risk of zoonosis, spreading the disease through the food chain. The purpose of this study was to analyze microbial contamination in bedding material and other matrices as well as potential antimicrobial resistances in chicken production facilities, and also to identify the sampling techniques and assays used. This study evidences the available data published, following the PRISMA methodology. Among the environmental samples, surface swabs were frequently used as a passive sampling technique. Morphological identification was performed in all studies. From all the matrices, the bedding material was the most contaminated. Most studies focused on bacterial contamination, with Salmonella sp. and Campylobacter sp. being commonly reported and three studies evidenced fungal contamination, being Penicillium sp.- and Aspergillus sp.-dominant. Mycotoxin assessment was only performed in one study, being identified in all bedding samples. The screening for bacteria resistance evidenced bacteria multidrug resistance; however, fungal susceptibility to azoles was not assessed in any of the analyzed studies. Briefly, this review evidences the microbial contamination in poultry facilities, emphasizing animals' bedding as a potential source of contamination. Additionally, this study contributes to a sampling and analysis protocol proposal to assess the microbial contamination in this setting. Additionally, the knowledge gaps identified highlight the need of further research regarding microbial contamination and toxicological potential on animals' bedding in order to mitigate the exposure in poultry pavilions.

Unveiling the Occupational Exposure to Microbial Contamination in Conservation–Restoration Settings

Assuring a proper environment for the fulfillment of professional activities is one of the Sustainable Development Goals and is contemplated in the One Health approach assumed by the World Health Organization. This particular study is applied to an often neglected sector of our society—the conservators/restorers—despite the many health issues reported by these professionals. Three different specialties (textiles, paintings and wood sculpture) and locations were selected for evaluation by placement of electrostatic dust cloths. After treatment of the samples, bacterial and fungal contamination were assessed, as well as mycotoxin determination, the presence of azole-resistant strains and cytotoxicity of the microorganisms encountered. Bacteria were only present in one of medias used and showed relatively low numbers. The highest level of contamination by fungi was identified in one of the textiles settings. The textile area also showed the highest variability for fungi. Aspergillus sp. are one indicator of possible environmental issues, and A. sections Fumigati and Circumdati were particularly relevant in two of the settings and identified in all of them. No mycotoxins were detected and the large majority of the fungi identified were non-cytotoxic. Overall, these can be considered low-contaminated environments but attention should be given to the Aspergillus sp. contamination. Additional studies are needed not only to make these results more robust, but also to test if the environmental sampling alone is the best approach in a setting where there is very little movement and dust displacement and where professionals are in very close proximity to the artefacts being treated, which may suggest the existence of a micro-atmosphere worth evaluating and comparing to the obtained results.

Development of an Indexed Score to Identify the Most Suitable Sampling Method to Assess Occupational Exposure to Fungi

The sampling approach is of utmost importance to obtain data regarding microbial viability and truly assess workers’ potential health effects. The purpose of this assessment is to create a score which will provide up-to-date information to identify the most suitable sampling method to assess occupational exposure to fungi. Data from a sampling campaign performed at Firefighters Headquarters (FFH) was analysed and a score was calculated from one (1) to three (3) for five (5) distinct sample parameters: (a) accuracy; (b) complexity of the field work; (c) cost; (d) complexity in laboratory work; and (e) time taken since the fieldwork until obtaining the fungal contamination characterization. The statistical analysis allowed us to conclude that settled dust and Andersen six-stage were the best sampling methods to perform the assessment of the occupational exposure to fungi at FFH, when considering the number of species. As for the final score, the results showed that surface swabs were the best sampling method. The results obtained for surface swabs highlights the low complexity of this processing combined with the fact that it is a low-cost sampling method. This study reinforces the need to use a wide array of sampling methods when assessing occupational exposure to fungal contamination to ensure an accurate risk characterization.

Six Feet under Microbiota: Microbiologic Contamination and Toxicity Profile in Three Urban Cemeteries from Lisbon, Portugal

Cemeteries are potential environmental reservoirs of pathogenic microorganisms from organic matter decomposition. This study aimed to characterize the microbial contamination in three cemeteries, and more specifically in grave diggers’ facilities. One active sampling method (impingement method) and several passive sampling methods (swabs, settled dust, settled dust filters and electrostatic dust cloths—EDC) were employed. The molecular detection of Aspergillus sections and SARS-CoV-2, as well as mycotoxin analysis, screening of azole resistance, and cytotoxicity measurement were also conducted. Total bacteria contamination was 80 CFU·m⁻² in settled dust samples, reached 849 CFU·m⁻² in EDC and 20,000 CFU·m⁻² in swabs, and ranged from 5000 to 10,000 CFU·m⁻² in filters. Gram-negative bacteria (VRBA) were only observed in in settled dust samples (2.00 × 10⁵ CFU·m⁻²). Regarding Aspergillus sp., the highest counts were obtained in DG18 (18.38%) and it was not observed in azole-supplemented SDA media. SARS-CoV-2 and the targeted Aspergillus sections were not detected. Mycophenolic acid was detected in one settled dust sample. Cytotoxic effects were observed for 94.4% filters and 5.6% EDC in A549 lung epithelial cells, and for 50.0% filters and 5.6% EDC in HepG2 cells. Future studies are needed in this occupational setting to implement more focused risk management measures.

Microbial Occupational Exposure Assessments in Sawmills—A Review

The composition of airborne microflora in sawmills may vary to a great degree depending on the kind of timber being processed and the technology of production being used. Cases of allergy alveolitis and asthma have been reported in woodworkers who were exposed to wood dust largely infected with microorganisms. The aim of this review article is to identify studies where the microbial occupational exposure assessment was performed in sawmills and the characteristics of the contamination found, as well as to identify which sampling methods and assays were applied. This study reports the search of available data published regarding microbial occupational exposure assessment in environmental samples from sawmills, following the Preferred Reporting Items for Systematic Reviews (PRISMA) methodology. The most used sampling method was air sampling, impaction being the most common method. Regarding analytical procedures for microbial characterization, morphological identification of fungi and bacteria was the most frequent approach. Screening for fungal susceptibility to azoles was performed in two studies and four studies applied molecular tools. Regarding microbial contamination, high fungal levels were frequent, as well as high bacteria levels. Fungal identification evidenced Penicillium as the most frequent genera followed by Aspergillus sp. Mycotoxins were not assessed in any of the analyzed studies. Microbial occupational exposure assessment in sawmills is crucial to allow this risk characterization and management.

Cytotoxicity of Aspergillus Section Fumigati Isolates Recovered from Protection Devices Used on Waste Sorting Industry

Safe working conditions must be guaranteed during waste sorting, which is crucial to maximizing recycling and reuse, in order to minimize workers’ exposure to chemical and biological hazards. This study determines the contribution of Aspergillus section Fumigati to the overall cytotoxicity of filtering respiratory protection devices (FRPD) and mechanic protection gloves (MPG) collected in 2019 from different workstations in one waste sorting industry in Portugal. The cytotoxicity of 133 Aspergillus section Fumigati isolates was determined as IC50 in human A549 epithelial lung cells and swine kidney cells, using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Aspergillus section Fumigati cytotoxicity results were compared with previous total cytotoxicity data from FRPD and MPG samples. A significant correlation was detected between the total cytotoxicity of samples and cytotoxicity of Aspergillus section Fumigati isolates in A549 cells (rS = −0.339, p = 0.030). The cytotoxicity of Aspergillus section Fumigati isolates explained 10.7% of the total cytotoxicity of the sample. On the basis of the comparison of cytotoxicity levels, it was possible to determine the contribution of Aspergillus section Fumigati isolates for the total cytotoxicity of protection devices used in the waste sorting industry. The results support in vitro toxicology as a relevant approach in risk assessments regarding cytotoxicity in passive sampling, and thus, useful in determining the contribution of relevant microbial contaminants to overall cytotoxicity. This approach can provide valuable answers in dose/response studies, and support innovations in risk characterization and their translation into occupational policies.

Genetic Diversity and Dispersal of Aspergillus fumigatus in Arctic Soils

Aspergillus fumigatus is a saprophytic mold and an opportunistic pathogen with a broad geographic and ecological distribution. A. fumigatus is the most common etiological agent of aspergillosis, affecting over 8,000,000 individuals worldwide. Due to the rising number of infections and increasing reports of resistance to antifungal therapy, there is an urgent need to understand A. fumigatus populations from local to global levels. However, many geographic locations and ecological niches remain understudied, including soil environments from arctic regions. In this study, we isolated 32 and 52 A. fumigatus strains from soils in Iceland and the Northwest Territories of Canada (NWT), respectively. These isolates were genotyped at nine microsatellite loci and the genotypes were compared with each other and with those in other parts of the world. Though significantly differentiated from each other, our analyses revealed that A. fumigatus populations from Iceland and NWT contained evidence for both clonal and sexual reproductions, and shared many alleles with each other and with those collected from across Europe, Asia, and the Americas. Interestingly, we found one triazole-resistant strain containing the TR₃₄ /L98H mutation in the cyp51A gene from NWT. This strain is closely related to a triazole-resistant genotype broadly distributed in India. Together, our results suggest that the northern soil populations of A. fumigatus are significantly influenced by those from other geographic regions.

Selection and Amplification of Fungicide Resistance in Aspergillus fumigatus in Relation to DMI Fungicide Use in Agronomic Settings: Hotspots versus Coldspots

Aspergillus fumigatus is a ubiquitous saprophytic fungus. Inhalation of A. fumigatus spores can lead to Invasive Aspergillosis (IA) in people with weakened immune systems. The use of triazole antifungals with the demethylation inhibitor (DMI) mode of action to treat IA is being hampered by the spread of DMI-resistant "ARAf" (azole-resistant Aspergillus fumigatus) genotypes. DMIs are also used in the environment, for example, as fungicides to protect yield and quality in agronomic settings, which may lead to exposure of A. fumigatus to DMI residues. An agronomic setting can be a "hotspot" for ARAf if it provides a suitable substrate and favourable conditions for the growth of A. fumigatus in the presence of DMI fungicides at concentrations capable of selecting ARAf genotypes at the expense of the susceptible wild-type, followed by the release of predominantly resistant spores. Agronomic settings that do not provide these conditions are considered "coldspots". Identifying and mitigating hotspots will be key to securing the agronomic use of DMIs without compromising their use in medicine. We provide a review of studies of the prevalence of ARAf in various agronomic settings and discuss the mitigation options for confirmed hotspots, particularly those relating to the management of crop waste.

Cytotoxicity of Aspergillus Section Fumigati Isolated from Health Care Environments

This study analyzed 57 Aspergillus section Fumigati (AF) isolates collected by active and passive sampling (N = 450) in several health care facilities and from biological sampling of health care workers (N = 25) and controls (N = 22) in Portugal. All isolates were cultured in different media and screened for azole resistance. Cytotoxicity was assessed for 40 isolates in lung epithelial cells and kidney cells using the MTT assay. Aspergillus section Fumigati was prevalent in the health care facilities and in nasal swabs from health care workers and controls. All AF isolates reduced cell viability and presented medium to high cytotoxicity, with cytotoxicity being significantly higher in A549 lung epithelial cells. The cytotoxicity of isolates from air and nasal swab samples suggested the inhalation route as a risk factor. Notably, 42% of AF isolates exhibited a pattern of reduced susceptibility to some of the most used antifungals available for the treatment of patients infected with these fungi. In sum, the epidemiology and clinical relevance of Aspergillus section Fumigati should continue to be addressed. A deeper understanding of the mechanisms underlying Aspergillus-mediated cytotoxicity is necessary.

Aspergillus Section Fumigati in Firefighter Headquarters

Background: Aspergillus section Fumigati is one of the Aspergillus sections more frequently related to respiratory symptoms and by other health outcomes. This study aimed to characterize Aspergillus section Fumigati distribution in eleven firefighter headquarters (FFHs) to obtain an accurate occupational exposure assessment. Methods: A sampling approach protocol was performed using active (impaction method) and passive sampling methods (floor surfaces swabs, electrostatic dust collectors (EDCs), and settled dust). All samples were analysed by culture-based methods and passive sampling was used for molecular detection of Aspergillus section Fumigati. Results: Of all the matrices, the highest counts of Aspergillus sp. were obtained on settled dust filters (3.37% malt extract agar—MEA, 19.09% dichloran glycerol—DG18) followed by cleaning cloths (1.67% MEA; 7.07% DG18). Among the Aspergillus genus, the Fumigati section was predominant in Millipore and EDC samples in MEA (79.77% and 28.57%, respectively), and in swabs and settled dust filters in DG18 (44.76% and 30%, respectively). The Fumigati section was detected more frequently in DG18 (33.01%) compared to MEA (0.33%). The Fumigati section was observed in azole supplemented media (itraconazole and voriconazole) in several passive sampling methods employed and detected by qPCR in almost all passive samples, with EDCs being the matrix with the highest prevalence (n = 61; 67.8%). Conclusion: This study confirms that Aspergillus sp. is widespread and the Fumigati section is present in all FFHs. The presence of fungi potentially resistant to azoles in the FFHs was also observed. Further studies are needed to identify the best corrective and preventive measures to avoid this section contamination in this specific occupational environment.

Azole-resistant Aspergillus fumigatus in the environment: Identifying key reservoirs and hotspots of antifungal resistance

Aspergillus fumigatus is an opportunistic human pathogen that causes aspergillosis, a spectrum of environmentally acquired respiratory illnesses. It has a cosmopolitan distribution and exists in the environment as a saprotroph on decaying plant matter. Azoles, which target Cyp51A in the ergosterol synthesis pathway, are the primary class of drugs used to treat aspergillosis. Azoles are also used to combat plant pathogenic fungi. Recently, an increasing number of azole-naive patients have presented with pan-azole-resistant strains of A. fumigatus. The TR34/L98H and TR46/Y121F/T289A alleles in the cyp51A gene are the most common ones conferring pan-azole resistance. There is evidence that these mutations arose in agricultural settings; therefore, numerous studies have been conducted to identify azole resistance in environmental A. fumigatus and to determine where resistance is developing in the environment. Here, we summarize the global occurrence of azole-resistant A. fumigatus in the environment based on available literature. Additionally, we have created an interactive world map showing where resistant isolates have been detected and include information on the specific alleles identified, environmental settings, and azole fungicide use. Azole-resistant A. fumigatus has been found on every continent, except for Antarctica, with the highest number of reports from Europe. Developed environments, specifically hospitals and gardens, were the most common settings where azole-resistant A. fumigatus was detected, followed by soils sampled from agricultural settings. The TR34/L98H resistance allele was the most common in all regions except South America where the TR46/Y121F/T289A allele was the most common. A major consideration in interpreting this survey of the literature is sampling bias; regions and environments that have been extensively sampled are more likely to show greater azole resistance even though resistance could be more prevalent in areas that are under-sampled or not sampled at all. Increased surveillance to pinpoint reservoirs, as well as antifungal stewardship, is needed to preserve this class of antifungals for crop protection and human health.

Selective Flamingo Medium for the Isolation of Aspergillus fumigatus

For various studies in the clinic as well as the environment, it is essential to be able to selectively isolate Aspergillus fumigatus from samples containing bacteria as well as various other fungi (mainly Mucorales). Six agar media were compared for effectiveness in selectively isolating Aspergillus fumigatus from agricultural plant waste, woodchip waste, green waste, soil, grass and air samples collected in The Netherlands at a 48 °C incubation. The Flamingo Medium incubated at 48 °C, provided the most effective condition for the isolation of A. fumigatus from environmental samples, since it effectively inhibited the growth of competing fungi (mainly Mucorales) present in the environmental samples. Flamingo Medium reduced the number of colonies of Mucorales species by 95% and recovered an average of 20-30% more A. fumigatus colonies compared to the other media. We further confirmed that Flamingo Medium can inhibit the growth of clinical Mucorales, which occasionally present in patient's tissue and can also be used for clinical applications. We suggest the use of Flamingo Medium as an efficient method for the study of A. fumigatus from important environmental niches for which there is increasing interest. Additionally, it can also be used in the clinic to isolate A. fumigatus especially from tissue contaminated with Mucorales.

Azole-Resistant Aspergillus fumigatus Harboring the TR34/L98H Mutation: First Report in Portugal in Environmental Samples

Introduction: The frequency in detection of azole-resistant Aspergillus fumigatus isolates has increased since 2010. In Portugal, the section Fumigati is one of the most frequent, and resistant strains to have been found in clinical and environmental contexts. Although several cryptic species within the Fumigati section show intrinsic resistance to azoles, one factor driving (acquired) resistance is selective pressure deriving from the extensive use of azoles. This is particularly problematic in occupational environments where high fungal loads are expected, and where there is an increased risk of human exposure and infection, with impact on treatment success and disease outcome. The mechanisms of resistance are diverse, but mainly associated with mutations in the cyp51A gene. Despite TR₃₄/L98H being the most frequent mutation described, it has only been detected in clinical specimens in Portugal. Methods: We analyzed 99 A. fumigatus isolates from indoor environments (healthcare facilities, spas, one dairy and one waste sorting unit) collected from January 2018 to February 2019 in different regions of Portugal. Isolates were screened for resistance to itraconazole, voriconazole and posaconazole by culture, and resistance was confirmed by broth microdilution. Sequencing of the cyp51A gene and its promoter was performed to detect mutations associated with resistance. Results: Overall, 8.1% of isolates were able to grow in the presence of at least one azole, and 3% (isolated from the air in a dairy and from filtering respiratory protective devices in a waste sorting industry) were pan-azole-resistant, bearing the TR₃₄/L98H mutation. Conclusion: For the first time in Portugal, we report environmental isolates bearing the TR₃₄/L98H mutation, isolated from occupational environments. Environmental surveillance of the emergence of azole-resistant A. fumigatus sensu stricto strains is needed, to ensure proper and timely implementation of control policies that may have a positive impact on public and occupational health.

Culture Media and Sampling Collection Method for Aspergillus spp. Assessment: Tackling the Gap between Recommendations and the Scientific Evidence

Culturing is still the most widely used method for determining fungal growth. Thus, is important to identify the most suitable culture media to assess Aspergillus spp. The aim of this study was to analyze data obtained from previous studies, aiming at identifying the most suitable culture media (malt extract agar (MEA) or dichloran-glycerol agar (DG18) to assess Aspergillus spp. isolation and growth. This study was conducted by using environmental samples (n = 1153). Most of the active sampling methods (air samples) were impacted directly onto both culture media. As for passive sampling methods, fungi were extracted from environmental matrices inoculated onto both media. Overall, total Aspergillus counts were higher in MEA (n = 617, 53.5%) than in DG18 (n = 536, 46.5%). Regarding Aspergillus sections, significant associations were detected with the media (χ2 (7) = 241.118, p < 0.001), the sampling approach (p < 0.001, 95% CI = (0.3 × 10−4), and the indoor environment (p < 0.001, 95% CI = (0.3 × 10−4)). As such, sampling approach and the culture media should be accurately selected when dealing with Aspergillus spp. exposure assessment.

Settleable Dust and Bioburden in Portuguese Dwellings

Monitoring campaigns in several buildings have shown that occupants exposed to contaminated indoor air generally exhibit diverse health symptoms. This study intends to assess settleable dust loading rates and bioburden in Portuguese dwellings by passive sampling onto quartz fiber filters and electrostatic dust cloths (EDCs), respectively. Settled dust collected by EDCs was analyzed by culture-based methods (including azole-resistance screening) and qPCR, targeting four different toxigenic Aspergillus sections (Flavi, Fumigati, Circumdati, and Nidulantes). Dust loading rates and bioburden showed higher variability in the summer season. In both seasons, Penicillium sp. was the one with the highest prevalence (59.1% winter; 58.1% summer), followed by Aspergillus sp. in winter (13.0%). Fungal contamination increased in the winter period, while bacterial counts decreased. Aspergillus sections Circumdati and Nidulantes, detected in voriconazole supplemented media, and Aspergillus sections Fumigati and Nidulantes, detected by molecular tools, were found in the winter samples. This study reinforces the importance of applying: (a) Passive sampling methods in campaigns in dwellings; (b) two different culture media (MEA and DG18) to assess fungi; (c) in parallel, molecular tools targeting the most suitable indicators of fungal contamination; and (d) azole resistance screening to unveil azole resistance detection in fungal species.