Limited evidence of fungicide-driven triazole-resistant Aspergillus fumigatus in Hamilton, Canada

Assessing thermal adaptation of a global sample of Aspergillus fumigatus: Implications for climate change effects

Aspergillus fumigatus is a common environmental mold and a major cause of opportunistic infections in humans. It's distributed among many ecological niches across the globe. A major virulence factor of A. fumigatus is its ability to grow at high temperature. However, at present, little is known about variations among strains in their growth at different temperatures and how their geographic origins may impact such variations. In this study, we analyzed 89 strains from 12 countries (Cameroon, Canada, China, Costa Rica, France, India, Iceland, Ireland, New Zealand, Peru, Saudi Arabia, and USA) representing diverse geographic locations and temperature environments. Each strain was grown at four temperatures and genotyped at nine microsatellite loci. Our analyses revealed a range of growth profiles, with significant variations among strains within individual geographic populations in their growths across the temperatures. No statistically significant association was observed between strain genotypes and their thermal growth profiles. Similarly geographic separation contributed little to differences in thermal adaptations among strains and populations. The combined analyses among genotypes and growth rates at different temperatures in the global sample suggest that most natural populations of A. fumigatus are capable of rapid adaptation to temperature changes. We discuss the implications of our results to the evolution and epidemiology of A. fumigatus under increasing climate change.

Aspergillus fumigatus sternal osteomyelitis following cardiac surgery: Case report and literature review

BACKGROUND

Sternal osteomyelitis caused by Aspergillus spp is uncommon in cardiac surgery patients requiring sternotomy.

CASE PRESENTATION

We report a 77-year-old male with a history of poorly controlled diabetes who was diagnosed with Aspergillus sternal osteomyelitis, three months following an uneventful coronary artery bypass surgery. He underwent multiple debridement surgeries and was treated with voriconazole. Despite a complicated post-operative course, the patient responded well to voriconazole with clinical and biochemical evidence of remission. Unfortunately, he died of an unrelated cause due to decompensated heart failure.

DISCUSSION

Though uncommon, Aspergillus sternal osteomyelitis should be considered in the differential diagnosis of immunocompetent patients with post-operative sternal wound infections and negative bacterial tissue cultures. Management should include a combination of medical and surgical therapy.

Genetic Diversity and Azole Resistance Among Natural Aspergillus fumigatus Populations in Yunnan, China

The emergence and spread of azole resistance alleles in clinical and environmental isolates of Aspergillus fumigatus is a global human health concern and endangers the "One Health" approach in our fight against antifungal resistance (AFR) in this pathogen. A major challenge to combat AFR in A. fumigatus is the massive aerial dispersal ability of its asexual spores. Our recent fine-scale survey of greenhouse populations of A. fumigatus near Kunming, Yunnan, China, suggested that the use of azole fungicides for plant protection was likely a major driver of the high-frequency azole-resistant A. fumigatus (ARAF) in greenhouses. Here, we investigated the potential spread of those ARAF and the structure of geographic populations of A. fumigatus by analyzing 452 isolates from 19 geographic locations across Yunnan. We found lower frequencies of ARAF in these outdoor populations than those in greenhouses near Kunming, but there were abundant new alleles and new genotypes, including those associated with azole resistance, consistent with multiple independent origins of ARAF across Yunnan. Interestingly, among the four ecological niches, the sediments of a large lake near Kunming were found to have the highest frequency of ARAF (~ 43%). While most genetic variations were observed within the 19 local populations, statistically significant genetic differentiations were found between many subpopulations within Yunnan. Furthermore, similar to greenhouse populations, these outdoor populations of A. fumigatus in Yunnan were significantly different from those in other parts of the world. Our results call for increased attention to local and regional studies of this fungal pathogen to help develop targeted control strategies against ARAF.

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.

Molecular Epidemiology of Azole-Resistant Aspergillus fumigatus in France Shows Patient and Healthcare Links to Environmentally Occurring Genotypes

Resistance of the human pathogenic fungus Aspergillus fumigatus to antifungal agents is on the rise. However, links between patient infections, their potential acquisition from local environmental sources, and links to global diversity remain cryptic. Here, we used genotyping analyses using nine microsatellites in A. fumigatus, in order to study patterns of diversity in France. In this study, we genotyped 225 local A. fumigatus isolates, 112 azole susceptible and 113 azole resistant, collected from the Bourgogne-Franche-Comté region (Eastern France) and sampled from both clinical (n = 34) and environmental (n = 191) sources. Azole-resistant clinical isolates (n = 29) were recovered mainly from cystic fibrosis patients and environmental isolates (n = 84) from market gardens and sawmills. In common with previous studies, the TR₃₄/L98H allele predominated and comprised 80% of resistant isolates. The genotypes obtained for these local TR₃₄/L98H isolates were integrated into a broader analysis including all genotypes for which data are available worldwide. We found that dominant local TR₃₄/L98H genotypes were isolated in different sample types at different dates (different patients and types of environments) with hospital air and patient's isolates linked. Therefore, we are not able to rule out the possibility of some nosocomial transmission. We also found genotypes in these same environments to be highly diverse, emphasizing the highly mixed nature of A. fumigatus populations. Identical clonal genotypes were found to occur both in the French Eastern region and in the rest of the world (notably Australia), while others have not yet been observed and could be specific to our region. Our study demonstrates the need to integrate patient, healthcare, and environmental sampling with global databases in order to contextualize the local-scale epidemiology of antifungal resistant aspergillosis.

Prevalence of Azole-Resistant Aspergillus fumigatus is Highly Associated with Azole Fungicide Residues in the Fields

Triazole resistance in Aspergillus fumigatus is a growing public health concern. In addition to its emergence in the therapy of invasive aspergillosis by triazole medicines, it has been frequently detected in agricultural fields all over the world. Here, we explore the potential link between residues of azole fungicides with similar chemical structure to triazole medicines in soil and the emergence of resistant A. fumigatus (RAF) through 855 500 km² monitoring survey in Eastern China covering 6 provinces. In total, 67.3%, 15.2%, 12.3%, 2.9%, 1.5%, 0.4%, and 0.3% of the soil samples contained these five fungicides (tebuconazole, difenoconazole, propiconazole, hexaconazole, and prochloraz) of 0-100, 100-200, 200-400, 400-600, 600-800, 800-1000, and >1000 ng/g, respectively. The fractions of samples containing RAF isolates were 2.4%, 5.2%, 6.4%, 7.7%, 7.4%, 14.3%, and 20.0% of the samples with total azole fungicide residues of 0-100, 100-200, 200-400, 400-600, 600-800, 800-1000, and >1000 ng/g, respectively. We find that the prevalence of RAFs is positively (P < 0.0001) correlated with residual levels of azole fungicides in soils. Our results suggest that the use of azole fungicides in agriculture should be minimized and the intervals between treatments expanded to reduce the selective pressure toward the development of resistance in A. fumigatus in agricultural fields.

Variations in sexual fitness among natural strains of the opportunistic human fungal pathogen Aspergillus fumigatus

Aspergillus fumigatus is a ubiquitous ascomycete fungus, naturally inhabiting the soil and compost piles. Its conidia readily disperse into the atmosphere and cause opportunistic infections known as aspergillosis. With the emerging resistance to many antifungal drugs, our understanding of A. fumigatus epidemiology has become increasingly important for developing effective control and treatment strategies. As a pathogen capable of both sexual and asexual reproduction, mutations causing drug resistance and increased virulence could be spread rapidly in A. fumigatus populations. However, relatively little is known about the distributions of sexual reproductive fitness among natural strains of A. fumigatus. Here we investigated the formation of sexual reproductive structure (i.e. cleistothecia) and sexual spore viability among 60 natural strains of A. fumigatus. These strains were from six geographically distant countries (India, China, Canada, Cameroon, Saudi Arabia, and New Zealand), with 10 strains (including five MAT1-1 strains and five MAT1-2 strains) from each country. These strains were crossed in all combinations with strains of the opposite mating type. In addition, all 60 strains were crossed with either AFB62-1 (MAT1-1) or AFIR928 (MAT1-2), two reference supermater strains. Of the 900 crosses among the 60 natural strains, 136 crosses (15.1%) produced cleistothecia. Our analyses revealed that strains from China had the highest average ability to form cleistothecia, followed by those from New Zealand, Saudi Arabia, India, Canada, and Cameroon. Among the crosses that produced cleistothecia, about 40% produced viable ascospores, with the rate of ascospore germination varied significantly among crosses. Interestingly, neither the ability to form cleistothecia nor ascospore germination rate showed any distinct relationships with either geographic or genetic distance between parental strains. Our results suggest that genetic exchange among geographically and genetically divergent strains of A. fumigatus are possible. However, the rates of genetic exchange likely vary among strains and populations in nature.

Comparative Genome Sequence Analyses of Geographic Samples of Aspergillus fumigatus-Relevance for Amphotericin B Resistance

Amphotericin B (AMB) is a major fungicidal polyene agent that has a broad spectrum of action against invasive fungal infections. AMB is typically used as the last-line drug against serious and life-threatening infections when other drugs have failed to eliminate the fungal pathogens. Recently, AMB resistance in Aspergillus fumigatus has become more evident. For example, a high rate of AMB resistance (96%) was noted in the A. fumigatus population in Hamilton, Ontario, Canada. AMB-resistant strains have also been found in other countries. However, the mechanism of AMB resistance remains largely unknown. Here, we investigated the potential genes and mutations associated with AMB resistance using whole-genome sequences and examined AMB resistance distribution among genetic populations. A total of 196 whole-genome sequences representing strains from 11 countries were examined. Analyses of single nucleotide polymorphisms (SNPs) at the whole-genome level revealed that these strains belonged to three divergent genetic clusters, with the majority (90%) of AMB resistant strains located in one of the three clusters, Cluster 2. Our analyses identified over 60 SNPs significantly associated with AMB resistance. Together, these SNPs represent promising candidates from which to investigate the putative molecular mechanisms of AMB resistance and for their potential use in developing rapid diagnostic markers for clinical screening of AMB resistance in A. fumigatus.

Fungal species concepts in the genomics era

The 140 000 or so fungal species reported so far are heterogeneously defined based on varying criteria such as morphological, physiological, mating, and (or) molecular features. Incongruences are common among traits used to separating closely related species and it is often difficult to compare fungal taxonomic groups defined based on different species recognition criteria. Though DNA sequence-based classification and identification have been made, a consensus has not been reached, primarily due to intrinsic limitations in the proposed one or a few genes. Here, I argue that the fundamental reason for the observed inconsistencies is that speciation is a stochastic process with the emergence and fixation of different traits influenced differently by many non-deterministic factors such as population size, random mutation, mode(s) of reproduction, selection imposed by interacting biotic and abiotic factors, and chance events. Each species concept attempts to capture one or a few traits emerged in the continuous process of speciation. I propose that a genome sequence-based classification and identification system could unify and stabilize fungal taxonomy and help integrate taxonomy with other fields of fungal biology. The genomic species concept could be similarly argued for other groups of eukaryotic microbes as well as for plants and animals.

Contemporary Gene Flow is a Major Force Shaping the Aspergillus fumigatus Population in Auckland, New Zealand

Aspergillus fumigatus is a globally distributed opportunistic fungal pathogen capable of causing highly lethal invasive aspergillosis in immunocompromised individuals. Recent studies have indicated that the global population consists of multiple, divergent genetic clusters that are geographically broadly distributed. However, most of the analyzed samples have come from continental Eurasia and the Americas where the effects of ancient versus recent factors are difficult to distinguish. Here, we investigated environmental A. fumigatus isolates from Auckland, New Zealand, a geographically isolated population, and compared them with those from other parts of the world to determine the relative roles of historical differentiation and recent gene flow in shaping A. fumigatus populations. Our data suggest that the Auckland A. fumigatus population contains both unique indigenous genetic elements as well as genetic elements that are similar to those from other regions such as Europe, Africa, and North America. Though the hypothesis of random recombination was rejected, we found abundant evidence for phylogenetic incompatibility and recombination within the Auckland A. fumigatus population. Additionally, susceptibility testing identified two triazole-resistant strains, one of which contained the globally distributed mutation TR₃₄/L98H in the cyp51A gene. Our results suggest that contemporary gene flow, likely due to anthropogenic factors, is a major force shaping the New Zealand A. fumigatus population.

Determination of azole fungal residues in soils and detection of Aspergillus fumigatus-resistant strains in market gardens of Eastern France

Medical azole antifungals are major compounds used to prevent and to treat invasive aspergillosis (IA). Azole fungicides, called DMI (14-alpha demethylase inhibitors), are also widely used for crop protection and have been reported to be linked to azole-resistant A. fumigatus (aR-Af) development in the environment. The aim of this study was to determine whether or not market gardens that spray DMIs in Eastern France are also affected by the presence of aR-Af. Forty aR-Afs were detected in soils in only two of the four market gardens using DMIs, with 23% (7/30) and 10% (3/30) of soils containing aR-Af. A total of 87.5% of these isolates had the TR34/L98H mutation and 22.5% the TR46/Y121F/T289A mutation on the cyp51A gene. Analyses of residual azole concentrations in soils showed the presence of difenoconazole for up to 2 years after spraying, but only in soils of market gardens where aR-Af was detected. It is very important to identify professional activities that could lead to aR-Af development and to develop preventive measures for at-risk patients living near professional activities using DMIs. We have to better understand why, in some cases, the use of DMI is not linked to aR-Af. Measures should be taken to avoid the use of DMI conferring cross-resistance to preserve the efficiency of human therapeutics.

Widespread amphotericin B-resistant strains of Aspergillus fumigatus in Hamilton, Canada

Purpose

Amphotericin B (AMB) is one of the major antifungal drugs used in the management of aspergillosis and is especially recommended for treating triazole-resistant strains of Aspergillus fumigatus. However, relatively little is known about the AMB susceptibility patterns of A. fumigatus in many parts of the world. This study aims to describe the AMB susceptibility patterns in Hamilton, Ontario, Canada.

Methods

The in vitro susceptibilities of 195 environmental and clinical A. fumigatus isolates to AMB were tested by the broth microdilution method as per the Clinical and Laboratory Standards Institute’s guidelines. Catalase-generated oxygen bubbles trapped by Triton X-100 were used to quantify catalase activity in a representative group of isolates.

Results

Of the 195 isolates, 188 (96.4%) had the minimum inhibitory concentration (MIC) of AMB ≥2 mg/L, with approximately 80% and 20% of all clinical and environmental isolates having MICs of ≥ 4 mg/L. Overall, the clinical isolates were less susceptible to AMB than environmental isolates (P-value <0.001). The strain with the highest AMB MIC (16 mg/L) had one of the highest catalase activities. However, there was no correlation between AMB MIC and catalase activity in our sample.

Conclusion

The widespread AMB resistance suggests that using AMB in the management of A. fumigatus infections in Hamilton would likely result in treatment failure. Although high catalase activity may have contributed to AMB resistance in some isolates, the mechanism(s) for the observed AMB resistance in Hamilton is unknown and likely complex.