Utility of a microsatellite assay for identifying clonally related outbreak isolates of Aspergillus fumigatus

Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive Future Potential

Fungal infections pose an increasing threat to public health. New pathogens and changing epidemiology are a pronounced risk for nosocomial outbreaks. To investigate clonal transmission between patients and trace the source, genotyping is required. In the last decades, various typing assays have been developed and applied to different medically important fungal species. While these different typing methods will be briefly discussed, this review will focus on the development and application of short tandem repeat (STR) genotyping. This method relies on the amplification and comparison of highly variable STR markers between isolates. For most common fungal pathogens, STR schemes were developed and compared to other methods, like multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis. The pros and cons of STR typing as compared to the other methods are discussed, as well as the requirements for the development of a solid STR typing assay. The resolution of STR typing, in general, is higher than MLST and AFLP, with WGS SNP analysis being the gold standard when it comes to resolution. Although most modern laboratories are capable to perform STR typing, little progress has been made to standardize typing schemes. Allelic ladders, as developed for Aspergillus fumigatus, facilitate the comparison of STR results between laboratories and develop global typing databases. Overall, STR genotyping is an extremely powerful tool, often complimentary to whole genome sequencing. Crucial details for STR assay development, its applications and merit are discussed in this review.

Insights into Aspergillus fumigatus Colonization in Cystic Fibrosis and Cross-Transmission between Patients and Hospital Environments

BACKGROUND

Approximately 60% of individuals with cystic fibrosis (CF) are affected by Aspergillus fumigatus infection. This condition is correlated with a decline in lung function and is identified as an independent risk factor contributing to hospital admissions among CF patients. This study investigates the dynamic interplay of A. fumigatus within the context of CF patients, tracing its evolution over time, with a specific emphasis on colonization dynamics.

METHODS

An analysis was conducted on 83 sequential A. fumigatus isolates derived from sputum samples of six patients receiving care at a renowned CF hospital in Brazil. Employing microsatellite genotyping techniques, alongside an investigation into cyp51A gene mutations, this research sheds light on the genetic variations, colonization, and resistance of A. fumigatus within the CF respiratory environment.

RESULTS

Our research findings indicate that CF patients can harbor A. fumigatus strains from the same clonal complexes for prolonged periods. Additionally, we identified that clinical isolates have the potential to spread among patients in the same healthcare facility, evidencing hospital contamination. Two patients who underwent long-term Itraconazole treatment did not show phenotypic resistance. However, one of these patients exhibited mutations in the cyp51A gene, indicating the need to monitor resistance to azoles in these patients colonized for long periods by A. fumigatus. We also observed co-colonization or co-infection involving multiple genotypes in all patients over time.

CONCLUSION

This comprehensive examination offers valuable insights into the pathogenesis of A. fumigatus infections in CF patients, potentially shaping future therapeutic strategies and management approaches. This enhanced understanding contributes to our knowledge of A. fumigatus impact on disease progression in individuals with cystic fibrosis. Additionally, the study provides evidence of cross-contamination among patients undergoing treatment at the same hospital.

Azole resistance mechanisms and population structure of the human pathogen Aspergillus fumigatus on retail plant products

Aspergillus fumigatus is a ubiquitous saprotroph and human-pathogenic fungus that is life-threatening to the immunocompromised. Triazole-resistant A. fumigatus was found in patients without prior treatment with azoles, leading researchers to conclude that resistance had developed in agricultural environments where azoles are used against plant pathogens. Previous studies have documented azole-resistant A. fumigatus across agricultural environments, but few have looked at retail plant products. Our objectives were to determine if azole-resistant A. fumigatus is prevalent in retail plant products produced in the United States (U.S.), as well as to identify the resistance mechanism(s) and population genetic structure of these isolates. Five hundred twenty-five isolates were collected from retail plant products and screened for azole resistance. Twenty-four isolates collected from compost, soil, flower bulbs, and raw peanuts were pan-azole resistant. These isolates had the TR34/L98H, TR46/Y121F/T289A, G448S, and H147Y cyp51A alleles, all known to underly pan-azole resistance, as well as WT alleles, suggesting that non-cyp51A mechanisms contribute to pan-azole resistance in these isolates. Minimum spanning networks showed two lineages containing isolates with TR alleles or the F46Y/M172V/E427K allele, and discriminant analysis of principle components identified three primary clusters. This is consistent with previous studies detecting three clades of A. fumigatus and identifying pan-azole-resistant isolates with TR alleles in a single clade. We found pan-azole resistance in U.S. retail plant products, particularly compost and flower bulbs, which indicates a risk of exposure to these products for susceptible populations and that highly resistant isolates are likely distributed worldwide on these products.IMPORTANCEAspergillus fumigatus has recently been designated as a critical fungal pathogen by the World Health Organization. It is most deadly to people with compromised immune systems, and with the emergence of antifungal resistance to multiple azole drugs, this disease carries a nearly 100% fatality rate without treatment or if isolates are resistant to the drugs used to treat the disease. It is important to determine the relatedness and origins of resistant A. fumigatus isolates in the environment, including plant-based retail products, so that factors promoting the development and propagation of resistant isolates can be identified.

Aspergillus Outbreak in an Intensive Care Unit: Source Analysis with Whole Genome Sequencing and Short Tandem Repeats

Whole genome sequencing (WGS) is widely used for outbreak analysis of bacteriology and virology but is scarcely used in mycology. Here, we used WGS for genotyping Aspergillus fumigatus isolates from a potential Aspergillus outbreak in an intensive care unit (ICU) during construction work. After detecting the outbreak, fungal cultures were performed on all surveillance and/or patient respiratory samples. Environmental samples were obtained throughout the ICU. WGS was performed on 30 isolates, of which six patient samples and four environmental samples were related to the outbreak, and twenty samples were unrelated, using the Illumina NextSeq 550. A SNP-based phylogenetic tree was created from outbreak samples and unrelated samples. Comparative analysis (WGS and short tandem repeats (STRs), microsatellite loci analysis) showed that none of the strains were related to each other. The lack of genetic similarity suggests the accumulation of Aspergillus spores in the hospital environment, rather than a single source that supported growth and reproduction of Aspergillus fumigatus. This supports the hypothesis that the Aspergillus outbreak was likely caused by release of Aspergillus fumigatus spores during construction work. Indeed, no new Aspergillus cases were observed in the ICU after cessation of construction. This study demonstrates that WGS is a suitable technique for examining inter-strain relatedness of Aspergillus fumigatus in the setting of an outbreak investigation.

Comparison of Multi-locus Genotypes Detected in Aspergillus fumigatus Isolated from COVID Associated Pulmonary Aspergillosis (CAPA) and from Other Clinical and Environmental Sources

Background: Aspergillus fumigatus is a saprophytic fungus, ubiquitous in the environment and responsible for causing infections, some of them severe invasive infections. The high morbidity and mortality, together with the increasing burden of triazole-resistant isolates and the emergence of new risk groups, namely COVID-19 patients, have raised a crescent awareness of the need to better comprehend the dynamics of this fungus. The understanding of the epidemiology of this fungus, especially of CAPA isolates, allows a better understanding of the interactions of the fungus in the environment and the human body. Methods: In the present study, the M3 markers of the STRAf assay were used as a robust typing technique to understand the connection between CAPA isolates and isolates from different sources (environmental and clinical-human and animal). Results: Of 100 viable isolates that were analyzed, 85 genotypes were found, 77 of which were unique. Some isolates from different sources presented the same genotype. Microsatellite genotypes obtained from A. fumigatus isolates from COVID+ patients were all unique, not being found in any other isolates of the present study or even in other isolates deposited in a worldwide database; these same isolates were heterogeneously distributed among the other isolates. Conclusions: Isolates from CAPA patients revealed high heterogeneity of multi-locus genotypes. A genotype more commonly associated with COVID-19 infections does not appear to exist.

Madurella mycetomatis grains within a eumycetoma lesion are clonal

Eumycetoma is a neglected tropical infection of the subcutaneous tissue, characterized by tumor-like lesions and most commonly caused by the fungus Madurella mycetomatis. In the tissue, M. mycetomatis organizes itself in grains, and within a single lesion, thousands of grains can be present. The current hypothesis is that all these grains originate from a single causative agent, however, this hypothesis was never proven. Here, we used our recently developed MmySTR assay, a highly discriminative typing method, to determine the genotypes of multiple grains within a single lesion. Multiple grains from surgical lesions obtained from 11 patients were isolated and genotyped using the MmySTR panel. Within a single lesion, all tested grains shared the same genotype. Only in one single grain from one patient, a difference of one repeat unit in one MmySTR marker was noted relative to the other grains from that patient. We conclude that within these lesions the grains originate from a single clone and that the inherent unstable nature of the microsatellite markers may lead to small genotypic differences.

Molecular typing of clinical and environmental Aspergillus fumigatus isolates from Iran using microsatellites

Background and Purpose

Because of the growing incidence of Aspergillus infection, typing methods of Aspergillus species are increasingly being used. Accordingly, studying the spread and population dynamics of strains isolating from clinical and environment, from a single host to large-scale ecosystems is definitely needed. In the current study, we carried out a genetic analysis of nine microsatellite loci in isolates from different regions of Iran to compare and explore the genetic diversity between environmental and clinical A. fumigatus strains.

Materials and Methods

Sixty-six clinical (n=43) and environmental (n= 23) isolates of A. fumigatus, have collected from six cities of Iran. All A. fumigatus isolates identified based on macroscopic and microscopic characters, the ability to grow at above 45°C, and confirmed using DNA sequencing of the partial b-tubulin gene. Sixty-six A. fumigatus isolates were subjected by microsatellite typing using three separate multiplex PCRs with a panel of nine short tandem repeats (STR) to evaluate the genetic relatedness.

Results

The STR typing of 66 A. fumigatus isolates revealed 38 distinct genotypes distributed among environmental and clinical isolates. We identified 12 clones including 40 different isolates representing 60% of all isolates tested, which each clone included 2-7 isolates.

Conclusion

The STR typing is considered as a valuable tool with excellent discriminatory power to study the molecular epidemiology and genotypic diversity of A. fumigatus isolates. These findings show that the high genetic diversity observed of Iranian A. fumigatus isolates with those outside Iran and formed a separate cluster.

Clonal Expansion of Environmental Triazole Resistant Aspergillus fumigatus in Iran

Azole-resistance in Aspergillus fumigatus is a worldwide medical concern complicating the management of aspergillosis (IA). Herein, we report the clonal spread of environmental triazole resistant A. fumigatus isolates in Iran. In this study, 63 A. fumigatus isolates were collected from 300 compost samples plated on Sabouraud dextrose agar supplemented with itraconazole (ITR) and voriconazole (VOR). Forty-four isolates had the TR₃₄/L98H mutation and three isolates a TR₄₆/Y121F/T289A resistance mechanism, while two isolates harbored a M172V substitution in cyp51A. Fourteen azole resistant isolates had no mutations in cyp51A. We found that 41 out of 44 A. fumigatus strains with the TR₃₄/L98H mutation, isolated from compost in 13 different Iranian cities, shared the same allele across all nine examined microsatellite loci. Clonal expansion of triazole resistant A. fumigatus in this study emphasizes the importance of establishing antifungal resistance surveillance studies to monitor clinical Aspergillus isolates in Iran, as well as screening for azole resistance in environmental A. fumigatus isolates.

Investigation of the Relationships Between Clinical and Environmental Isolates of Aspergillus fumigatus by Multiple-locus Variable Number Tandem Repeat Analysis During Major Demolition Work in a French Hospital

Background

Genotyping is needed to explore the link between clinical cases from colonization of invasive aspergillosis (IA) and major building construction. Attempts to correlate Aspergillus fumigatus strains from clinical infection or colonization with those found in the environment remain controversial due to the lack of a large prospective study. Our aim in this study was to compare the genetic diversity of clinical and environmental A. fumigatus isolates during a demolition period.

Methods

Fungal contamination was monitored daily for 11 months in 2015. Environmental surveillance was undertaken indoors and outdoors at 8 locations with automatic agar samplers. IA infection cases were investigated according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group criteria. Isolates were identified by amplification and sequencing of the β- tubulin gene. They were genotyped by multiple-locus variable number tandem repeat analysis (MLVA). The phylogenetic relationships between isolates were assessed by generating a minimum spanning tree.

Results

Based on 3885 samples, 394 A. fumigatus isolates (383 environmental and 11 clinical) were identified and genotyped using MLVA. Clinical isolates were collected from patients diagnosed as having probable IA (n = 2), possible IA (n = 1), or bronchial colonization (n = 6). MLVA generated 234 genotypes. Seven clinical isolates shared genotypes identical to environmental isolates.

Conclusions

Among the diversity of genotypes described, similar genotypes were found in clinical and environmental isolates, indicating that A. fumigatus infection and colonization may originate from hospital environments.

Microsatellite Stability in STR Analysis Aspergillus fumigatus Depends on Number of Repeat Units

More than a decade ago a short tandem repeat-based typing method was developed for the fungus Aspergillus fumigatus. This STRAf assay is based on the analysis of nine short tandem repeat markers. Interpretation of this STRAf assay is complicated when there are only one or two differences in tandem repeat markers between isolates, as the stability of these markers is unknown. To determine the stability of these nine markers, a STRAf assay was performed on 73–100 successive generations of five clonally expanded A. fumigatus isolates. In a total of 473 generations we found five times an increase of one tandem repeat unit. Three changes were found in the trinucleotide repeat marker STRAf 3A, while the other two were found in the trinucleotide repeat marker STRAf 3C. The di- or tetranucleotide repeats were not altered. The altered STRAf markers 3A and 3C demonstrated the highest number of repeat units (≥50) as compared to the other markers (≤26). Altogether, we demonstrated that 7 of 9 STRAf markers remain stable for 473 generations and that the frequency of alterations in tandem repeats is positively correlated with the number of repeats. The potential low level instability of STRAf markers 3A and 3C should be taken into account when interpreting STRAf data during an outbreak.

Comparison of Two Highly Discriminatory Typing Methods to Analyze Aspergillus fumigatus Azole Resistance

Aspergillus fumigatus molecular typing has become increasingly more important for detecting outbreaks as well as for local and global epidemiological investigations and surveillance. Over the years, many different molecular methods have been described for genotyping this species. Some outstanding approaches are based on microsatellite markers (STRAf assay, which is the current gold standard), or based on sequencing data (TRESP typing improved in this work with a new marker and was renamed TRESPERG). Both methodologies were used to type a collection of 212 A. fumigatus isolates that included 70 azole resistant strains with diverse resistance mechanisms from different geographic locations. Our results showed that both methods are totally reliable for epidemiological investigations showing similar stratification of the A. fumigatus population. STRAf assay offered higher discriminatory power (D = 0.9993) than the TRESPERG typing method (D = 0.9972), but the latter does not require specific equipment or skilled personnel, allowing for a prompt integration into any clinical microbiology laboratory. Among azole resistant isolates, two groups were differentiated considering their resistance mechanisms: cyp51A single point mutations (G54, M220, or G448), and promoter tandem repeat integrations with or without cyp51A modifications (TR₃₄/L98H, TR₄₆/Y121F/A289T, or TR₅₃). The genotypic differences were assessed to explore the population structure as well as the genetic relationship between strains and their azole resistance profile. Genetic cluster analyses suggested that our A. fumigatus population was formed by 6–7 clusters, depending on the methodology. Also, the azole susceptible and resistance population showed different structure and organization. The combination of both methodologies resolved the population structure in a similar way to what has been described in whole-genome sequencing works.

Elevated MIC Values of Imidazole Drugs against Aspergillus fumigatus Isolates with TR34/L98H/S297T/F495I Mutation

The use of azole fungicides in agriculture is believed to be one of the main reasons for the emergence of azole resistance in Aspergillus fumigatus Though widely used in agriculture, imidazole fungicides have not been linked to resistance in A. fumigatus This study showed that elevated MIC values of imidazole drugs were observed against A. fumigatus isolates with TR₃₄/L98H/S297T/F495I mutation, but not among isolates with TR₃₄/L98H mutation. Short-tandem-repeat (STR) typing analysis of 580 A. fumigatus isolates from 20 countries suggested that the majority of TR₃₄/L98H/S297T/F495I strains from China were genetically different from the predominant major clade comprising most of the azole-resistant strains and the strains with the same mutation from the Netherlands and Denmark. Alignments of sterol 14α-demethylase sequences suggested that F495I in A. fumigatus was orthologous to F506I in Penicillium digitatum and F489L in Pyrenophora teres, which have been reported to be associated with imidazole resistance. In vitro antifungal susceptibility testing of different recombinants with cyp51A mutations further confirmed the association of the F495I mutation with imidazole resistance. In conclusion, this study suggested that environmental use of imidazole fungicides might confer selection pressure for the emergence of azole resistance in A. fumigatus.

Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How?

Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.

A Pseudo-outbreak of Aspergillosis at a Tertiary Care Hospital: Thinking Beyond the Infection Control Risk Assessment

In the modern era of carefully monitored renovations, construction-relatedAspergillusoutbreaks have decreased. We investigated an increase in clinical cultures growingAspergillusspecies, determining that contamination of the mycology lab caused a pseudo-outbreak. A major construction site was appropriately sealed, but unrecognized staff traffic may have facilitated laboratory contamination.

Infect Control Hosp Epidemiol2016;1–4

A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP)

Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed. A. fumigatus isolates were characterized by PCR amplification and sequencing with a panel of three TRESP encoding genes: cell surface protein A; MP-2 antigenic galactomannan protein; and hypothetical protein with a CFEM domain. The allele sequence repeats of each of the three targets were combined to assign a specific genotype. For the evaluation of this method, 126 unrelated A. fumigatus strains were analyzed and 96 different genotypes were identified, showing a high level of discrimination [Simpson’s index of diversity (D) 0.994]. In addition, 49 azole resistant strains were analyzed identifying 26 genotypes and showing a lower D value (0.890) among them. This value could indicate that these resistant strains are closely related and share a common origin, although more studies are needed to confirm this hypothesis. In summary, a novel genotyping method for A. fumigatus has been developed which is reproducible, easy to perform, highly discriminatory and could be especially useful for studying outbreaks.

Azole-resistant Aspergillus fumigatus in Denmark: a laboratory-based study on resistance mechanisms and genotypes

Azole-resistant Aspergillus fumigatus originating from the environment as well as induced during therapy are continuously emerging in Danish clinical settings. We performed a laboratory-based retrospective study (2010-2014) of azole resistance and genetic relationship of A. fumigatus at the national mycology reference laboratory of Denmark. A total of 1162 clinical and 133 environmental A. fumigatus isolates were identified by morphology, thermotolerance and/or β-tubulin sequencing. Screening for azole resistance was carried out using azole agar, and resistant isolates were susceptibility tested by the EUCAST (European Committee on Antimicrobial Susceptibility Testing) E.Def 9.2 reference method and CYP51A sequenced. Genotyping was performed for outbreak investigation and, when appropriate, short tandem repeat Aspergillus fumigatus microsatellite assay. All 133 environmental A. fumigatus isolates were azole susceptible. However, from 2010 to 2014, there was an increasing prevalence of azole resistance (from 1.4 to 6% isolates (p <0.001) and 1.8 to 4% patients (p <0.05)) among the clinical isolates, with the well-known environmental CYP51A variant TR34/L98H responsible for >50% of the azole resistance mechanisms. Among 184 Danish A. fumigatus isolates, 120 unique genotypes were identified and compared to a collection of 1822 international genotypes. Seven (5.8%) Danish genotypes were shared between isolates within Denmark but with different origin, 19 (15.8%) were shared with foreign genotypes, and two (11.8%) of 17 genotypes of isolates carrying the TR34/L98H resistance mechanisms were identical to two Dutch TR34/L98H isolates. Our findings underlines the demand for correct identification and susceptibility testing of clinical mould isolates. Furthermore, although complex, genotyping supported the hypotheses regarding clonal expansion and the potential of a single origin for the TR34/L98H clone.

Microsatellite Typing of Aspergillus flavus Strains in a Tunisian Onco-hematology Unit

Aspergillus flavus is the most common species associated with invasive aspergillosis in Tunisia. The molecular epidemiology of the species is poorly documented. We used five highly discriminative microsatellite markers for the genotyping of clinical and hospital environmental A. flavus strains to assess whether IA could be hospital-acquired in the onco-hematology unit of the Farhat Hached teaching hospital of Sousse, Tunisia. The genotyping of 18 clinical isolates, collected from sputa of 17 acute leukemia patients, and 81 isolates, collected in these patients' hospital environment and food, identified 57 isolates that were grouped in 10 clones, each of them including 2-17 isolates. The remaining 42 isolates showed a unique genotype. Two main transmission scenarios were observed: (1) the same clone was isolated from different patients; (2) the same clone was isolated from a patient, its hospital environment and/or food. These findings strongly suggest the occurrence of hospital-acquired A. flavus infection/colonization in the investigated onco-hematology unit.

Molecular Epidemiology of Invasive Aspergillosis: Lessons Learned from an Outbreak Investigation in an Australian Hematology Unit

Suspected nosocomial Aspergillus fumigatus infections in an Australian hematology unit were investigated by molecular typing of clinical and environmental isolates using polymerase chain reaction fingerprinting, CSP typing, and multilocus microsatellite typing. Only multilocus microsatellite typing revealed that all isolates were genetically distinct. The selection of an appropriate typing method is essential for effective outbreak investigations.

Isolate-dependent growth, virulence, and cell wall composition in the human pathogen Aspergillus fumigatus

The ubiquitous fungal pathogen Aspergillus fumigatus is a mediator of allergic sensitization and invasive disease in susceptible individuals. The significant genetic and phenotypic variability between and among clinical and environmental isolates are important considerations in host-pathogen studies of A. fumigatus-mediated disease. We observed decreased radial growth, rate of germination, and ability to establish colony growth in a single environmental isolate of A. fumigatus, Af5517, when compared to other clinical and environmental isolates. Af5517 also exhibited increased hyphal diameter and cell wall β-glucan and chitin content, with chitin most significantly increased. Morbidity, mortality, lung fungal burden, and tissue pathology were decreased in neutropenic Af5517-infected mice when compared to the clinical isolate Af293. Our results support previous findings that suggest a correlation between in vitro growth rates and in vivo virulence, and we propose that changes in cell wall composition may contribute to this phenotype.

Azole-resistant Aspergillus fumigatus isolate with the TR34/L98H mutation in both a fungicide-sprayed field and the lung of a hematopoietic stem cell transplant recipient with invasive aspergillosis

A French farmer developed invasive aspergillosis with azole-resistant Aspergillus fumigatus with the TR34/L98H mutation following a hematopoietic stem cell transplantation. He had worked in fungicide-sprayed fields where a non-genetically related A. fumigatus TR34/L98H isolate was collected. If azole resistance detection increases, voriconazole as first-line therapy might be questioned in agricultural areas.

Genetic and virulence variation in an environmental population of the opportunistic pathogen Aspergillus fumigatus

Environmental populations of the opportunistic pathogen Aspergillus fumigatus have been shown to be genotypically diverse and to contain a range of isolates with varying pathogenic potential. In this study, we combined two RAPD primers to investigate the genetic diversity of environmental isolates from Manchester collected monthly over 1 year alongside Dublin environmental isolates and clinical isolates from patients. RAPD analysis revealed a diverse genotype, but with three major clinical isolate clusters. When the pathogenicity of clinical and Dublin isolates was compared with a random selection of Manchester isolates in a Galleria mellonella larvae model, as a group, clinical isolates were significantly more pathogenic than environmental isolates. Moreover, when relative pathogenicity of individual isolates was compared, clinical isolates were the most pathogenic, Dublin isolates were the least pathogenic and Manchester isolates showed a range in pathogenicity. Overall, this suggests that the environmental population is genetically diverse, displaying a range in pathogenicity, and that the most pathogenic strains from the environment are selected during patient infection.

Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011

BACKGROUND

Mucormycosis is a fungal infection caused by environmentally acquired molds. We investigated a cluster of cases of cutaneous mucormycosis among persons injured during the May 22, 2011, tornado in Joplin, Missouri.

METHODS

We defined a case as a soft-tissue infection in a person injured during the tornado, with evidence of a mucormycete on culture or immunohistochemical testing plus DNA sequencing. We conducted a case-control study by reviewing medical records and conducting interviews with case patients and hospitalized controls. DNA sequencing and whole-genome sequencing were performed on clinical specimens to identify species and assess strain-level differences, respectively.

RESULTS

A total of 13 case patients were identified, 5 of whom (38%) died. The patients had a median of 5 wounds (range, 1 to 7); 11 patients (85%) had at least one fracture, 9 (69%) had blunt trauma, and 5 (38%) had penetrating trauma. All case patients had been located in the zone that sustained the most severe damage during the tornado. On multivariate analysis, infection was associated with penetrating trauma (adjusted odds ratio for case patients vs. controls, 8.8; 95% confidence interval [CI], 1.1 to 69.2) and an increased number of wounds (adjusted odds ratio, 2.0 for each additional wound; 95% CI, 1.2 to 3.2). Sequencing of the D1-D2 region of the 28S ribosomal DNA yielded Apophysomyces trapeziformis in all 13 case patients. Whole-genome sequencing showed that the apophysomyces isolates were four separate strains.

CONCLUSIONS

We report a cluster of cases of cutaneous mucormycosis among Joplin tornado survivors that were associated with substantial morbidity and mortality. Increased awareness of fungi as a cause of necrotizing soft-tissue infections after a natural disaster is warranted.

Diversity and specificity of microsatellites within Aspergillus section Fumigati

BACKGROUND

Microsatellites (or short tandem repeats, STRs) are the genetic markers of choice for studying Aspergillus fumigatus molecular epidemiology due to its reproducibility and high discrimination power. However, the specificity of these markers must be investigated in a group of isolates from closely related species. The aim of this work was to test a microsatellite-based PCR multiplex previously designed for A. fumigatus in a set of species belonging to section Fumigati, namely Aspergillus fumigatiaffinis, Aspergillus lentulus, Aspergillus novofumigatus, Aspergillus unilateralis, Aspergillus viridinutans, Neosartorya fischeri, Neosartorya hiratsukae, Neosartorya pseudofischeri and Neosartorya udagawae.

RESULTS

The reference A. fumigatus strain ATCC 46645 was easily genotyped in standard conditions showing a final electrophoretic profile of 8 expected peaks corresponding to each microsatellite locus. Inversely, no peaks were observed for all other species from section Fumigati, with an exception for marker MC6b in A. unilateralis. By screening the genome sequence of Neosartorya fischeri NRRL 181, the results showed that MC3, MC6a and MC7 might be employed for N. fischeri genotyping since these markers present several repeats of each motif. The accumulation of insertions and deletions was frequently observed in the genomic regions surrounding the microsatellites, including those where the A. fumigatus primers are located. The amplification of microsatellite markers in less stringent amplification conditions resulted in a distinct electrophoretic profile for species within section Fumigati.

CONCLUSIONS

Therefore, the microsatellite-based PCR multiplex allow simple identification of A. fumigatus and, with a slight modification of temperature conditions, it also allows discriminating other pathogenic species within section Fumigati, particularly A. fumigatiaffinis, N. fischeri and N. udagawae.

Molecular epidemiology of Aspergillus fumigatus isolates harboring the TR34/L98H azole resistance mechanism

A rapid emergence of azole resistance has been observed in Aspergillus fumigatus in The Netherlands over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves the TR(34)/L98H mutations in cyp51A. This resistance mechanism is now also increasingly being found in other countries. Therefore, genetic markers were used to gain more insights into the origin and spread of this genotype. Studies of 142 European isolates revealed that those with the TR(34)/L98H resistance mechanism showed less genetic variation than azole-susceptible isolates or those with a different genetic basis of resistance and were assigned to only four CSP (putative cell surface protein) types. Sexual crossing experiments demonstrated that TR(34)/L98H isolates could outcross with azole-susceptible isolates of different genetic backgrounds, suggesting that TR(34)/L98H isolates can undergo the sexual cycle in nature. Overall, our findings suggest a common ancestor of the TR(34)/L98H mechanism and subsequent migration of isolates harboring TR(34)/L98H across Europe.

Molecular epidemiology of Aspergillus fumigatus: an in-depth genotypic analysis of isolates involved in an outbreak of invasive aspergillosis

We recently reported an outbreak of invasive aspergillosis in the major heart surgery unit of Hospital Gregorio Marañón, Madrid, Spain (T. Peláez, P. Muñoz, J. Guinea, M. Valerio, M. Giannella, C. H. W. Klaassen, and E. Bouza, Clin. Infect. Dis., in press). Aspergillus fumigatus was isolated from clinical samples from 10 patients admitted to the unit during the outbreak period (surgical wound invasive aspergillosis, n = 2; probable pulmonary invasive aspergillosis, n = 4; colonization, n = 4). In the study described here, we have studied the genotypic diversity of the A. fumigatus isolates found in the air and clinical samples. We used short tandem repeats of A. fumigatus (STRAf) typing to analyze the genotypes found in the 168 available A. fumigatus isolates collected from the clinical samples (n = 109) from the patients and from the environmental samples taken from the air of the unit (n = 59). The genotypic variability of A. fumigatus was higher in environmental than in clinical samples. Intrasample variability was also higher in environmental than in clinical samples: 2 or more different genotypes were found in 26% and 89% of clinical and environmental samples, respectively. We found matches between environmental and clinical isolates in 3 of the 10 patients: 1 patient with postsurgical invasive aspergillosis and 2 patients with probable pulmonary invasive aspergillosis. A total of 7 genotypes from 3 different patients and the air grouped together in 2 clusters. Clonally related genotypes and microvariants were detected in both clinical and environmental samples. STRAf typing proved to be a valuable tool for identifying the source of invasive aspergillosis outbreaks and for studying the genotypic diversity of clinical and environmental A. fumigatus isolates.

High resolution genotyping of clinical Aspergillus flavus isolates from India using microsatellites

BACKGROUND

Worldwide, Aspergillus flavus is the second leading cause of allergic, invasive and colonizing fungal diseases in humans. However, it is the most common species causing fungal rhinosinusitis and eye infections in tropical countries. Despite the growing challenges due to A. flavus, the molecular epidemiology of this fungus has not been well studied. We evaluated the use of microsatellites for high resolution genotyping of A. flavus from India and a possible connection between clinical presentation and genotype of the involved isolate.

METHODOLOGY/PRINCIPAL FINDINGS

A panel of nine microsatellite markers were selected from the genome of A. flavus NRRL 3357. These markers were used to type 162 clinical isolates of A. flavus. All nine markers proved to be polymorphic displaying up to 33 alleles per marker. Thirteen isolates proved to be a mixture of different genotypes. Among the 149 pure isolates, 124 different genotypes could be recognized. The discriminatory power (D) for the individual markers ranged from 0.657 to 0.954. The D value of the panel of nine markers combined was 0.997. The multiplex multicolor approach was instrumental in rapid typing of a large number of isolates. There was no correlation between genotype and the clinical presentation of the infection.

CONCLUSIONS/SIGNIFICANCE

There is a large genotypic diversity in clinical A. flavus isolates from India. The presence of more than one genotype in clinical samples illustrates the possibility that persons may be colonized by multiple genotypes and that any isolate from a clinical specimen is not necessarily the one actually causing infection. Microsatellites are excellent typing targets for discriminating between A. flavus isolates from various origins.

Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus

Background

Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus.

Results

We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8) of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89). The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST). The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France.

Conclusions

MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a clear separation between isolates according to their geographic origin rather than their respective hosts.

The Aspergillus fumigatus cspA gene encoding a repeat-rich cell wall protein is important for normal conidial cell wall architecture and interaction with host cells

cspA (for cell surface protein A) encodes a repeat-rich glycophosphatidylinositol (GPI)-anchored cell wall protein (CWP) in the pathogenic fungus Aspergillus fumigatus. The number of repeats in cspA varies among isolates, and this trait is used for typing closely related strains of A. fumigatus. We have previously shown that deletion of cspA is associated with rapid conidial germination and reduced adhesion of dormant conidia. Here we show that cspA can be extracted with hydrofluoric acid (HF) from the cell wall, suggesting that it is a GPI-anchored CWP. The cspA-encoded CWP is unmasked during conidial germination and is surface expressed during hyphal growth. Deletion of cspA results in weakening of the conidial cell wall, whereas its overexpression increases conidial resistance to cell wall-degrading enzymes and inhibits conidial germination. Double mutant analysis indicates that cspA functionally interacts with the cell wall protein-encoding genes ECM33 and GEL2. Deletion of cspA together with ECM33 or GEL2 results in strongly reduced conidial adhesion, increased disorganization of the conidial cell wall, and exposure of the underlying layers of chitin and beta-glucan. This is correlated with increasing susceptibility of the DeltacspA, DeltaECM33, and DeltacspA DeltaECM33 mutants to conidial phagocytosis and killing by human macrophages and hyphal damage induced by neutrophils. However, these strains did not exhibit altered virulence in mice with infected lungs. Collectively, these results suggest a role for cspA in maintaining the strength and integrity of the cell wall.

Microsatellite typing to trace Aspergillus flavus infections in a hematology unit

Assessing the relatedness of strains isolated from patients and their environment is instrumental in documenting the source of preventable health care-associated life-threatening Aspergillus flavus human infection clusters. The present study aimed at identifying and selecting suitable microsatellite markers for A. flavus typing. This typing scheme was then applied to investigate the A. flavus epidemiology within a hematology unit in Sfax, Tunisia. Use of a combination of five markers made it possible to discern clusters of isolates and to substantiate the genetic diversity of A. flavus within clusters. Isolates from Tunisia and Marseille, France, displayed distinct haplotypes, indicating a highly significant geographical structuring of A. flavus. The typing of clinical and environmental A. flavus isolates in a hematology unit provided insights into its hospital epidemiology. From a heterogeneous genetic background, a cluster indicative of a clonal propagation episode within the unit could be identified. In two patients with invasive aspergillosis, the same genotype was found in clinical and environmental isolates, indicating hospital-acquired colonization and infection. In further studies, this novel microsatellite typing scheme might be instrumental in illuminating important epidemiological issues about A. flavus population genetics or epidemiology, including tracing the sources and routes of transmission.

The first documented case of Aspergillus cardiac surgical site infection in Sweden: an epidemiology study using arbitrarily primed PCR

Here we report two rare cases of severe thoracic Aspergillus fumigatus infections after lung and heart surgery at the same thoracic intensive care unit at the same time. The main objective was to identify a possible source of transmission. With arbitrarily primed polymerase chain reaction a patient-to-patient transmission could rapidly be ruled out as the cause of the first documented case of aspergillosis after open-heart surgery in Sweden. Although no definitive source was identified, a genetically similar strain was found in a contaminated supply room.

Comparison of multiple typing methods for Aspergillus fumigatus

As part of studies on the spread of infections, risk factors and prevention, several typing methods were developed to investigate the epidemiology of Aspergillus fumigatus. In the present study, 52 clinical isolates of A. fumigatus from 12 airway specimens from patients with invasive aspergillosis (hospitalized in three different centres) were characterized by short tandem repeat (STR) typing and multilocus sequence typing (MLST). These isolates were previously typed by random amplified polymorphic DNA (RAPD), sequence-specific DNA polymorphism (SSDP), microsatellite polymorphism (MSP) and multilocus enzyme electrophoresis (MLEE). STR typing identified 30 genotypes and, for most patients, all isolates were grouped in one cluster of the unweighted pair group method with arithmetic mean dendrogram. Using MLST, 16 genotypes were identified among 50 isolates, while two isolates appeared untypeable. RAPD, MSP, SSDP and MLEE allowed identification of eight, 14, nine and eight genotypes, respectively. Combining the results of these methods led to the delineation of 25 genotypes and a similar clustering pattern as with STR typing. In general, STR typing led to similar results to the previous combination of RAPD, SSDP, MSP and MLEE, but had a higher resolution, whereas MLST was less discriminatory and resulted in a totally different clustering pattern. Therefore, this study suggests the use of STR typing for research concerning the local epidemiology of A. fumigatus, which requires a high discriminatory power.

Utility of a proposed CSP typing nomenclature for Australian Aspergillus fumigatus isolates: Identification of additional CSP types and suggested modifications

A recently developed CSP typing scheme and proposed nomenclature was applied to a collection of 164 clinical and environmental Aspergillus fumigatus isolates from Melbourne, Australia. Fifteen CSP variants were observed overall, including three that were not reported in the original nomenclature that described 19 CSP variants, raising the possibility of phylogeographic differences between the Australian and the previously studied European and North American A. fumigatus populations. However, those CSP variants that were common between this and the previous studies appeared to have a broadly similar prevalence. The presence of an additional CCT codon in the 3' flanking region of some CSP variants was also observed in homologous Neosartorya fischeri sequence, suggesting that the absence of this codon in other isolates is due to codon deletion, rather than its presence representing a duplication. We recommend a number of modifications to the proposed CSP type nomenclature to accommodate these new findings.

Interlaboratory reproducibility of a single-locus sequence-based method for strain typing of Aspergillus fumigatus

Seven international laboratories tested the recently proposed single-locus typing strategy for Aspergillus fumigatus subtyping for interlaboratory reproducibility. Comparative sequence analyses of portions of the locus AFUA_3G08990, encoding a putative cell surface protein (denoted CSP), was performed with a panel of Aspergillus isolates. Each laboratory followed very different protocols for extraction of DNA, PCR, and sequencing. Results revealed that the CSP typing method was a reproducible and portable strain typing method.

MLST versus microsatellites for typing Aspergillus fumigatus isolates

In recent years, there has been a clear and growing tendency to use exact typing methods for discrimination between microbial isolates. Exact typing methods that yield an unambiguous typing result offer a number of advantages over conventional methods in the generation of typing data that is reproducible, portable and exchangeable. Two such methods are multi-locus sequence typing (MLST) and microsatellite-based typing. Here I will discuss the basic principles of both methods and compare them from a practical and performance point of view with respect to typing Aspergillus fumigatus isolates. Microsatellites offer the best available typing option by outperforming MLST in terms of speed, throughput, costs and discriminatory power. This latter advantage of microsatellites is a direct consequence of their inherent instability. This (in)stability of individual microsatellite markers and alleles should be taken into account in the interpretation of microsatellite-based typing data.

Simple and highly discriminatory microsatellite-based multiplex PCR for Aspergillus fumigatus strain typing

The answers to important questions concerning Aspergillus fumigatus pathogenicity, transmissions routes and efficacy of treatments require highly discriminating and reproducible genotyping methods. The present study was aimed at improving microsatellite methodology for A. fumigatus typing by reducing the task of strain identification to a single multiplex reaction and by selecting highly accurate short tandem repeat polymorphisms. A set of eight primer pairs was used for the genotype determination of 116 clinical isolates of A. fumigatus obtained from three healthcare centres. A new, automated and highly discriminatory typing method is described for A. fumigatus strains. The optimized multiplex PCR was successfully performed with all tested clinical strains and showed a discriminatory power of 0.9997 among presumably unrelated isolates. The comparison of groups of strains from different health centres showed that 99.6% of the genotypic variation was present within groups. Strains with the same genotype were isolated from the same patient, sometimes recovered more than 1 year later. A few cases of patients at the same clinic unit carrying strains of identical genotype strongly suggested colonization by A. fumigatus during their hospitalization. Specific measures must therefore be taken in order to prevent and restrict such incidents.