New restriction fragment length polymorphism (RFLP) markers for Aspergillus fumigatus

A Comparison of Microsatellites in Phytopathogenic Aspergillus Species in Order to Develop Markers for the Assessment of Genetic Diversity among Its Isolates

The occurrence of Microsatellites (SSRs) has been witnessed in most of the fungal genomes however its abundance varies across species. In the present study, we analyzed the frequency of SSRs in the whole genome and transcripts of two phyto-pathogenic (Aspergillus niger and Aspergillus terreus) and compared them with two non-pathogenic (Aspergillus nidulans and Aspergillus oryzae) Aspergillus. Higher relative abundance and relative density of SSRs were observed in the whole genome and transcript sequences of the pathogenic Aspergillus when compared to the non-pathogenic. The relative abundance and density of SSRs were positively correlated with the G+C content of transcripts. Among the different classes of SSR, the percentage of tetra-nucleotide SSRs were maximum in A. niger (36.7%) and A. oryzae (35.9%) whereas A. nidulans and A. terreus preferred tri-nucleotide SSRs (38.2 and 42.1%) in whole genome sequences. In transcripts, tri-nucleotide SSRs were the most abundant whereas di-nucleotide SSRs were the least favored. Motif conservation study among the transcripts revealed conservation of only 27% motif within Aspergillus species. Furthermore, a similar relationship among the Ascomycetes was obtained on the basis of motif conservation and conserved genes (rDNA). To analyze the diversity present within the Indian isolates of Aspergillus, primers were successfully designed for 692 motifs in A. niger and A. terreus of which 20 were selected for diversity analysis. Among all the markers amplified, 10 markers (83.3%) were polymorphic, whereas remaining two markers (16.6%) were monomorphic. Ten polymorphic markers acquired in this investigation showed the utility of recently created SSR markers in the assessment of genetic diversity among various isolates of Aspergillus.

A review molecular typing methods for Aspergillus flavus isolates

Aspergillus flavus is the second most important Aspergillus species causing human infections. The importance of this fungus increases in regions with a dry and hot climate. Small phylogenetic studies in Aspergillus flavus indicate that the morphological species contains several genetically isolated species. Different genotyping methods have been developed and employed in order to better understand the genetic and epidemiological relationships between environmental and clinical isolates. Understanding pathogen distribution and relatedness is essential for determining the epidemiology of nosocomial infections and aiding in the design of rational pathogen control methods. Typing techniques can also give us a deeper understanding of the colonization pattern in patients. Most of these studies focused on Aspergillus fumigatus because it is medically the most isolated species. To date, there has not been any publication exclusively reviewing the molecular typing techniques for Aspergillus flavus in the literature. This article reviews all these different available methods for this organism.

Molecular typing of Aspergillus species

Aspergillus species are widely distributed fungi that release large amounts of airborne conidia, which are dispersed in the environment. Several Aspergillus species have been described as human pathogens. Molecular techniques have been developed to investigate the epidemiological relation between environmental and clinical isolates. Several typing methods have been described for Aspergillus species, most of them with reference to Aspergillus fumigatus. Here, we summarise all the different available molecular typing techniques for Aspergillus. The performance of these techniques is evaluated with respect to their practical feasibility, and their interpretation and discriminatory power assessed. For A. fumigatus isolates, a large extent of genetic variability is demonstrated and therefore fingerprinting techniques with high discriminatory power and high reproducibility are required for this species. Afut1-restriction fragment length polymorphism and microsatellite typing showed the highest discriminatory power. In addition, the microsatellites show excellent reproducibility. Other typing techniques are still useful for smaller epidemiological problems and for less well-equipped laboratories.

Multilocus sequence typing of the pathogenic fungus Aspergillus fumigatus

A multilocus sequence typing (MLST) scheme was devised for Aspergillus fumigatus. The system involved sequencing seven gene fragments and was applied to a panel of 100 isolates of A. fumigatus from diverse sources. Thirty different sequence types were found among the 100 isolates, and 93% of the isolates differed from the other isolates by only one allele sequence, forming a single clonal cluster as indicated by the eBURST algorithm. The discriminatory power of the MLST method was only 0.93. These results strongly indicate that A. fumigatus is a species of a relatively recent origin, with low levels of sequence dissimilarity. Typing methods based on variable numbers of tandem repeats offer higher levels of strain discrimination. Mating type data for the 100 isolates showed that 71 isolates were type MAT1-2 and 29 isolates were MAT1-1.

Molecular typing of aspergilli: Recent developments and outcomes

Aspergillus spp. have been the subject of numerous epidemiological studies. The most useful typing techniques are DNA based methods including the random amplified polymorphic DNA technique, microsatellite length polymorphisms, restriction fragment length polymorphism (RFLP) analysis using retrotransposon-like sequences as probes, and multilocus sequence typing. The results of typing clinical isolates indicate that most of the invasive aspergillosis (IA) patients were infected by a single strain. Genetic analysis could not discriminate between clinical and environmental isolates of Aspergillus. fumigatus, indicating that every strain present in the environment is a potential pathogen if it encounters the appropriate host. The source of infection can also be monitored by typing. Typing studies led to the discovery of a new pathogenic species, A. lentulus, and to the identification of several species not known previously to be pathogenic. Typing studies revealed the existence of two genetically isolated groups within a global A. fumigatus population. Aspergillus fumigatus was found to be the first example of a true cosmopolitan fungus. Additionally, the results obtained in several studies support the premise that recombination played an important role in A. fumigatus populations. The discovery of functional mating type genes in A. fumigatus indicates that past or recent sexual processes could be responsible for the observed recombining population structure.

Taf1: a class II transposon of Aspergillus fumigatus

Aspergillus fumigatus is an important medical pathogen that lacks a known sexual cycle. Transposons may provide an important mechanism for the generation of genetic diversity in this organism. Here, we describe Taf1, the first class II transposon to be identified in A. fumigatus. Taf1, a member of the mariner superfamily and pogo family of transposons, is distinguished by the presence of extremely long (89 bp) inverted repeats that flank the transposase coding sequence. Taf1 is present in different locations and copy number among clinical strains of A. fumigatus and is transcribed. Analysis of multiple insertion sequences within a single strain suggests that Taf1 elements undergo inactivation by a repeat induced polymorphism-like mechanism. Taf1 insertion patterns were extremely stable despite multiple stressors including heat shock, serial passage, and infection in mice. Thus Taf1 may be useful for strain identification and molecular typing.

In vitro evolution of itraconazole resistance in Aspergillus fumigatus involves multiple mechanisms of resistance

We investigated the evolution of resistance to the antifungal drug itraconazole in replicate populations of Aspergillus fumigatus that were founded from a strain with a genotype of sensitivity to a single drug and then propagated under uniform conditions. For each population, conidia were serially transferred 10 times to agar medium either with or without itraconazole. After 10 transfers in medium supplemented with itraconazole, 10 itraconazole-resistant mutant strains were isolated from two populations. These mutant strains had different growth rates and different levels of itraconazole resistance. Analysis of the ergosterol contents of these mutants showed that they accumulate ergosterol when they are grown in the presence of itraconazole. The replacement of the CYP51A gene of the wild-type strain changed the susceptibility pattern of this strain to one of itraconazole resistance only when CYP51A genes with N22D and M220I mutations were used as selectable marker genes. Real-time quantitative reverse transcription-PCR was used to assess the levels of expression of the Afumdr1, Afumdr2, Afumdr3, Afumdr4, AtrF transporter, CYP51A, and CYP51B genes in these mutant strains. Most mutants showed either constitutive high-level expression or induction upon exposure of Afumdr3, Afumdr4, and AtrF to itraconazole. Our results suggest that overexpression of drug efflux pumps and/or selection of drug target site mutations are at least partially responsible for itraconazole resistance and could be considered mechanisms for the emergence of clinical resistance to this drug.

Combined used of RAPD and touchdown PCR for epidemiological studies of Aspergillus fumigatus

INTRODUCTION

Aspergillus fumigatus is a filamentous fungus that acts as an opportunistic pathogen and has emerged as a major problem in immunosuppressed patients. Nosocomial outbreaks of aspergillosis are becoming more frequent, but their identification and epidemiological characterization is slow and difficult.

OBJECTIVE

Description of a fast, sensitive, specific method to identify and fingerprint A. fumigatus using methodology available in clinical laboratories.

METHODS

We studied several strains of A. fumigatus isolated from patients with invasive aspergillosis (n = 4), the hospital environment (n = 5) and reference cultures (n = 1), as well as other close phylogenetic fungal species from patients (n = 1), hospital environment (n = 6) and reference cultures (n = 1). A. fumigatus was identified by both touchdown PCR and conventional phenotyping methods. Genotyping was performed with random amplification of polymorphic DNA (RAPD) analysis, comparing the results from two primers (OPZ-19 and R-108) and different amplification protocols with regard to band resolution and reproducibility.

RESULTS

Touchdown PCR and phenotype results were identical. Best RAPD results were obtained with the R-108 primer and considerably longer ramp times between annealing and extension.

CONCLUSION

RAPD analysis is a fast, reliable tool for DNA fingerprinting. Patterns may be easier to repeat and interpret when longer ramp times are used. Touchdown PCR combined with RAPD analysis is a sensitive, accurate method for managing clinical outbreaks of Aspergillus fumigatus.

Madurella mycetomatis strains from mycetoma lesions in Sudanese patients are clonal

Molecular diversity among clinical isolates of Madurella mycetomatis, the prime fungal agent of human mycetoma in Sudan, could possibly explain the diverse clinical presentations of this severely debilitating infectious disease. In addition, culture-independent DNA-mediated typing tests need to be developed for this organism, since M. mycetomatis DNA, but not the organism itself, can be identified in soil, the material from which infections are thought to originate. A collection of 38 different clinical M. mycetomatis isolates was characterized by large-scale random amplification of polymorphic DNA using 20 different primer species. These analyses, involving at least 2,600 annealing sites, showed a complete lack of DNA fingerprint variation among the various isolates. From the resulting homogeneous DNA fingerprints, seven fragments were cloned and sequenced, and novel, species-specific PCR restriction fragment length polymorphism (RFLP) tests were designed. The seven PCR RFLP tests were successfully performed on the 38 different M. mycetomatis strains. However, again all M. mycetomatis DNA patterns obtained appeared to be identical, whereas patterns produced using DNAs from other fungal species were clearly discriminatory. These results suggest that there is little genetic variation among clinically relevant M. mycetomatis strains from Sudan. The data tentatively imply that different manifestations of mycetoma are due to differences in host susceptibility rather than differential virulence of the causative agent.