Fusarium:Molecular Diversity and Intrinsic Drug Resistance

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Different colonization patterns of Aspergillus terreus in patients with cystic fibrosis

Due to the abnormal viscosity of airway secretions, patients with cystic fibrosis (CF) are athigh risk of fungal colonization of the respiratory tract. Aspergillus fumigatus is by far the most common fungal specie encountered in the CF context, but other species are increasingly reported such as Scedosporium spp. or Geosmithia argillacea, as well as other aspergilli including Aspergillus terreus. In our experience, this saprophytic fungus ranks the third among the filamentous fungi colonizing the respiratory tract of CF patients. Additionally, although relatively uncommon, infections caused by A. terreus present a high mortality rate due to its usually low susceptibility to systemic antifungals. Nevertheless, little is known about the epidemiology of A. terreus colonization/infections. In the present study, nine short tandem repeats of A. terreus were used to genotype 122 clinical isolates recovered from sputum samples from five patients with CF followed-up in two distinct hospitals in France (Angers and Giens hospitals). Sputum samples were collected over a two-month to seven-year period depending on the patients, and for each sample, all the obtained isolates were studied, with a maximum of five per sample. Three colonization patterns were observed. The first colonization pattern consisted of a chronic colonization (defined as the presence of the same genotype in at least two successive samples collected over a minimum period of two months) by a largely dominant genotype associated with two or three other genotypes found occasionally (patient 4) or over a short period (patient 3). The second colonization pattern consisted of a chronic colonization by two distinct genotypes simultaneously detected (patients 1 and 2). For the last patient (patient 5), who was followed during four years, 16 isolates recovered from 6 sputum samples were analyzed, corresponding to 8 genetically distinct genotypes which succeeded to each other. Numerous questions therefore raise from these different colonization patterns, regarding (i) the origin of the contamination of the patients by this relatively uncommon environmental fungus, (ii) the differences between genotypes in their ability to chronically colonize the airways of the CF patients, or (iii) the differences between CF patients in their individual susceptibility to same genotypes

Different colonization patterns of Aspergillus terreus in patients with cystic fibrosis

Patients with cystic fibrosis (CF) are at high risk of colonization of the respiratory tract by filamentous fungi, mainly Aspergillus fumigatus, but also other Aspergillus species including A. terreus. In our experience, this last fungus ranks the third among the filamentous fungi colonizing the respiratory tract of CF patients. Additionally, although uncommon, infections caused by A. terreus present a high mortality rate due to its usually low susceptibility to systemic antifungals. The recent development of a microsatellite typing system allowed us to investigate the molecular epidemiology of the airway colonization by this fungus in CF. Nine short tandem repeats of A. terreus were used to genotype multiple and sequential isolates from sputum samples from CF patients followed-up in Angers and Giens hospitals (France). Sputum samples were collected over a 2 month to 7 year period, and for each sample, all the obtained isolates were studied, with a maximum of five per sample. Thus a total of 122 isolates was studied, corresponding to 47 samples collected from 5 distinct patients. Three colonization patterns were observed. The first one consisted of a chronic colonization (presence of the same genotype in at least two successive samples collected over a minimum period of two months) by a largely dominant genotype associated with two or three other genotypes found occasionally (patient 1) or over a short period (patient 2). The second pattern consisted of a chronic colonization by two distinct genotypes simultaneously detected (patients 3 and 4). For the last patient (patient 5), 16 isolates recovered from 6 sputum samples collected during four years were analyzed, corresponding to 8 distinct genotypes which succeeded to each other. Numerous questions rise from these different colonization patterns, relatively uncommon environmental fungus; and (ii) differences between genotypes in their ability to chronically colonize the airways of the CF patients or differences between CF patients in their individual susceptibility to same genotypes. Strikingly, some genotypes shared by some patients were responsible for a chronic colonization in some patients while they rapidly disappear in other patients. A multicenter study should be conducted combining genetic study of the host and genotyping of fungal isolates, searching for predisposing factors to the airway colonization by A. terreus

Epidemiology of airway colonization by Scedosporium apiospermum during cystic fibrosis

With a frequency of about 10%, species of the Scedosporium apiospermum complex (which comprises at least five distinct species with different antifungal susceptibility patterns) rank the second among the filamentous fungi colonizing the airways in cystic fibrosis (CF). Additionally, it is clearly established that these fungi may disseminate in case of immunodeficiency and that a chronic colonization of the airways by these pathogens may hinder the success of lung transplantation. In this study, we develop a new genotyping method to investigate the epidemiology of the airway colonization by these fungi. 63 multiple and sequential isolates of S. apiospermum collected from 9 CF patients, and selected among those previously studied by random amplification of polymorphic DNA (RAPD), were analyzed using the automated typing system DiversiLab (bioMérieux) based on PCR amplification of repetitive sequences. The DiversiLab Aspergillus rep-PCR kit which uses specific primers designed for Aspergillus fumigatus, was compared with the pan-fungus DiversiLab Fungal kit. Amplification products were separated by capillary electrophoresis on Agilent B2100 bioanalyzer, leading to single profiles for each isolate which were then compared using the DiversiLab software. In addition, species identification of these isolates was clarified by sequencing the betatubulin gene. Results obtained with both kits were comparable. Nevertheless, differentiation was easier using the DiversiLab Fungal kit. Additionally, rep-PCR usually confirmed the colonization patterns described by RAPD. Only two patients showed distinct genotypes. For Patient 2, two isolates were analyzed which were undistinguishable by RAPD, but rep-PCR revealed that they belonged to distinct genotypes, suggesting a transient colonization. For Patient 8 which showed by RAPD two distinct genotypes, 5 genotypes were found by rep-PCR with a dominant one represented by 5 isolates and two very close genotypes (corresponding to 3 isolates), while 4 other isolates belonged to two distant genotypes. In conclusion, the automated typing system DiversiLab proved to be an easy and efficient method to investigate the molecular epidemiology of the airway colonization by S. apiospermum in CF. Our results also confirm the capacity of the different species from the S. apiospermum complex to chronically colonize the airways of CF patients

Epidémiologie moléculaire de la colonisation par Aspergillus terreus des patients atteints de mucoviscidose

organisé par l'association Vaincre la mucoviscidoseNational audienc

Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of<i> Candida auris</i>

Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks