Semi-automated repetitive sequence-based PCR amplification for species of the<i>Scedosporium apiospermum</i>complex

Matray, Olivier; Mouhajir, Abdelmounaim; Giraud, Sandrine; Godon, Charlotte; Gargala, Gilles; Labbé, F.; Rougeron, Amandine; Zouhair, Rachid; Bouchara, Jean‐Philippe; Favennec, Loïc

doi:10.1093/mmy/myv080

Cited by 14 publications

(7 citation statements)

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“…rep-PCR has been previously used successfully for species and/or strain differentiation in several fungal groups, including Candida and Aspergillus species, as well as dermatophytes and some dimorphic fungi (25,26,27,28,29). Recently, Matray et al (23) showed that this method also allows species identification within the Scedosporium apiospermum species complex, another group of sibling species encountered in patients with CF, as well as in CGD patients. rep-PCR analysis of our set of isolates revealed a clustering consistent with data from ITS or beta-tubulin sequencing, thereby demonstrating that this method is also suitable for species identification within the R. argillacea complex.…”

Section: Discussionmentioning

confidence: 99%

“…DNA was quantified using a NanoDrop spectrometer (Thermo Fisher Scientific, Illkirsch, France) for a target value of Ն25 ng/ml. PCR amplification of repetitive DNA sequences was realized using the DiversiLab fungal kit (bioMérieux) as described previously (23). Amplicons were separated by capillary electrophoresis on an Agilent 2100 bioanalyzer (Massy, France).…”

Section: Methodsmentioning

confidence: 99%

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Long-Term Rasamsonia argillacea Complex Species Colonization Revealed by PCR Amplification of Repetitive DNA Sequences in Cystic Fibrosis Patients

et al. 2016

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The aim of this work was to document molecular epidemiology of Rasamsonia argillacea species complex isolates from cystic fibrosis (CF) patients. In this work, 116 isolates belonging to this species complex and collected from 26 CF patients and one patient with chronic granulomatous disease were characterized using PCR amplification assays of repetitive DNA sequences and electrophoretic separation of amplicons (rep-PCR). Data revealed a clustering consistent with molecular species identification. A single species was recovered from most patients. Rasamsonia aegroticola was the most common species, followed by R. argillacea sensu stricto and R. piperina, while R. eburnea was not identified. Of 29 genotypes, 7 were shared by distinct patients while 22 were patient specific. In each clinical sample, most isolates exhibited an identical genotype. Genotyping of isolates recovered from sequential samples from the same patient confirmed the capability of R. aegroticola and R. argillacea isolates to chronically colonize the airways. A unique genotype was recovered from two siblings during a 6-month period. In the other cases, a largely dominant genotype was detected. Present results which support the use of rep-PCR for both identification and genotyping for the R. argillacea species complex provide the first molecular evidence of chronic airway colonization by these fungi in CF patients.R asamsonia argillacea, which was first reported in clinical practice as a Penicillium species, then reclassified in the genus Geosmithia, and finally reassigned in 2013 to the new genus Rasamsonia, is now considered an emerging pathogen (1). Since its first report in humans as Penicillium emersonii (2), there has been an increasing number of cases reported in both dogs (3, 4, 5) and humans (6). Nevertheless, it is likely that the number of human infections caused by this fungus has long been underestimated because of the lack of specificity of its morphological features and to subsequent misidentifications with some Penicillium or Paecilomyces species.Only six species were previously recognized in the genus Rasamsonia described in 2012, i.e., R. argillacea, R. composticola, R. brevistipitata, R. byssochlamydoides, R. cylindrospora, and R. emersonii (7). However, multilocus sequence analysis of several R. argillacea isolates revealed a clustering which superimposed some phenotypic differences. Therefore, R. argillacea is now considered a species complex comprising four distinct species: R. argillacea sensu stricto, R. piperina, R. aegroticola, and R. eburnea (8).Infections caused by species of the R. argillacea complex have been reported in various clinical contexts in human. Chronic granulomatous disease (CGD) (9, 10, 11) and cystic fibrosis (CF) (12,13,14,15,16,17) are the major underlying clinical conditions. Rasamsonia infections may also occur in bone marrow transplant recipients (18, 19) but also may occur in the absence of any predisposing factors, as evidenced by the pulmonary and aortic graft infection reported by Doyon et al. (...

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Long-Term Rasamsonia argillacea Complex Species Colonization Revealed by PCR Amplification of Repetitive DNA Sequences in Cystic Fibrosis Patients

et al. 2016

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“…apiospermum strains. Our results detected a close relationship between the environmental strains from Thailand and the clinical strains from France [15], China and Japan [28]. Therefore, French, Chinese and Japan isolates originated in Thailand also.…”

Section: Discussionmentioning

confidence: 57%

“…[13]. The MLST scheme amplifies sequences at five genetic loci–actin (ACT), calmodulin exons 3 and 4 (CAL), the second largest subunit of RNA polymerase II gene (RPB2), ß-tubulin exons 2–4 (BT2), and manganese superoxide dismutase (SOD2) and has been found to have strong repeatability [13–15]. The allele types (ATs) and sequences types (STs) numbers of the consensus MLST scheme can be obtained through the Fungal MLST Database (http://mlst.mycologylab.org/).…”

Section: Introductionmentioning

confidence: 99%

Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand

2017

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The Scedosporium apiospermum species complex is an emerging filamentous fungi that has been isolated from environment. It can cause a wide range of infections in both immunocompetent and immunocompromised individuals. We aimed to study the genetic variation and relationships between 48 strains of S. apiospermum sensu stricto isolated from soil in Bangkok, Thailand. For PCR, sequencing and phylogenetic analysis, we used the following genes: actin; calmodulin exons 3 and 4; the second largest subunit of the RNA polymerase II; ß-tubulin exon 2–4; manganese superoxide dismutase; internal transcribed spacer; transcription elongation factor 1α; and beta-tubulin exons 5 and 6. The present study is the first phylogenetic analysis of relationships among S. apiospermum sensu stricto in Thailand and South-east Asia. This result provides useful information for future epidemiological study and may be correlated to clinical manifestation.

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“…Nucleotide sequence-based analysis is the current gold standard for fungal identification; rDNA internal transcribed spacer (ITS) sequencing appropriately identifies the main species in Scedosporium , but the partial β-tubulin gene ( BT2 ) is required to differentiate closely related species [ 8 , 9 ]. Matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS) has become available for the first-line identification of filamentous fungi, as its accuracy is comparable to that of DNA sequencing, but it is not routinely available at many medical centers [ 10 ].…”

Section: Scedosporiosismentioning

confidence: 99%

Recent Advances in the Treatment of Scedosporiosis and Fusariosis

McCarthy

Katragkou

Iosifidis

et al. 2018

JoF

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Species of Scedosporium and Fusarium are considered emerging opportunistic pathogens, causing invasive fungal diseases in humans that are known as scedosporiosis and fusariosis, respectively. These mold infections typically affect patients with immune impairment; however, cases have been reported in otherwise healthy individuals. Clinical manifestations vary considerably, ranging from isolated superficial infection to deep-seated invasive infection—affecting multiple organs—which is often lethal. While there have been a number of advances in the detection of these infections, including the use of polymerase chain reaction (PCR) and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS), diagnosis is often delayed, leading to substantial morbidity and mortality. Although the optimal therapy is controversial, there have also been notable advances in the treatment of these diseases, which often depend on a combination of antifungal therapy, reversal of immunosuppression, and in some cases, surgical resection. In this paper, we review these advances and examine how the management of scedosporiosis and fusariosis may change in the near future.

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Semi-automated repetitive sequence-based PCR amplification for species of theScedosporium apiospermumcomplex

Cited by 14 publications

References 38 publications

Long-Term Rasamsonia argillacea Complex Species Colonization Revealed by PCR Amplification of Repetitive DNA Sequences in Cystic Fibrosis Patients

Long-Term Rasamsonia argillacea Complex Species Colonization Revealed by PCR Amplification of Repetitive DNA Sequences in Cystic Fibrosis Patients

Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand

Recent Advances in the Treatment of Scedosporiosis and Fusariosis

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