This study looked for correlations between molecular identification, clinical manifestation, and morphology for Trichophyton interdigitale and Trichophyton mentagrophytes. For this purpose, a total of 110 isolates were obtained from Czech patients with various clinical manifestations of dermatophytosis. Phenotypic characters were analyzed, and the strains were characterized using multilocus sequence typing. Among the 12 measured/scored phenotypic features, statistically significant differences were found only in growth rates at 37 °C and in the production of spiral hyphae, but none of these features is diagnostic. Correlations were found between T. interdigitale and higher age of patients and between clinical manifestations such as tinea pedis or onychomychosis. The MLST approach showed that internal transcribed spacer (ITS) genotyping of T. mentagrophytes isolates has limited practical benefits because of extensive gene flow between sublineages. Based on our results and previous studies, there are few taxonomic arguments for preserving both species names. The species show a lack of monophyly and unique morphology. On the other hand, some genotypes are associated with predominant clinical manifestations and sources of infections, which keep those names alive. This practice is questionable because the use of both names confuses identification, leading to difficulty in comparing epidemiological studies. The current identification method using ITS genotyping is ambiguous for some isolates and is not user-friendly. Additionally, identification tools such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry fail to distinguish these species. To avoid further confusion and to simplify identification in practice, we recommend using the name T. mentagrophytes for the entire complex. When clear differentiation of populations corresponding to T. interdigitale and Trichophyton indotineae is possible based on molecular data, we recommend optionally using a variety rank: T. mentagrophytes var. interdigitale and T. mentagrophytes var. indotineae.
Species in the T. mentagrophytes complex lack support from usual taxonomic methods and simple identification tools are missing or inaccurate. To avoid recurring confusions, we propose naming the entire complex as T. mentagrophytes and optionally use rank variety to classify the observed variability.
- Klíčová slova
- anthropophilic dermatophytes, dermatophytosis, multigene phylogeny, skin infections, zoophilic dermatophytes,
- MeSH
- Arthrodermataceae MeSH
- DNA fungální genetika chemie MeSH
- fenotyp MeSH
- fylogeneze MeSH
- mezerníky ribozomální DNA genetika chemie MeSH
- multilokusová sekvenční typizace veterinární MeSH
- sekvenční analýza DNA veterinární MeSH
- tinea * diagnóza veterinární MeSH
- Trichophyton MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- DNA fungální MeSH
- mezerníky ribozomální DNA MeSH
UNLABELLED: Analysis of mycobiome from formalin-fixed, paraffin-embedded (FFPE) biopsies should preferentially detect only fungi which are actually present in the intestine wall, in contrast to stool samples, which are limited by the diet composition. Next generation sequencing provides the advantage of analyzing many species from a single sample. Consequently, canonical correspondence analysis divided fungal genera present in FFPE intestinal tissues into three well-defined experimental groups (negative controls - NC, Crohn's disease - CD, ulcerative colitis - UC). Simultaneously, the analysis showed that particular fungal genera are associated with these experimental groups and several fungal genera occurred in all experimental groups equally. Our results also showed a noticeable increase of Ascomycota proportion from NC, through CD to UC. Fungal genera Malassezia, Cladosporium and Toninia occurred in all experimental groups assuming that they are common components of the intestinal mycobiome. Other fungal genera found only in the NC experimental group were non-pathogenic and might bring some benefits. In contrast, CD and UC samples were characterized by an accumulation of genera with inhibitive effects on growth of other fungal genera and the presence of opportunistic pathogens. Furthermore, a decrease in the fungal genus Malassezia in inflammatory tissues was observed; Specifically, the UC experimental group showed a connection between the presence of Candida and seven time's lower amounts of Malassezia (compared to amounts found in NC). The CD experimental group was characterized by the simultaneous presence of Engyodontium album with Lecanicillium, and indicates a possible pathogenic effect of Ramularia in disease development. LAY SUMMARY: Mycobiome analysis of formalin-fixed and paraffin-embedded biopsies may highlight actual fungal genera composition in the intestinal wall. Interestingly, experimental groups of Crohn's disease and ulcerative colitis clearly differed by structure of their mycobiomes.
- Klíčová slova
- Crohn's disease, FFPE samples, NGS, mycobiome, ulcerative colitis,
- MeSH
- Ascomycota * MeSH
- biopsie MeSH
- dospělí MeSH
- idiopatické střevní záněty * diagnóza MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- mykobiom * MeSH
- senioři MeSH
- střeva MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
UNLABELLED: In recent years, increased rates of yeast infections in humans and animals have been recognized worldwide. Since animals may represent a source of yeast infections for humans, knowing the antifungal susceptibility profile of yeast isolates from milk and evaluating their pathogenic potential would be of great medical importance. Therefore, the aim of this survey was to study yeast diversity in milk samples, analyze the hemolytic and phospholipase activities of isolates and determine minimal inhibition concentration (MIC) for fluconazole, voriconazole and flucytosine. Out of 66 yeast isolates obtained from 910 individual raw milk samples from subclinically infected cows, 26 different yeast species were determined based on sequencing of the D1/D2 and ITS regions. Among them, Pichia kudriavzevii (formerly known as Candida krusei), Kluyveromyces marxianus (formerly known as Candida kefyr) and Debaryomyces hansenii (formerly known as Candida famata) were the most commonly identified. Hemolysin and/or phospholipase activity was observed in 66.7% of isolates. The elevated MIC for fluconazole was determined in 16 isolates from 11 species. The findings of this study demonstrate that yeast isolates from raw milk have the potential to express virulence attributes such as hemolysin and phospholipase, and additionally, some of these strains showed elevated MIC to fluconazole or to flucytosine. LAY SUMMARY: We identified 66 yeast isolates, including 26 different yeast species from 910 individual milk samples. Our results indicate that individual milk samples may serve as a source of yeasts with the potential to trigger infection and may have reduced sensitivity to tested antifungal agents.
- Klíčová slova
- Candida sp, antifungal susceptibility, mastitis, milk, virulence factors, yeast,
- MeSH
- antifungální látky * farmakologie MeSH
- faktory virulence * genetika MeSH
- flukonazol farmakologie MeSH
- mikrobiální testy citlivosti veterinární MeSH
- mléko MeSH
- skot MeSH
- vorikonazol MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- antifungální látky * MeSH
- faktory virulence * MeSH
- flukonazol MeSH
- vorikonazol MeSH
Animal or human protothecosis belongs to rather rare, endemic, pro-inflammatory infections. It is caused by achlorophyllous algae of the genus Prototheca. Especially, P. bovis (formerly P. zopfii genotype 2) is often inflected as a non-bacterial causative agent of dairy cattle mastitis. In this study, we present a multiplex real-time PCR (qPCR) system for rapid and exact Prototheca spp. detection and quantification. Limit of detection, diagnostic sensitivity, and specificity were determined. For the first time, specific sequences of AccD (encoding acetyl CoA reductase) for P. bovis, cox1 (encoding cytochrome C oxidase subunit 1) for P. wickerhamii, cytB (encoding cytochrome B) for P. blashkeae and atp6 (encoding transporting ATPase F0 subunit 6) for P. ciferrii (formerly P. zopfii genotype 1) were used for species identification and quantification together with 28S rRNA sequence detecting genus Prototheca. The developed qPCR assay was applied to 55 individual cow milk samples from a herd suspected of protothecosis, 41 bulk milk samples from different Czech farms, 16 boxed milk samples purchased in supermarkets and 21 environmental samples originating from a farm suspected of protothecosis. Our work thus offers the possibility to diagnose protothecosis in the samples, where bacterial mastitis is the most commonly presumed and thereby assisting adequate corrective measures to be taken.
- Klíčová slova
- limit of detection, Prototheca bovis, milk, real-time PCR,
- MeSH
- DNA chemie izolace a purifikace MeSH
- farmy MeSH
- klonování DNA MeSH
- kvantitativní polymerázová řetězová reakce metody MeSH
- limita detekce MeSH
- mikrobiologie životního prostředí MeSH
- mlékárenství MeSH
- mléko mikrobiologie MeSH
- multiplexová polymerázová řetězová reakce metody MeSH
- plazmidy genetika MeSH
- Prototheca genetika růst a vývoj izolace a purifikace MeSH
- senzitivita a specificita MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- Názvy látek
- DNA MeSH
UNLABELLED: Arthroderma is the most diverse genus among dermatophytes encompassing species occurring in soil, caves, animal burrows, clinical material and other environments. In this study, we collected ex-type, reference and authentic strains of all currently accepted Arthroderma species and generated sequences of three highly variable loci (ITS rDNA, β-tubulin, and translation elongation factor 1-α). The number of accepted species was expanded to 27. One novel species, A. melbournense (ex-type strain CCF 6162T = CBS 145858T), is described. This species was isolated from toenail dust collected by a podiatrist in Melbourne, during an epidemiological study of four geographical regions of Eastern Australia. Trichophyton terrestre, Chrysosporium magnisporum, and Chrysosporium oceanitis are transferred to Arthroderma. Typification is provided for T. terrestre that is not conspecific with any of the supposed biological species from the former T. terrestre complex, that is, A. insingulare, A. lenticulare and A. quadrifidum. A multi-gene phylogeny and reference sequences provided in this study should serve as a basis for future phylogenetic studies and facilitate species identification in practice. LAY ABSTRACT: The genus Arthroderma encompasses geophilic dermatophyte species that infrequently cause human and animal superficial infections. Reference sequences from three genetic loci were generated for all currently accepted Arthroderma species and phylogeny was constructed. Several taxonomic novelties are introduced. The newly provided data will facilitate species identification and future taxonomic studies.
- Klíčová slova
- Arthroderma, Trichophyton terrestre, geophilic dermatophytes, keratinophilic fungi, multigene phylogeny,
- MeSH
- Arthrodermataceae klasifikace genetika MeSH
- DNA fungální genetika MeSH
- elongační faktor 1 genetika MeSH
- fylogeneze * MeSH
- geny hub genetika MeSH
- lidé MeSH
- mezerníky ribozomální DNA genetika MeSH
- Microsporum klasifikace genetika MeSH
- Trichophyton klasifikace genetika MeSH
- tubulin genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Austrálie MeSH
- Názvy látek
- DNA fungální MeSH
- elongační faktor 1 MeSH
- mezerníky ribozomální DNA MeSH
- tubulin MeSH
Interlaboratory evaluations of Mucorales qPCR assays were developed to assess the reproducibility and performance of methods currently used. The participants comprised 12 laboratories from French university hospitals (nine of them participating in the Modimucor study) and 11 laboratories participating in the Fungal PCR Initiative. For panel 1, three sera were each spiked with DNA from three different species (Rhizomucor pusillus, Lichtheimia corymbifera, Rhizopus oryzae). For panel 2, six sera with three concentrations of R. pusillus and L. corymbifera (1, 10, and 100 genomes/ml) were prepared. Each panel included a blind negative-control serum. A form was distributed with each panel to collect results and required technical information, including DNA extraction method, sample volume used, DNA elution volume, qPCR method, qPCR template input volume, qPCR total reaction volume, qPCR platform, and qPCR reagents used. For panel 1, assessing 18 different protocols, qualitative results (positive or negative) were correct in 97% of cases (70/72). A very low interlaboratory variability in Cq values (SD = 1.89 cycles) were observed. For panel 2 assessing 26 different protocols, the detection rates were high (77-100%) for 5/6 of spiked serum. There was a significant association between the qPCR platform and performance. However, certain technical steps and optimal combinations of factors may also impact performance. The good reproducibility and performance demonstrated in this study support the use of Mucorales qPCR as part of the diagnostic strategy for mucormycosis.
- Klíčová slova
- Mucorales PCR, circulating DNA, interlaboratory assay, standardization,
- MeSH
- diagnostické techniky molekulární normy MeSH
- DNA fungální genetika MeSH
- klinické laboratorní techniky přístrojové vybavení metody normy MeSH
- kvantitativní polymerázová řetězová reakce normy MeSH
- lidé MeSH
- Mucorales genetika MeSH
- mukormykóza krev diagnóza MeSH
- nemocnice univerzitní statistika a číselné údaje MeSH
- odchylka pozorovatele MeSH
- reprodukovatelnost výsledků MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- multicentrická studie MeSH
- Geografické názvy
- Francie MeSH
- Názvy látek
- DNA fungální MeSH
Quantitative real-time PCR (qPCR) is increasingly used to detect Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia (PCP), but there are differences in the nucleic acids targeted, DNA only versus whole nucleic acid (WNA), and also the target genes for amplification. Through the Fungal PCR Initiative, a working group of the International Society for Human and Animal Mycology, a multicenter and monocenter evaluation of PCP qPCR assays was performed. For the multicenter study, 16 reference laboratories from eight different countries, performing 20 assays analyzed a panel consisting of two negative and three PCP positive samples. Aliquots were prepared by pooling residual material from 20 negative or positive- P. jirovecii bronchoalveolar lavage fluids (BALFs). The positive pool was diluted to obtain three concentrations (pure 1:1; 1:100; and 1:1000 to mimic high, medium, and low fungal loads, respectively). The monocenter study compared five in-house and five commercial qPCR assays testing 19 individual BALFs on the same amplification platform. Across both evaluations and for all fungal loads, targeting WNA and the mitochondrial small sub-unit (mtSSU) provided the earliest Cq values, compared to only targeting DNA and the mitochondrial large subunit, the major surface glycoprotein or the beta-tubulin genes. Thus, reverse transcriptase-qPCR targeting the mtSSU gene could serve as a basis for standardizing the P. jirovecii load, which is essential if qPCR is to be incorporated into clinical care pathways as the reference method, accepting that additional parameters such as amplification platforms still need evaluation.
- Klíčová slova
- Pneumocystis jirovecii, Cq, threshold, DNA, PCP, diagnosis, efficiency, panel specimens, pneumocystosis, qPCR, quantification, quantification cycles, standardization, whole nucleic acids,
- MeSH
- bronchoalveolární lavážní tekutina mikrobiologie MeSH
- diagnostické techniky molekulární metody normy MeSH
- DNA fungální genetika MeSH
- kvantitativní polymerázová řetězová reakce normy MeSH
- lidé MeSH
- Pneumocystis carinii genetika MeSH
- pneumocystová pneumonie diagnóza mikrobiologie MeSH
- senzitivita a specificita MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- multicentrická studie MeSH
- Názvy látek
- DNA fungální MeSH
Aspergillus moulds are increasingly being recognised as significant human pathogens that can cause life-threatening infections in the context of host immune dysregulation, particularly in the lung. It is now clear that there is a close relationship between infection susceptibility and the fine regulation of pulmonary immunity and inflammation. While the contribution of IL-17/Th17 responses to both physiological and pathological lung inflammation is now well established, the cellular interactions, soluble factors, and signalling pathways that determine Th17 cell responses to fungal infection remain unclear. Here, we identify potential key mediators of fungus-DC-T cell interactions in the respiratory tract, with a focus on the DC-derived cytokines thought to exert a major influence on generation of pathological Th17 cells. We review recent data indicating a crucial role for Aspergillus-induced autophagy in lung DCs on subsequent T-cell polarization and modulation of 'stemness', which appears critical for avoiding pathological lung inflammation and promoting disease resolution.
- Klíčová slova
- Aspergillus, IL-2, Inflammation, Th17,
- MeSH
- Aspergillus imunologie patogenita MeSH
- autofagie MeSH
- buňky Th17 imunologie MeSH
- cytokiny metabolismus MeSH
- dendritické buňky imunologie MeSH
- interakce hostitele a patogenu * MeSH
- lidé MeSH
- modely nemocí na zvířatech MeSH
- plicní aspergilóza farmakoterapie patologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- cytokiny MeSH
Species of Scedosporium and Lomentospora are considered as emerging opportunists, affecting immunosuppressed and otherwise debilitated patients, although classically they are known from causing trauma-associated infections in healthy individuals. Clinical manifestations range from local infection to pulmonary colonization and severe invasive disease, in which mortality rates may be over 80%. These unacceptably high rates are due to the clinical status of patients, diagnostic difficulties, and to intrinsic antifungal resistance of these fungi. In consequence, several consortia have been founded to increase research efforts on these orphan fungi. The current review presents recent findings and summarizes the most relevant points, including the Scedosporium/Lomentospora taxonomy, environmental distribution, epidemiology, pathology, virulence factors, immunology, diagnostic methods, and therapeutic strategies.
- MeSH
- antifungální látky farmakologie terapeutické užití MeSH
- Ascomycota klasifikace účinky léků genetika fyziologie MeSH
- chirurgie operační MeSH
- ekologie MeSH
- faktory virulence MeSH
- imunokompromitovaný pacient MeSH
- interakce hostitele a patogenu imunologie MeSH
- kombinovaná terapie MeSH
- lidé MeSH
- mnohočetná fungální léková rezistence genetika MeSH
- molekulární typizace MeSH
- mykózy diagnóza mikrobiologie patologie terapie MeSH
- oportunní infekce diagnóza mikrobiologie patologie terapie MeSH
- Scedosporium klasifikace účinky léků genetika fyziologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- antifungální látky MeSH
- faktory virulence MeSH
A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help exclude IA. Conversely, when testing more invasive samples (BAL, biopsy, CSF) emphasis is placed on confirming disease, so analytical specificity is paramount. This multicenter study examined the analytical specificity of PCR methods for detecting IA by blind testing a panel of DNA extracted from a various fungal species to explore the range of Aspergillus species that could be detected, but also potential cross reactivity with other fungal species. Positivity rates were calculated and regression analysis was performed to determine any associations between technical specifications and performance. The accuracy of Aspergillus genus specific assays was 71.8%, significantly greater (P < .0001) than assays specific for individual Aspergillus species (47.2%). For genus specific assays the most often missed species were A. lentulus (25.0%), A. versicolor (24.1%), A. terreus (16.1%), A. flavus (15.2%), A. niger (13.4%), and A. fumigatus (6.2%). There was a significant positive association between accuracy and using an Aspergillus genus PCR assay targeting the rRNA genes (P = .0011). Conversely, there was a significant association between rRNA PCR targets and false positivity (P = .0032). To conclude current Aspergillus PCR assays are better suited for detecting A. fumigatus, with inferior detection of most other Aspergillus species. The use of an Aspergillus genus specific PCR assay targeting the rRNA genes is preferential.
- Klíčová slova
- Aspergillus PCR, analytical specificity, cross reactivity, detection range,
- MeSH
- Aspergillus klasifikace genetika izolace a purifikace MeSH
- diagnostické techniky molekulární metody MeSH
- invazivní plicní aspergilóza diagnóza MeSH
- lidé MeSH
- polymerázová řetězová reakce metody MeSH
- senzitivita a specificita MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
