RESUMEN
Cryptococcosis is a fungal infection burdened by a high case-fatality rate in immunocompromised patients. Once limited to human immunodeficiency virus (HIV)-infected patients, the epidemiology of cryptococcosis has evolved in recent years and new risk factors have emerged. It is therefore essential to identify these risk factors in order to improve prevention and therapeutic efficacy. We conducted a retrospective observational study including all cases of cryptococcosis between January 2016 and December 2022, diagnosed at the University Hospital of Marseille. During the study period 15 cases of cryptococcosis were diagnosed. Six patients were HIV-infected. Nine patients had one or more comorbidities including liver cirrhosis, type 2 diabetes mellitus, primary immunodeficiency disorder, chronic lymphocytic leukemia and solid organ transplantation. Ten patients had central nervous system cryptococcosis, four had pulmonary cryptococcosis and one patient had extra-pulmonary disseminated cryptococcosis. Of the three patients with liver cirrhosis, two patients died with a post-mortem diagnosis. Our data suggest that emerging risk factors are probably underestimated by clinicians. It emphasizes the need for cryptococcal antigenemia as part of syndromic investigation of any unexplained fever or neurological symptoms in an at-risk patient. Early diagnosis and treatment are essential for patient's survival.
Asunto(s)
Criptococosis , Hospitales Universitarios , Huésped Inmunocomprometido , Humanos , Criptococosis/epidemiología , Criptococosis/diagnóstico , Masculino , Femenino , Estudios Retrospectivos , Hospitales Universitarios/estadística & datos numéricos , Persona de Mediana Edad , Adulto , Anciano , Factores de Riesgo , Francia/epidemiología , Infecciones por VIH/complicaciones , Infecciones por VIH/epidemiología , Cirrosis Hepática/complicaciones , Cirrosis Hepática/epidemiologíaRESUMEN
Because data on the fungal gut community structure of African children are scarce, we aimed to describe it by reanalysing rRNA ITS1 and ITS2 metabarcoding data from a study designed to assess the influence of microbiota in malaria susceptibility in Malian children from the Dogon country. More specifically, we aimed to establish the core gut mycobiome and compare the gut fungal community structure of breastfed children, aged 0-2 years, with other age groups. Briefly, DNA was extracted from 296 children's stool samples. Both rRNA ITS1 and ITS2 genomic barcodes were amplified and subjected to Illumina MiSeq sequencing. The ITS2 barcode generated 1,975,320 reads and 532 operational taxonomic units (OTUs), while the ITS1 barcode generated 647,816 reads and 532 OTUs. The alpha diversity was significantly higher by using the ITS1 compared to the ITS2 barcode (p < 0.05); but, regardless of the ITS barcode, we found no significant difference between breastfed children, aged 0-2 years, compared to the other age groups. The core gut mycobiome of the Malian children included Saccharomyces cerevisiae, Candida albicans, Pichia kudriavzevii, Malassezia restricta, Candida tropicalis and Aspergillus section Aspergillus, which were present in at least 50% of the 296 children. Further studies in other African countries are warranted to reach a global view of African children's core gut mycobiome.
RESUMEN
Tinea capitis (TC) is still a frequent dermatophytosis in France, both autochthonous and imported. A nationwide retrospective survey was performed and a total of 4395 TC cases were recorded within 36 French mycology laboratories during a 6-year period. TC is a disease that occurs in childhood with 85% of the cases occurring before 10 years old and 94% before the age of 15. Anthropophilic origin was predominant with 779 cases of Trichophyton tonsurans (32.6%), 738 cases of Trichophyton soudanense/T. violaceum (31%), and 445 cases of Microsporum audouinii (19.2%). Of note, T. tonsurans represents more than 80% of the cases in the French West Indies (Martinique and Guadeloupe). By contrast, zoophilic species were less prevalent with mainly M. canis (10.3%) confirming the shift from zoophilic to anthropophilic species observed in many centers during the last decades. During this survey, diagnosis methods were also collected. Most labs had a classical process for the diagnosis: microscopic direct examination associated to cultures on Sabouraud and Sabouraud-cycloheximide media (incubated between 25 ± 5°C for at least 3 weeks) in all laboratories. Identification of the causal dermatophyte was performed by microscopic and macroscopic examination of the cultures in 100% of the labs, with various specific culture media available when fructification was insufficient (mainly malt or potato-dextrose agar, or Borelli medium). New techniques were also implemented with the introduction of MALDI-TOF mass spectrometry identification in more than two third of the labs, and molecular identification available if necessary in half of the labs.
A total of 4395 tinea capitis cases were recorded within 36 French mycology laboratories during a 6-year period. An anthropophilic origin was predominant with 33%, 31%, and 18.8% of cases due to Trichophyton tonsurans, T. soudanense/T. violaceum, and Microsporum audouinii, respectively.
Asunto(s)
Microsporum , Tiña del Cuero Cabelludo , Humanos , Tiña del Cuero Cabelludo/epidemiología , Tiña del Cuero Cabelludo/microbiología , Tiña del Cuero Cabelludo/tratamiento farmacológico , Estudios Retrospectivos , Francia/epidemiología , Niño , Microsporum/aislamiento & purificación , Adolescente , Preescolar , Masculino , Femenino , Arthrodermataceae/aislamiento & purificación , Arthrodermataceae/clasificación , Trichophyton/aislamiento & purificación , Prevalencia , Encuestas y Cuestionarios , Lactante , AdultoRESUMEN
OBJECTIVES: We aimed to describe features and outcomes of cryptococcosis among HIV-seronegative individuals in a large surveillance network for cryptococcosis in France. METHODS: We included incident cases of cryptococcosis in HIV-seronegative individuals from 2005 to 2020. We compared patient characteristics, disease presentations, cryptococcal antigen results, and induction antifungal treatments according to underlying disease. We examined factors associated with 90-day mortality. Among patients with disseminated infections, we investigated whether receipt of flucytosine and polyene combination was associated with lower mortality. RESULTS: Among 652 individuals, 209 (32.1%) had malignancy, 130 (19.9%) were solid-organ transplant recipients, 204 (31.3%) had other immunocompromising conditions, and 109 (16.7%) had no reported underlying factor. The commonest presentations were disseminated infections (63.3%, 413/652) and isolated pulmonary infections (25.3%, 165/652). Solid-organ transplant patients were most likely to have disseminated infections and a positive serum cryptococcal antigen result. Patients with malignancy were older and less likely to receive a flucytosine-containing regimen for disseminated infections than others (58.7%, 78/133 vs. 73.2%, 194/265; p 0.029). The crude 90-day case-fatality ratio was 27.2% (95% CI, 23.5%-31.1%). Age ≥60 years (aOR: 2.75 [1.78-4.26]; p < 0.001), meningitis/fungaemia (aOR: 4.79 [1.80-12.7]; p 0.002), and malignancy (aOR: 2.4 [1.14-5.07]; p 0.02) were associated with higher 90-day mortality. Receipt of flucytosine and polyene combination was associated with lower 90-day mortality (aOR: 0.40 [0.23-0.71]; p 0.002) in multivariable analysis and inverse probability of treatment weighted analysis (aOR: 0.45 [0.25-0.80]; p 0.006). DISCUSSION: HIV-seronegative individuals with cryptococcosis comprise a wide range of underlying conditions with different presentations and outcomes, requiring a tailored approach to diagnosis and management.
Asunto(s)
Antifúngicos , Criptococosis , Humanos , Francia/epidemiología , Femenino , Masculino , Criptococosis/epidemiología , Criptococosis/mortalidad , Persona de Mediana Edad , Adulto , Estudios Transversales , Antifúngicos/uso terapéutico , Anciano , Flucitosina/uso terapéutico , Seronegatividad para VIH , Polienos/uso terapéutico , Adulto Joven , Huésped InmunocomprometidoRESUMEN
BACKGROUND: The first-line diagnosis of malaria in Mali is based on the use of rapid diagnostic tests (RDT) that detect the Histidin Rich Protein 2 (HRP2) antigen specific to Plasmodium falciparum. Our study, based on a real-time polymerase chain reaction (qPCR) gold standard, aimed to describe the distribution of the Plasmodium species in each administrative region of Mali and to assess the performance of RDTs. METHODS: We randomly selected 150 malaria-negative and up to 30 malaria-positive RDTs in 41 sites distributed in 9 regions of Mali. DNA extracted from the RDT nitrocellulose strip was assayed with a pan-Plasmodium qPCR. Positive samples were then analyzed with P. falciparum-, P. malariae-, P. vivax-, or P. ovale-specific qPCRs. RESULTS: Of the 1496 RDTs, 258 (18.6%) were positive for Plasmodium spp., of which 96.9% were P. falciparum. The P. vivax prevalence reached 21.1% in the north. RDT displayed acceptable diagnostic indices; the lower CI95% bounds of Youden indices were all ≥0.50, except in the north (Youden index 0.66 (95% CI [0.44-0.82]) and 0.63 (95% CI [0.33-0.83]. CONCLUSIONS: Overall, RDT diagnostic indices are adequate for the biological diagnosis of malaria in Mali. We recommend the use of RDTs detecting P. vivax-specific antigens in the north.
Asunto(s)
Malaria Falciparum , Malaria Vivax , Malaria , Plasmodium , Humanos , Prueba de Diagnóstico Rápido , Malí/epidemiología , Plasmodium vivax/genética , Pruebas Diagnósticas de Rutina , Sensibilidad y Especificidad , Malaria/diagnóstico , Plasmodium/genética , Malaria Vivax/epidemiología , Malaria Falciparum/diagnóstico , Reacción en Cadena en Tiempo Real de la PolimerasaRESUMEN
Among 1107 cryptococcosis cases from the French surveillance network (2005-2020), the proportion of HIV-seronegative individuals has recently surpassed that of HIV-seropositive individuals. We observed marked differences in patient characteristics, disease presentations, cryptococcal antigen results, infecting species, and mortality according to HIV serostatus.
RESUMEN
Mucormycosis is known to be a rare opportunistic infection caused by fungal organisms belonging to the Mucorales order, which includes the Syncephalastrum species. These moulds are rarely involved in clinical diseases and are generally seen as contaminants in clinical laboratories. However, in recent years, case reports of human infections due to Syncephalastrum have increased, especially in immunocompromised hosts. In this study, we described two new Syncephalastrum species, which were isolated from human nails and sputum samples from two different patients. We used several methods for genomic and phenotypic characterisation. The phenotypic analysis relied on the morphological features, analysed both by optical and scanning electron microscopy. We used matrix-assisted laser desorption-ionization time-of-flight mass spectrometry, energy-dispersive X-ray spectroscopy, and BiologTM technology to characterise the proteomic, chemical mapping, and carbon source assimilation profiles, respectively. The genomic analysis relied on a multilocus DNA sequence analysis of the rRNA internal transcribed spacers and D1/D2 large subunit domains, fragments of the translation elongation factor-1 alpha, and the ß-tubulin genes. The two novel species in the genus Syncephalastrum, namely S. massiliense PMMF0073 and S. timoneanum PMMF0107, presented a similar morphology: irregular branched and aseptate hyphae with ribbon-like aspects and terminal vesicles at the apices all surrounded by cylindrical merosporangia. However, each species displayed distinct phenotypic and genotypic features. For example, S. timoneanum PMMF0107 was able to assimilate more carbon sources than S. massiliense PMMF0073, such as adonitol, α-methyl-D-glucoside, trehalose, turanose, succinic acid mono-methyl ester, and alaninamide. The polyphasic approach, combining the results of complementary phenotypic and genomic assays, was instrumental for describing and characterising these two new Syncephalastrum species.
RESUMEN
BACKGROUND: Freshwater snails of the genera Bulinus spp., Biomphalaria spp., and Oncomelania spp. are the main intermediate hosts of human and animal schistosomiasis. Identification of these snails has long been based on morphological and/or genomic criteria, which have their limitations. These limitations include a lack of precision for the morphological tool and cost and time for the DNA-based approach. Recently, Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry, a new tool used which is routinely in clinical microbiology, has emerged in the field of malacology for the identification of freshwater snails. This study aimed to evaluate the ability of MALDI-TOF MS to identify Biomphalaria pfeifferi and Bulinus forskalii snail populations according to their geographical origin. METHODS: This study was conducted on 101 Bi. pfeifferi and 81 Bu. forskalii snails collected in three distinct geographical areas of Senegal (the North-East, South-East and central part of the country), and supplemented with wild and laboratory strains. Specimens which had previously been morphologically described were identified by MALDI-TOF MS [identification log score values (LSV) ≥ 1.7], after an initial blind test using the pre-existing database. After DNA-based identification, new reference spectra of Bi. pfeifferi (n = 10) and Bu. forskalii (n = 5) from the geographical areas were added to the MALDI-TOF spectral database. The final blind test against this updated database was performed to assess identification at the geographic source level. RESULTS: MALDI-TOF MS correctly identified 92.1% of 101 Bi. pfeifferi snails and 98.8% of 81 Bu. forskalii snails. At the final blind test, 88% of 166 specimens were correctly identified according to both their species and sampling site, with LSVs ranging from 1.74 to 2.70. The geographical source was adequately identified in 90.1% of 91 Bi. pfeifferi and 85.3% of 75 Bu. forskalii samples. CONCLUSIONS: Our findings demonstrate that MALDI-TOF MS can identify and differentiate snail populations according to geographical origin. It outperforms the current DNA-based approaches in discriminating laboratory from wild strains. This inexpensive high-throughput approach is likely to further revolutionise epidemiological studies in areas which are endemic for schistosomiasis.
Asunto(s)
Biomphalaria , Esquistosomiasis , Animales , Humanos , Bulinus , Esquistosomiasis/epidemiología , Caracoles , Espectrometría de Masas , ADN , Rayos LáserRESUMEN
Vulvovaginal candidiasis (VVC) alongside with antifungal resistance are becoming a major clinical problem in recent years. A prospective study aimed to evaluate the diversity of yeast strains associated with VVC in Tebessa city (northeastern Algeria) and investigate their susceptibility patterns. Over two months, yeasts were isolated on chromogenic medium from twenty-nine non-pregnant women with symptomatic VVC. The isolates were characterized with MALDI-TOF MS and antifungal susceptibility testing was performed for nine antifungal drugs using SensititreTM YeastOneTM YO10. Twenty-nine non-duplicate yeasts were recovered and the mass spectrometry profiles showed reliable scores of which four genera and five different species were identified. Candida albicans accounted for 65.5 % (n = 19) of the total number of isolates, followed by C. glabrata with 20.7% (n = 6). For the remaining non-albicans Candida (NCA) species, Kluyveromyces marxianus with 6.9% (n = 2), Pichia kudriavzevii and Saccharomyces cerevisiae with one isolate each. The antifungal susceptibilities showed wild type MICs of C. albicans to amphotericin B, azoles and echinocandins. In addition, four C. albicans isolates were resistant to flucytosine. For C. glabrata isolates, 100% non-WT phenotype was found for both posaconazole and itraconazole. For the very first time, the obtained outcomes bring out new data concerning the epidemiology of yeasts causing VVC in Algeria and their antimicrobial susceptibility profiles.
Asunto(s)
Candidiasis Vulvovaginal , Femenino , Humanos , Candidiasis Vulvovaginal/epidemiología , Candidiasis Vulvovaginal/tratamiento farmacológico , Candidiasis Vulvovaginal/microbiología , Antifúngicos/farmacología , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Estudios Prospectivos , Argelia/epidemiología , Candida/genética , Candida albicans , Pruebas de Sensibilidad MicrobianaRESUMEN
Aspergillosis of the newborn remains a rare but severe disease. We report four cases of primary cutaneous Aspergillus flavus infections in premature newborns linked to incubators contamination by putative clonal strains. Our objective was to evaluate the ability of matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) coupled to convolutional neural network (CNN) for clone recognition in a context where only a very small number of strains are available for machine learning. Clinical and environmental A. flavus isolates (n = 64) were studied, 15 were epidemiologically related to the four cases. All strains were typed using microsatellite length polymorphism. We found a common genotype for 9/15 related strains. The isolates of this common genotype were selected to obtain a training dataset (6 clonal isolates/25 non-clonal) and a test dataset (3 clonal isolates/31 non-clonal), and spectra were analysed with a simple CNN model. On the test dataset using CNN model, all 31 non-clonal isolates were correctly classified, 2/3 clonal isolates were unambiguously correctly classified, whereas the third strain was undetermined (i.e., the CNN model was unable to discriminate between GT8 and non-GT8). Clonal strains of A. flavus have persisted in the neonatal intensive care unit for several years. Indeed, two strains of A. flavus isolated from incubators in September 2007 are identical to the strain responsible for the second case that occurred 3 years later. MALDI-TOF is a promising tool for detecting clonal isolates of A. flavus using CNN even with a limited training set for limited cost and handling time.
Cutaneous aspergillosis is a rare but potentially fatal disease of the prematurely born infant. We described here several cases due to Aspergillus flavus and have linked them to environnemental strains using MLP genotyping and MALDI-TOF mass spectrometry coupled with artificial intelligence.
Asunto(s)
Aspergilosis , Infección Hospitalaria , Animales , Aspergillus flavus/genética , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/veterinaria , Infección Hospitalaria/veterinaria , Unidades de Cuidado Intensivo Neonatal , Aspergilosis/diagnóstico , Aspergilosis/veterinariaRESUMEN
Invasive fungal diseases are a public health problem. They affect a constantly increasing number of at-risk patients, and their incidence has risen in recent years. These opportunistic infections are mainly due to Candida sp. but less common or rare yeast infections should not be underestimated. These so-called "less common" yeasts include Ascomycota of the genera Candida (excluding the five major Candida species), Magnusiomyces/Saprochaete, Malassezia, and Saccharomyces, and Basidiomycota of the genera Cryptococcus (excluding the Cryptococcus neoformans/gattii complex members), Rhodotorula, and Trichosporon. The aim of this review is to (i) inventory the less common yeasts isolated in humans, (ii) provide details regarding the specific anatomical locations where they have been detected and the clinical characteristics of the resulting infections, and (iii) provide an update on yeast taxonomy. Of the total of 239,890 fungal taxa and their associated synonyms sourced from the MycoBank and NCBI Taxonomy databases, we successfully identified 192 yeasts, including 127 Ascomycota and 65 Basidiomycota. This repertoire allows us to highlight rare yeasts and their tropism for certain anatomical sites and will provide an additional tool for diagnostic management.
RESUMEN
Background Fungal infections mainly caused by Candida krusei are increasing rapidly and represent a serious public health problem in human immunodeficiency virus (HIV)-infected patients. This study aimed to investigate the antifungal susceptibility profile and virulence factors in C. krusei isolated from HIV-infected patients. Methodology Isolates were identified by biochemical and molecular methods. The antifungal resistance profile was established based on the antifungal susceptibility test performed using the Sensititre YeastOne™ (Thermo Fisher Scientific, Waltham, MA) microdilution technique. The production of phospholipase and proteinase was detected by standard methods. Biofilm formation was performed by the microtiter plate method. Results A total of 73 isolates of C. krusei were recovered from stool, oral swabs, vaginal swabs, and urine samples. The highest number of C. krusei isolates (49, 67.05%)was recovered from stool samples. A total of 32.56% of the C. krusei isolates were multidrug-resistant (MDR). The patients living with HIV and not receiving antiretroviral treatment displayed the highest number of C. krusei isolates (29, 39.76%), whereas the patients living with HIV on antiretroviral therapy exhibited the lowest number of C. krusei isolates (2, 2.72%). All isolates were categorized as strong biofilm producers. Among the production of hydrolytic enzymes, 25 (58.13%) and 24 (55.81%) of C. krusei isolates were classified as strong phospholipase and proteinase producers, respectively. Conclusion The C. krusei isolates obtained in this study were MDR and strongly expressed biofilm formation and both phospholipase and proteinase hydrolytic enzymes. The results show how pathogenic C. krusei is in the HIV-infected population and will contribute toward the management of C. krusei-related infections, which may help improve the life quality of people living with HIV.
RESUMEN
The majority of Candida species are known as non-pathogenic yeasts and rarely involved in human diseases. However, recently case reports of human infections caused by non-albicans Candida species have increased, mostly in immunocompromised hosts. Our study aimed to describe and characterize as thoroughly as possible, a new species of the Metschnikowia clade, named here Candida massiliensis (PMML0037), isolated from a clinical sample of human sputum. We targeted four discriminant genetic regions: "Internal Transcribed Spacers" of rRNA, D1/D2 domains (28S large subunit rRNA) and part of the genes encoding Translation Elongation Factor 1-α and ß-tubulin2. The genetic data were compared to morphological characters, from scanning electron microscopy (TM 4000 Plus, SU5000), physiological, including the results of oxidation and assimilation tests of different carbon sources by the Biolog system, and chemical mapping by Energy-Dispersive X-ray Spectroscopy. Lastly, the in vitro antifungal susceptibility profile was performed using the E-test™ exponential gradient method. The multilocus analysis supported the genetic position of Candida massiliensis (PMML0037) as a new species of the Metschnikowia clade, and the phenotypic analysis highlighted its unique morphological and chemical profile when compared to the other Candida/Metschnikowia species included in the study.
Asunto(s)
Candida , Metschnikowia , Humanos , ADN Espaciador Ribosómico/genética , ADN Espaciador Ribosómico/química , Filogenia , ADN de Hongos/genética , ADN de Hongos/química , Levaduras/genética , ARN Ribosómico/genética , Metschnikowia/genética , ARN Ribosómico 28S , Análisis de Secuencia de ADN , Técnicas de Tipificación MicológicaRESUMEN
Introduction: Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date. Methods: In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics. Results: Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples. Conclusion: This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.
Asunto(s)
Bacterias , Microbiota , Femenino , Humanos , Estudios Prospectivos , Estudios Retrospectivos , Bacterias/genética , Reacción en Cadena en Tiempo Real de la PolimerasaRESUMEN
AIMS: The rare yeast species Lodderomyces elongisporus, Kodamaea ohmeri, Cyberlindnera fabianii, and Wickerhamomyces anomalus are increasingly implicated in severe mycoses in immunocompromised patients. This study aimed to assess the prevalence of uncommon yeast species in Côte d'Ivoire. METHODS: The yeast isolates from superficial samples, mainly vaginal swabs, were collected at the Pasteur Institute of Abidjan in a study on the molecular epidemiology of clinical yeast species. Identification relied on MALDI-TOF MS and ITS sequence analysis. Antifungal susceptibility testing was performed using the CLSI method. RESULTS: Of the 315 strains analysed from 227 outpatients, 14 belonged to 4 uncommon species: Lodderomyces elongisporus, Kodamaea ohmeri, Cyberlindnera fabianii, and Wickerhamomyces anomalus. None exhibited elevated fluconazole, amphotericin B, caspofungin, ketoconazole, or flucytosin MIC. CONCLUSIONS: The presence of these rare yeasts represents a risk in immunocompromised people. Their adequate and timely identification is a priority. Overall, enhancing the mycoses diagnostic capacities in Côte d'Ivoire, and more generally in African clinical laboratories with limited resources is a critical aim.
Asunto(s)
Hongos , Micosis , Femenino , Humanos , Côte d'Ivoire/epidemiología , Levaduras , Micosis/epidemiologíaRESUMEN
Mycoviruses are viruses that selectively infect and multiply in fungal cells. Malassezia is the most abundant fungus on human skin and is associated with a variety of conditions, including atopic eczema, atopic dermatitis, dandruff, folliculitis, pityriasis versicolor, and seborrheic dermatitis. Here, we conducted mycovirome studies on 194 public transcriptomes of Malassezia (2,568,212,042 paired-end reads) screened against all available viral proteins. Transcriptomic data were assembled de novo resulting in 1,170,715 contigs and 2,995,306 open reading frames (ORFs) that were subsequently tracked for potential viral sequences. Eighty-eight virus-associated ORFs were detected in 68 contigs from 28 Sequence Read Archive (SRA) samples. Seventy-five and thirteen ORFs were retrieved from transcriptomes of Malassezia globosa and Malassezia restricta, respectively. Phylogenetic reconstructions revealed three new mycoviruses belonging to the Totivirus genus and named Malassezia globosa-associated-totivirus 1 (MgaTV1); Malassezia restricta-associated-totivirus 1 (MraTV1) and Malassezia restricta-associated-totivirus 2 (MraTV2). These viral candidates extend our understanding of the diversity and taxonomy of mycoviruses as well as their co-evolution with their fungal hosts. These results reflected the unexpected diversity of mycoviruses hidden in public databases. In conclusion, this study sheds light on the discovery of novel mycoviruses and opens the door to study their impact on disease caused by the host fungus Malassezia and globally, their implication in clinical skin disorders.
Asunto(s)
Dermatitis Atópica , Virus Fúngicos , Malassezia , Totivirus , Humanos , Malassezia/genética , Virus Fúngicos/genética , FilogeniaRESUMEN
In order to assess the knowledge and experience of fungal infections (FIs) among clinicians in Senegal, a cross-sectional survey was carried out among medical practitioners in Senegal via a questionnaire designed with "Google Forms" between 24 January and 24 April 2022. A total of 100 clinicians responded to the questionnaire. Clinicians in the 31- 40-year-old age group formed the majority of respondents (51%). Male respondents were predominant (72%). Forty-one percent of respondents were general practitioners, 40% were specialist doctors, and the rest were residents. Dermatologists were the most common at 15% (6/40). In terms of clinicians' general knowledge of fungi, FIs and their therapeutic management, an average of 70% correct answers was recorded. The majority (70%) of respondents cared for between two to four different categories of patients at risk of invasive FIs (IFIs) at a time, with diabetes predominating. Eighty percent confirmed that they had been confronted with FIs, including 43% with superficial FIs, 3% with subcutaneous FIs and 5% with IFIs. Thirty-four percent of doctors stated that they had never suspected an IFI. Candidiasis was the most commonly mentioned mycosis by doctors. To support the diagnosis of these FIs, 22% of the clinicians said that they had recourse only to the clinical diagnosis. In total, 79% of clinicians responded that they had never used an antifungal chemoprophylaxis. In addition, 28% and 22% of practicing physicians chose a combination of antifungals for the chemoprophylaxis of invasive candidiasis and invasive aspergillosis, respectively. This survey shows that both clinicians' knowledge and experience of fungi, antifungals, FIs and their therapeutic management, as well as chemoprophylaxis, need to be improved. Indeed, half of the clinicians seem to be unaware of the incidence of FIs, in particular IFIs, which, nevertheless, represent some of the deadliest infectious diseases in the world.
Asunto(s)
Candidiasis Invasiva , Infecciones Fúngicas Invasoras , Médicos , Humanos , Masculino , Adulto , Antifúngicos/uso terapéutico , Senegal/epidemiología , Estudios Transversales , Hongos , Infecciones Fúngicas Invasoras/diagnóstico , Infecciones Fúngicas Invasoras/tratamiento farmacológico , Infecciones Fúngicas Invasoras/epidemiología , Candidiasis Invasiva/tratamiento farmacológicoRESUMEN
Understanding the transmission of Schistosoma hæmatobium in the Senegal River Delta requires knowledge of the snails serving as intermediate hosts. Accurate identification of both the snails and the infecting Schistosoma species is therefore essential. Cercarial emission tests and multi-locus (COX1 and ITS) genetic analysis were performed on Bulinus forskalii snails to confirm their susceptibility to S. hæmatobium infection. A total of 55 Bulinus forskalii, adequately identified by MALDI-TOF mass spectrometry, were assessed. Cercarial shedding and RT-PCR assays detected 13 (23.6%) and 17 (31.0%), respectively, Bulinus forskalii snails parasitized by S. hæmatobium complex fluke. Nucleotide sequence analysis identified S. hæmatobium in 6 (11.0%) using COX1 and 3 (5.5%) using ITS2, and S. bovis in 3 (5.5%) using COX1 and 3 (5.5%) using ITS2. This result is the first report of infection of Bulinus forskalii by S. hæmatobium complex parasites in Senegal using innovative and more accurate identification methods to discriminate this snail and characterize its infection by S. hæmatobium.
Asunto(s)
Bulinus , Schistosoma haematobium , Animales , Bulinus/parasitología , Schistosoma haematobium/genética , Senegal , Schistosoma/genética , Caracoles/parasitología , RíosRESUMEN
Humans are constantly exposed to micromycetes, especially filamentous fungi that are ubiquitous in the environment. In the presence of risk factors, mostly related to an alteration of immunity, the non-dermatophyte fungi can then become opportunistic pathogens, causing superficial, deep or disseminated infections. With new molecular tools applied to medical mycology and revisions in taxonomy, the number of fungi described in humans is rising. Some rare species are emerging, and others more frequent are increasing. The aim of this review is to (i) inventory the filamentous fungi found in humans and (ii) provide details on the anatomical sites where they have been identified and the semiology of infections. Among the 239,890 fungi taxa and corresponding synonyms, if any, retrieved from the Mycobank and NCBI Taxonomy databases, we were able to identify 565 moulds in humans. These filamentous fungi were identified in one or more anatomical sites. From a clinical point of view, this review allows us to realize that some uncommon fungi isolated in non-sterile sites may be involved in invasive infections. It may present a first step in the understanding of the pathogenicity of filamentous fungi and the interpretation of the results obtained with the new molecular diagnostic tools.