Freshwater snail-borne parasitic diseases in Africa.

BACKGROUND: Freshwater snails are the first obligatory intermediate hosts in the trematode life cycle. Several parasitic diseases transmitted by these snails are endemic in Africa, and their distribution closely follows that of the intermediate hosts. These diseases represent a major public health problem and cause significant socio-economic losses in Africa, particularly schistosomiasis and fascioliasis. In this review, we will describe the main roles of freshwater snails in the life cycle of trematode parasites, and the geographical distribution of these diseases in Africa. We will also discuss the different techniques for detecting parasitic infections in snails, as well as the various methods of controlling snails and the larval stages of parasites. METHODS: We carried out a literature search for articles dealing with parasitic diseases transmitted by freshwater snail hosts in Africa. The search was conducted in databases such as PubMed, Web of Science and Google Scholar using various search terms combined by Boolean operators. Our search was limited to peer-reviewed articles less than 10 years old. Articles published to date in the fields of control of parasitic diseases transmitted by freshwater snails were included. Results were presented in narrative and in table format. RESULTS: The results of the database search identified 1007 records. We included 84 studies in this review. These studies generally focused on freshwater snails and the diseases they transmit. We described the geographical distribution of 43 freshwater species belonging to nine snail families, as well as the parasites that infect them. Several methods for diagnosing parasites in their snail hosts have been described, including microscopic and molecular methods, as well as antibody and protein barcode-based techniques. Molluscicides have been described as the main strategy for snail control. CONCLUSION: This study highlights several elements of knowledge about diseases transmitted by freshwater snails and their distribution. A good understanding of snail infection detection techniques and existing control methods is an essential component in adapting control strategies for these diseases.

Urogenital schistosomiasis in schoolchildren in the lake zones of Kankossa and Oued Rawdha, southern Mauritania: The first parasitological and malacological survey.

BACKGROUND: Urogenital schistosomiasis due to Schistosoma haematobium is a major public health problem in Mauritania, but little is known about its epidemiology in many areas of the country, particularly in the lake zones. The objectives of the present parasitological and malacological study were to assess the prevalence and intensity of urogenital schistosomiasis among school children in Kankossa and Oued Rawdha lakes, southern Mauritania, and determine the species of intermediate host snails and the prevalence of snails with schistosome. METHODS: A school-based epidemiological survey was conducted in two villages in the lake areas of Kankossa and Oued Rawdha. Urine samples were collected from 450 state primary school children and Koranic school children and examined for the presence of S. haematobium eggs using filtration technique. Water bodies adjacent to human settlement were surveyed for Bulinus and Biomphalaria snails that may potentially be intermediate hosts of S. haematobium. Morphological, molecular, and proteomic (i.e. matrix-assisted laser desorption ionization time-of-flight mass spectrometry [MALDI-TOF MS]) identification of collected snails were conducted, and their infection status was assessed by real-time polymerase chain reaction (RT-PCR) using the highly repetitive DraI gene. RESULTS: The prevalence of urogenital schistosomiasis was 35.6% and 15.8% in Kankossa and Oued Rawdha villages, respectively, corresponding to 'moderate' prevalence (i.e., 10-49% infected schoolchildren). Urogenital schistosomiasis prevalence was higher in boys (30.0%) than in girls (21.2%; P < 0.05), and in Koranic schools pupils (37.1%) than in state schools (20.5%; P < 0.05) pupils. Multiple regression analysis showed that sex (odds ratio [OR]: 1.64; 95% confidence interval [95% CI]: 1.06-2.57; P = 0.03) and Koranic school level (OR: 1.79; 95% CI: 1.06-3.04; P = 0.03) were independently and significantly associated with urogenital schistosomiasis. Based on molecular and proteomic identification, both B. senegalensis and B. umbilicatus colonized the water bodies of Oued Rawdha, whereas both B. forskalii and B. truncatus colonized those of Kankossa. The DraI RT-PCR detected S. haematobium complex DNA in 8 of 66 (12.1%) analysed snails: one B. truncatus and one B. forskalii in Kankossa and five B. senegalensis and one B. umbilicatus in Oued Rawdha. CONCLUSION: Urogenital schistosomiasis is moderately prevalent in the lake zones of Kankossa and, to a lesser extent, Oued Rawdha, located in southern Mauritania. Mass drug administration campaigns with praziquantel should be conducted to reduce the prevalence of urogenital schistosomiasis among school-aged children in the lake zone of Kankossa and Oued Rawdha village. Further parasitological and malacological studies should be conducted in other villages located in the Mauritanian lakes in the southern Sahelian zones and the northern oasis areas to strengthen our knowledge of the current epidemiological situation and implement appropriate urogenital schistosomiasis control strategies.

Direct 16S/ITS rRNA Gene PCR Followed by Sanger Sequencing for Detection of Mycetoma Causative Agents in Dakar, Senegal: A Pilot Study Among Patients with Mycetoma Attending Aristide Le Dantec University Hospital.

Mycetoma can be caused either by fungi or aerobic Actinomycetes. A precise identification of the causal agents is critical for the therapeutic outcome. Thus, this study aimed to identify the pathogens of mycetoma using 16S/ITS rRNA gene polymerase chain reaction (PCR) followed by Sanger sequencing directly on grains. In sum, 32 samples including 15 black grains, 12 red grains, and five white/yellow grains collected from patients with mycetoma at the Aristide Le Dantec University Hospital in Dakar, Senegal, between October 2014 and September 2020 were submitted to PCR/sequencing. For black grain eumycetoma, the ITS rRNA region was targeted. Similarly, the 16S rRNA gene was targeted for red grain actinomycetoma. These two regions were targeted in parallel for white/yellow grains, which could be of either bacterial or fungal origin. The age of the patients ranged from 14 to 72 years with a mean age of 36 ± 14 years. Thirteen (86%) of the 15 samples with black grains, were successfully sequenced with only one established eumycetoma pathogen, Madurella mycetomatis identified in 11 (73%). Cladosporium sphaerospermum was identified in one sample. For the 16S rRNA sequencing of red grains, a 58.3% (7/12) success rate was obtained with Actinomadura pelletieri identified in six samples. Among the five samples sequenced twice, the 16S rRNA allowed us to identify the causative agent in 2 cases, A. madurae in one, and A. geliboluensis in the other. The ITS rRNA identified 3 fungi, of which none was a mycetoma agent. Overall, direct 16S/ITS rRNA sequencing of the grains for detecting and identifying mycetoma pathogens was successful in 59.4% of cases. Fungi, led by M. mycetomatis, were the predominant pathogens identified. Two probable new mycetoma agents, C. sphaerospermum, and A. geliboluensis were identified and both deserve to be confirmed in further studies.

Cryptococcosis at the university hospital of Marseille: A case series.

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.

Malian Children's Core Gut Mycobiome.

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.

Epidemiology and management of tinea capitis in France: A 6-year nationwide retrospective survey.

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.

Features of cryptococcosis among 652 HIV-seronegative individuals in France: a cross-sectional observational study (2005-2020).

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.

Cryptococcus neoformans Infections Differ Among Human Immunodeficiency Virus (HIV)-Seropositive and HIV-Seronegative Individuals: Results From a Nationwide Surveillance Program in France.

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.

Evaluation of the Performance of Rapid Diagnostic Tests for Malaria Diagnosis and Mapping of Different Plasmodium Species in Mali.

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.

Syncephalastrum massiliense sp. nov. and Syncephalastrum timoneanum sp. nov. Isolated from Clinical Samples.

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.

MALDI-TOF mass spectrometry identification and antifungal susceptibility testing of yeasts causing vulvovaginal candidiasis (VVC) in Tebessa (Northeastern Algeria).

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.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry traces the geographical source of Biomphalaria pfeifferi and Bulinus forskalii, involved in schistosomiasis transmission.

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.

Nosocomial transmission of Aspergillus flavus in a neonatal intensive care unit: Long-term persistence in environment and interest of MALDI-ToF mass-spectrometry coupled with convolutional neural network for rapid clone recognition.

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.

A Repertoire of the Less Common Clinical Yeasts.

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.

Antifungal Resistance Profile, Biofilm Formation, and Virulence Factor Production in Candida krusei Isolates From HIV-Infected Patients in Cameroon.

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.

Candida massiliensis sp. nov. Isolated from a Clinical Sample.

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.

Preliminary landscape of Candidatus Saccharibacteria in the human microbiome.

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.

Evaluation of knowledge and experience of fungal infections (mycoses) among clinical doctors in Senegal.

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.

Tracking Mycoviruses in Public RNAseq Datasets of Malassezia: Three Original Totiviruses Revealed.

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.