Metagenomics reveals an abundance of black yeast-like fungi in the skin microbiome.

BACKGROUND: The skin is the first line of defence against communities of resident viruses, bacteria and fungi. The composition of the microbiome might change with factors related to the environment and host. The microbiome is dominated by bacteria. Dermatophytes and yeasts are the predominant fungi that are also involved in opportunistic infections of skin, hair and nails. Among environmental fungi, Chaetothyriales (black yeasts and relatives) are enriched by hydrocarbon pollution in domesticated habitats and comprise numerous species that cause mild-to-severe disease. METHODS: We investigated the presence of black fungi in the skin microbiome by conducting an analysis in the publicly available metagenomic SRA database (NCBI). We focused on the causative agents of chromoblastomycosis and phaeohyphomycosis and used barcodes and padlock probe sequences as diagnostic tools. RESULTS: A total of 132,159,577 MB was analysed and yielded 18,360 reads that matched with 24 species of black fungi. Exophiala was the most prevalent genus, and Cyphellophora europaea was the most abundant species. CONCLUSION: This study reveals the abundant presence of Chaetothyriales on the skin without necessarily being associated with infection. Most of the detected causal agents are known from mild skin diseases, while also species were revealed that had been reported from CARD9-deficient patients.

Case report: First case of fungemia caused by Papiliotrema laurentii in a patient with SARS-CoV-2 infection.

Previously considered saprobe and non-pathogenic, the fungus Papiliotrema laurentii (formerly known as Cryptococcus laurentii), is rarely associated with human infection. Nevertheless, there has been an increase in reported infections by non-neoformans cryptococci. After a literature search on the Cochrane Library, LILACS, SciELO, MEDLINE, PubMed, and PMC (PubMed Central) databases, we conclude that this is the first case report of fungemia and probable meningitis caused by Papiliotrema laurentii in a previously immunocompetent host with associated COVID-19.

Brazilian artisanal Colonial cheese: characterization, microbiological safety, and survival of Salmonella enterica serovar Enteritidis during ripening.

The artisanal Colonial cheese is typical of the southern region of Brazil and dates back to the colonization by Italian and German immigrants. Produced with raw milk, it is the main cheese produced by more than 15,200 small rural proprieties. The consumer increasingly appraises food with territorial valorization, demanding specific sanitary norms for this type of cheese. This work aimed to know the physical-chemical characteristics of the cheeses produced in the west of Santa Catarina State, to study the ripening time to reach microbiological safety, and to experimentally observe the survival of Salmonella enterica serovar Enteritidis ATCC 13076 during the ripening. The physical-chemical characterization was performed with 129 samples of cheeses. Five dairies were selected for evaluation of the ripening process. Salmonella survival using a challenge test was performed on three batches prepared in a pilot plant. The cheeses were classified as high (15.4%), medium (74.6%), and low moisture (9.2%), and concerning fat content as semi-fat (37.5%) and fat (62.5%). Salmonella challenge test demonstrated their survival for up to 28 days, depending on the initial contamination. The ripening monitoring showed that thermotolerant coliforms could be a good indicator of the process because they are the most persistent microorganisms.

Isolation of Beauveria Strains and Their Potential as Control Agents for Lema bilineata Germar (Coleoptera: Chrysomelidae).

Lema bilineata Germar (Coleoptera: Chrysomelidae) was recently reported to damage Physalis peruviana crops in Brazil. Given the potential for inflicting damage on other Solanaceae species and the lack of alternatives for controlling this pest, we assessed the pathogenicity of 15 Beauveria isolates against L. bilineata adults in vitro. In addition, three of these isolates were tested for their ovicidal effect against L. bilineata eggs. Fungal strains were isolated from mummified corpses of L. bilineata collected in a non-commercial field in Paraná, Brazil. The isolates were identified as Beauveria bassiana using molecular markers. Lema bilineata adults were susceptible to conidial suspensions of all these isolates at a concentration of 108 conidia mL-1. Deaths caused by fungal extrusion were confirmed. Three strains were found to be more virulent against L. bilineata adults and showed ovicidal effects. This is the first study on entomopathogenic fungi isolated from dead insects collected from P. peruviana crops and tested against L. bilineata carried out in Brazil. The results obtained in the laboratory indicate the high potential of the use of three B. bassiana strains against L. bilineata as a biocontrol agent.

Environmental prospecting of black yeast-like agents of human disease using culture-independent methodology.

Melanized fungi and black yeasts in the family Herpotrichiellaceae (order Chaetothyriales) are important agents of human and animal infectious diseases such as chromoblastomycosis and phaeohyphomycosis. The oligotrophic nature of these fungi enables them to survive in adverse environments where common saprobes are absent. Due to their slow growth, they lose competition with common saprobes, and therefore isolation studies yielded low frequencies of clinically relevant species in environmental habitats from which humans are thought to be infected. This problem can be solved with metagenomic techniques which allow recognition of microorganisms independent from culture. The present study aimed to identify species of the family Herpotrichiellaceae that are known to occur in Brazil by the use of molecular markers to screen public environmental metagenomic datasets from Brazil available in the Sequence Read Archive (SRA). Species characterization was performed with the BLAST comparison of previously described barcodes and padlock probe sequences. A total of 18,329 sequences was collected comprising the genera Cladophialophora, Exophiala, Fonsecaea, Rhinocladiella and Veronaea, with a focus on species related to the chromoblastomycosis. The data obtained in this study demonstrated presence of these opportunists in the investigated datasets. The used techniques contribute to our understanding of environmental occurrence and epidemiology of black fungi.

Environmental Screening of Fonsecaea Agents of Chromoblastomycosis Using Rolling Circle Amplification.

Chromoblastomycosis is a chronic, cutaneous or subcutaneous mycosis characterized by the presence of muriform cells in host tissue. Implantation disease is caused by melanized fungi related to black yeasts, which, in humid tropical climates, are mainly members of the genus Fonsecaea. In endemic areas of Brazil, F. pedrosoi and F. monophora are the prevalent species. The current hypothesis of infection is traumatic introduction via plant materials, especially by plant thorns. However, isolation studies have demonstrated a low frequency of the agents in environmental substrates. The present study aimed to detect F. pedrosoi and F. monophora in shells of babassu coconuts, soil, plant debris, and thorns from endemic areas of chromoblastomycosis in Maranhão state, northern Brazil, using Rolling Circle Amplification (RCA) with padlock probes as a new environmental screening tool for agents of chromoblastomycosis. In addition to molecular screening, the environmental samples were analyzed by fungal isolation using mineral oil flotation. The limit of detection of the RCA method was 2.88 × 107 copies of DNA per sample for the used padlock probes, indicating that this represents an efficient and sensitive molecular tool for the environmental screening of Fonsecaea agents. In contrast, with isolation from the same samples using several selective methods, no agents of chromoblastomycosis were recovered.

Selective isolation of agents of chromoblastomycosis from insect-associated environmental sources.

Chromoblastomycosis is a neglected disease characterized by cutaneous, subcutaneous or disseminated lesions. It is considered an occupational infectious disease that affects mostly rural workers exposed to contaminated soil and vegetal matter. Lesions mostly arise after a traumatic inoculation of herpotrichiellaceous fungi from the Chaetothyriales order. However, the environmental niche of the agents of the disease remains obscure. Its association with insects has been predicted in a few studies. Therefore, the present work aimed to analyze if social insects, specifically ants, bees, and termites, provide a suitable habitat for the fungi concerned. The mineral oil flotation method was used to isolate the microorganisms. Nine isolates were recovered and phylogenetic analysis identified two strains as potential agents of chromoblastomycosis, i.e., Fonsecaea pedrosoi CMRP 3076, obtained from a termite nest (n = 1) and Rhinocladiella similis CMRP 3079 from an ant exoskeleton (n = 1). In addition, we also identified Fonsecaea brasiliensis CMRP 3445 from termites (n = 1), Exophiala xenobiotica CMRP 3077 from ant exoskeleton (n = 1), Cyphellophoraceae CMRP 3103 from bees (n = 1), Cladosporium sp. CMRP 3119 from bees (n = 1), Hawksworthiomyces sp. CMRP 3102 from termites (n = 1), and Cryptendoxyla sp. from termites (n = 2). The environmental isolate of F. pedrosoi CMRP 3076 was tested in two animal models, Tenebrio molitor and Wistar rat, for its pathogenic potential with fungal retention in T. molitor tissue. In the Wistar rat, the cells resembling muriform cells were observed 30 d after inoculation.

Case report: First case of fungemia caused by Papiliotrema laurentii in a patient with SARS-CoV-2 infection

ABSTRACT Previously considered saprobe and non-pathogenic, the fungus Papiliotrema laurentii (formerly known as Cryptococcus laurentii), is rarely associated with human infection. Nevertheless, there has been an increase in reported infections by non-neoformans cryptococci. After a literature search on the Cochrane Library, LILACS, SciELO, MEDLINE, PubMed, and PMC (PubMed Central) databases, we conclude that this is the first case report of fungemia and probable meningitis caused by Papiliotrema laurentii in a previously immunocompetent host with associated COVID-19.

New Insights on Environmental Occurrence of Pathogenic Fungi Based on Metagenomic Data from Brazilian Cerrado Biome

Abstract: Cerrado is the second largest biome in Brazil and majorly contributes to the country's grain production. Previous studies on soil metagenomics from the Cerrado revealed an outstanding microbial diversity. In this study, the abundance of pathogenic fungi was analyzed using metagenomic sequences of the Cerrado soils under native vegetation, and under agriculture with no-tillage and conventional tillage. In total, 128,627 sequences of fungi were identified, with 43,439 representing pathogenic fungi and were distributed as follows: native 17,301 (40%), no-tillage 13,780 (32%), and conventional tillage 12,358 (28%). We identified 41 pathogenic fungal species associated with human and animal infections. The data analysis revealed that the native soils had a higher relative abundance of fungal sequences, similar to pathogenic species sequences, in relation to the total eukaryotic sequences, than the conventional tillage and no-tillage treatments, which observed a reduction in fungal abundance because of anthropogenic activities.