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Background Vulvovaginal candidiasis (VVC) is a common and debilitating long-term illness affecting million women worldwide. This disease is caused mainly by Candida albicans and a lesser extent by other species, including the two phylogenetically closely related pathogens Candida africana and Candida dubliniensis. Objectives In this study, we report detailed molecular epidemiological data about the occurrence of these two pathogenic yeasts in Iranian patients affected by VVC, or its chronic recurrent form (RVVC), and provide, for the first time, data on the antifungal activity of two new drugs, efinaconazole (EFN) and luliconazole (LUL). Methods A total of 133 vaginal yeast isolates, presumptively identified as C. albicans by phenotypic and restriction analysis of rDNA, were further analyzed by using a specific molecular method targeting the HWP1 gene. All C. africana and C. dubliniensis isolates were also tested for their in-vitro susceptibility to a panel of modern and classical antifungal drugs. Results and conclusions Based on the molecular results, among 133 germ-tube positive isolates, we identify 119 C. albicans (89.47%), 11 C. africana (8.27%), and 3 C. dubliniensis (2.26%) isolates. C. africana and C. dubliniensis showed low MIC values for most of the antifungal drugs tested, especially for EFN and LUL, which exhibited a remarkable antifungal activity. High MIC values were observed only for nystatin and terbinafine. Although C. albicans remains the most common Candida species recovered from Iranian VVC/RVVC patients, our data show that its prevalence may be slightly overestimated due to the presence of difficult-to-identify closely related yeast, especially C. africana.

Candida tropicalis is a human pathogenic yeast frequently isolated in Latin America and Asian-Pacific regions, although recent studies showed that it is also becoming increasingly widespread throughout several African and south-European countries. Nevertheless, relatively little is known about its global patterns of genetic variation as most of existing multilocus sequence typing (MLST) data come from Asia and there are no genotyped African isolates.We report detailed genotyping data from a large set of C. tropicalis isolates recovered from different clinical sources in Italy, Egypt and Cameroon in order to expand the allele/genotype library of MLST database (https://pubmlst.org/ctropicalis), and to explore the genetic diversity in this species.A total of 103 C. tropicalis isolates were genotyped using the MLST scheme developed for this species. All isolates were also tested for in vitro susceptibility to various antifungals to assess whether certain genotypes were associated with drug-resistance.A total of 104 different alleles were detected across the MLST-loci investigated. The allelic diversity found at these loci resulted in 51 unique MLST genotypes of which 36 (70.6%) were novel. Global optimal eBURST analysis identified 18 clonal complexes (CCs) and confirm the existence of a specific Italian-cluster (CC36). Three CCs were also statistically associated with fluconazole resistance, which was elevated in Cameroon and Egypt. Our data show high genetic diversity in our isolates suggesting that the global population structure of C. tropicalis is still poorly understood. Moreover, its clinical impact in Italy, Egypt and Cameroon appears to be relevant and should be carefully considered.

Background The genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic soil and plant fungi, although pathogenic species capable of causing human infections are also present. The whole-genomes of disease-causing species have already been sequenced and annotated but no comprehensive genomic resources for environmental Sporothrix species are available, thus limiting our understanding of the evolutionary origin of virulence-related genes and pathogenicity. Result The genome assembly of four environmental Sporothrix species resulted in genome size of ~ 30.9 Mbp in Sporothrix phasma, ~ 35 Mbp in S. curviconia, ~ 38.7 Mbp in S. protearum, and ~ 39 Mbp in S. variecibatus, with a variable gene content, ranging from 8142 (S. phasma) to 9502 (S. variecibatus). The analysis of mobile genetic elements showed significant differences in the content of transposable elements within the sequenced genomes, with the genome of S. phasma lacking several class I and class II transposons, compared to the other Sporothrix genomes investigated. Moreover, the comparative analysis of orthologous genes shared by clinical and environmental Sporothrix genomes revealed the presence of 3622 orthogroups shared by all species, whereas over 4200 genes were species-specific single-copy gene products. Carbohydrate-active enzyme analysis revealed a total of 2608 protein-coding genes containing single and/or multiple CAZy domains, resulting in no statistically significant differences among pathogenic and environmental species. Nevertheless, some families were not found in clinical species. Furthermore, for each sequenced Sporothrix species, the mitochondrial genomes was assembled in a single circular DNA molecule, ranging from 25,765 bp (S. variecibatus) to 58,395 bp (S. phasma). Conclusion In this study, we present four annotated genome assemblies generated using PacBio SMRT sequencing data from four environmental species: S. curviconia, S. phasma, S. protearum and S. variecibatus with the aim to provide a starting point for future comparative genome evolution studies addressing species diversification, ecological/host adaptation and origin of pathogenic lineages within the genus Sporothrix.

Background Candida sp. represent the most common cause of fungal infections worldwide. In the present work, we have evaluated the activity of an essential oil extracted from pistachio hulls against a number of standard and clinical strains of Candida sp. Methods C. albicans ATCC 64550, C. parapsilosis ATCC 22019, 4 clinical strains of C. albicans, 3 clinical strains of C. parapsilosis and 3 clinical strains of C. glabrata were used. All clinical isolates were identified by species-specific PCR-based methods. Susceptibility studies were performed using pistachio hull essential oil alone or in combination with antifungal compounds. The interactions between pistachio hull essential oil and selected antifungal compounds were also evaluated using the checkerboard method and the mechanisms of interaction investigated by droplet size distribution. Results Pistachio hull essential oil was fungicidal at the concentrations between 2.50 and 5.0 mg/ml. D-limonene and 3-Carene were the components with major activity. An antagonistic effect was observed with all combinations tested. Conclusion The antifungal activity of pistachio hull essential oil could be used to help control resistance in Candida species. More studies need to be performed to elucidate the mechanisms responsible for the activity of pistachio hull essential oil.

An autochthonous case of lymphocutaneous sporotrichosis caused by Sporothrix schenckii is reported. The patient developed skin lesions localized along the lymphatics that appeared after he suffered an injury while collecting wicker canes in marshy water. The fungus was identified as Sporothrix schenckii by MALDI-TOF and sequencing. Phylogenetic analysis was also performed. Low MIC values were detected for all tested echinocandins and azoles except for fluconazole. The patient was treated with itraconazole without significant improvement. A regression of lesions was observed after 3 months of therapy with voriconazole. Few cases of sporotrichosis have been reported in Europe. However, several cases of sporotrichosis have been described in Italy. The incidence of sporotrichosis in Italy may be underestimated and microbiologists, and clinicians must be aware of this fungal infection.

Cryptococcosis is a human infection caused mainly by two species of the Cryptococcus genus, Cryptococcus neoformans and Cryptococcus gattii, whose populations contain several phylogenetically related haploid (VN/VG-types) and hybrid genotypes. Here, we report the whole-genome sequencing of a Nigerian C. neoformans VNII, Mat-α, strain with a rare multilocus-sequence-type (MLST) genotype (ST43).

Elucidating population structure and levels of genetic diversity and recombination is necessary to understand the evolution and adaptation of species. Candida albicans is the second most frequent agent of human fungal infections worldwide, causing high-mortality rates. Here we present the genomic sequences of 182 C. albicans isolates collected worldwide, including commensal isolates, as well as ones responsible for superficial and invasive infections, constituting the largest dataset to date for this major fungal pathogen. Although, C. albicans shows a predominantly clonal population structure, we find evidence of gene flow between previously known and newly identified genetic clusters, supporting the occurrence of (para)sexuality in nature. A highly clonal lineage, which experimentally shows reduced fitness, has undergone pseudogenization in genes required for virulence and morphogenesis, which may explain its niche restriction. Candida albicans thus takes advantage of both clonality and gene flow to diversify., The fungal pathogen Candida albicans can undergo a parasexual process that may contribute to genetic diversity, but its actual relevance is unclear. Here, Ropars et al. analyse the genomic sequences of 182 C. albicans isolates collected worldwide and find evidence of gene flow and thus parasexuality in nature.

Although the epidemiology of pathogenic Candida species causing invasive human diseases is changing, Candida albicans still remains the most common cause of bloodstream infections worldwide. The propensity of this pathogen to cause infections is undoubtedly the result of its unique genetic plasticity that allow it to adapt and respond quickly to a myriad of changing conditions both in the host and in the environment. For this reason, we decided to investigate the genetic diversity of this important fungal pathogen in a particular category of patients with severe neurological deficits including the hospital environments where they are hospitalized. Genetic diversity of 21 C. albicans isolates recovered from blood, hands of healthcare workers and hospital environments was evaluated by using multilocus sequence typing (MLST) which revealed a high genetic heterogeneity with a set of 18 diploid sequence types (DSTs) recovered among 21 isolates investigated. Interestingly, 13 of these 18 MLST genotypes were completely new and added to the C. albicans MLST central database. Six eBURST clonal complexes (CC-1, CC-2, CC-6, CC-9, CC-27 and CC-42) and three singletons contained all DSTs found in this study. Among all the new DSTs identified, DST3388 was the most intriguing as this genotype was recovered from a typical C. albicans isolate clustering within the MLST-Clade 13, the most divergent evolutionary lineage within C. albicans population containing only isolates with unusual phenotypes originally known as Candida africana. In conclusion, the results of this study expand our understanding of the molecular epidemiology and global population structure of C. albicans suggesting that further studies on different categories of patients and hospital environments are needed to better understand how the population of this species adapts and evolves in heterogeneous hosts and changing environments.

Background: Hepatitis C virus (HCV) NS3 resistance-associated substitutions (RASs) reduce HCV susceptibility to protease inhibitors. Little is known about NS3 RASs in viral isolates from the liver of chronic hepatitis C (CHC) patients infected with HCV genotype-1a (G1a). Aim: The objective of this work was to study NS3 variability in isolates from the serum and liver of HCV-G1a-infected patients naïve to direct-acting antivirals (DAAs). Methods: NS3 variability of HCV-G1a isolates from the serum and liver of 11 naïve CHC patients, and from sera of an additional 20 naïve CHC patients, was investigated by next-generation sequencing. Results: At a cutoff of 1%, NS3 RASs were detected in all the samples examined. At a cutoff of 15%, they were found in 54.5% (6/11) and 27.3% (3/11) of the paired liver and serum samples, respectively, and in 22.5% (7/31) of the overall serum samples examined. Twenty-six out of thirty-one (84%) patients showed NS3 variants with multiple RASs. Phylogenetic analysis showed that NS3 sequences clustered within 2 clades, with 10/31 (32.2%) patients infected by clade I, 15/31 (48.8%) by clade II, and 6/31 (19.3%) by both clades. Conclusions: Though the number of patients examined was limited, NS3 variants with RASs appear to be major components of both intrahepatic and circulating viral quasispecies populations in DAA-naïve patients.

In this study, using multilocus microsatellite analysis, we report the genetic characterization of 27 Candida parapsilosis isolates recovered in two different periods of time (2007-2009 and 2011-2012) from infants hospitalized in the neonatal intensive care unit of a hospital in Messina, Italy. The results revealed the persistence and dominance of a particular infectious genotype among NICU patients and highlight the power of the used microsatellite markers in clarifying epidemiologic associations, detect micro-evolutionary variations and facilitating the recognition of outbreaks. © 2012 Elsevier B.V.

This study aimed to elucidate the genetic relatedness and epidemiology of 127 clinical and environmental Candida glabrata isolates from Europe and Africa using multilocus microsatellite analysis. Each isolate was first identified using phenotypic and molecular methods and subsequently, six unlinked microsatellite loci were analyzed using automated fluorescent genotyping. Genetic relationships were estimated using the minimum-spanning tree (MStree) method. Microsatellite analyses revealed the existence of 47 different genotypes. The fungal population showed an irregular distribution owing to the over-representation of genetically different infectious haplotypes. The most common genotype was MG-9, which was frequently found in both European and African isolates. In conclusion, the data reported here emphasize the role of specific C. glabrata genotypes in human infections for at least some decades and highlight the widespread distribution of some isolates, which seem to be more able to cause disease than others., This research was supported in part by the EU Mare Nostrum (EUMN-III Call) program of the European Union, grant agreement number 2011-4050/001-EMA2. Dr Sanae Rharmitt was the recipient of a scholarship (10 months) signed within the EUMN program for PhD students (F.S. 1.04.11.01 UORI) under the supervision of Prof Orazio Romeo., info:eu-repo/semantics/publishedVersion

Cryptococcus neoformans and Cryptococcus gattii are encapsulated yeasts able to cause fatal neurological infections in both human and other mammals. Cryptococcosis is the most common fungal infection of the central nervous system and has a huge burden in sub-Saharan Africa and South East Asia. Bird excreta are considered an environmental reservoir for C. neoformans in urban areas, therefore a study aimed at isolating and characterizing this yeast is important in disease management. In this study, one hundred samples of pigeon droppings were collected in Jos, Plateau State, Nigeria. C. neoformans was isolated from three samples and initially identified using standard phenotypic and biochemical tests. Molecular analysis revealed that all three isolates belonged to C. neoformans genotype VNII, mating type α and were assigned to the sequence type ST43 by multilocus sequence typing analysis. This study reports, for the first time, the molecular characterization of C. neoformans in Nigeria, where little is still known about the environmental distribution of the genotypes, serotypes and mating types of this important human pathogen.

Given the lack of comprehensive molecular epidemiology studies in Reggio Calabria and Messina, Italy, we decided to perform an extensive environmental sampling to describe the current molecular epidemiology of C. neoformans/C. gattii species complex in southern Italy. In this study, we report the occurrence of serotypes, genotypes and mating-types of isolates of the C. neoformans/C. gattii species complex recovered from environmental sources. In addition, a number of environmental C. neoformans var. grubii strains, isolated in 1997 by our laboratory, were also retrospectively examined in order to compare their genotypes with those recently found and to infer the possible epidemiological changes in our country. One hundred and twenty-two isolates were identified as being C. neoformans, whereas only one was found to belong to C. gattii serotype B, genotype VGI and mating-type alpha. Our data revealed that all environmental isolates of C. neoformans recovered here as well as those previously isolated in 1997 belong to serotype A and genotype VNI and posses a mating-type alpha allele.

Fungal nosocomial infections continue to be a serious problem among hospitalized patients, decreasing quality of life and adding millions of euros to healthcare costs. The aim of this study was to describe the pattern of fungi associated with the hands of healthcare workers and to genotype Candida parapsilosis isolates in order to understand whether their high clinical prevalence stems from endemic nosocomial genotypes or from the real emergence of epidemiologically-unrelated strains. Approximately 39% (50/129) of healthcare workers were positive for yeasts and among 77 different fungal isolates recovered, C. parapsilosis was the most frequent (44/77; 57%). Twenty-seven diverse genotypes were obtained by microsatellite analysis of 42 selected blood and hand isolates. Most of the isolates from hands showed a new, unrelated, genotype, whereas a particular group of closely related genotypes prevailed in blood samples. Some of the latter genotypes were also found on the hands of healthcare workers, indicating a persistence of these clones within our hospital. C. parapsilosis genotypes from the hands were much more heterogeneous than clinical ones, thus reflecting a high genetic diversity among isolates, which is notably unusual and unexpected for this species.

We performed a molecular study to determine the occurrence of Candida albicans, Candida africana , and Candida dubliniensis in different clinical samples. The study provides new insights into the epidemiology of candidiasis in hospitalized patients in three hospitals in southern Italy. It also reports the first detailed epidemiological data concerning the occurrence of C. africana in clinical samples.

The authors developed a new, simple, and reliable PCR/restriction fragment length polymorphism technique, using amplification of the hyphal wall protein 1 gene of Candida albicans and its gene homologue in Candida dubliniensis , to differentiate the two species of Candida . Performed with a new primer set, CRR-f/CRR-r, PCR produced two different fragments: one of 1,180 bp for C. albicans , and one of 930 bp for C. dubliniensis .

BACKGROUND: Our aim was to identify risk factors for the development of neonatal Candida liver abscess and to find useful information to better manage this potentially fatal complication. METHODS: A computerized search was conducted using PubMed. Overall, three articles describing the history of seven infants were finally considered. The characteristics of these seven cases were analyzed together with those of three new cases that we treated in the recent past. RESULTS: All the neonates were premature. Previous antibiotic use was reported in all the cases, umbilical venous catheterization in 9/10 and total parenteral nutrition in 8/10. Candida albicans was isolated in 9/10. All the patients presented with aspecific signs of sepsis. Liver abscesses were described as "microabscesses" or "miliary abscesses" in three cases, as solitary lesion in two cases. In one case two lesions and in one four lesions were reported. Three infants died. CONCLUSIONS: Liver ultrasonography should be performed in all the neonates with signs of sepsis, especially in the presence of candidemia and/or hepatomegaly and/or significant change in liver enzymes. Umbilical venous catheter should be removed, and peripheral IV access should be used until there is documented clearance from the blood with three or more negative blood cultures.

The authors report the molecular characterization of Candida parapsilosis isolates recovered from the blood and venous central catheter tips of patients admitted to different care units of the Polyclinic Hospital, University of Messina, Italy. Among 97 presumed C. parapsilosis isolates examined, 94 were identified as C. parapsilosis sensu stricto and the remaining 3 isolates were found to belong to the cryptic species Candida orthopsilosis which was recovered only from blood cultures of neonates (

During a survey of the prevalence of Candida spp. in Jos, Plateau State, Nigeria, two atypical C. albicans isolates were recovered. These two yeasts were germ tube positive, chlamydospore-negative and gave a green color on CHROMagar Candida. Molecular analysis performed by amplification of the hwp1 gene showed that these two isolates belonged to C. africana, a newly proposed Candida species closely related to C. albicans. Based on the presence or absence of an intron in DNA sequences encoding rRNA, the two C. africana, including all C. albicans isolates examined, were found to belong to genotype A and no other genotypes or species such as C. dubliniensis were found. To our knowledge, this is the first isolation of C. africana in Nigeria.

We describe a case of mycetoma caused by Actinomadura pelletieri with simultaneous involvement of the spine, abdominal wall and retroperitoneal space in a man who had suffered from ‘Madura foot’ 10 years earlier. The characteristics of this case were analysed and contextualized among those of other cases of mycetoma caused by other micro-organisms found through a review of the international literature. The rarity of the disease in industrialized countries and its possible atypical presentations may hinder a prompt diagnosis. Culture techniques that allow detection of slow-growing fungi and actinomycetes should be routinely used when dealing with tissue samples from patients from tropical and subtropical regions with chronic granulomatous infections.

In this study, we investigated phylogenetic relationships among Italian Sporothrix schenckii isolates, by comparing their partial calmodulin sequences. In this analysis, we used 26 environmental strains of S. schenckii, plus two autochthonous clinical isolates. The results showed that our clinical strains grouped with S. schenckii sensu stricto isolates, whereas all 26 environmental isolates co-clustered with Sporothrix albicans (now regarded as a synonym of Sporothrix pallida), a non-pathogenic species closely related to S. schenckii. Furthermore, the group of environmental strains was found to be quite heterogeneous and further subdivided into two subgroups. The data reported here also showed that molecular methods, for specific identification of S. schenckii, developed before the description of its closely related species should be used with caution because of the possibility of false positive results, which could lead to inappropriate antifungal therapy. This study improves our understanding of the distribution of these new closely related Sporothrix species which also showed significant differences in antifungal susceptibilities.

We have developed a multiplex PCR protocol for the detection of Candida glabrata and its closely related species Candida nivariensis and Candida bracarensis. The method uses four PCR primers, targeting the ITS1 region and the 5.8S ribosomal RNA gene. The combination of these primers yielded unique results to all Candida species tested. The PCR assay we developed was found to be a rapid, specific and easy to perform method and it will be useful for characterizing large numbers of isolates for epidemiological studies.

The authors report here a polymerase chain reaction-based assay using a single primer pair (CR-f/CR-r), allowing discrimination between Candida africana and Candida albicans by using the hwp1 gene. The method also identifies Candida dubliniensis because it produces 3 different DNA fragments: approximately 700 bp for C. africana, 941 bp for C. albicans, and 569 for C. dubliniensis.

One atypical isolate of the pathogenic yeast Candida albicans was isolated from an Italian patient with vulvovaginitis. The strain, germ tube positive and chlamydospore-negative showed white-thin turquoise colonies on Candida ID 2 medium. The yeast was identified as Candida africana by using morphological and biochemical tests. On the basis of the molecular results obtained in this study as well as in other studies, C. africana cannot be yet considered as a new species of Candida. It is possible that C. africana represents a new variant of C. albicans like the well-known Candida stellatoidea. To our knowledge, this is the first isolation of C. africana in Italy.

Sporotrichosis is a mycotic infection rarely encountered in European countries, including Italy. We describe lymphocutaneous sporotrichosis in an immunocompetent 64-year-old male Italian mason. The patient had linear nodules along the right upper arm with severe lymphadenopathy in the same arm. Sporothrix schenckii was identified by phenotypic and molecular methods. Treatment with itraconazole and methylprednisolone followed by administration of itraconazole alone successfully cured the infection. To our knowledge, this is the first documented report of sporotrichosis from Calabria and Sicily, extreme southern Italy.