Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in t... more Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in the host. The morphological shift between mycelial/yeast phases is crucial for its virulence, but the transcriptional networks implicated in dimorphic transition are still not fully understood. Here, we report the global transcriptomic differences occurring between mould and yeast phases of S. schenckii, including changes in gene expression profiles associated with these distinct cellular phenotypes. Moreover, we also propose a new genome annotation, which reveals a more complex transcriptional architecture than previously assumed. Using RNA-seq, we identified a total of 17 307 genes, of which 11 217 were classified as protein-encoding genes, whereas 6090 were designated as non-coding RNAs (ncRNAs). Approximately ~71 % of all annotated genes were found to overlap and the different-strand overlapping type was the most common. Gene expression analysis revealed that 8795 genes were different...
Background The genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic... more 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 tr...
Background: Sporotrichosis is a subcutaneous mycosis with worldwide distribution and caused by se... more Background: Sporotrichosis is a subcutaneous mycosis with worldwide distribution and caused by seven pathogenic species of Sporothrix genus: S. schenckii sensu stricto, S. brasiliensis, S. globosa and S. luriei (clinical clade), and the species S. mexicana, S. pallida and S. chilensis (environmental clade). Isolates of the same species of Sporothrix may have different pathogenicities; however, few isolates of this fungus have been studied. Thus, the aim of this work was to analyze the clinical and anatomopathological changes in immunocompetent and immunosuppressed BALB/c mice infected with clinical and environmental isolates of seven different species of Sporothrix, from both clades. One human clinical isolate of S. schenckii sensu stricto, S. brasiliensis, S. globosa, S. luriei, S. mexicana and S. chilensis species and one environmental isolate of S. pallida were inoculated subcutaneously in immunocompetent mice and the same isolates of S. brasiliensis and S.schenckii sensu stricto...
Current Pharmacogenomics and Personalized Medicine
Background: The heterogeneity of some diseases, such as cancer, makes the decisions on therapeuti... more Background: The heterogeneity of some diseases, such as cancer, makes the decisions on therapeutic strategy very challenging. In this context, pathway analysis can support the identification of the best treatment and indeed prevent the issues arising from the trial and error process, in terms of best overall efficacy and lowest toxicity, ultimately saving time and resources. In a pathway, each gene is represented by a node and the pathway analysis can be performed using algorithms that interpolate data from different sources (i.e. sequencing, microarray, drug efficacy and interactions). Objective: The purpose of this study was to evaluate the effects of erbb2 amplification on HER2- positive breast cancer and to predict, with a pathway based computational approach, the efficacy of a therapy with Trastuzumab and Palbociclib, alone or in combination. Methods: One of the available and most integrated algorithms is PHENSIM that was used in this study to evaluate the gene dysregulations c...
African Journal of Microbiology Research, Aug 30, 2013
ABSTRACT Although rare and emerging, Candida bracariensis and Candida nivariensis are two newly d... more ABSTRACT Although rare and emerging, Candida bracariensis and Candida nivariensis are two newly described species in the Candida glabrata complex which share similar phenotypic features and could be misdiagnosed. We examined 34 clinical isolates of C. glabrata using a multiplex PCR method for the presence of this newly described cryptic species. All study isolates were confirmed to be C. glabrata and none verified as either C. bracariensis or C. nivariensis
Abstract Here, we sequenced the faecal microbiome of a local pig breed by using whole-metagenome ... more Abstract Here, we sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Metagenomic data revealed that the faecal microbiome consists of a complex and intricate admixture of microbes belonging to all domains of life, including viruses. Most of sequencing reads were mapped to multiple reference sequences of Bacteria (99.35%) whereas the remaining reads (0.65%) were assigned to different microbes belonging to Archaea, Eukarya, and viruses. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found. BLAST homology search showed that viral reads could be assigned to a total of 13 viral families of which 7 were present in all metagenomes. Bioinformatics analysis identified a catalogue of microbial genes encoding 231,428 unique proteins grouped in 3,169 functional groups and involved in 275 biochemical pathways. This study represents a first attempt to explore the faecal microbiome of a local pig breed in order to expand our knowledge about the taxonomic and functional profiles of microbes associated with this rare and endangered-maintained pig breed. Highlights Sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Bioinformatics analysis identified a catalogue of microbial genes. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found.
European Journal of Clinical Microbiology & Infectious Diseases, 2020
An autochthonous case of lymphocutaneous sporotrichosis caused by Sporothrix schenckii is reporte... more 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, Crypt... more 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, Mata, strain with a rare multilocus-sequence-type (MLST) genotype (ST43). Keyword Cryptococcus Á C. neoformans Á Cryptococcosis Á Next-generation sequencing Á Whole-genome assembly A recent study in Nigeria, where more than 20% of HIV-infected patients have a positive cryptococcal antigenemia, revealed that the environment of this country is mainly contaminated by C. neoformans VNII strains belonging to a rare MLST genotype (ST43) [1].
Hepatitis C virus (HCV) NS3 resistance-associated substitutions (RASs) reduce HCV susceptibility ... more 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). 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). 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. 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 ...
In an era in which antimicrobial resistance is increasing at an alarming pace, it's very impo... more In an era in which antimicrobial resistance is increasing at an alarming pace, it's very important to find new antimicrobial agents effective against pathogenic microrganisms resistant to traditional treatments. Among the notable breakthroughs in the past years of research in natural-drug discovery there is the identification and testing of flavonoids, a group of plant-derived substances capable of promoting many beneficial effects on humans. These compounds show different biological activities such as inhibition of neuroinflammation and tumor growth as well as antidepressant, antiarthritic, anti-hypercholesterolemic, antidiabetic, antiulcer and antiasthmatic activities. However, one of the most important effects of these phytochemicals is, undoubtedly, their antimicrobial activity against many microbial pathogens. In recent years, hundreds of scientific papers reported the inhibitory effects of flavonoids against pathogenic fungi but none of these has ever considered the inexor...
Data deposition: The data sets supporting the conclusions of this article have been deposited in ... more Data deposition: The data sets supporting the conclusions of this article have been deposited in the Transcriptome Shotgun Assembly (TSA) database under accession numbers GEVV02000000 (CBS 11016 strain) and GEVW02000000 (GE1 strain), associated with BioProject IDs PRJNA327731 and PRJNA327736, respectively. The raw reads used for the transcriptome analysis have also been deposited in the NCBI Sequence Read Archive (SRA) under the following accession numbers SRR3747616 and SRR3745408.
This study aimed at investigating the genetic diversity of a panel of Candida africana strains re... more This study aimed at investigating the genetic diversity of a panel of Candida africana strains recovered from vaginal samples in different countries. All fungal strains were heterozygous at the mating-type-like locus and belonged to the genotype A of Candida albicans. Moreover, all examined C. africana strains lack N-acetylglucosamine assimilation and sequence analysis of the HXK1 gene showed a distinctive polymorphism that impair the utilization of this amino sugar in this yeast. Multi-locus sequencing of seven housekeeping genes revealed a substantial genetic homogeneity among the strains, except for the CaMPIb, SYA1 and VPS13 loci which contributed significantly to the classification of our set of C. africana strains into six existing diploid sequence types. Amplified fragment length polymorphism fingerprint analysis yielded greater genotypic heterogeneity among the C. africana strains. Overall the data reported here show that in C. africana genetic diversity occurs and the existence of this intriguing group of C. albicans strains with specific phenotypes associated could be useful for future comparative studies in order to better understand the genetics and evolution of this important human pathogen.
Sporothrix globosa is a thermo-dimorphic fungus belonging to a pathogenic clade that also include... more Sporothrix globosa is a thermo-dimorphic fungus belonging to a pathogenic clade that also includes Sporothrix schenckii, which causes human and animal sporotrichosis. Here, we present the first genome assemblies of two S. globosa strains providing data for future comparative genomic studies in pathogenic Sporothrix species.
Cryptococcus neoformans and Cryptococcus gattii are encapsulated yeasts able to cause fatal neuro... more 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.
In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterran... more In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterranean basin, an extensive environmental survey was carried out during 2012-2015. A total of 302 sites located in 12 countries were sampled, 6436 samples from 3765 trees were collected and 5% of trees were found to be colonized by cryptococcal yeasts. Cryptococcus neoformans was isolated from 177 trees and C. gattii from 13. Cryptococcus neoformans colonized 27% of Ceratonia, 10% of Olea, Platanus and Prunus trees and a lower percentage of other tree genera. The 13 C. gattii isolates were collected from five Eucalyptus, four Ceratonia, two Pinus and two Olea trees. Cryptococcus neoformans was distributed all around the Mediterranean basin, whereas C. gattii was isolated in Greece, Southern Italy and Spain, in agreement with previous findings from both clinical and environmental sources. Among C. neoformans isolates, VNI was the prevalent molecular type but VNII, VNIV and VNIII hybrid strains were also isolated. With the exception of a single VGIV isolate, all C. gattii isolates were VGI. The results confirmed the presence of both Cryptococcus species in the Mediterranean environment, and showed that both carob and olive trees represent an important niche for these yeasts.
Sporothrix pallida is considered to be a mostly avirulent environmental fungus, phylogenetically ... more Sporothrix pallida is considered to be a mostly avirulent environmental fungus, phylogenetically closely related to the well-known pathogen Sporothrix schenckii . Here, we present the first assembly of its genome, which provides a valuable resource for future comparative genomic studies between nonpathogenic and pathogenic Sporothrix spp.
European Journal of Clinical Microbiology & Infectious Diseases, 2016
This study aimed to elucidate the genetic relatedness and epidemiology of 127 clinical and enviro... more 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. harmless to humans and for a long time regarded as a non-34 pathogenic saprophyte of the normal flora of healthy individ-35 uals [1]. However, in recent decades, this view has been grad-36 ually weakened as a growing number of clinical reports have 37 shown that this fungus is, on the contrary, an important path-38 ogen [2-4]. 39 The increase in patients with an impaired immune system, 40 in addition to the widespread use of immunosuppressive ther-41 apies and broad-spectrum antibiotic drugs, has greatly contrib-42 uted to rendering C. glabrata one of the most commonly iso-43 lated yeasts among all non-C. albicans species that infect 44 humans [2-4]. However, although Candida albicans remains 45 the most frequently isolated fungal pathogen in humans, 46 C. glabrata has been reported to be an significant cause of * O. Romeo
Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in t... more Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in the host. The morphological shift between mycelial/yeast phases is crucial for its virulence, but the transcriptional networks implicated in dimorphic transition are still not fully understood. Here, we report the global transcriptomic differences occurring between mould and yeast phases of S. schenckii, including changes in gene expression profiles associated with these distinct cellular phenotypes. Moreover, we also propose a new genome annotation, which reveals a more complex transcriptional architecture than previously assumed. Using RNA-seq, we identified a total of 17 307 genes, of which 11 217 were classified as protein-encoding genes, whereas 6090 were designated as non-coding RNAs (ncRNAs). Approximately ~71 % of all annotated genes were found to overlap and the different-strand overlapping type was the most common. Gene expression analysis revealed that 8795 genes were different...
Background The genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic... more 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 tr...
Background: Sporotrichosis is a subcutaneous mycosis with worldwide distribution and caused by se... more Background: Sporotrichosis is a subcutaneous mycosis with worldwide distribution and caused by seven pathogenic species of Sporothrix genus: S. schenckii sensu stricto, S. brasiliensis, S. globosa and S. luriei (clinical clade), and the species S. mexicana, S. pallida and S. chilensis (environmental clade). Isolates of the same species of Sporothrix may have different pathogenicities; however, few isolates of this fungus have been studied. Thus, the aim of this work was to analyze the clinical and anatomopathological changes in immunocompetent and immunosuppressed BALB/c mice infected with clinical and environmental isolates of seven different species of Sporothrix, from both clades. One human clinical isolate of S. schenckii sensu stricto, S. brasiliensis, S. globosa, S. luriei, S. mexicana and S. chilensis species and one environmental isolate of S. pallida were inoculated subcutaneously in immunocompetent mice and the same isolates of S. brasiliensis and S.schenckii sensu stricto...
Current Pharmacogenomics and Personalized Medicine
Background: The heterogeneity of some diseases, such as cancer, makes the decisions on therapeuti... more Background: The heterogeneity of some diseases, such as cancer, makes the decisions on therapeutic strategy very challenging. In this context, pathway analysis can support the identification of the best treatment and indeed prevent the issues arising from the trial and error process, in terms of best overall efficacy and lowest toxicity, ultimately saving time and resources. In a pathway, each gene is represented by a node and the pathway analysis can be performed using algorithms that interpolate data from different sources (i.e. sequencing, microarray, drug efficacy and interactions). Objective: The purpose of this study was to evaluate the effects of erbb2 amplification on HER2- positive breast cancer and to predict, with a pathway based computational approach, the efficacy of a therapy with Trastuzumab and Palbociclib, alone or in combination. Methods: One of the available and most integrated algorithms is PHENSIM that was used in this study to evaluate the gene dysregulations c...
African Journal of Microbiology Research, Aug 30, 2013
ABSTRACT Although rare and emerging, Candida bracariensis and Candida nivariensis are two newly d... more ABSTRACT Although rare and emerging, Candida bracariensis and Candida nivariensis are two newly described species in the Candida glabrata complex which share similar phenotypic features and could be misdiagnosed. We examined 34 clinical isolates of C. glabrata using a multiplex PCR method for the presence of this newly described cryptic species. All study isolates were confirmed to be C. glabrata and none verified as either C. bracariensis or C. nivariensis
Abstract Here, we sequenced the faecal microbiome of a local pig breed by using whole-metagenome ... more Abstract Here, we sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Metagenomic data revealed that the faecal microbiome consists of a complex and intricate admixture of microbes belonging to all domains of life, including viruses. Most of sequencing reads were mapped to multiple reference sequences of Bacteria (99.35%) whereas the remaining reads (0.65%) were assigned to different microbes belonging to Archaea, Eukarya, and viruses. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found. BLAST homology search showed that viral reads could be assigned to a total of 13 viral families of which 7 were present in all metagenomes. Bioinformatics analysis identified a catalogue of microbial genes encoding 231,428 unique proteins grouped in 3,169 functional groups and involved in 275 biochemical pathways. This study represents a first attempt to explore the faecal microbiome of a local pig breed in order to expand our knowledge about the taxonomic and functional profiles of microbes associated with this rare and endangered-maintained pig breed. Highlights Sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Bioinformatics analysis identified a catalogue of microbial genes. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found.
European Journal of Clinical Microbiology & Infectious Diseases, 2020
An autochthonous case of lymphocutaneous sporotrichosis caused by Sporothrix schenckii is reporte... more 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, Crypt... more 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, Mata, strain with a rare multilocus-sequence-type (MLST) genotype (ST43). Keyword Cryptococcus Á C. neoformans Á Cryptococcosis Á Next-generation sequencing Á Whole-genome assembly A recent study in Nigeria, where more than 20% of HIV-infected patients have a positive cryptococcal antigenemia, revealed that the environment of this country is mainly contaminated by C. neoformans VNII strains belonging to a rare MLST genotype (ST43) [1].
Hepatitis C virus (HCV) NS3 resistance-associated substitutions (RASs) reduce HCV susceptibility ... more 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). 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). 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. 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 ...
In an era in which antimicrobial resistance is increasing at an alarming pace, it's very impo... more In an era in which antimicrobial resistance is increasing at an alarming pace, it's very important to find new antimicrobial agents effective against pathogenic microrganisms resistant to traditional treatments. Among the notable breakthroughs in the past years of research in natural-drug discovery there is the identification and testing of flavonoids, a group of plant-derived substances capable of promoting many beneficial effects on humans. These compounds show different biological activities such as inhibition of neuroinflammation and tumor growth as well as antidepressant, antiarthritic, anti-hypercholesterolemic, antidiabetic, antiulcer and antiasthmatic activities. However, one of the most important effects of these phytochemicals is, undoubtedly, their antimicrobial activity against many microbial pathogens. In recent years, hundreds of scientific papers reported the inhibitory effects of flavonoids against pathogenic fungi but none of these has ever considered the inexor...
Data deposition: The data sets supporting the conclusions of this article have been deposited in ... more Data deposition: The data sets supporting the conclusions of this article have been deposited in the Transcriptome Shotgun Assembly (TSA) database under accession numbers GEVV02000000 (CBS 11016 strain) and GEVW02000000 (GE1 strain), associated with BioProject IDs PRJNA327731 and PRJNA327736, respectively. The raw reads used for the transcriptome analysis have also been deposited in the NCBI Sequence Read Archive (SRA) under the following accession numbers SRR3747616 and SRR3745408.
This study aimed at investigating the genetic diversity of a panel of Candida africana strains re... more This study aimed at investigating the genetic diversity of a panel of Candida africana strains recovered from vaginal samples in different countries. All fungal strains were heterozygous at the mating-type-like locus and belonged to the genotype A of Candida albicans. Moreover, all examined C. africana strains lack N-acetylglucosamine assimilation and sequence analysis of the HXK1 gene showed a distinctive polymorphism that impair the utilization of this amino sugar in this yeast. Multi-locus sequencing of seven housekeeping genes revealed a substantial genetic homogeneity among the strains, except for the CaMPIb, SYA1 and VPS13 loci which contributed significantly to the classification of our set of C. africana strains into six existing diploid sequence types. Amplified fragment length polymorphism fingerprint analysis yielded greater genotypic heterogeneity among the C. africana strains. Overall the data reported here show that in C. africana genetic diversity occurs and the existence of this intriguing group of C. albicans strains with specific phenotypes associated could be useful for future comparative studies in order to better understand the genetics and evolution of this important human pathogen.
Sporothrix globosa is a thermo-dimorphic fungus belonging to a pathogenic clade that also include... more Sporothrix globosa is a thermo-dimorphic fungus belonging to a pathogenic clade that also includes Sporothrix schenckii, which causes human and animal sporotrichosis. Here, we present the first genome assemblies of two S. globosa strains providing data for future comparative genomic studies in pathogenic Sporothrix species.
Cryptococcus neoformans and Cryptococcus gattii are encapsulated yeasts able to cause fatal neuro... more 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.
In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterran... more In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterranean basin, an extensive environmental survey was carried out during 2012-2015. A total of 302 sites located in 12 countries were sampled, 6436 samples from 3765 trees were collected and 5% of trees were found to be colonized by cryptococcal yeasts. Cryptococcus neoformans was isolated from 177 trees and C. gattii from 13. Cryptococcus neoformans colonized 27% of Ceratonia, 10% of Olea, Platanus and Prunus trees and a lower percentage of other tree genera. The 13 C. gattii isolates were collected from five Eucalyptus, four Ceratonia, two Pinus and two Olea trees. Cryptococcus neoformans was distributed all around the Mediterranean basin, whereas C. gattii was isolated in Greece, Southern Italy and Spain, in agreement with previous findings from both clinical and environmental sources. Among C. neoformans isolates, VNI was the prevalent molecular type but VNII, VNIV and VNIII hybrid strains were also isolated. With the exception of a single VGIV isolate, all C. gattii isolates were VGI. The results confirmed the presence of both Cryptococcus species in the Mediterranean environment, and showed that both carob and olive trees represent an important niche for these yeasts.
Sporothrix pallida is considered to be a mostly avirulent environmental fungus, phylogenetically ... more Sporothrix pallida is considered to be a mostly avirulent environmental fungus, phylogenetically closely related to the well-known pathogen Sporothrix schenckii . Here, we present the first assembly of its genome, which provides a valuable resource for future comparative genomic studies between nonpathogenic and pathogenic Sporothrix spp.
European Journal of Clinical Microbiology & Infectious Diseases, 2016
This study aimed to elucidate the genetic relatedness and epidemiology of 127 clinical and enviro... more 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. harmless to humans and for a long time regarded as a non-34 pathogenic saprophyte of the normal flora of healthy individ-35 uals [1]. However, in recent decades, this view has been grad-36 ually weakened as a growing number of clinical reports have 37 shown that this fungus is, on the contrary, an important path-38 ogen [2-4]. 39 The increase in patients with an impaired immune system, 40 in addition to the widespread use of immunosuppressive ther-41 apies and broad-spectrum antibiotic drugs, has greatly contrib-42 uted to rendering C. glabrata one of the most commonly iso-43 lated yeasts among all non-C. albicans species that infect 44 humans [2-4]. However, although Candida albicans remains 45 the most frequently isolated fungal pathogen in humans, 46 C. glabrata has been reported to be an significant cause of * O. Romeo
Candida albicans is the most common opportunistic pathogen causing severe fungal infection in hum... more Candida albicans is the most common opportunistic pathogen causing severe fungal infection in humans, especially in immunocompromised patients. Crucial to its success as a pathogen is the substantial dynamism of its genome which readily undergoes genetic changes generating new strains. Candida africana is a low virulence biovariant of C. albicans possessing peculiar vaginal tropism. This particular strain is unable to form chlamydospores, structures whose biological function is still unknown. In this study we sequenced the whole mRNA and assembled the transcriptomes of a strong C. albicans chlamydospore-producing strain (GE1) and a natural chlamydospore-negative C. africana strain (CBS11016), under specific experimental conditions. Here we showed the assembly results obtained using two strategies: a de novo and a genome-guided approach using Trinity program (v2.2.0). The assembled transcriptomes were evaluated using BUSCO, QUAST and rnaQUAST. De novo transcriptomes were assembled in 10681 (C. albicans) and 9612 (C. africana) contigs (≥200bp) whereas the assemblies produced by genome-guided option consisted of 21656 and 19160 contigs (≥200bp), respectively. Quality analysis showed that the de novo approach produced more complete transcriptomes despite the availability of a good reference genome. In conclusion, this study provides general guidance for transcriptome assembly of RNA-Seq data from closely related Candida yeast and emphasize the efficacy of the de novo assembly also when a sequenced reference genome of reasonable quality exists.
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Papers by Orazio Romeo
unable to form chlamydospores, structures whose biological function is still unknown. In this study we sequenced the whole mRNA and assembled the transcriptomes of a strong C. albicans chlamydospore-producing strain (GE1) and a natural chlamydospore-negative C. africana strain (CBS11016), under specific experimental conditions. Here we showed the assembly results obtained using two strategies: a de novo and a genome-guided approach using Trinity program (v2.2.0). The assembled transcriptomes were evaluated using BUSCO, QUAST and rnaQUAST. De novo transcriptomes were assembled in 10681 (C. albicans) and 9612 (C. africana) contigs (≥200bp) whereas the assemblies produced by genome-guided option consisted of 21656 and 19160 contigs (≥200bp), respectively. Quality analysis showed that the de novo approach produced more complete transcriptomes despite the availability of a good reference genome. In conclusion, this study provides general guidance for transcriptome assembly of RNA-Seq data from closely related Candida yeast and emphasize the efficacy of the de novo assembly also when a sequenced reference genome of reasonable quality exists.