Publicação
Development of a framework for identification of Candida Species and detection of antifungal resistance
| Resumo: | Invasive fungal infections affect millions of people around the world, and they are associated with high mortality rates, which in some cases can reach 90%. These infections have a high incidence in immunosuppressed patients. The most frequent pathogens that cause this type of infections belong to the Candida genus. Most of them have the ability to develop molecular mechanisms to fight antifungal treatment, which leads to the increase of antifungal resistance. The remarkable evolution in speed and cost of sequencing technologies, such as Next-Generation Sequencing, allowed whole genomes to be sequenced in a single run, becoming a solution with advantages over traditional methods. In the last years, the number of sequenced genomes increased dramatically. However, the number of bioinformatics systems to treat and analyze these data did not follow this growth, especially in clinical mycology. So, to address the lack of bioinformatics solutions applied to clinical mycology, a framework has been developed to allow the identification and detection of antifungal resistance in different species of the Candida genus. The framework is prepared to receive sequencing files from Illumina platforms and has the ability to identify a high range of fungi species. The detection of antifungal resistance is available for Candida albicans, Candida glabrata, Candida parapsilosis and Candida tropicalis, regarding ERG11 and FKS1 genes. The framework developed can be a great solution for any microbiology laboratory equipped with Next-Generation Sequencing platforms. |
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| Autores principais: | Oliveira, Ana Patrícia Mota de |
| Assunto: | Antifungal resistance detection Candida species Fungi identification Next-Generation Sequencing Espécies de Candida Identificação de fungos Resistência aos antifúngicos |
| Ano: | 2019 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | Invasive fungal infections affect millions of people around the world, and they are associated with high mortality rates, which in some cases can reach 90%. These infections have a high incidence in immunosuppressed patients. The most frequent pathogens that cause this type of infections belong to the Candida genus. Most of them have the ability to develop molecular mechanisms to fight antifungal treatment, which leads to the increase of antifungal resistance. The remarkable evolution in speed and cost of sequencing technologies, such as Next-Generation Sequencing, allowed whole genomes to be sequenced in a single run, becoming a solution with advantages over traditional methods. In the last years, the number of sequenced genomes increased dramatically. However, the number of bioinformatics systems to treat and analyze these data did not follow this growth, especially in clinical mycology. So, to address the lack of bioinformatics solutions applied to clinical mycology, a framework has been developed to allow the identification and detection of antifungal resistance in different species of the Candida genus. The framework is prepared to receive sequencing files from Illumina platforms and has the ability to identify a high range of fungi species. The detection of antifungal resistance is available for Candida albicans, Candida glabrata, Candida parapsilosis and Candida tropicalis, regarding ERG11 and FKS1 genes. The framework developed can be a great solution for any microbiology laboratory equipped with Next-Generation Sequencing platforms. |
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