Blood-borne fungal pathogens nucleic-acids detection

Scope: design human fungal pathogens universal primers, i.e. design nucleic-acid reagents (primers and probes) for the detection and quantification of any fungal species belonging to the set of documented human pathogens.

List of blood-borne fungi:

• Mucorales, aka Zygomycetes (Rhizopus, Mucor, Lichthemia, Cunninghamella)
• Hyaline hyphomycetes (Aspergillus, Fusarium)
• Dematiaceous hyphomycetes (Alternaria, Scedosporium, Aureobasidium)
• Yeasts and yeast-like (Candida, Cryptococcus, Malessezia, Pneumocystis jirovecii)
• Dimorphic fungi (Histoplasma, Blastomyces, Coccidioides)
• Dermatophytes (Trichophyton, Microsporum)

Resources

Data

• the Fungal 28S rRNAs sequence dataset of the Ribosomal Database Project release 11.5 (RDP);
• the SILVA SSU and LSU Ref NR 99 data;
• the EMBL-EBI RNAcentral, in particular its hgnc.fasta data;
• the [biocore / sortmerna] (https://github.com/biocore/sortmerna/tree/master/data/rRNA_databases) github repository;

Software packages

• The R environment for statistical computing;
• EMBOSS: The European Molecular Biology Open Software Suite EMBOSS;
• Samtools;
• Clustal Omega;
• primer3;

Requirements

• qRT-PCR reagents for detecting circulating fungal ribososomal RNA;
• 18S, 28S and 5.8S;
• Amplicons size ~ 150 nt;

Notes

• Ribosome Small Subunit (SSU) rRNA: 18S.
• Ribosome Large Subunit (LSU) rRNA: 28S and 5.8S.

workflow.

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