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Unknown B

OK so it’s a Fusarium species, but which one?

This is a critically ill patient and the clinician needs a definitive species identification to optimize antifungal treatment.

Current Fusarium species identification is based on multilocus sequence data (Guarro 2013, O’Donnell et al. 2015, van Diepeningen et al. 2015).  ITS and D1/D2 sequences are too conserved to resolve species limits of most fusaria. O’Donnell et al. (2015) recommend avoiding ITS or D1/D2 sequences from an unknown isolate to query GenBank, because >50% of the sequences from Fusarium species are misidentified in this database.

Identifications based on morphology and/or ITS and D1/D2 sequences should be reported as species complexes. Sequencing of EF-1α, RPB1 and/or RPB2 is required for accurate species identification.

Here is your EF-1α gene partial sequence ready to perform a pairwise sequence alignment.

tggcaagtcg accaccgtaa gtcaaaccct catcgcgatc tgcttatctc gggtcgtgga accccgcctg gcatctcggg cggggtattc atcattcact tcatgctgac aatcatctac agaccggtca cttgatctac cagtgcggtg gtatcgacaa gcgaaccatc gagaagttcg agaaggttgg tgacatctcc cccgatcgcg ccttgatatt ccacatcgaa ttccctgtcg aattccctcc atcgcgatac gctctgcgcc cgcttctccc gagtcccaaa atttttgcgg tccgaccgta atttttttgg tggggcattt accccgccac tcgggcgacg ttggacaaag ccctgatccc tgcacacaaa aacaccaaat cctcttggcg cgcatcatca cgtggttcac gacagacgct aactggtcca acaataggaa gccgctgagc tcggtaaggg ttccttcaag tacgcctggg tccttgacaa gctcaaggcc gagcgtgagc gtggtatcac catcgacatt gccctctgga agttcgagac tccccgctac tatgtcaccg tcattggtat gttgctgtca cctctctcac acatgtctca ccactaacaa

Now copy the above sequence, go to one of the databases listed below and perform a search.

CBS-KNAW Fungal Biodiversity Centre Link to external website
To perform a pairwise sequence alignment use the link provided, select the Pairse DNA alignments box, check the disclaimer box, paste the above sequence into the “align” box, hit the “start alignment" box.

FUSARIUM-ID at Pennsylvania State University Link to external website
To perform a pairwise sequence alignment use the link provided, select Fusarium-ID, check that the data set selected is for the EF-1α gene, paste sequence into the “enter query sequence” box and hit the Start Search.

Hopefully you will get the right answer.

References:

  1. Guarro, J. 2013. Fusariosis, a complex infection caused by a high diversity of fungal species refractory to treatment. Eur. J. Clin. Microbiol. Infect. Dis. 32: 1491-1500.
  2. O’Donnell, K., T.J. Ward, V.A.R.G. Robert et al. 2015. DNA sequence-based identification of Fusarium: Current status and future directions. Phytoparasitica 43: 583-595.
  3. van Diepeningen, A.D., B. Brankovics, J. Iltes et al. 2015. Diagnosis of Fusarium infections: approaches to identification by the clinical mycology laboratory. Curr. Fungal Infect. Rep. 9: 135-143.

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