Medical Fusarium: novel species or uncertain identifications?

Y. Song*, S. Hu, G.S. de Hoog, X. Liu, X. Meng, R. Xue, A.D. van Diepeningen, L. Fokkens, S. Gao

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)

Abstract

Fungal infections increasingly threaten human health, particularly in immuno compromised patients. Identification of etiologic agents of infection is important for effective treatment. Here, we study a set of 48 Fusarium strains, most of which had been collected from Chinese hospitals over two decades. Sequences of cam, rpb2, tub2, and tef1-α, singly or multilocus, did not entirely match with the described taxa; therefore, the species problem and correctness of identification became a research question. Blast searches in multiple dedicated databases did not always provide identical species assignments. Results remained variable when compared with phylogeny with 636sequences identified in recent literature, including sequences from 41 type strains. Assignment to specific species within a species complex based on > 1000 single-copy orthologs was also variable for some species. Previously published MALDI-ToF data provided identification that matched sequence-based identification at the species complex level, but performed poorly with lineages within the complexes. Different methods of identification yielded dissimilar results. Some previously identified strains in earlier publications deviated more from the reference than our clinical strains. We further tested species boundaries using levels of admixture and found highadmixture levels between F. fujikuroi, F. nisikadoi and F. oxysporum species complexes. It is concluded that species complexes can be recognised hylogenetically by BLAST and by MALDI-ToF, but the high intraspecific diversity of these fungi interferes with the unequivocal assignment of individual isolates to particular lineages. At a higher taxonomic level, most clinical strains were found to belong to F. fujikuroi, F. oxysporum and F. solani (Neocosmospora) complexes,irrespective of the method used for identification. To determine whether these complexes were particularly over represented in clinical strains, we compared this data in a larger dataset of 216clinical isolates to those in environmental samples. We found that clinical strains are enriched forthe F. solani complex (Neocosmospora) and less for F. oxysporum and F. fujikuroi complexes,suggesting that among these opportunistic human pathogens, F. solani is particularly equipped to survive in clinical settings.
Original languageEnglish
Pages (from-to)2263-2283
Number of pages21
JournalMycosphere
Volume14
Issue number1
DOIs
Publication statusPublished - 27 Dec 2023

Fingerprint

Dive into the research topics of 'Medical Fusarium: novel species or uncertain identifications?'. Together they form a unique fingerprint.

Cite this