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J Mycol Med. 2019 Jan 28. pii: S1156-5233(18)30301-9. doi: 10.1016/j.mycmed.2019.01.003. [Epub ahead of print]

Molecular identification of Fusarium species complexes: Which gene and which database to choose in clinical practice?

Author information

1
Laboratoire de parasitologie mycologie, CHRU de Nancy, université de Lorraine, 54000 Nancy, France; Laboratoire de biologie médicale, hôpitaux privés de Metz, 13, rue de la gendarmerie, 57000 Metz, France.
2
Laboratoire de parasitologie mycologie, CHRU de Nancy, université de Lorraine, 54000 Nancy, France.
3
Laboratoire de parasitologie mycologie, CHRU de Nancy, université de Lorraine, 54000 Nancy, France; SIMPA, université de Lorraine, 54000 Nancy, France.
4
Laboratoire de parasitologie mycologie, CHRU de Nancy, université de Lorraine, 54000 Nancy, France; SIMPA, université de Lorraine, 54000 Nancy, France. Electronic address: a.debourgogne@chru-nancy.fr.

Abstract

Identification of Fusarium at the level of the species complex is difficult with phenotypic methods, so it is necessary to use molecular sequencing methods. This study presents, for 33 isolates distributed among the four major species complexes, the performance of five identification schemes involving ITS (internal transcribed spacer), EF1α (translation elongation factor 1 alpha), RPB1 (largest subunit of RNA polymerase) and RPB2 (second largest subunit of RNA polymerase) genes and two databases: GenBank and Fusarium MLST (MultiLocus Sequence Typing). In our practice, the identification of the fungus from a culture is performed with EF1α and from a primary sample with ITS, using in both cases the specific database Fusarium MLST.

KEYWORDS:

EF1α; Fusarium MLST; Fusarium species complex; Molecular identification

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