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Gangneux JP, Guegan H, Vandenborght LE, et al. A European ECMM-ESCMID survey on goals and practices for mycobiota characterisation using next-generation sequencing. Mycoses. 2019;62(12):1096-1099doi: 10.1111/myc.12999.
Gangneux, J. P., Guegan, H., Vandenborght, L. E., Buffet-Bataillon, S., Enaud, R., & Delhaes, L. (2019). A European ECMM-ESCMID survey on goals and practices for mycobiota characterisation using next-generation sequencing. Mycoses, 62(12), 1096-1099. https://doi.org/10.1111/myc.12999
Gangneux, Jean-Pierre, et al. "A European ECMM-ESCMID survey on goals and practices for mycobiota characterisation using next-generation sequencing." Mycoses vol. 62,12 (2019): 1096-1099. doi: https://doi.org/10.1111/myc.12999
Gangneux JP, Guegan H, Vandenborght LE, Buffet-Bataillon S, Enaud R, Delhaes L. A European ECMM-ESCMID survey on goals and practices for mycobiota characterisation using next-generation sequencing. Mycoses. 2019 Dec;62(12):1096-1099. doi: 10.1111/myc.12999. Epub 2019 Oct 21. PMID: 31498487.
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Mycoses. 2019 Dec;62(12):1096-1099. doi: 10.1111/myc.12999. Epub 2019 Oct 21.

A European ECMM-ESCMID survey on goals and practices for mycobiota characterisation using next-generation sequencing.

Mycoses

Jean-Pierre Gangneux, Hélène Guegan, Louise-Eva Vandenborght, Sylvie Buffet-Bataillon, Raphael Enaud, Laurence Delhaes

Affiliations

  1. CHU Rennes, Univ Rennes, Inserm, Irset (Institut de Recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
  2. CHU de Bordeaux, Université de Bordeaux, Inserm, Center for Cardiothoracic Research of Bordeaux, U1045, CIC 1401, Bordeaux, France.

PMID: 31498487 DOI: 10.1111/myc.12999

Abstract

Although substantial efforts have been made to investigate about the composition of the microbiota, fungi that constitute the mycobiota play a pivotal role in maintaining microbial communities and physiological processes in the body. Here, we conducted an international survey focusing on laboratory's current procedures regarding their goals and practices of mycobiota characterisation using NGS. A questionnaire was proposed to laboratories affiliated to working groups from ECMM (NGS study group) and ESCMID (ESGHAMI and EFISG study groups). Twenty-six questionnaires from 18 countries were received. The use of NGS to characterise the mycobiota was not in routine for most of the laboratories (N = 23, 82%), and the main reason of using NGS was primary to understand the pathophysiology of a dysbiosis (N = 20), to contribute to a diagnosis (N = 16) or to implement a therapeutic strategy (N = 12). Other reported reasons were to evaluate the exposome (environmental studies) (N = 10) or to investigate epidemics (N = 8). Sputum is the main sample studied, and cystic fibrosis represents a major disease studied via the analysis of pulmonary microbiota. No consensus has emerged for the choice of the targets with 18S, ITS1 and ITS2 used alternatively among the laboratories. Other answers are detailed in the manuscript. We report a photography of mycobiota analysis that may become a major tool in the near future. We can draw some conclusions on the diversity of approaches within the answers of the 27 laboratories and underline the need for standardisation.

© 2019 Blackwell Verlag GmbH.

Keywords: Europe; digestive tract infections; fungi; lung infections; microbiota; mycobiota

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