A European ECMM‐ESCMID survey on goals and practices for mycobiota characterisation using next‐generation sequencing. Issue 12 (21st October 2019)

• Record Type: Journal Article
• Authors: Gangneux, Jean‐Pierre; Guegan, Hélène; Vandenborght, Louise‐Eva; Buffet‐Bataillon, Sylvie; Enaud, Raphael; Delhaes, Laurence
• Other Names: Lackner Michaela investigator.; Freiberger Tomas investigator.; Hare Rasmus investigator.; Leth Mortensen Klaus investigator.; Hedayati Mohammad T. investigator.; Moran Gary investigator.; Vehreschild Maria investigator.; Steinmann Jörg investigator.; Delhaes Laurence investigator.; Botterel Françoise investigator.; Gangneux Jean‐Pierre investigator.; Roilides Emmanuel investigator.; Ben‐Ami Ronen investigator.; Lo Cascio Giuliana investigator.; Treviño‐Rangel Rogelio de Jesús investigator.; Meis Jacques investigator.; Melchers Willem investigator.; Hornung Bastian investigator.; Sabino Raquel investigator.; Barac Aleksandra investigator.; Chotirmall Sanjay H investigator.; Rello Jordi investigator.; Martin‐Gomez M.Teresa investigator.; Alastruey‐Izquierdo Ana investigator.; Wongsuk Thanwa investigator.; Karahan Zeynep Ceren investigator.
• Is Part Of: Mycoses. Volume 62:Issue 12(2019)
• Page Start: 1096
• Page End: 1099
• Publication Date: 2019-10-21
• Subjects: digestive tract infections -- Europe -- fungi -- lung infections -- microbiota -- mycobiota; Pathogenic fungi -- Periodicals; Medical mycology -- Periodicals; 616.969
• DOI: 10.1111/myc.12999
• Languages: English
• ISSNs: 0933-7407

Abstract

Summary: 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.