Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing.
Adolescent
Adult
Aged
Antifungal Agents
/ pharmacology
Basidiomycota
/ drug effects
Child
Child, Preschool
DNA, Fungal
/ genetics
DNA, Ribosomal
/ genetics
Female
France
/ epidemiology
Genome, Fungal
Genotype
Genotyping Techniques
Humans
Infant
Male
Middle Aged
Mycological Typing Techniques
Phylogeny
Sequence Analysis, DNA
Trichosporonosis
/ epidemiology
Whole Genome Sequencing
Young Adult
Trichosporon asahii
IGS sequencing
emerging yeast
epidemiology of trichosporonosis
whole genome sequencing
Journal
Mycoses
ISSN: 1439-0507
Titre abrégé: Mycoses
Pays: Germany
ID NLM: 8805008
Informations de publication
Date de publication:
Sep 2020
Sep 2020
Historique:
received:
30
03
2020
revised:
28
05
2020
accepted:
28
05
2020
pubmed:
9
6
2020
medline:
13
7
2021
entrez:
8
6
2020
Statut:
ppublish
Résumé
Trichosporonosis is a rare invasive infection in humans mainly due to Trichosporon asahii, and especially recovered from patients having haematological malignancy. Since 2012, IGS1 region sequencing is used as a genotyping method to distinguish isolates, with high frequency of one haplotype worldwide and a geographic specificity for some haplotypes. We compared the IGS1 genotyping method and whole genome sequencing (WGS) to study the relationship between clinical isolates involved in two grouped cases in France. IGS1 sequencing and antifungal susceptibility testing were performed for 54 clinical isolates. Clinical data for 28 isolates included in surveillance programs were analysed. Whole genome was sequenced for 32 clinical isolates and the type strain. All isolates were intrinsically resistant to flucytosine, while voriconazole had the most potent in vitro activity. The majority of the isolates was recovered from patients with haematological malignancies (42.86%), with a high proportion of children (<15 yrs-old, 32.14%) and a high mortality rate at three months (46.15%). Based on the WGS analysis, isolates exhibiting IGS1 haplotype 1, 3 and 7 belonged to different clades. Five isolates recovered during the first grouped cases had the same IGS1 haplotype and shared 99% of SNPs similarity. For the second grouped cases, four isolates had 98.7% of SNPs similarity while the isolate recovered 4 years earlier was totally unlinked. We confirmed the usefulness of IGS1 sequencing for grouped cases infection of T. asahii. We underlined its limitation for the study of population structure and the utility of WGS analysis for the study of epidemiologically unrelated isolates.
Sections du résumé
BACKGROUND
BACKGROUND
Trichosporonosis is a rare invasive infection in humans mainly due to Trichosporon asahii, and especially recovered from patients having haematological malignancy. Since 2012, IGS1 region sequencing is used as a genotyping method to distinguish isolates, with high frequency of one haplotype worldwide and a geographic specificity for some haplotypes.
OBJECTIVES
OBJECTIVE
We compared the IGS1 genotyping method and whole genome sequencing (WGS) to study the relationship between clinical isolates involved in two grouped cases in France.
METHODS
METHODS
IGS1 sequencing and antifungal susceptibility testing were performed for 54 clinical isolates. Clinical data for 28 isolates included in surveillance programs were analysed. Whole genome was sequenced for 32 clinical isolates and the type strain.
RESULTS
RESULTS
All isolates were intrinsically resistant to flucytosine, while voriconazole had the most potent in vitro activity. The majority of the isolates was recovered from patients with haematological malignancies (42.86%), with a high proportion of children (<15 yrs-old, 32.14%) and a high mortality rate at three months (46.15%). Based on the WGS analysis, isolates exhibiting IGS1 haplotype 1, 3 and 7 belonged to different clades. Five isolates recovered during the first grouped cases had the same IGS1 haplotype and shared 99% of SNPs similarity. For the second grouped cases, four isolates had 98.7% of SNPs similarity while the isolate recovered 4 years earlier was totally unlinked.
CONCLUSIONS
CONCLUSIONS
We confirmed the usefulness of IGS1 sequencing for grouped cases infection of T. asahii. We underlined its limitation for the study of population structure and the utility of WGS analysis for the study of epidemiologically unrelated isolates.
Substances chimiques
Antifungal Agents
0
DNA, Fungal
0
DNA, Ribosomal
0
Banques de données
GENBANK
['ALBS00000000', 'MN936175']
Types de publication
Comparative Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
942-951Subventions
Organisme : Santé Publique France
Organisme : Institut Pasteur
Informations de copyright
© 2020 Blackwell Verlag GmbH.
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