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Sci Rep. 2019 Feb 22;9(1):2563. doi: 10.1038/s41598-019-38768-4.

Within-Host Genomic Diversity of Candida albicans in Healthy Carriers.

Author information

1
Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris, France.
2
Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France.
3
Unité de Parasitologie-Mycologie, Service de Microbiologie clinique, Hôpital Necker-Enfants-Malades, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France.
4
Center for Bioinformatics, BioStatistics and Integrative Biology (C3BI), USR 3756 IP CNRS, Institut Pasteur, Paris, France.
5
Department of Biology, Ecole Polytechnique, Palaiseau, France.
6
Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris, France. bougnoux@pasteur.fr.
7
Unité de Parasitologie-Mycologie, Service de Microbiologie clinique, Hôpital Necker-Enfants-Malades, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France. bougnoux@pasteur.fr.

Abstract

Genomic variations in Candida albicans, a major fungal pathogen of humans, have been observed upon exposure of this yeast to different stresses and experimental infections, possibly contributing to subsequent adaptation to these stress conditions. Yet, little is known about the extent of genomic diversity that is associated with commensalism, the predominant lifestyle of C. albicans in humans. In this study, we investigated the genetic diversity of C. albicans oral isolates recovered from healthy individuals, using multilocus sequencing typing (MLST) and whole genome sequencing. While MLST revealed occasional differences between isolates collected from a single individual, genome sequencing showed that they differed by numerous single nucleotide polymorphisms, mostly resulting from short-range loss-of-heterozygosity events. These differences were shown to have occurred upon human carriage of C. albicans rather than subsequent in vitro manipulation of the isolates. Thus, C. albicans intra-sample diversity appears common in healthy individuals, higher than that observed using MLST. We propose that diversifying lineages coexist in a single human individual, and this diversity can enable rapid adaptation under stress exposure. These results are crucial for the interpretation of longitudinal studies evaluating the evolution of the C. albicans genome.

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