Comparative genomics of infective Saccharomyces cerevisiae strains reveals their food origin

Abstract

Fungal infections are less studied than viral or bacterial infections and often more difficult to treat. Saccharomyces cerevisiae is usually identified as an innocuous human-friendly yeast; however, this yeast can be responsible for infections mainly in immunosuppressed individuals. S. cerevisiae is a relevant organism widely used in the food industry. Therefore, the study of food yeasts as the source of clinical infection is becoming a pivotal question for food safety. In this study, we demonstrate that S. cerevisiae strains cause infections to spread mostly from food environments. Phylogenetic analysis, genome structure analysis, and phenotypic characterization showed that the key sources of the infective strains are food products, such as bread and probiotic supplements. We observed that the adaptation to host infection can drive important phenotypic and genomic changes in these strains that could be good markers to determine the source of infection. These conclusions add pivotal evidence to reinforce the need for surveillance of food-related S. cerevisiae strains as potential opportunistic pathogens.

Figure 1

ML Phylogeny of the clinical strains and representatives of the principal clades described in Peter et al. 2018. The strains from this study are colored in a brown and bigger font. The origin and name of the strains are in Table 1. The clusters described by Peter et al. 2018 are represented by colored semi-circles with their name. In supplementary Table S1 there is more information about these strains.

Figure 2

(a) PCA analysis performed on the SNP matrix of the strains included in this study. (b) Heterozygous SNP density plot of the studied strains. Strains codes are as follows: MIXED GROUP: 2.2.1:black; FBMI.18: deep blue; FBMI.34:firebrick red; AQ2593:grey; AQ2723; light coral; AQ2654:plum; AQ435;brown; AQ2582:olive green; AQ2580:yellow. WINE: AQ2587:black; AQ2657:deep blue; AQ2724:firebrick red; AQ2584:grey; AQ593:plum. OTHERS: AQ2720:black; AQ2717:blue; AQ2885:grey; AQ2722:plum; AQ2721:olive green. Ploidy and aneuploidy data are included in supplementary Table S2.

Figure 3

Weight loss along the fermentation for the Clinical-Bakery strains. Up: a long-time weight loss. Wine strains were used as a control. Down: weight loss at the end of the fermentation by isolation origin. Mann Witney test: Ns non-significant, *< 0.05, ****< 0.0001.

Figure 4

Growth at pH 2.5 (up) and in the presence of bile acids (down) relative to their growth in YNB. Values were calculated with the AUC (area under the growth curve). The isolation environment and the phylogenetic group were indicated for each strain. M Mixed-clinical bakery. W wine-boulardii. T-test for independent samples: ***< 0.001.