The distribution of drug resistance varies across the Saccharomycotina yeast phylogeny

To examine patterns of evolution of resistance, we plotted the resistance of 532 yeast species to eight different antifungal drugs [9] on the yeast phylogeny (Fig 1) [1]; the majority of strains were natural or environmental isolates (494 of 532 or 93%) with only 38 out of the 532 (7%) isolated from mammalian-associated environments (S1 Table). The antifungal resistance profiles of these mammalian-associated yeasts did not significantly differ from the rest of the dataset for any antifungal drug (S1 Table). Resistance to fluconazole was by far the most common, with 34.2% (182/532) of species tested being resistant (S2 Table). Resistance to voriconazole was the next most frequent (92/532 or 17.2%), followed by caspofungin (69/532 or 13.0%), amphotericin B (53/532 or 9.8%), itraconazole (46/532 or 8.6%), terbinafine (42/532 or 7.9%), 5-fluorocytosine (41/532 or 7.7%), and posaconazole (33/532 or 6.2%) (S2 Table). Out of 264 yeasts with resistance to any drug, over half (148) were resistant to two or more drugs. Of the yeasts that were resistant to a single drug, 42.2% (49/116) were resistant to fluconazole (S2 Table). We note that each species in our dataset is represented by a single strain. Since differences in resistance between strains of pathogenic yeasts have been observed [32–34], the resistance phenotype recorded for the strains examined in our study may not be always representative of the entire species.

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Fig 1. Resistance profiles to antifungal drugs vary throughout the Saccharomycotina subphylum.

Resistance to some drugs is lineage-specific (e.g., 5-fluorocytosine resistance), but resistance to others is broadly distributed (e.g., fluconazole resistance). Dark colors denote resistance, light colors denote susceptibility, and no color denotes absence of testing. Yeast species names are omitted for easier visualization, but they can be found in S4 Fig. The colors of the different branches of the phylogeny correspond to the 12 taxonomic orders [1,83]. Drug resistance data obtained using the microdilution technique described in Desnos-Ollivier et al. [9]. Note that this visualization of antifungal drug resistance profiles does not consider within-species variation in drug resistance. There are 1,154 strains in the phylogeny, 532 with known values of resistance to antifungals.

https://doi.org/10.1371/journal.pgen.1012091.g001

In general, resistance to any of the eight antifungal drugs was rare in the 111 yeasts in the order Serinales (which includes the genus Metschnikowia, C. auris, as well as C. albicans and its relatives) (S3 Table). Resistance to 5-fluorocytosine was rare outside of the Lipomycetales and Trigonopsidales orders, while caspofungin resistance was rare only within the Serinales, Pichiales, and Saccharomycetales. In contrast, resistance to the azoles (including fluconazole), terbinafine, and amphotericin B tended to be relatively evenly distributed throughout the phylogeny, with only a few exceptions (S3 Table).

Notably, using the D measure developed by Fritz and Purvis [35], we found that the distributions of resistance to different antifungal drugs across the yeast phylogeny were neither randomly distributed nor were explained entirely by evolutionary history (Table 1). This pattern of sporadic resistance suggests that resistance to these drugs (or functional analogs of these drugs) repeatedly arose during yeast evolution and was likely adaptive. Both the broad distribution and the repeated evolution of antifungal resistance are particularly surprising, considering that 93% of yeast species examined are represented by natural isolates and have never been observed in the clinic (S1 Table).

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Table 1. The distributions of resistance to antifungal drugs are not explained by evolutionary history.

https://doi.org/10.1371/journal.pgen.1012091.t001

A random forest algorithm identifies gene and sequence features predictive of resistance

To identify genomic, phenotypic, and ecological features linked to the repeated evolution of drug resistance, we trained a random forest algorithm on genomic, metabolic growth, and isolation environment data from the Y1000 + Project [1,31]. Training on metabolic growth and isolation environment data yielded accuracies of 54–75% (average 63%) and 47–63% (average 55%), respectively (S4 Table). The features that, on average, most contributed to accuracy for resistance across all the drugs tested were growth on salicin and cellobiose for the models trained on metabolic data, while Arthropoda animal type and having a microbe association were the most informative traits for models trained on isolation environment data (S5 Table). The highest accuracy values were obtained when predicting resistance to 5-fluorocytosine in models trained on metabolic data, largely because there are numerous growth substrates (likely unrelated to drug resistance) that show the same clade-specific distribution as 5-fluorocytosine (S4 Table). The metabolic and environmental features that most contributed to accuracy for fluconazole resistance were growth on glucosamine and isolation from grasses, respectively (S1 Fig).

When trained on genomic data (i.e., on variation in InterPro functional annotations across the genomes of species), models predicted resistance to each of the eight antifungals with ~54–75% accuracy (Figs 2, S2). Fluconazole resistance was predicted most accurately (75.2%) and itraconazole resistance was predicted least accurately (53.1%) (Figs 2, S2). Although all the azoles belong to the same drug class, their level of correlation across yeasts was not very high as the numbers of yeasts resistant to posaconazole and itraconazole were considerably lower than those to fluconazole—only 19 yeasts were resistant to all 4 azoles while 195 yeasts were resistant to one or more azoles. However, resistance to voriconazole was more common and had higher overlap with fluconazole resistance—87/92 species that were resistant to voriconazole were also resistant to fluconazole. Anticipating that the higher accuracy in predicting fluconazole resistance would afford the best potential to uncover insights into the mechanisms of the evolution of drug resistance, we chose to focus on fluconazole resistance going forward.

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Fig 2. A random forest algorithm predicts resistance to fluconazole with moderate accuracy from variation in InterPro functional annotations (n = 532).

Accuracy is shown in the form of cross-validated balanced accuracy over 20 down-sampled runs (value insight rectangle in bottom left of each panel). The confusion matrix (bottom right) shows yeasts predicted correctly to be sensitive (true negatives, top left), yeasts predicted to be resistant but are not (false positives, top right), yeasts correctly predicted to be resistant (true positives, bottom right), and yeasts correctly predicted to be sensitive (false negatives, bottom left). The Receiver Operating Characteristic (ROC) curve (upper right) shows the true positive rate over false positive rate with changing classification thresholds. The feature importance graph (left) shows the InterPro annotations that are most informative for predicting resistance to each drug. Note that the most informative genomic features were not linked to known drug resistance genes.

https://doi.org/10.1371/journal.pgen.1012091.g002

The most well-characterized genomic determinants of azole resistance in the major human pathogen C. albicans are non-synonymous variants in Erg11. Erg11 is the drug target of the azole class of drugs, and resistance can arise by both mutations that impede the drug’s ability to bind to the protein, as well as copy number variants of ERG11 or its regulators [10–13,29,36–41]. Therefore, we expected to see this gene (or other genes in the ergosterol pathway) in the top features of this model. However, we found that the top features for predicting fluconazole resistance implicated neither Erg11, which ranked 129^th in prediction importance, nor other genes in the ergosterol pathway.

Rather, the most informative genomic features were linked to cell wall-associated functional annotations. The flocculin type 3 repeat (IPR025928; the top feature), which is found in diverse proteins, including in the flocculation proteins Flo5, Flo9, and Flo10 in S. cerevisiae [42] (Fig 2), mediates cell-cell adhesion and the formation of multicellular clumps, also called flocs [42]. Previous research has found that increasing the number of repeats in these genes linearly increases the adhesion properties of their protein products, as well as the fraction of flocculating cells, which could make cells less accessible to antifungal drugs [43]. The X8 domain (IPR012946; the second top feature) is less well characterized in fungi, but some proteins with this domain are known to be involved in cell wall biosynthesis [44]. The third top feature was the myosin head domain (IPR001609), and some myosins have been demonstrated to regulate membrane permeability of fungi, thereby altering their susceptibility to antifungal drugs [45]. Based on the known biology of these genes, we hypothesize that variation in genomic factors related to the composition and integrity of the cell wall and membrane might impact natural drug resistance by changing both the structure of colonies of different species (flocculin repeats) and altering the accessibility and permeability of the cell membranes to antifungal drugs.

Variation in the presence/absence in InterPro functional annotations is only one of the many dimensions of genomic variation that differentiate Saccharomycotina species. For example, amino acid mutations in the Erg11 protein are the most commonly characterized causes of resistance to fluconazole in clinical isolates of most yeast human pathogens [11–14,30,38,46], yet sequence variation is not accounted for in the InterPro dataset. Therefore, we next focused on predicting fluconazole resistance solely from Erg11 amino acid sequence variation across Saccharomycotina yeast species.

Different random forest models yield similar fluconazole resistance prediction accuracies and implicate the same Erg11 sites

To test whether variation in specific sites of the Erg11 protein sequence contributed to fluconazole resistance prediction accuracy, we identified and aligned Erg11 orthologs across the yeast subphylum using the MAFFT sequence alignment algorithm [47]. We then trained random forest models to predict fluconazole resistance based on data from (a) both InterPro gene functional annotations and Erg11 MAFFT alignment sites, and (b) just Erg11 MAFFT alignment sites. We found that accuracy of prediction remained similar (75.1% when using both InterPro functional annotations and Erg11 sites, and 73.6% when using just Erg11 sites) (Fig 3). The fact that Erg11 results in similar predictive accuracy as a genome-wide ensemble of functional annotation variation data is consistent with the central role of Erg11 as an azole drug target.

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Fig 3. Training a random forest algorithm on the multiple sequence alignment of the known resistance protein Erg11 identifies numerous sites predictive of resistance to fluconazole.

Using an integer-encoded multisequence alignment of Erg11 in all Saccharomycotina yeasts as input data, the random forest algorithm predicted resistance to fluconazole with moderate accuracy (A). Adding in the InterPro annotations slightly increased accuracy, but residues in the alignment remained some of the most important features (B). Accuracy is shown in the form of confusion matrices (matrix in the bottom right in each panel), which show yeasts predicted correctly to be sensitive (true negatives, top left corner of the matrix), yeasts predicted to be resistant but are not (false positives, top right), yeasts correctly predicted to be resistant (true positives, bottom right), and yeasts correctly predicted to be sensitive (false negatives, bottom left). Receiver Operating Characteristic (ROC) curves (top left in each panel) show the true positive rate over false positive rate with changing classification thresholds. Feature importance graphs (left) show the residues or InterPro annotations that are most informative for predicting growth on fluconazole. The accuracies in the bottom left corner of each panel are cross-validated balanced accuracy over 20 down-sampled runs. 527 yeasts had a high-quality hit for an ERG11 sequence and drug resistance data, but the remaining 5 that had drug resistance data but no high quality ERG11 sequence were still included in the analysis with an empty input for the ERG11 sequence.

https://doi.org/10.1371/journal.pgen.1012091.g003

To explore the effects of different methods of aligning and encoding the Erg11 sequence on the training of the random forest algorithm, we used several different methods, including (a) a different sequence alignment algorithm, Muscle5 [48]; (b) one-hot encoding presence and absence of each variant in the alignment; (c) a sequence alignment derived from the superposition of structural models of all Erg11 proteins present in Saccharomycotina yeast species; and (d) an alignment-free, k-mer-based (k = 3) approach to encode all Erg11 protein sequences from Saccharomycotina yeast species. None of these methods substantially influenced prediction accuracy (S3 Fig). Importantly, all methods identified many of the same sites in the Erg11 protein as the top predictive features: the three different alignment methods (MAFFT, Muscle5, and structural sequence alignment) all identified same top three most informative sites; and, when using one-hot encoding, seven out of top ten variants were located at 5 sites that were also seen in the top 10 sites of all three alignment methods (S3 Fig). Similarly, four of the top five most informative k-mers in the k-mer based method were within two residues of sites in the C. albicans Erg11 sequence that were in the top ten most informative sites in the alignment-based methods. These results indicate that diverse methods all identify the same few sites that are most informative for predicting fluconazole resistance.

Some top sites in Erg11 that predict fluconazole resistance have been experimentally shown to confer resistance

To examine whether variation at sites predicted by our models can actually confer fluconazole resistance, we examined data from a recent deep mutational scan experiment measuring the effect of individual amino acid substitutions across 206 sites in C. albicans Erg11 on fluconazole resistance [27]. Five of our ten most informative sites were tested in these experiments: our top two sites, Y477 and A313, as well as M372, S506, and V404 (numbering based on the C. albicans strain CBS 562 protein sequence). Variants at four of those five sites resulted in significantly increased resistance to fluconazole, including variants in the top site, Y477, and in sites A313, S506, and V404 (Fig 4A). While we have not demonstrated that variants in our top sites are causal, the inclusion of several experimentally verified resistance-conferring variants among our informative sites (e.g., Y477F, A313L, and V404T) shows that at least some resistance-conferring variants are being captured by our random forest models.

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Fig 4. The most informative Erg11 sites have been experimentally shown to confer resistance and were generally less conserved than sites previously found to confer fluconazole resistance in clinical isolates.

(A) Variant frequencies across Erg11 protein sequences from Saccharomycotina yeasts (n = 530) for five of the most informative sites identified by a random forest algorithm trained to predict fluconazole resistance. Over- and under-representation of a given variant is shown when either >44% (over) or <24% (under) of fluconazole-resistant yeasts contained the indicated amino acid substitution. Experimental evidence for fluconazole resistance to each amino acid substitution was taken from Bedard et al. [27]. (B) Experimentally verified [27] or clinically characterized amino acid substitution frequencies across Saccharomycotina. (C) Per-site conservation of all aligned residues of Erg11 across Saccharomycotina yeasts. Amino acid positions implicated in fluconazole resistant clinical cases (red) are significantly more conserved than the top ten most informative sites identified by our random forest algorithm (blue) (box plot; p = 0.00024, Mann Whitney U Test). (D) Crystal structure of C. albicans Erg11 showing spatial distributions of the classifier’s top ten most informative (blue) and clinical resistance-conferring (red) residues. Other views of the crystal structure are shown in S7 Fig.

https://doi.org/10.1371/journal.pgen.1012091.g004

There are several other natural variants present at these sites that do not appear to confer fluconazole resistance but differ in their frequencies between drug-resistant and -sensitive yeasts; some of these variants are more common in fluconazole-resistant yeasts, while others are more common in fluconazole-sensitive ones. For example, variant A313S was present in the Erg11 sequences of 71 assayed yeasts and coincided with a fluconazole-resistance phenotype 71.8% of the time; conversely, S506Q was present in 191 yeasts and coincided with a fluconazole-susceptibility phenotype 84.2% of the time. Such patterns of variation, where a variant disproportionality associates with either a resistance or susceptibility phenotype, inform our random forest models and are used by them to predict fluconazole resistance (Fig 4A).

Top Erg11 sites identified by random forest models are more variable and spatially separated from those conferring fluconazole resistance in the clinic

When using the MAFFT Erg11 multiple sequence alignment to predict fluconazole resistance, the ten sites with the highest feature importance corresponded to C. albicans Erg11 residues Y477, A313, M372, T411, F170, T191, S506, N187, V404, and M189 (from most important (0.011 relative importance) to least important (0.0055 relative importance)) (Fig 3). Interestingly, none of these residues overlapped with sites harboring 36 Erg11 mutations previously implicated in drug resistance of clinical isolates [11–13,30,37,39–41,46,49–51]. Twenty-five of the 36 sites had zero importance in predicting fluconazole resistance using the MAFFT alignment, and the remaining 11 had relative importances of 0.0038 or less (Fig 4B, S6 and S7 Tables). The minimal contribution of mutations known to confer resistance in clinical settings to our predictions reflects the stronger evolutionary conservation at all these sites (mean Jensen-Shannon divergence (JSD) = 0.76) (S7 Table). In contrast, evolutionary conservation at our top ten most-informative sites was significantly lower (mean JSD = 0.64; p = 0.00024, Mann Whitney U Test; Fig 4C). Only variable sites are expected to be informative for predicting fluconazole resistance in machine learning models, and sites with no variation are simply uninformative for predicting variation in resistance. These results raise the hypothesis that variants contributing to drug resistance in natural isolates across entire lineages may differ substantially from mutations found to confer resistance in specific pathogens in clinical settings.

Mapping the ten most informative residues for predicting fluconazole onto the high-resolution crystal structure of C. albicans Erg11 (5v5z) shows that all ten sites cluster separately from previous clinical variants (Figs 4D, S7). This pattern of spatial segregation, considered in conjunction with the higher sequence conservation of sites that harbor clinical variants across Erg11 protein sequences from Saccharomycotina yeasts, suggests that structural constraints may be limiting variation at those sites seen almost exclusively in clinical contexts. Indeed, resistance-conferring clinical mutations all occur within 12Å or less of the Erg11 active site or the natively bound heme (both of which are involved in azole binding), and sites in these functionally important regions are less likely to tolerate variation (mean JSD = 0.75 of 213 residues within 12 Å of heme or bound itraconazole in 5v5z). Therefore, differing levels of sequence conservation observed between the ten most informative residues and sites harboring the fluconazole resistance-conferring clinical mutations in Saccharomycotina Erg11 proteins may be the result of biophysical constraints in the Erg11 structure itself.

Erg11 variants informative for predicting fluconazole resistance are less destabilizing than clinical and experimental resistance-conferring variants

Sites harboring resistance-conferring mutations in the clinic are highly conserved while the ten most informative residues identified by our random forest models are less conserved. This raises the question of whether these two types of sites are evolving under different levels of biophysical constraint. To test this hypothesis, we performed an in silico deep mutational scan of C. albicans Erg11 to evaluate the impact of every possible amino acid substitution on the predicted structural stability of the Erg11 protein (Fig 5A; Methods). We found that Erg11 amino acid variants observed in natural isolates of Saccharomycotina are predicted to have significantly lower mean mutational effects per site (i.e., lower changes in their free energy of folding (i.e., ∆∆G)) compared to variants that are never seen (Fig 5B). This distinction also holds when considering these variants individually, with naturally occurring Erg11 variants being substantially less energetically perturbing than variants that are never observed across Saccharomycotina (Fig 5C). These observations are consistent with a model of Erg11 protein sequence evolution where purifying selection acts against variants that substantially disrupt the energetic stability of Erg11.

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Fig 5. Erg11 variants naturally present in Saccharomycotina yeasts, especially those used that best predict fluconazole resistance, are less destabilizing than other Erg11 variants, as well as previously known clinical variants.

(A) In silico deep mutational scan results of the heme-bound form of C. albicans Erg11. Heatmap intensities represent the degree to which each amino acid substitution is predicted to affect the stability of the folded protein relative to wild type (DDG). Positive DDG values are destabilizing, and negative DDG values are hyper-stabilizing. (B) The mean predicted DDG per site, for just those amino acid substitutions that are either present (green) or wholly absent in 1,150 Saccharomycotina yeasts. Natural variation is significantly less destabilizing than variation that is never seen (box plot; p = 0.00000000, Mann Whitney U Test). (C) Mutational effects for every possible Erg11 mutation. Erg11 variants known to confer fluconazole resistance (red) are significantly more destabilizing than variants naturally present across Saccharomycotina (green).

https://doi.org/10.1371/journal.pgen.1012091.g005

Interestingly, if we consider known resistance-conferring mutations identified in the clinic or experimentally determined (i.e., fluconazole resistance-conferring variants identified through an experimental deep mutational scan of 206 sites in C. albicans Erg11 [27]), they also are significantly more energetically unfavorable than naturally occurring Erg11 variants present in Saccharomycotina yeasts; indeed, they are energetically indistinguishable from those variants that are never observed across Saccharomycotina. In contrast to the resistance-conferring clinical and experimental mutations, the predicted mutational effects of the 50 most informative variants from the one-hot encoded model are significantly lower and rank among the most energetically conservative variants seen across Saccharomycotina yeasts (Fig 5C).

Thus, while biophysical constraints render clinically- or experimentally-determined fluconazole resistance variants uninformative for predicting resistance from natural Erg11 sequences of Saccharomycotina yeasts, machine learning approaches can nevertheless leverage natural variation to accurately predict resistance.

Shared evolutionary history does not explain the association of individual Erg11 variants with fluconazole resistance

One potential explanation for the observed associations is that the top Erg11 sites may simply reflect the phylogenetic relationships of the species tested (even though the pattern of drug resistance itself is not explained by shared evolutionary history; Table 1). To evaluate whether the individual Erg11 amino acid sites identified by the random forest model are not themselves influenced by phylogeny, we applied a logistic model to measure the association of variants at every Erg11 site with the presence/absence of fluconazole resistance, both with and without correcting for phylogenetic relatedness (Methods; S6 Fig).

We next compared these results to the most informative sites identified by our random forest classifier. Among the top 10 informative sites highlighted above (Fig 3A), all sites are significantly associated with fluconazole drug resistance both before and after accounting for phylogeny (Fig 6). We then went on to examine the Erg11 sites ranked among both the top 50 in terms of Gini importance and SHAP values. This set comprised 33 shared sites, only three of which were not statistically significant after accounting for phylogeny (S8 Fig). Moreover, four of the 33 sites are statistically significant only after phylogenetic correction (S7 Fig). Thus, not only do these results confirm that the sites identified by the classifier are robust to phylogenetic non-independence, but they also reveal the surprising finding that the random forest classifier may sometimes even be able to correct for bias in the data resulting from phylogenetic structure (even though phylogenetic information was not explicitly used to train the algorithm).

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Fig 6. The most informative sites identified by the random forest classifier are robustly associated with fluconazole resistance in a phylogenetic logistic regression.

Manhattan plot showing each amino acid position of C. albicans Erg11 and the site’s corresponding association with fluconazole resistance following logistic regression with phylogenetic correction. Highlighted are the Top 10 sites from the random forest classifier based upon their Gini- and SHAP-measured feature importance. Also shown are the Erg11 residues that are within 12 Å of the bound heme along with residues specifically implicated in clinical cases of fluconazole-resistant strains of C. albicans from the FungAMR database [84].

https://doi.org/10.1371/journal.pgen.1012091.g006

Strain selection

The goal of our study was to characterize variation in resistance across the diversity of yeast species in the Saccharomycotina subphylum. Given the large number of yeast species, only one strain was typically examined per species (usually the type strain). Note that we have genomic, metabolic, and isolation environment data from 1,154 yeast strains (representing at least 1,051 species) [1]. From those 1,154 yeasts, we were able to retrieve drug resistance data for 532 through the study of Desnos-Ollivier et al. [9] (see also Antifungal resistance data matrix section below).

Genomic data matrix

Using InterProScan gene functional annotations generated by the Y1000 + Project [1], a data matrix was built with counts of each unique InterPro ID number in each genome (https://figshare.com/s/739a5de80d5ce89dbd10). Each genome was its own row, and the number of each InterPro ID (N = 12,242) present in one or more of the 1,154 yeast genomes was its own column. A python script recorded the number of each InterPro ID for each genome and put them in the appropriate cells of the data matrix.

Metabolic data matrix

Our metabolic data matrix contained 122 traits from 893 yeast strains (out of the 1,154 total) from 885 species in the subphylum [1,71] (S4 Table). The list of traits in the data matrix included growth on different carbon and nitrogen sources, such as galactose, raffinose, and urea, as well as on environmental conditions, such as growth at different temperatures and salt concentrations. The percentage of missing data in the data matrix was 37.5% (40,906 missing values out of 108,946 total). Less thoroughly studied traits tended to have more missing data than more commonly found and/or thoroughly studied traits.

Environmental data matrix

The isolation environments for 1,088 (94%) out of the 1,154 yeasts examined were gathered from strain databases, species descriptions, or from The Yeasts: A Taxonomic Study [1,72] (S5 Table) and converted into a hierarchical binary trait matrix using a controlled vocabulary containing all the unique environmental descriptors [31]. Strains without isolation environments were either domesticated via crossing or subculturing or lacked information in our searches. The ontology contains six broad isolation environment categories: animal, plant, environmental, fungal, industrial products, and victuals (food or drink). Within these categories, more specific controlled vocabulary annotations are connected to each strain: for example, an isolation environment reported as “Drosophila hibisci on Hibiscus heterophyllus” is associated in our ontology with the animal subclass “Drosophila hibisci” and the plant subclass “Hibiscus heterophyllus”.

Gene sequence data matrix

To retrieve the Erg11 protein sequence(s) from each genome, we used HMMR3 (version 3.1b2) hmmsearch [73]. The sequence alignment profile was constructed with hmmbuild [73] from several documented copies of Erg11 in different species across Saccharomycotina yeasts. Four of the 1,154 yeasts had annotated copies of Erg11 that were highly divergent and aligned poorly with the others. The sequences of these four yeasts were therefore excluded from our subsequent analyses. MAFFT version 7 [47] was then used to align the amino acid sequences of Erg11 from the remaining 1,150 yeasts across the subphylum. The resulting multiple sequence alignment was integer-encoded, with each amino acid as well as gaps in the alignment being represented by a different integer. The alignment was then converted into a data matrix where each column represented a different site of the alignment, and each column represented each species. In cases where two copies were found in a genome, the one with the highest sequence similarity score to the HMM profile used to search for Erg11 was used. For the four yeasts with the highly divergent Erg11 sequences, their rows in the dataset were left empty. To examine the impact of different multiple sequence alignment methods on the accuracy and the identification of the most important sites of our classifier, we also generated Erg11 sequence alignments using Muscle5 [48] and protein structure-guided approach (see section on Erg11 structural alignment below).

Antifungal resistance data matrix

Our drug resistance data matrix contained eight traits from 532 yeasts in the subphylum. The data were sourced from information available for each of the sequenced strains from the CBS strain database. These data were gathered from strains studied as part of the published descriptions of species, additional data on strains obtained by previous studies done in the Westerdijk Fungal Biodiversity Institute (CBS), or additional data provided by the depositors of the strains in the CBS culture collection.

The methods for determining whether a strain was resistant are described in Desnos-Oliver et al. [9]; briefly, drug resistance was assessed for each strain using a microdilution technique according to the procedure and criteria established by the Antifungal Susceptibility Testing Subcommittee of EUCAST (AFST-EUCAST) [9]. MIC was measured as a 50% (or 90% for amphotericin B) reduction in growth compared to the strain grown in a drug-free well. As suggested by EUCAST recommendations, for fluconazole an MIC higher than or equal to 8 µg/mL was defined as resistance, while for voriconazole it was an MIC higher than 0.25 µg/mL. Previous research looking at mutations in target genes was used to determine that an MIC of over 8 µg/mL would be considered resistant for caspofungin and 0.5 µg/mL. Finally, for the remainder of the drugs, the resistance threshold was determined by the MIC at which 90% of clinical isolates were inhibited: ≥ 0.5 µg/mL for itraconazole and posaconazole, ≥ 0.25 µg/mL for Amphotericin B, and ≥8 µg/mL for Terbinafine.

Classifying resistance to different antifungals using machine learning algorithms trained on genomic, metabolic, and/or environmental data

To test whether we could classify resistance to eight different antifungal drugs from genomic, metabolic, and isolation environment data, we used a random forest algorithm. For each resistance profile, we trained the algorithm separately on a given dataset to evaluate the accuracy of classification and identify the most important predictive features. Although the task being performed is classification, and the random forest algorithm that we use is a classifier, we refer to the results of these analyses throughout this study as “predictions” for ease of understanding.

We trained a machine learning algorithm built by an XGBoost (1.7.3) [74] random forest classifier (XGBRFClassifier()) with the parameters max_depth = 12 and n_estimators = 100; all other parameters were in their default settings. The max_depth parameter specifies the depth of each decision tree, determining how complex the random forest will be to prevent overfitting while maintaining accuracy. The n_estimators parameter specifies the number of decision trees in the forest. After testing the increase in accuracy while increasing each of these parameters, we found that having a higher max_depth or more decision trees per random forest did not further increase accuracy.

Since drug resistance is typically relatively rare, our datasets tended to be highly unbalanced. Before training the random forest algorithm, down-sampling by randomly choosing an equal number of non-resistant species as resistant species was first employed to balance the datasets. The random forest algorithm was then trained on 90% of the data, and used the remaining 10% for cross-validation, using the RepeatedStratifiedKFold and cross_val_score functions from the sklearn.model_selection (1.2.1) package. Cross validation is a method for assessing accuracy involving 10 trials, each of which holds back a random 10% of the training data for testing. We also used the cross_val_predict() function from Sci-Kit Learn separately to generate the confusion matrices; these matrices show the numbers of strains correctly predicted to be resistant or sensitive to a specific antifungal drug (true positives and true negatives, respectively) and incorrectly predicted (false positives, predicted to be resistant but are in reality sensitive; and false negatives, predicted to be sensitive but are in reality resistant). This function also employs a 10-fold cross validation step, but it keeps track of which species are classified as true/false positives and true/false negatives during each of these 10 trials, while entering the final results into a confusion matrix. Top features were automatically generated by the XGBRFClassifier function using Gini importance, which uses node impurity (the amount of variance in resistance for strains that either are or are not resistant to this drug). All these metrics, as well as total balanced accuracy (for which 50% would be equivalent to randomly guessing), were recorded and saved, and then the process was repeated 20 times with new randomly chosen down-sampled datasets each time to account for variation in the yeasts chosen to represent examples of drug-sensitive strains.

Receiver Operating Characteristic (ROC) curves, which plot the true positive rate against the false positive rate, were also generated for each prediction analysis to visualize the accuracy of the algorithm in predicting resistance to a given drug; values of the area under the curve (AUC) greater than 0.5 in these plots indicate better than random classification. Non-down-sampled datasets were used for this analysis, to fully capture the error in the whole dataset. As above, a 10-fold cross validation step was employed such that the model was tested and trained on different subsets on the dataset for each run, i.e., the model was never tested on the data used for its training.

Erg11 sequence conservation

The Jenson-Shannon entropy metric of protein sequence conservation was generated from the MAFFT MSA using score_conservation.py [75].

Structural alignments of Saccharomycotina Erg11

Hypothetical structural models for all Erg11 proteins found in the Y1000 + Project genomic dataset from the Saccharomycotina subphylum were generated using ESMFold as implemented by ColabFold (v.1.5). ESMFold was chosen over other alternative methods (e.g., over methods such as AlphaFold or homology modeling) for its greater speed and comparable accuracy [76]. A structural MSA was generated from the resulting ESMfold protein models using FoldMason (foldmason easy-msa --report-mode 1 --refine-iters 5) [77].

C. albicans Erg11 protein structure

A protein structure for the apo form of C. albicans Erg11 was retrieved from the PDB (5v5z) [78]. The amino acid sequence of the structure was checked and edited to match the Erg11 sequence of the C. albicans strain CBS 632 present in the Y1000 + Project (only one amino acid difference was amended). All protein model images were generated using ChimeraX (v1.7) [79].

C. albicans Erg11 in silico deep mutational scanning

The apo form of C. albicans Erg11 (5v5z) was relaxed in complex with the native heme using Rosetta 3.13. Briefly the structure was cleaned and renumbered using clean_pdb.py and pdb_renumber.py. The cleaned structure was minimized with heme (-nstruct 20, -relax:cartesian true, -default_max_cycles 200), and the lowest energy structure was chosen.

All-way, in silico mutagenesis (deep mutational scanning) was conducted using Rosetta 3.13 (cartesian_ddg) and energy minimization protocols and parameterizations previously benchmarked to optimize replication of experimental ΔΔG (DDG) measurements (parser:protocol cartesianrelaxprep.xml) [80]. Three replicates were performed for each substitution (ddg::iterations 3) and the mean change of free energy of folding (ΔG) was derived from the mean difference between wild type and each amino acid substitution (ΔΔG = ΔG (mutant) - ΔG (wild type)) across replicates.

Phylogenetic signal analysis

The strength of the phylogenetic signal for drug resistance was evaluated using the D measure developed by Fritz and Purvis [35], as implemented in the phylo.d function that is part of the caper (v 1.0.3) R package [81]. The strength of the phylogenetic signal was measured separately for each antifungal drug on a pruned species tree. The D measure statistically evaluates whether the distribution of a trait on a phylogeny is best explained from shared, phylogenetic history (“Brownian”) or from random occurrences over the tree (“random”).

Association testing

To test for associations between amino acid state and trait state, we began with the Erg11 multiple sequence alignment generated using the MAFFT alignment. Gaps and ambiguous characters in the alignment (e.g., “-”, “X”) were treated as missing data and excluded from the association testing performed at each site. Then, for each aligned position in the Erg11 alignment, the observed amino-acid states were treated as categorical predictors (site_state) with a baseline set to the most frequent amino acid observed at that site, while the trait state was a binary vector representing all the species (trait). We then fit both a standard logistic regression (glm(trait ~ site_state)) and a phylogenetic logistic regression (phyloglm(trait ~ site_state, species_tree, MPLE)) to these data [82]. For each model, effect and significance per site were assessed by a likelihood ratio test (LRT), resulting in a p-value for each of the two tests (p_std for glm; p_phylo for phyloglm). All p-values were subsequently corrected for multiple testing using Benjamini–Hochberg (BH) applied separately to p_std and p_phylo, producing p_adj_std and p_adj_phylo. The p_adj_std and p_adj_phylo values were then used to characterize each site for phylogenetic independence as follows:

1. “Robust association”: p_adj_std < 0.05 and p_adj_phylo < 0.05
2. “Explained by phylogeny”: p_adj_std < 0.05 and p_adj_phylo ≥ 0.05
3. “Revealed by phylogeny”: p_adj_std ≥ 0.05 and p_adj_phylo < 0.05.