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The evolution of drug resistance in clinical isolates of Candida albicans.

Ford CB, Funt JM, Abbey D, Issi L, Guiducci C, Martinez DA, Delorey T, Li BY, White TC, Cuomo C, Rao RP, Berman J, Thompson DA, Regev A - Elife (2015)

Bottom Line: Studies in clinical isolates have implicated multiple mechanisms in resistance, but have focused on large-scale aberrations or candidate genes, and do not comprehensively chart the genetic basis of adaptation.LOH events were commonly associated with acquired resistance, and SNPs in 240 genes may be related to host adaptation.Conversely, most aneuploidies were transient and did not correlate with drug resistance.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Broad Institute of MIT and Harvard, Cambridge, United States.

ABSTRACT
Candida albicans is both a member of the healthy human microbiome and a major pathogen in immunocompromised individuals. Infections are typically treated with azole inhibitors of ergosterol biosynthesis often leading to drug resistance. Studies in clinical isolates have implicated multiple mechanisms in resistance, but have focused on large-scale aberrations or candidate genes, and do not comprehensively chart the genetic basis of adaptation. Here, we leveraged next-generation sequencing to analyze 43 isolates from 11 oral candidiasis patients. We detected newly selected mutations, including single-nucleotide polymorphisms (SNPs), copy-number variations and loss-of-heterozygosity (LOH) events. LOH events were commonly associated with acquired resistance, and SNPs in 240 genes may be related to host adaptation. Conversely, most aneuploidies were transient and did not correlate with drug resistance. Our analysis also shows that isolates also varied in adherence, filamentation, and virulence. Our work reveals new molecular mechanisms underlying the evolution of drug resistance and host adaptation.

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Emergence of increased drug resistance often coincides with reduction infitness in the absence of drug, but an increase in the presence ofdrug.(A) For each patient (panel) shown is the fitness(‘Materials and methods’) of each strain (Y axis, mean ±STDV), ordered from the progenitor to evolved isolates (left to right, Xaxis). Fitness is calculated relative to an ENO1::YFP SC5314 referenceisolate. The MIC of each strain is shown in the gray boxes on top (white:low; black: high, color bar at bottom). Green: isolates with aneuploidies;Blue: euploid isolates. (B) Shown is the mean differencebetween fitness in the absence and presence of drug (Y axis, error bars are± STDV; n > 3) for isolates (X axis) thatshowed a decrease in fitness (Figure7A) in the absence of drug concomitant with an increase in MIC(asterisks), and flanking isolates in Patient 1 and 59 (ordered from theprogenitor to evolved isolates, left to right, X axis). The difference infitness is calculated as the difference in selection coefficient(s, Y axis) between matching competition experiments inRPMI and those in RPMI with one half the MIC for fluconazole (Table 1) for each isolate tested (Xaxis). Negative values indicate that the strain had higher fitness in thepresence of fluconazole vs assays without fluconazole. For each assay, thefluconazole-resistant isolate 4639 ENO1::YFP was used asthe reference strain.DOI:http://dx.doi.org/10.7554/eLife.00662.020
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fig7: Emergence of increased drug resistance often coincides with reduction infitness in the absence of drug, but an increase in the presence ofdrug.(A) For each patient (panel) shown is the fitness(‘Materials and methods’) of each strain (Y axis, mean ±STDV), ordered from the progenitor to evolved isolates (left to right, Xaxis). Fitness is calculated relative to an ENO1::YFP SC5314 referenceisolate. The MIC of each strain is shown in the gray boxes on top (white:low; black: high, color bar at bottom). Green: isolates with aneuploidies;Blue: euploid isolates. (B) Shown is the mean differencebetween fitness in the absence and presence of drug (Y axis, error bars are± STDV; n > 3) for isolates (X axis) thatshowed a decrease in fitness (Figure7A) in the absence of drug concomitant with an increase in MIC(asterisks), and flanking isolates in Patient 1 and 59 (ordered from theprogenitor to evolved isolates, left to right, X axis). The difference infitness is calculated as the difference in selection coefficient(s, Y axis) between matching competition experiments inRPMI and those in RPMI with one half the MIC for fluconazole (Table 1) for each isolate tested (Xaxis). Negative values indicate that the strain had higher fitness in thepresence of fluconazole vs assays without fluconazole. For each assay, thefluconazole-resistant isolate 4639 ENO1::YFP was used asthe reference strain.DOI:http://dx.doi.org/10.7554/eLife.00662.020

Mentions: To explore the possibility that some of the mutations reflect adaptation to otherfactors besides drug, we next measured phenotypes associated to virulence andinteraction with the host (‘Materials and methods’). Adhesion,filamentation, and virulence in a C. elegans model of infection(Jain et al., 2013) were measured for alarge panel of isolates (Figure 6, Figure 6—figure supplement 1, Figure 6—source data1). Additionally, we measured competitive fitness in standard tissueculture medium (RPMI) with and without drug in vitro (Figure 7).10.7554/eLife.00662.017Figure 6.Filamentation, adhesion and virulence increase concurrently withfitness.


The evolution of drug resistance in clinical isolates of Candida albicans.

Ford CB, Funt JM, Abbey D, Issi L, Guiducci C, Martinez DA, Delorey T, Li BY, White TC, Cuomo C, Rao RP, Berman J, Thompson DA, Regev A - Elife (2015)

Emergence of increased drug resistance often coincides with reduction infitness in the absence of drug, but an increase in the presence ofdrug.(A) For each patient (panel) shown is the fitness(‘Materials and methods’) of each strain (Y axis, mean ±STDV), ordered from the progenitor to evolved isolates (left to right, Xaxis). Fitness is calculated relative to an ENO1::YFP SC5314 referenceisolate. The MIC of each strain is shown in the gray boxes on top (white:low; black: high, color bar at bottom). Green: isolates with aneuploidies;Blue: euploid isolates. (B) Shown is the mean differencebetween fitness in the absence and presence of drug (Y axis, error bars are± STDV; n > 3) for isolates (X axis) thatshowed a decrease in fitness (Figure7A) in the absence of drug concomitant with an increase in MIC(asterisks), and flanking isolates in Patient 1 and 59 (ordered from theprogenitor to evolved isolates, left to right, X axis). The difference infitness is calculated as the difference in selection coefficient(s, Y axis) between matching competition experiments inRPMI and those in RPMI with one half the MIC for fluconazole (Table 1) for each isolate tested (Xaxis). Negative values indicate that the strain had higher fitness in thepresence of fluconazole vs assays without fluconazole. For each assay, thefluconazole-resistant isolate 4639 ENO1::YFP was used asthe reference strain.DOI:http://dx.doi.org/10.7554/eLife.00662.020
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4383195&req=5

fig7: Emergence of increased drug resistance often coincides with reduction infitness in the absence of drug, but an increase in the presence ofdrug.(A) For each patient (panel) shown is the fitness(‘Materials and methods’) of each strain (Y axis, mean ±STDV), ordered from the progenitor to evolved isolates (left to right, Xaxis). Fitness is calculated relative to an ENO1::YFP SC5314 referenceisolate. The MIC of each strain is shown in the gray boxes on top (white:low; black: high, color bar at bottom). Green: isolates with aneuploidies;Blue: euploid isolates. (B) Shown is the mean differencebetween fitness in the absence and presence of drug (Y axis, error bars are± STDV; n > 3) for isolates (X axis) thatshowed a decrease in fitness (Figure7A) in the absence of drug concomitant with an increase in MIC(asterisks), and flanking isolates in Patient 1 and 59 (ordered from theprogenitor to evolved isolates, left to right, X axis). The difference infitness is calculated as the difference in selection coefficient(s, Y axis) between matching competition experiments inRPMI and those in RPMI with one half the MIC for fluconazole (Table 1) for each isolate tested (Xaxis). Negative values indicate that the strain had higher fitness in thepresence of fluconazole vs assays without fluconazole. For each assay, thefluconazole-resistant isolate 4639 ENO1::YFP was used asthe reference strain.DOI:http://dx.doi.org/10.7554/eLife.00662.020
Mentions: To explore the possibility that some of the mutations reflect adaptation to otherfactors besides drug, we next measured phenotypes associated to virulence andinteraction with the host (‘Materials and methods’). Adhesion,filamentation, and virulence in a C. elegans model of infection(Jain et al., 2013) were measured for alarge panel of isolates (Figure 6, Figure 6—figure supplement 1, Figure 6—source data1). Additionally, we measured competitive fitness in standard tissueculture medium (RPMI) with and without drug in vitro (Figure 7).10.7554/eLife.00662.017Figure 6.Filamentation, adhesion and virulence increase concurrently withfitness.

Bottom Line: Studies in clinical isolates have implicated multiple mechanisms in resistance, but have focused on large-scale aberrations or candidate genes, and do not comprehensively chart the genetic basis of adaptation.LOH events were commonly associated with acquired resistance, and SNPs in 240 genes may be related to host adaptation.Conversely, most aneuploidies were transient and did not correlate with drug resistance.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Broad Institute of MIT and Harvard, Cambridge, United States.

ABSTRACT
Candida albicans is both a member of the healthy human microbiome and a major pathogen in immunocompromised individuals. Infections are typically treated with azole inhibitors of ergosterol biosynthesis often leading to drug resistance. Studies in clinical isolates have implicated multiple mechanisms in resistance, but have focused on large-scale aberrations or candidate genes, and do not comprehensively chart the genetic basis of adaptation. Here, we leveraged next-generation sequencing to analyze 43 isolates from 11 oral candidiasis patients. We detected newly selected mutations, including single-nucleotide polymorphisms (SNPs), copy-number variations and loss-of-heterozygosity (LOH) events. LOH events were commonly associated with acquired resistance, and SNPs in 240 genes may be related to host adaptation. Conversely, most aneuploidies were transient and did not correlate with drug resistance. Our analysis also shows that isolates also varied in adherence, filamentation, and virulence. Our work reveals new molecular mechanisms underlying the evolution of drug resistance and host adaptation.

Show MeSH
Related in: MedlinePlus