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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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Related in: MedlinePlus

Deletion mutants of recurrently mutated genes reveal changes in relativefitness.Shown is the fitness (‘Materials and methods’) for eachdeletion mutant strain and the corresponding wild-type strain (Y axis, mean± STDV). The wild-type parental strain (SN250) is on the far left (redbar and dashed line). Fitness is calculated relative to an ENO1::YFP SC5314reference isolate. Locus names are given for the mutant isolates (X axis).Asterisks denote statistical significance (* < 0.05, **< 0.01, *** < 0.001, ****< 0.0001) by one-way ANOVA with Holm–Sidak correction formultiple comparisons.DOI:http://dx.doi.org/10.7554/eLife.00662.021
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fig8: Deletion mutants of recurrently mutated genes reveal changes in relativefitness.Shown is the fitness (‘Materials and methods’) for eachdeletion mutant strain and the corresponding wild-type strain (Y axis, mean± STDV). The wild-type parental strain (SN250) is on the far left (redbar and dashed line). Fitness is calculated relative to an ENO1::YFP SC5314reference isolate. Locus names are given for the mutant isolates (X axis).Asterisks denote statistical significance (* < 0.05, **< 0.01, *** < 0.001, ****< 0.0001) by one-way ANOVA with Holm–Sidak correction formultiple comparisons.DOI:http://dx.doi.org/10.7554/eLife.00662.021

Mentions: Consistent with a role in host adaptation, 5 of the 22 deletion mutants reduced invitro fitness in a culture medium thought to approximate in vivo conditions (Figure 8, ‘Materials and methods’).Three were significantly more fit than the WT parental strain (SN250, red, Figure 8), including CCN1, thatencodes a G1 cyclin required for hyphal growth maintenance (Loeb et al., 1999) and orf19.4471, an orthologof Saccharomyces cerevisiae VPS64, which is required forcytoplasm-to-vacuole targeting of proteins (Bonangelino et al., 2002), is involved in recycling pheromone receptors(Kemp and Sprague, 2003), and isidentified as an ‘aneuploidy-tolerating mutant’ (Torres et al., 2010). Among the least fit were cell wallprotein genes (HYR1, HYR3, andPIR1; De Groot et al.,2003).10.7554/eLife.00662.021Figure 8.Deletion mutants of recurrently mutated genes reveal changes in relativefitness.


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)

Deletion mutants of recurrently mutated genes reveal changes in relativefitness.Shown is the fitness (‘Materials and methods’) for eachdeletion mutant strain and the corresponding wild-type strain (Y axis, mean± STDV). The wild-type parental strain (SN250) is on the far left (redbar and dashed line). Fitness is calculated relative to an ENO1::YFP SC5314reference isolate. Locus names are given for the mutant isolates (X axis).Asterisks denote statistical significance (* < 0.05, **< 0.01, *** < 0.001, ****< 0.0001) by one-way ANOVA with Holm–Sidak correction formultiple comparisons.DOI:http://dx.doi.org/10.7554/eLife.00662.021
© Copyright Policy
Related In: Results  -  Collection

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

fig8: Deletion mutants of recurrently mutated genes reveal changes in relativefitness.Shown is the fitness (‘Materials and methods’) for eachdeletion mutant strain and the corresponding wild-type strain (Y axis, mean± STDV). The wild-type parental strain (SN250) is on the far left (redbar and dashed line). Fitness is calculated relative to an ENO1::YFP SC5314reference isolate. Locus names are given for the mutant isolates (X axis).Asterisks denote statistical significance (* < 0.05, **< 0.01, *** < 0.001, ****< 0.0001) by one-way ANOVA with Holm–Sidak correction formultiple comparisons.DOI:http://dx.doi.org/10.7554/eLife.00662.021
Mentions: Consistent with a role in host adaptation, 5 of the 22 deletion mutants reduced invitro fitness in a culture medium thought to approximate in vivo conditions (Figure 8, ‘Materials and methods’).Three were significantly more fit than the WT parental strain (SN250, red, Figure 8), including CCN1, thatencodes a G1 cyclin required for hyphal growth maintenance (Loeb et al., 1999) and orf19.4471, an orthologof Saccharomyces cerevisiae VPS64, which is required forcytoplasm-to-vacuole targeting of proteins (Bonangelino et al., 2002), is involved in recycling pheromone receptors(Kemp and Sprague, 2003), and isidentified as an ‘aneuploidy-tolerating mutant’ (Torres et al., 2010). Among the least fit were cell wallprotein genes (HYR1, HYR3, andPIR1; De Groot et al.,2003).10.7554/eLife.00662.021Figure 8.Deletion mutants of recurrently mutated genes reveal changes in relativefitness.

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