Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Evolution of antifungal-drug resistance: mechanisms and pathogen fitness

Key Points

  • Like other microorganisms, fungi exist in populations that are adaptable. Under the selection imposed by antifungal drugs, initially drug-sensitive fungal pathogens frequently evolve resistance.

  • Although molecular mechanisms of resistance to antifungal drugs are well characterized, it is the evolutionary processes, the divergent mechanisms that arise by mutation and the impact on the fitness of the pathogen that determine the fate of resistance in fungal pathogen populations.

  • In fungi, unlike bacteria, drug-resistance (and other) genes do not usually spread horizontally among widely divergent taxa. The prevailing pattern is that antifungal-drug resistance evolves repeatedly in isolated populations.

  • The evidence for the evolution of resistance in real time comes from two different types of study: those that monitor fungal populations in patients undergoing antifungal drug therapy; and, in replicate, artificial cultures containing an antifungal drug.

  • A crucial factor in the evolution of resistance to drugs is whether different resistance mechanisms that occur in combination result in increased fitness in the presence of a drug, compared with the same mechanisms when they occur in isolation.

  • In the development of new antifungal drugs, the evolutionary potential for resistance can be predicted by subjecting known target genes to the Barlow–Hall procedure for mutagenic PCR and artificial recombination, and by allowing pathogen populations to evolve under artificial conditions designed to favour as many different mechanisms of resistance as possible.

  • Possible avenues for managing antifungal drug resistance in the future include developing methods to channel fungal evolution so that the pathogen population becomes more vulnerable to existing drugs, and interfering with the ability of the fungal population to produce phenotypic variation, which might be subject to natural selection and therefore impede evolvability.


Like other microorganisms, fungi exist in populations that are adaptable. Under the selection imposed by antifungal drugs, drug-sensitive fungal pathogens frequently evolve resistance. Although the molecular mechanisms of resistance are well-characterized, there are few measurements of the impact of these mechanisms on pathogen fitness in different environments. To predict resistance before a new drug is prescribed in the clinic, the full spectrum of potential resistance mutations and the interactions among combinations of divergent mechanisms can be determined in evolution experiments. In the search for new strategies to manage drug resistance, measuring the limits of adaptation might reveal methods for trapping fungal pathogens in evolutionary dead ends.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Chemical structures of some antifungal drugs and their targets.
Figure 2: Fitness landscapes for antifungal-drug-resistance mechanisms.


  1. 1

    Sanglard, D. & Odds, F. C. Resistance of Candida species to antifungal agents: molecular mechanisms and clinical consequences. Lancet Infect. Dis. 2, 73–85 (2002). This article reviews antifungal resistance mechanisms, the methods for measuring resistance, and surveys resistance detected in the clinic. Includes an assessment of the threat posed by antifungal resistance.

    CAS  Article  Google Scholar 

  2. 2

    Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. & Doolittle, W. F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972–977 (2000).

    CAS  Article  Google Scholar 

  3. 3

    Sanglard, D. Resistance of human fungal pathogens to antifungal drugs. Curr. Opin. Microbiol. 5, 379–385 (2002).

    CAS  Article  Google Scholar 

  4. 4

    Lupetti, A., Danesi, R., Campa, M., Del Tacca, M. & Kelly, S. Molecular basis of resistance to azole antifungals. Trends Mol. Med. 8, 76–81 (2002).

    CAS  Article  Google Scholar 

  5. 5

    Cowen, L. E. et al. Population genomics of drug resistance in Candida albicans. Proc. Natl Acad. Sci. USA 99, 9284–9928 (2002). Shows how altered patterns of gene expression become entrenched with the evolution of resistance and how these patterns might be channelled in a limited number of ways.

    CAS  Article  Google Scholar 

  6. 6

    Barker, K. S. et al. Genome-wide expression profiling reveals genes associated with amphotericin B and fluconazole resistance in experimentally induced antifungal resistant isolates of Candida albicans. J. Antimicrob. Chemother. 54, 376–385 (2004).

    CAS  Article  Google Scholar 

  7. 7

    DeRisi, J. et al. Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. FEBS Lett. 470, 156–160 (2000).

    CAS  Article  Google Scholar 

  8. 8

    Rogers, P. D. & Barker, K. S. Genome-wide expression profile analysis reveals coordinately regulated genes associated with stepwise acquisition of azole resistance in Candida albicans clinical isolates. Antimicrob. Agents Chemother. 47, 1220–1227 (2003).

    CAS  Article  Google Scholar 

  9. 9

    Reference method for broth dilution antifungal susceptibility testing of yeasts. Approved standard. NCCLS document M27-A. National Committee for Clinical Laboratory Standards, Wayne, Pennsylvania (1997).

  10. 10

    Casadevall, A. & Pirofski, L. A. The damage-response framework of microbial pathogenesis. Nature Rev. Microbiol. 1, 17–24 (2003).

    CAS  Article  Google Scholar 

  11. 11

    Cowen, L. E., Kohn, L. M. & Anderson, J. B. Divergence in fitness and evolution of drug resistance in experimental populations of Candida albicans. J. Bacteriol. 183, 2971–2978 (2001).

    CAS  Article  Google Scholar 

  12. 12

    Anderson, J. B. et al. Mode of selection and experimental evolution of antifungal drug resistance in Saccharomyces cerevisiae. Genetics 163, 1287–1298 (2003). Examples of parallel evolution of antifungal-drug resistance at the molecular level with two different selection regimens.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13

    Pfaller, M. A., Sheehan, D. J. & Rex, J. H. Determination of fungicidal activities against yeasts and molds: lessons learned from bactericidal testing and the need for standardization. Clin. Microbiol. Rev. 17, 268–280 (2004).

    CAS  Article  Google Scholar 

  14. 14

    Matsumori, N., Yamaji, N., Matsuoka, S., Oishi, T. & Murata, M. Amphotericin B covalent dimers forming sterol-dependent ion-permeable membrane channels. J. Am. Chem. Soc. 124, 4180–4181 (2002).

    CAS  Article  Google Scholar 

  15. 15

    White, T. C., Marr, K. A. & Bowden, R. A. Clinical, cellular, and molecular factors that contribute to antifungal drug resistance. Clin. Microbiol. Rev. 11, 382–402 (1998).

    CAS  Article  Google Scholar 

  16. 16

    Kurtz, M. B. et al. Characterization of echinocandin-resistant mutants of Candida albicans: genetic, biochemical, and virulence studies. Infect. Immun. 64, 3244–3251 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    Hernandez, S. et al. Caspofungin resistance in Candida albicans: correlating clinical outcome with laboratory susceptibility testing of three isogenic isolates serially obtained from a patient with progressive Candida esophagitis. Antimicrob. Agents Chemother. 48, 1382–1383 (2004).

    CAS  Article  Google Scholar 

  18. 18

    Levin, B. R. & Bergstrom, C. T. Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. Proc. Natl Acad. Sci. USA 97, 6981–6985 (2000).

    CAS  Article  Google Scholar 

  19. 19

    Fincham, J. R. S., Day, P. R. & Radford, A. Fungal Genetics 4th edn (University of California Press, Berkeley, 1979). Still the most authoritative and comprehensive treatment of fungal transmission genetics.

    Google Scholar 

  20. 20

    Pfaller, M. A. Nosocomial candidiasis: emerging species, reservoirs, and modes of transmission. Clin. Infect. Dis. 22, S89–S94 (1996).

    Article  Google Scholar 

  21. 21

    Pontecorvo, G. The parasexual cycle in fungi. Annu. Rev. Microbiol. 10, 393–400 (1956).

    CAS  Article  Google Scholar 

  22. 22

    Milgroom, M. G. Recombination and the multilocus structure of fungal populations. Annu. Rev. Phytopathology 34, 457–477 (1996).

    CAS  Article  Google Scholar 

  23. 23

    Anderson, J. B. & Kohn, L. M. Genotyping, gene genealogies, and genomics bring fungal population genetics above ground. Trends Ecol. Evol. 13, 444–449 (1998).

    CAS  Article  Google Scholar 

  24. 24

    Anderson, J. B. et al. Infrequent genetic exchange and recombination in the mitochondrial genome of Candida albicans. J. Bacteriol. 183, 865–872 (2001).

    CAS  Article  Google Scholar 

  25. 25

    Burt, A., Carter, D. A., Koenig, G. L., White, T. J. & Taylor, J. W. Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis. Proc. Natl Acad. Sci. USA 93, 770–773 (1996).

    CAS  Article  Google Scholar 

  26. 26

    Graser, Y. et al. Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination. Proc. Natl Acad. Sci. USA 93, 12473–12477 (1996).

    CAS  Article  Google Scholar 

  27. 27

    Taylor, J. W., Geiser, D. M., Burt, A. & Koufopanou, V. The evolutionary biology and population genetics underlying fungal strain typing. Clin. Microbiol. Rev. 12, 126–146 (1999).

    CAS  Article  Google Scholar 

  28. 28

    Taylor, J. W. et al. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol. 31, 21–32 (2000).

    CAS  Article  Google Scholar 

  29. 29

    White, T. C. Increased mRNA levels of ERG16, CDR, and MDR1 correlate with increases in azole resistance in Candida albicans isolates from a patient infected with human immunodeficiency virus. Antimicrob. Agents Chemother. 41, 1482–1487 (1997). A well-documented example of drug-resistance evolution in a fungal population present in the body of a patient. Shows how different mechanisms of resistance can accumulate in an evolutionary lineage of a fungal pathogen.

    CAS  Article  Google Scholar 

  30. 30

    Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Rev. Genet. 4, 457–469 (2003). An excellent manual for experimental evolution including a 'how to' guide and the underlying principles of the process.

    CAS  Article  Google Scholar 

  31. 31

    Zeyl, C. Budding yeast as a model organims for population genetics. Yeast 16, 773–784 (2000).

    CAS  Article  Google Scholar 

  32. 32

    Andersson, D. I. Persistence of antibiotic resistant bacteria. Curr. Opin. Microbiol. 6, 452–456 (2003).

    CAS  Article  Google Scholar 

  33. 33

    Levin, B. R., Perrot, V. & Walker, N. Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. Genetics 154, 985–997 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Maisnier-Patin, S. & Andersson, D. I. Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution. Res. Microbiol. 155, 360–369 (2004).

    CAS  Article  Google Scholar 

  35. 35

    Paquin, C. & Adams, J. Frequency of fixation of adaptive mutations is higher in evolving diploid than haploid yeast populations. Nature 302, 495–500 (1983).

    CAS  Article  Google Scholar 

  36. 36

    Cowen, L. E. et al. Evolution of drug resistance in experimental populations of Candida albicans. J. Bacteriol. 182, 1515–1522 (2000).

    CAS  Article  Google Scholar 

  37. 37

    Hall, B. G. Innovation: predicting the evolution of antibiotic resistance genes. Nature Rev. Microbiol. 2, 430–435 (2004). Shows how the principles of experimental evolution can be applied to single genes to establish the potential reach of evolutionary change.

    CAS  Article  Google Scholar 

  38. 38

    Sanglard, D., Ischer, F., Koymans, L. & Bille, J. Amino acid substitutions in the cytochrome P-450 lanosterol 14α-demethylase (CYP51A1) from azole-resistant Candida albicans clinical isolates contribute to resistance to azole antifungal agents. Antimicrob. Agents Chemother. 42, 241–253 (1998).

    CAS  Article  Google Scholar 

  39. 39

    White, T. C. The presence of an R467K amino acid substitution and loss of allelic variation correlate with an azole-resistant lanosterol 14α demethylase in Candida albicans. Antimicrob. Agents Chemother. 41, 1488–1494 (1997).

    CAS  Article  Google Scholar 

  40. 40

    Markovich, S., Yekutiel, A., Shalit, I., Shadkchan, Y. & Osherov, N. Genomic approach to identification of mutations affecting caspofungin susceptibility in Saccharomyces cerevisiae. Antimicrob. Agents Chemother. 48, 3871–3876 (2004).

    CAS  Article  Google Scholar 

  41. 41

    Kondrashov, A. S. Classification of hypotheses on the advantage of amphimixis. J. Hered. 84, 372–387 (1993).

    CAS  Article  Google Scholar 

  42. 42

    Johnson, M. D., MacDougall, C., Ostrosky-Zeichner, L., Perfect, J. R. & Rex, J. H. Combination antifungal therapy. Antimicrob. Agents Chemother. 48, 693–715 (2004).

    CAS  Article  Google Scholar 

  43. 43

    Singh, N. & Heitman, J. Antifungal attributes of immunosuppressive agents: new paradigms in management and elucidating the pathophysiologic basis of opportunistic mycoses in organ transplant recipients. Transplantation 77, 795–800 (2004).

    CAS  Article  Google Scholar 

  44. 44

    Cruz, M. C. et al. Calcineurin is essential for survival during membrane stress in Candida albicans. EMBO J. 21, 546–559 (2002).

    CAS  Article  Google Scholar 

  45. 45

    Sanglard, D., Ischer, F., Marchetti, O., Entenza, J. & Bille, J. Calcineurin A of Candida albicans: involvement in antifungal tolerance, cell morphogenesis and virulence. Mol. Microbiol. 48, 959–976 (2003).

    CAS  Article  Google Scholar 

  46. 46

    Matthews, R. C. & Burnie, J. P. Recombinant antibodies: a natural partner in combinatorial antifungal therapy. Vaccine 22, 865–871 (2004).

    CAS  Article  Google Scholar 

  47. 47

    Vazquez, J. A. Combination antifungal therapy against Candida species: the new frontier — are we there yet? Med. Mycol. 41, 355–368 (2003).

    CAS  Article  Google Scholar 

  48. 48

    Kontoyiannis, D. P. & Lewis, R. E. Combination chemotherapy for invasive fungal infections: what laboratory and clinical studies tell us so far. Drug Resist. Updat. 6, 257–269 (2003).

    CAS  Article  Google Scholar 

  49. 49

    Cuenca-Estrella, M. Combinations of antifungal agents in therapy — what value are they? J. Antimicrob. Chemother. 54, 854–869 (2004).

    CAS  Article  Google Scholar 

  50. 50

    Anderson, J. B., Ricker, N. & Sirjusingh, C. Ploidy and evolution of antifungal drug resistance. Genetics 168, 1915–1923 (2004).

    CAS  Article  Google Scholar 

  51. 51

    Kirschner, M. & Gerhart, J. Evolvability. Proc. Natl Acad. Sci. USA 95, 8420–8427 (1998).

    CAS  Article  Google Scholar 

  52. 52

    Funk & Wagnall's Standard College Dictionary (Harcourt, Brace & World Inc., New York, 1963).

  53. 53

    Zeyl, C. Capturing the adaptive mutation in yeast. Res. Microbiol. 155, 217–223 (2004).

    CAS  Article  Google Scholar 

  54. 54

    Saupe, S. J. Molecular genetics of heterokaryon incompatibility in filamentous ascomycetes. Microbiol. Mol. Biol. Rev. 64, 489–502 (2000).

    CAS  Article  Google Scholar 

  55. 55

    Glass, N. L. & Kaneko, I. Fatal attraction: nonself recognition and heterokaryon incompatibility in filamentous fungi. Eukaryot. Cell 2, 1–8 (2003).

    CAS  Article  Google Scholar 

  56. 56

    Cortesi, P., McCulloch, C. E., Song, H., Lin, H. & Milgroom, M. G. Genetic control of horizontal virus transmission in the chestnut blight fungus, Cryphonectria parasitica. Genetics 159, 107–118 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57

    Fraser, J. A. & Heitman, J. Evolution of fungal sex chromosomes. Mol. Microbiol. 51, 299–306 (2004).

    CAS  Article  Google Scholar 

  58. 58

    Casselton, L. A. & Olesnicky, N. S. Molecular genetics of mating recognition in basidiomycete fungi. Microbiol. Mol. Biol. Rev. 62, 55–70 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59

    Herskowitz, I. Life cycle of the budding yeast Saccharomyces cerevisiae. Microbiol. Rev. 52, 536–553 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60

    Kronstad, J. W. & Staben, C. Mating type in filamentous fungi. Annu. Rev. Genet. 31, 245–276 (1997).

    CAS  Article  Google Scholar 

  61. 61

    Lockhart, S. R., Daniels, K. J., Zhao, R., Wessels, D. & Soll, D. R. Cell biology of mating in Candida albicans. Eukaryot. Cell 2, 49–61 (2003).

    CAS  Article  Google Scholar 

  62. 62

    Hull, C. M., Raisner, R. M. & Johnson, A. D. Evidence for mating of the 'asexual' yeast Candida albicans in a mammalian host. Science 289, 307–310 (2000).

    CAS  Article  Google Scholar 

  63. 63

    Miller, M. G. & Johnson, A. D. White-opaque switching in Candida albicans is controlled by mating-type locus homeodomain proteins and allows efficient mating. Cell 110, 293–302 (2002).

    CAS  Article  Google Scholar 

  64. 64

    Magee, B. B. & Magee, P. T. Induction of mating in Candida albicans by construction of MTLa and MTLα strains. Science 289, 310–313 (2000).

    CAS  Article  Google Scholar 

  65. 65

    Tsong, A. E., Miller, M. G., Raisner, R. M. & Johnson, A. D. Evolution of a combinatorial transcriptional circuit: a case study in yeasts. Cell 115, 389–399 (2003).

    CAS  Article  Google Scholar 

Download references


The author's research is supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada and an Operating Grant from the Canadian Institutes of Health Research.

Author information



Ethics declarations

Competing interests

The author declares no competing financial interests.

Related links

Related links











James B. Anderson's laboratory

Doctor Fungus

Saccharomyces cerevisiae Genome Database



The ability of a pathogen to continue to reproduce in the presence of an antifungal agent, here measured either as minimum inhibitory concentration or as fitness.


The extent to which an individual contributes genes to future generations, here measured as the number of generational doublings by a given fungal strain in a given environment in a set period of time or as an instantaneous rate of reproduction. In nature, ability to tolerate adverse environments, efficiency of sporulation and viability of offspring might also be important components of fitness.


The ability of a fungal strain to grow at drug concentrations above the minimum inhibitory concentration (MIC) in MIC tests.


The ability of the pathogen to survive while under inhibition by an agent.


Any fungal structure capable of dissemination and reproduction, including hyphal fragments, yeast cells or spores.


Occurs when fitness increases with the phenotypic value of a trait, for example, the higher the resistance, the higher the rate of reproduction.


A constitutive process in which the vegetative cells of filamentous fungi of the same, or closely related, species grow together and fuse with one another.


The capacity of an organism to express variation at the phenotypic level that might then be acted on by natural selection.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Anderson, J. Evolution of antifungal-drug resistance: mechanisms and pathogen fitness. Nat Rev Microbiol 3, 547–556 (2005).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing