Understanding Antimicrobial Resistance in Fungal Infections

Understanding Antimicrobial Resistance in Fungal Infections

November 1, 2024

Introduction

Antimicrobial resistance (AMR) is a growing concern in both human and veterinary medicine, particularly when it comes to fungal infections. As these infections become increasingly prevalent and challenging to treat, understanding the mechanisms behind AMR is critical. This post will explore the evolution of resistance genes in fungi, focusing on ATP-binding cassette (ABC) transporters. We will also discuss intrinsic resistance mechanisms and the role of transcription factors in shaping resistance profiles.

What is Antimicrobial Resistance in Fungi?

Antimicrobial resistance in fungi refers to the ability of fungal pathogens to withstand the effects of antifungal agents, rendering standard treatments ineffective. This resistance can arise through various mechanisms, complicating the management of fungal infections in both humans and animals. The incidence of invasive fungal infections has surged, particularly in immunocompromised individuals, and many existing antifungal therapies are limited by resistance.

Intrinsic resistance plays a crucial role here; certain fungal species naturally possess mechanisms that confer a baseline level of resistance to antifungal agents. This innate ability to resist certain drugs often complicates treatment options, necessitating a deeper understanding of both intrinsic and acquired resistance mechanisms to develop effective therapeutic strategies.

Evolution of Resistance

Fungal resistance evolves through a combination of genetic mutations, selective pressure from antifungal use, and environmental factors. One significant group involved in this process is the ATP-binding cassette (ABC) transporters, specifically the Pleiotropic Drug Resistance (PDR) transporters. These transporters act as efflux pumps, removing antifungal agents from fungal cells and thereby decreasing drug accumulation and efficacy (Harris, et al. 2021).

The evolution of resistance can be accelerated by the extensive use of antifungals in agriculture and human medicine. For instance, the application of azole fungicides in crop protection can create selective pressure, leading to the emergence of resistant fungal strains that can later affect human and animal health.

As fungi adapt to survive these pressures, their resistance mechanisms can become more sophisticated, resulting in strains that are not only resistant to commonly used antifungals but also difficult to manage clinically.

Mechanisms of Resistance

The mechanisms underlying antifungal resistance are complex and multifaceted. PDR transporters, a subset of ABC transporters, are integral in this process. These transporters can actively pump out a wide variety of antifungal agents out of the fungal cells, reducing their intracellular concentrations and thus their effectiveness.

Nearly all organisms possess multiple genes in the ABC transporter family, however only a few members of this gene family are involved in fungal drug resistance. For example, overexpression of two specific ABC transporter genes, CDR1 and CDR2, convey drug resistance in Candida albicans while the closely related CDR3 gene within the same species is uninvolved (Smriti, et al. 2002; Prasad, et al. 2015).

While genes like CDR1 provide certain fungi with the potential for antifungal resistance, sometimes the process requires a helping hand. Transcription factors are a class of proteins that play a significant role in resistance by enhancing the activity of AMR genes. The Fluconazole Resistance Protein 3 (FRP3) is a key transcription factor that regulates the expression of genes involved in resistance pathways. Upregulation of FRP3 can lead to increased ABC transporter, further complicating treatment efforts (Yang, et al. 2001).

Fungi may also develop AMR through mutations in the drug’s target site. Azoles are a class of antifungals that disrupt ergosterol synthesis, a key component of the fungal cell membrane. Through mutations in the drug’s target gene, certain fungi can evade the binding of azoles and retain their growth in the presence of azoles

Intrinsic resistance is another critical aspect of fungal AMR, as some fungal species inherently possess mechanisms that protect them from certain antifungals. For instance, the fungal pathogen species, Cryptococcus neoformans has intrinsic resistance to echinocandins, limiting treatment options even before exposure to antifungal agents.

The Connection Between Agricultural and Medical AMR

The relationship between agricultural practices and medical antimicrobial resistance is a growing concern. The use of antifungals in agriculture can lead to the selection of resistant fungal strains that may later infect humans and animals. For example, Aspergillus species, which can be found in agricultural settings, have developed resistance mechanisms through exposure to fungicides, creating a reservoir of resistant traits that can transfer to clinically relevant fungi.

This overlap is particularly troubling in veterinary medicine, where fungal pathogens can arise from agricultural environments, posing a risk to both animal and human health. One group of pathogens that are migrating from the agricultural environment to the clinical are Fusarium species. Fusarium is a genus of fungal pathogens that typically cause agricultural disease. More recently, these fungi have been observed in human and animal infections, causing keratitis infections and mycotoxin poisoning (Batista, et al. 2020; O’Donnell, et al. 2016). Alarmingly Fusarium are equipped with intrinsic resistances to virtually all available antifungal drugs, likely a product of their deep history as agricultural parasites and prolonged exposure to fungicides (Arikan, et al. 1999). Understanding this interconnectedness is vital for developing comprehensive strategies to combat AMR in both fields.

Next Generation Sequencing: The future of AMR detection

Next-generation sequencing (NGS) refers to a group of advanced DNA sequencing technologies that allow for the parallel sequencing of millions of DNA fragments. This capability provides comprehensive insights into the genetic material of organisms, making it possible to analyze entire genomes, metagenomes, or targeted regions of interest.

In the context of fungal AMR detection, NGS can be used to identify specific fungi present in a sample and assess their genetic makeup, including any resistance genes (Durand, et al. 2019). By identifying specific resistance genes, NGS can provide insights into how fungi are developing resistance, helping guide treatment decisions and avoid incorrect usage of antimicrobials.

Conclusion

Fungal pathogens can employ a variety of mechanisms to resist antimicrobial treatments. The rising incidence of antimicrobial resistance in fungal infections presents a significant challenge for both human and veterinary medicine. By understanding the mechanisms of resistance, including the role of PDR transporters, intrinsic resistance, and key transcription factors, we can better address this critical issue. Additionally, it is difficult to develop fungicides for veterinary use with minimal toxicity effects on the  patient due to genetic similarities between animals and fungi. Continued research, fungicidal stewardship, and surveillance are essential to identify emerging resistant strains and develop effective therapeutic strategies, ensuring better outcomes for humans and animals alike.

References

Arikan S, Lozano-Chiu M, Paetznick V, Nangia S, Rex JH. Microdilution susceptibility testing of amphotericin B, itraconazole, and voriconazole against clinical isolates of Aspergillus and Fusarium species. J Clin Microbiol. 1999 Dec;37(12):3946-51. doi: 10.1128/JCM.37.12.3946-3951.1999.

Batista BG, Chaves MA, Reginatto P, Saraiva OJ, Fuentefria AM. Human fusariosis: An emerging infection that is difficult to treat. Rev Soc Bras Med Trop. 2020;53:e20200013. doi: 10.1590/0037-8682-0013-2020.

Durand C, Maubon D, Cornet M, Wang Y, Aldebert D, Garnaud C. Can We Improve Antifungal Susceptibility Testing? Front Cell Infect Microbiol. 2021 Sep 10;11:720609. doi: 10.3389/fcimb.2021.720609.

Harris, A., Wagner, M., Du, D. et al. Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5. Nat Commun 12, 5254 (2021). https://doi.org/10.1038/s41467-021-25574-8.

Marichal P, Koymans L, Willemsens S, Bellens D, Verhasselt P, Luyten W, Borgers M, Ramaekers FCS, Odds FC, Vanden Bossche H. Contribution of mutations in the cytochrome P450 14α-demethylase (Erg11p, Cyp51p) to azole resistance in Candida albicans. Microbiology. 1999;145:2701–13. doi: 10.1099/00221287-145-10-2701.

O’Donnell K, Sutton DA, Wiederhold N, Robert VA, Crous PW, Geiser DM. Veterinary Fusarioses within the United States. J Clin Microbiol. 2016 Nov;54(11):2813-2819. doi: 10.1128/JCM.01607-16.

Prasad R, Banerjee A, Khandelwal NK, Dhamgaye S. The ABCs of Candida albicans Multidrug Transporter Cdr1. Eukaryot Cell. 2015;14(12):1154-64. doi: 10.1128/EC.00137-15.

Smriti,  Krishnamurthy, S., Dixit, B.L., Gupta, C.M., Milewski, S. and Prasad, R. (2002), ABC transporters Cdr1p, Cdr2p and Cdr3p of a human pathogen Candida albicans are general phospholipid translocators. Yeast, 19: 303-318. https://doi.org/10.1002/yea.818

Yang X, Talibi D, Weber S, Poisson G, Raymond M. Functional isolation of the Candida albicans FCR3 gene encoding a bZip transcription factor homologous to Saccharomyces cerevisiae Yap3p. Yeast. 2001;18(13):1217–1225. doi: 10.1002/yea.770.

Categories: Antimicrobial Resistance, Fungal Infections, Next-Gen DNA Sequencing Technology

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