The development of resistance to azoles of the clinical isolate Candida auris - the causative agent of candidaemia

Abstract

Candida auris is a new causative agent of fungal infections, which is actively spreading around the world and is featured by increased natural resistance to antifungal drugs. The presence of C. albicans ortholog genes in the C. auris genome suggests both the general origin of the species and possibly the general mechanisms of formation of resistance to antifungal drugs.

The aim is to determine the role in the formation of resistance to antifungal drugs (azoles, echinocandins) of single-nucleotide substitutions in the genes ERG11, ERG3 and FKS1 of the clinical isolate C. auris.

Material and methods. The object of the study is fluconazole resistant strain of C. auris RCPF 1821 (>256 gg/ml), the causative agent of the first case of candidaemia registered in the Russian Federation in an ICU patient, Moscow. Species identification was confirmed by MALDI-TOF mass spectrometry (Score Value range 1.704-1.898; identification category B) and by sequencing of the internal transcribed spacer region (ITS) of rDNA (GenBank MG706148) and the TEF1α gene locus (GenBank MG596888). Single nucleotide polymorphism (SNP) of the ERG11, ERG3, and FKS1 genes was determined during genome-wide sequencing of the strain using a MiSeq sequencer with 250 bp pair-terminal readings. The draft genome sequence was deposited at GenBank under accession number SBI000000000. The search for SNPs was performed in the Harvest Parsnp program.

Results and discussion. Phylogenomic reconstruction based on SNPs of the entire genome showed that the C. auris RCPF 1821 strain belongs to the Indo-Pakistani (South Asian) clade. Translated sequences of ERG11 the studied strain RCPG 1821 contained the amino acid substitutions F105L and K143R, which were previously associated with resistance formation in C. albicans. Alignment of the amino acid sequences of the C. auris RCPF 1821 ERG3 and FKS1 genes with the sequences of the corresponding C. albicans proteins did not reveal any mutations that could potentially be responsible for antifungal resistance.

Conclusion. Observed fluconazole resistance in C. auris was probably due to F105L and K143R mutations in ERG11 gene.

Keywords:Candida auris, antifungal resistance, next generation sequencing, single nucleotide polymorphism, ERG11, ERG3 and FKS1 genes

Funding. The study had no sponsor support.

Conflict of interests. The authors declare no conflict of interests.

For citation: Vasilyeva N.V., Taraskina A.E., Bogomolova T.S., Vybornova I.V., Pchelin I.M., Ryabinin I.A., Azarov D.V., Apalko S.V., Romaniuk S.A., Shcherbak S.G., Kruglov A.N. The development of resistance to azoles of the clinical isolate Candida auris - the causative agent of candidaemia. Infektsionnye bolezni: novosti, mneniya, obuchenie [Infectious Diseases: News, Opinions, Training]. 2020; 9 (2): 70-6. DOI: 10.33029/2305-3496-2020-9-2-70-76 (in Russian)

References

1. Klimko N., Kozlova Y., Khostelidi S. et al. The burden of serious fungal diseases in Russia. Mycose. 2015; 58 (suppl 5): 58-62.

2. GAFFI: Global Action Fund for Fungal Infections. URL: https://www.gaffi.org/

3. Cornely O.A., Lass-Flor C., Lagrou K., Arsic-Arsenijevic V., Hoenigl M. Improving outcome of fungal disease - guiding experts and patients towards excellence. Mycoses. 2017; 60: 420-5.

4. Vasilyeva N., Raush E., Bogomolova T.S., Shagdileeva E., Klimko N. Species distribution and susceptibility testing of Candida spp. isolated from patients with invasive candidosis in Russia. In: Mycoses. Special Issue: 7th Trends in Medical Mycology, 9-12 October 2015. Lisbon, Portugal. 2015; 58 (suppl S4): 149.

5. Munoz J.F., Gade L., Chow N.A., Loparev V.N., Juieng P., Farrer R.A., et al. Genomic basis of multidrug-resistance, mating, and virulence in Candida auris and related emerging species. Nat Commun. 2018; 9 (1): 5346.

6. Lu P.L., Liu W.L., Lo H.J., Wang F.D., Ko W.C., Hsueh P.R., et al. Are we ready for the global emergence of multidrug-resistant Candida auris in Taiwan? J Formos Med Assoc. 2017; 117: 462-70.

7. Jeffery-Smith A., Taori S.K., Schelenz S., et al. Candida auris: a review of the literature. Clin Microbiol Rev. 2017; 31 (1): e00029-17.

8. Riat A., Neofytos D., Coste A., et al. First case of Candida auris in Switzerland: discussion about preventive strategies. Swiss Med Wkly. 2018; 148: w14622.

9. Chowdhary A., Sharma C., Meis J.F. Candida auris: a rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally. PLoS Pathogens. 2017; 13 (5): e1006290.

10. Lockhart S.R., Etienne K.A., Vallabhaneni S., Farooqi J., Chowdhary A., Govender N.P., et al. Simultaneous emergence of multidrug-resistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clin Infect Dis. 2017; 64 (2): 134-40.

11. Sekyere J.O. Candida auris: a systematic review and meta-analysis of current updates on an emerging multidrug-resistant pathogen. Microbiol Open. 2018; 7: e578.

12. Cortegiani A., Misseri G., Fasciana T., Giammanco A., Giarratano A., Chowdhary A. Epidemiology, clinical characteristics, resistance, and treatment of infections by Candida auris. J Intensive Care. 2018; 6 (69): 1-13.

13. Vasilyeva N.V., Pchelin I.M., Ryabinin I.A., Raush E.R., Chilina G.A., Bogomolova T.S.. et al. The first Russian case of candidaemia due to Candida auris. 28th ECCMID. 2018.

14. Chatterjee S., Alampalli S.V., Nageshan R.K., Chettiar S.T., Joshi S., Tatu U.S. Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. BMC Genomics. 2015; 16: 686.

15. Pchelin I.M., Zlatogursky V.V., Rudneva M.V., et al. Reconstruction of phylogenetic relationships in dermatomycete genus Trichophyton Malmsten 1848 based on ribosomal internal transcribed spacer region, partial 28S rRNA and beta-tubulin genes sequences. Mycoses. 2016; 59: 566-75.

16. Pchelin I.M., Azarov D.V., Churina M.A., Scherbak S.G., Apalko S.V., Vasilyeva N.V., et al. Species boundaries in the Trichophyton mentag-rophytes/T. interdigitale species complex. Med Mycol. 2018; 57 (6): 781-9. DOI: 10.1093/mmy/myy115.

17. Kaas R.S., Leekitcharoenphon P., Aarestrup F.M., Lund 0. Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One. 2014; 9 (8): e104984.

18. Cowen L.E., Sanglard D., Howard S.J., Rogers P.D., Perlin D.S. Mechanisms of antifungal drug resistance. Cold Spring Harb Perspect Med. 2014; 5 (7): a019752.

19. Morio F., Jensen R.H., Le Pape P., Arendrup M.C. Molecular basis of antifungal drug resistance in yeasts. Int J Antimicrob Agents. 2017; 50 (5): 599-606.

20. Hargrove T.Y., Friggeri L., Wawrzak Z., Qi A., Hoekstra W.J., Schotz-inger R.J., et al. Structural analyses of Candida albicans sterol 14a-demethy-lase complexed with azole drugs address the molecular basis of azole-mediated inhibition of fungal sterol biosynthesis. J Biol Chem. 2017; 292 (16): 6728-43.

21. Healey K.R., Kordalewska M., Jimenez Ortigosa C., Singh A., Berrfo I., Chowdhary A., et al. Limited ERG11 mutations identified in isolates of Candida auris directly contribute to reduced azole susceptibility. Antimicrob Agents Chemother. 2018; 62 (10): e01427-18.

22. Prasad R., Goffeau A. Yeast ATP-binding cassette transporters conferring multidrugresistance. Annu Rev Microbiol. 2012; 66: 39-63.

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CHIEF EDITOR
Aleksandr V. Gorelov
Academician of the Russian Academy of Sciences, MD, Head of Infection Diseases and Epidemiology Department of the Scientific and Educational Institute of Clinical Medicine named after N.A. Semashko ofRussian University of Medicine, Ministry of Health of the Russian Federation, Professor of the Department of Childhood Diseases, Clinical Institute of Children's Health named after N.F. Filatov, Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation, Deputy Director for Research, Central Research Institute of Epidemiology, Rospotrebnadzor (Moscow, Russian Federation)

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