Mem Inst Oswaldo Cruz, Rio de Janeiro, VOLUME 121 | 2026
Research Articles
Circulation of fluconazole-resistant Candida auris in Peru confirmed by genomic analysis
1National Centre for Public Health, Instituto Nacional de Salud, National Reference Laboratory of Mycology, Lima, Peru
2National Centre for Public Health, Instituto Nacional de Salud, Innovation and Development Area, Lima, Peru
DOI: 10.1590/0074-02760260027
263 views
401 downloads
ABSTRACT
BACKGROUND Candida auris is an emerging fungal pathogen associated with invasive infections, notable for nosocomial spread and multidrug resistance. Despite its public health importance, genetic data from Peruvian isolates remain limited.
OBJECTIVES To perform a multi-isolate genomic analysis of Peruvian C. auris isolates, including epidemiological analysis, clade assignment, phylogenetic reconstruction, and characterisation of antifungal resistance-associated mutations.
METHODS Twenty clinical samples from hospitals in Lima and Callao were identified using MALDI-TOF and subjected to antifungal susceptibility testing. Genomic DNA was sequenced, and genomes meeting quality criteria (n = 19) were included in the analysis. Phylogenomic and ERG11 phylogenetic analyses were performed, and protein modelling combined with molecular docking was used to assess interactions with lanosterol 14-α-demethylase.
FINDINGS All analysed isolates belonged to clade IV and exhibited resistance to fluconazole. The ERG11 gene harboured four relevant mutations; notably, K143R was located within the hemi-binding region of lanosterol 14-α-demethylase and was predicted, based on molecular docking, to potentially alter fluconazole binding. These findings highlight the circulation of a resistant clade and underscore the need for strengthened genomic surveillance and antifungal stewardship strategies.
MAIN CONCLUSIONS This study expands the genomic data available for C. auris and reinforces the urgent need for sustained genomic surveillance to monitor and contain antifungal resistance.
REFERENCES
01. Satoh K, Makimura K, Hasumi Y, Nishiyama Y, Uchida K, Yamaguchi H. Candida auris sp nov, a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital. Microbiol Immunol. 2009; 53(1): 41-4. doi:10.1111/j.1348- 0421.2008.00083.x.
02. Rhodes J, Fisher MC. Global epidemiology of emerging Candida auris. Curr Opin Microbiol. 2019; 52: 84-9. doi:10.1016/j. mib.2019.05.008.
03. Ruiz-Gaitán A, Martínez H, Moret A, Calabuig E, Tasias M, Alastruey- Izquierdo A, et al. Detection and treatment of Candida auris in an outbreak situation: risk factors for developing colonization and candidemia by this new species in critically ill patients. Expert Rev Anti Infect Ther. 2019; 17(4): 295-305. doi:10.1080/14787 210.2019.1592675.
04. WHO - World Health Organization. WHO fungal priority pathogens list to guide research development and public health. Geneva: World Health Organization; 2022 [cited 2026 Apr 26]. Available from: https://www.who.int/publications/i/item/9789240060241.
05. WHO/PAHO - World Health Organization/Pan American Health Organization. Epidemiological alert: Candida auris outbreaks in health care services. 2016 [cited 2026 Jun 3]. Available from: https://www.paho.org.
06. Lockhart SR, Etienne KA, Vallabhaneni S, Farooqi J, Chowdhary A, Govender NP, et al. Simultaneous emergence of multidrugresistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clin Infect Dis. 2017; 64(2): 134-40. doi:10.1093/cid/ciw691.
07. Spruijtenburg B, Badali H, Abastabar M, Mirhendi H, Khodavaisy S, Sharifisooraki J, et al. Confirmation of fifth Candida auris clade by whole genome sequencing. Emerg Microbes Infect. 2022; 11(1): 2405-11. doi:10.1080/22221751.2022.2125349.
08. Chow NA, De Groot T, Badali H, Abastabar M, Chiller T, Meis JF. Potential fifth clade of Candida auris, Iran, 2018. Emerg Infect Dis. 2019; 25(9): 1780-1. doi:10.3201/eid2509.190686.
09. Suphavilai C, Ko KKK, Lim KM, Tan MG, Boonsimma P, Chu JJK, et al. Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study. Lancet Microbe. 2024; 5(9): 100878. doi:10.1016/S2666-5247(24)00101-0.
10. Sharma C, Kumar N, Meis JF, Pandey R, Chowdhary A. Draft genome sequence of a fluconazole-resistant Candida auris strain from a candidemia patient in India. Genome Announc. 2015; 3(4): e00722-15. doi:10.1128/genomeA.00722-15.
11. Chatterjee S, Alampalli SV, Nageshan RK, Chettiar ST, Joshi S, Tatu U. Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. BMC Genomics. 2015; 16(1): 686. doi:10.1186/s12864-015-1863-z.
12. Tse H, Tsang AKL, Chu YW, Tsang DNC. Draft genome sequences of 19 clinical isolates of Candida auris from Hong Kong. Microbiol Resour Announc. 2021; 10(1): e00308-20. doi:10.1128/ MRA.00308-20.
13. Pchelin IM, Azarov DV, Churina MA, Ryabinin IA, Vibornova IV, Apalko SV. Whole genome sequence of first Candida auris strain isolated in Russia. Med Mycol. 2020; 58(3): 414-6. doi:10.1093/ mmy/myz078.
14. Yagui M, Páucar-Miranda CJ, Sandoval-Ahumada R, López-Martínez RL, Terrel-Gutierrez L, Zurita-Macalapu S, et al. Primer reporte de Candida auris en Perú. An Fac Med. 2021; 82(1): 79-84. doi:10.15381/anales.v82i1.20739.
15. Cuicapuza D, Soto-Febres F, Neyra EV, Bustamante B. First draft genome sequence of Candidozyma auris from a human clinical isolate in a major metropolitan hospital in Lima, Peru. Microbiol Resour Announc. 2026; 15(3): e00538-25.doi:10.1128/mra.00538-25.
16. Panizo MM, Reviákina V, Montes W, González G. Mantenimiento y preservación de hongos en agua destilada y aceite mineral. Rev Soc Ven Microbiol. 2005; 25(1): 35-40.
17. Relloso MS, Nievas J, Taie SF, Farquharson V, Mujica MT, Romano V, et al. Evaluación de la espectrometría de masas: MALDI-TOF MS para la identificación rápida y confiable de levaduras. Rev Argent Microbiol. 2015; 47(2): 103-7. doi:10.1016/j.ram.2015.02.004.
18. CDC - Centres for Disease Control and Prevention. Antifungal susceptibility testing for Candida auris. 2024 [cited 2026 Apr 26]. Available from: https://www.cdc.gov/candida-auris/hcp/laboratories/ antifungal-susceptibility-testing.html.
19. Babraham Bioinformatics. FastQC: a quality control tool for high throughput sequence data. 2010 [cited 2026 Apr 26]. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
20. Bolger A, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114-20. doi:10.1093/bioinformatics/btu170.
21. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014; 15(3): R46. doi:10.1186/gb-2014-15-3-r46.
22. Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5): 455-77. doi:10.1089/cmb.2012.0021.
23. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9(11): e112963. doi:10.1371/journal.pone.0112963.
24. Alonge M, Lebeigle L, Kirsche M, Jenike K, Ou S, Aganezov S, et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 2022; 23(1): 258. doi:10.1186/s13059-022-02823-7.
25. Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA. 2020; 117(17): 9451-7. doi:10.1073/pnas.1921046117.
26. Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2004; 5(1): 4.10.1- 4.10.14. doi: 10.1002/0471250953.bi0410s05.
27. Haese-Hill W, Crouch K, Otto TD. Annotation and visualization of parasite, fungi and arthropod genomes with Companion. Nucleic Acids Res. 2024; 52(W1): W436-W442. doi: 10.1093/nar/gkae378.
28. Manni M, Berkeley M, Seppey M, Simão FA, Zdobnov EM. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021; 38(10): 4647-54. doi: 10.1093/molbev/msab199.
29. Emms D, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20(1): 238. doi: 10.1186/s13059-019-1832-y.
30. Katoh K, Misawa K, Kuma KI, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002; 30(14): 3059-66. doi:10.1093/nar/gkf436.
31. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020; 37(5): 1530-4. doi: 10.1093/molbev/msaa015.
32. Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018; 46(W1): W296-W303. doi: 10.1093/nar/gky427.
33. Martín P, Olivares J, Maass F, Valero E. Analytic approximations for special functions, applied to the modified Bessel functions I₂(x) and I₂/₃(x). Results Phys. 2018; 11: 1028-1034. doi: 10.1016/j. rinp.2018.10.029.
34. McGuffin LJ, Alharbi SMA. ModFOLD9: a web server for independent estimates of 3D protein model quality. J Mol Biol. 2024; 436(17): 168531. doi: 10.1016/j.jmb.2024.168531.
35. Laskowski RA, Hutchinson EG, Michie A, Wallace AC, Jones ML, Thornton JM. PDBsum: a web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci. 1997; 22(12): 488-90. doi: 10.1016/S0968-0004(97)01140-7.
36. Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC. GROMACS: fast, flexible, and free. J Comput Chem. 2005; 26(16): 1701-8. doi: 10.1002/jcc.20291.
37. Melinte V, Tudor AD, Bujoi AG, Radu MT, Văcăriou MC, Cismaru IM, et al. Candida auris outbreak in a multidisciplinary hospital in Romania during the post-pandemic era: potential solutions and challenges in surveillance and epidemiological control. Antibiotics. 2024; 13(4): 325. doi: 10.3390/antibiotics13040325.
38. Keighley C, Garnham K, Harch SAJ, Robertson M, Chaw K, Teng JC, et al. Candida auris: diagnostic challenges and emerging opportunities for the clinical microbiology laboratory. Curr Fungal Infect Rep. 2021; 15(3): 116-26. doi: 10.1007/s12281-021-00420-y.
39. Vinayagamoorthy K, Chakravarthy K, Prakash H. Prevalence, risk factors, treatment and outcome of multidrug-resistant Candida auris infections in COVID-19 patients: a systematic review. Mycoses. 2022; 65(6): 613-24. doi: 10.1111/myc.13447.
40. Siopi M, Georgiou P, Paranos P, Beredaki MI, Tarpatzi A, Kalogeropoulou E, et al. Increase in candidemia cases and emergence of fluconazole-resistant Candida parapsilosis and C. auris isolates in a tertiary care academic hospital during the COVID-19 pandemic, Greece, 2020 to 2023. Euro Surveill. 2024; 29(29): 2300661. doi: 10.2807/1560-7917.ES.2024.29.29.2300661.
41. Eix EF, Nett JE. Candida auris: epidemiology and antifungal strategy. Annu Rev Med. 2025; 76(1): 57-72. doi: 10.1146/annurevmed- 061523-021233.
42. Jamalian A, Freeke J, Chowdhary A, De Hoog S, Stielow JB, Meis JF. Fast and accurate identification of Candida auris by high resolution mass spectrometry. J Fungi. 2023; 9(2): 267. doi: 10.3390/jof9020267.
43. Zhu H, Liu M, Boekhout T, Wang Q. Improvement of a MALDITOF database for the reliable identification of Candidozyma auris (formally Candida auris) and related species. Microbiol Spectr. 2025; 13(1): e01444-24. doi: 10.1128/spectrum.01444-24.
44. Chowdhary A, Prakash A, Sharma C, Kordalewska M, Kumar A, Sarma S, et al. A multicentre study of antifungal susceptibility patterns among 350 Candida auris isolates (2009-2017) in India: role of ERG11 and FKS1 genes. J Antimicrob Chemother. 2018; 73(4): 891-9. doi: 10.1093/jac/dkx480.
45. Kim HY, Nguyen TA, Kidd S, Chambers J, Alastruey-Izquierdo A, Shin JH, et al. Candida auris: a systematic review to inform the World Health Organization fungal priority pathogens list. Med Mycol. 2024; 62(6): myae042. doi: 10.1093/mmy/myae042.
46. De Almeida JN, Francisco EC, Hagen F, Brandão IB, Pereira FM, Dias PHP, et al. Emergence of Candida auris in Brazil in a COVID- 19 intensive care unit. J Fungi (Basel). 2021; 7(3): 220. doi: 10.3390/jof7030220.
47. Misas E, Escandón P, Gade L, Caceres D, Hurst S, Le N, et al. Genomic epidemiology and antifungal-resistant characterization of Candida auris, Colombia, 2016-2021. mSphere. 2024; 9(2): e00562-23. doi: 10.1128/msphere.00577-23.
48. Du H, Bing J, Hu T, Ennis CL, Nobile CJ, Huang G. Candida auris: epidemiology, biology, antifungal resistance, and virulence. PLoS Pathog. 2020; 16(10): e1008921. doi:10.1371/journal.ppat.1008921.
49. Chow NA, Muñoz JF, Gade L, Berkow EL, Li X, Welsh RM, et al. Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses. mBio. 2020; 11(2): e03364-19. doi: 10.1128/mBio.03364-19.
50. Gifford H, Rhodes J, Farrer RA. The diverse genomes of Candida auris. Lancet Microbe. 2024; 5(9): 100903. doi: 10.1016/S2666- 5247(24)00135-6.
51. Zhang J, Li L, Lv Q, Yan L, Wang Y, Jiang Y. The fungal CYP51s: their functions, structures, related drug resistance, and inhibitors. Front Microbiol. 2019; 10: 691. doi: 10.3389/fmicb.2019.00691.
52. Kordalewska M, Perlin DS. Identification of drug resistant Candida auris. Front Microbiol. 2019; 10: 1918. doi: 10.3389/ fmicb.2019.01918.
53. Healey KR, Kordalewska M, Ortigosa CJ, Singh A, Berrío 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. doi: 10.1128/AAC.01427-18.
54. Pfaller MA, Messer SA, Deshpande LM, Rhomberg PR, Utt E, Castanheira M. Evaluation of synergistic activity of isavuconazole or voriconazole plus anidulafungin and the occurrence and genetic characterization of Candida auris detected in a surveillance program. Antimicrob Agents Chemother. 2021; 65(4): e02031-20. doi: 10.1128/AAC.02031-20.
55. Casimiro-Ramos A, Bautista-Crescencio C, Vidal-Montiel A, González GM, Hernández-García JA, Hernández-Rodríguez C, et al. Comparative genomics of the first resistant Candida auris strain isolated in Mexico: phylogenomic and pan-genomic analysis and mutations associated with antifungal resistance. J Fungi. 2024; 10(6): 392. doi: 10.3390/jof10060392.
56. Jacobs SE, Jacobs JL, Dennis EK, Taimur S, Rana M, Patel D, et al. Candida auris pan-drug-resistant to four classes of antifungal agents. Antimicrob Agents Chemother. 2022; 66(7): e00053-22. doi: 10.1128/AAC.00053-22.
Financial support: This research was supported by the Government of Peru through the budget allocated to the National Institute of Health.
+ Corresponding author: rolo.paredes.gago@gmail.com | 
https://orcid.org/0000-0002-4431-869X
Received 28 January 2026
Accepted 26 May 2026
HOW TO CITE
Paredes-Gago R, Nuñez-Llanos A, Cespedes-Roman C, Izarra-Rojas V, Hurtado V, Padilla-Rojas C, et al. Circulation of fluconazole-resistant Candida auris in Peru confirmed by genomic analysis. Mem Inst Oswaldo Cruz. 2026; 121: e260027.
HANDLING EDITOR
Ernesto Caffaren | https://orcid.org/0000-0002-8353-3034
