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Research Article

Evaluation of outbreak persistence caused by multidrug-resistant and echinocandin-resistant Candida parapsilosis using multidimensional experimental and epidemiological approaches

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Article: 2322655 | Received 09 Jan 2024, Accepted 20 Feb 2024, Published online: 05 Mar 2024

References

  • Daneshnia F, de Almeida Júnior JN, Ilkit M, et al. Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap. The Lancet Microbe. 2023;4:e470–e480. doi:10.1016/S2666-5247(23)00067-8
  • Witt LS, Misas E, Farley MM, et al. 2885. Increased incidence of fluconazole-resistant Candida parapsilosis bloodstream infections in Atlanta, Georgia 2021. Open Forum Infect Dis; 2023;10(Suppl. 2): ofad500.162.
  • McTaggart LR, Eshaghi A, Hota S, et al. First Canadian report of transmission of fluconazole-resistant Candida parapsilosis within two hospital networks confirmed by genomic analysis. J Clin Microbiol. 2023;62(1):e0116123.
  • Arastehfar A, Hilmioğlu-Polat S, Daneshnia F, et al. Clonal Candidemia outbreak by Candida parapsilosis Carrying Y132F in Turkey: evolution of a persisting challenge. Front Cell Infect Microbiol. 2021;11:676177. doi:10.3389/fcimb.2021.676177
  • Thomaz DY, de Almeida JNJ, Sejas ONE, et al. Environmental Clonal Spread of Azole-Resistant Candida parapsilosis with Erg11-Y132F mutation causing a large Candidemia outbreak in a Brazilian Cancer referral center. J fungi (Basel, Switzerland). 2021;7:259.
  • Ning Y, Xiao M, Perlin DS, et al. Decreased echinocandin susceptibility in Candida parapsilosis causing candidemia and emergence of a pan-echinocandin resistant case in China. Emerg Microbes Infect. 2023;12:2153086. doi:10.1080/22221751.2022.2153086
  • Siopi M, Papadopoulos A, Spiliopoulou A, et al. Pan-Echinocandin Resistant C. parapsilosis Harboring an F652S Fks1 alteration in a patient with Prolonged Echinocandin therapy. J fungi (Basel, Switzerland). 2022;8(9).
  • Arastehfar A, Daneshnia F, Hilmioglu-Polat S, et al. Genetically related micafungin-resistant Candida parapsilosis blood isolates harbouring novel mutation R658G in hotspot 1 of Fks1p: a new challenge? J Antimicrob Chemother. 2021;76:418–422.
  • Daneshnia F, Hilmioğlu-Polat S, Ilkit M, et al. Whole-genome sequencing confirms a persistent candidaemia clonal outbreak due to multidrug-resistant Candida parapsilosis. J Antimicrob Chemother. 2023;78:1488–1494. doi:10.1093/jac/dkad112
  • Doorley LA, Rybak JM, Berkow EL, et al. Candida parapsilosis Mdr1B and Cdr1B Are Drivers of Mrr1-mediated clinical fluconazole resistance. Antimicrob Agents Chemother. 2022;66:e0028922.
  • Daneshnia F, de Almeida Júnior JN, Arastehfar A, et al. Determinants of fluconazole resistance and echinocandin tolerance in C. parapsilosis isolates causing a large clonal candidemia outbreak among COVID-19 patients in a Brazilian ICU. Emerg Microbes Infect. 2022;11:2264–2274. doi:10.1080/22221751.2022.2117093
  • Ben-Ami R, Garcia-Effron G, Lewis RE, et al. Fitness and virulence costs of Candida albicans FKS1 hot spot mutations associated with echinocandin resistance. J Infect Dis. 2011;204:626–635. doi:10.1093/infdis/jir351
  • Papp C, Kocsis K, Tóth R, et al. Echinocandin-induced microevolution of Candida parapsilosis influences virulence and abiotic stress tolerance. mSphere. 2018;3:e00547–18.
  • Pryszcz LP, Németh T, Gácser A, et al. Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis. Genome Biol Evol. 2013;5:2382–2392. doi:10.1093/gbe/evt185
  • Bergin SA, Zhao F, Ryan AP, et al. Systematic analysis of copy number variations in the Pathogenic Yeast Candida parapsilosis identifies a Gene amplification in RTA3 that is associated with drug resistance. MBio. 2022;13(5):e0177722.
  • Ola M, O’Brien CE, Coughlan AY, et al. Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis. Genome Res. 2020;30:684–696. doi:10.1101/gr.257816.119
  • Arastehfar A, Ünal N, Hoşbul T, et al. Candidemia among Coronavirus disease 2019 patients in Turkey admitted to intensive care units: a retrospective multicenter study. Open forum Infect Dis. 2022;9:ofac078. doi:10.1093/ofid/ofac078
  • Jiang H, Lei R, Ding S-W, et al. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014;15:182. doi:10.1186/1471-2105-15-182
  • Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM; 2013. doi:10.48550/ARXIV.1303.3997
  • Auwera GAVde, O’Connor BD. (2020). Genomics in the cloud: using Docker, GATK, and WDL in Terra, First edition ed. O’Reilly, Beijing Boston Farnham Sebastopol Tokyo.
  • Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10. doi:10.1093/gigascience/giab008
  • Rausch T, Zichner T, Schlattl A, et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28:i333–i339. doi:10.1093/bioinformatics/bts378
  • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842. doi:10.1093/bioinformatics/btq033
  • Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–1313. doi:10.1093/bioinformatics/btu033
  • Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–W296. doi:10.1093/nar/gkab301
  • Vaser R, Adusumalli S, Leng SN, et al. SIFT missense predictions for genomes. Nat Protoc. 2016;11:1–9. doi:10.1038/nprot.2015.123
  • Lohse MB, Gulati M, Valle Arevalo A, et al. Assessment and Optimizations of Candida albicans In Vitro Biofilm Assays. Antimicrob Agents Chemother. 2017;61:e02749–16.
  • Carreté L, Ksiezopolska E, Pegueroles C, et al. Patterns of genomic variation in the opportunistic pathogen Candida glabrata suggest the existence of mating and a secondary association with humans. Curr Biol England. 2022;32(14):3219.
  • Siscar-Lewin S, Gabaldón T, Aldejohann AM, et al. Transient mitochondria dysfunction confers fungal cross-Resistance against Phagocytic killing and fluconazole. MBio. 2021;12:e0112821. doi:10.1128/mBio.01128-21
  • Timmer KD, Floyd DJ, Scherer AK, et al. Multiparametric profiling of Neutrophil function via a high-throughput flow cytometry-based assay. Cells. 2023;12; doi:10.3390/cells12050743
  • Derkacz D, Bernat P, Krasowska A. K143R amino acid substitution in 14-α-Demethylase (Erg11p) changes Plasma Membrane and cell wall structure of Candida albicans. Int J Mol Sci. 2022;23; doi:10.3390/ijms23031631
  • Ning Y, Dai R, Zhang L, et al. Copy number variants of ERG11: mechanism of azole resistance in Candida parapsilosis. The Lancet Microbe. England. 2023;74(8):2230–2238.
  • Morio F, Lombardi L, Binder U, et al. Precise genome editing using a CRISPR-Cas9 method highlights the role of CoERG11 amino acid substitutions in azole resistance in Candida orthopsilosis. J Antimicrob Chemother. 2019;74:2230–2238. doi:10.1093/jac/dkz204
  • Daneshnia F, Polat H, Ilkit S, et al. Determinants of fluconazole resistance and the efficacy of fluconazole and milbemycin oxim combination against Candida parapsilosis clinical isolates from Brazil and Turkey. Front fungal Biol. 2022;3:906681. doi:10.3389/ffunb.2022.906681
  • Bergin S, Doorley LA, Rybak JM, et al. Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes. bioRxiv. 2023;9:e58349.
  • Todd RT, Selmecki A. Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs. Elife. 2020;9:91–111.
  • Ponde NO, Lortal L, Ramage G, et al. Candida albicans biofilms and polymicrobial interactions. Crit Rev Microbiol. 2021;47:91–111. doi:10.1080/1040841X.2020.1843400