Copy number variants of ERG11: Mechanism of azole resistance in Candida parapsilosis

Abstract

Faranz Daneshnia and colleagues1Daneshnia F de Almeida Júnior, JN Ilkit M et al.Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap.Lancet Microbe. 2023; 4: e470-e480Summary Full Text Full Text PDF PubMed Scopus (0) Google Scholar reviewed challenges posed by emerging worldwide azole resistance in Candida parapsilosis and the resistance-related biological features of this pathogen. As discussed in the Review, the resistance caused by an increased copy number of ERG11 that has been observed in other Candida species is of global concern (eg, C albicans1Daneshnia F de Almeida Júnior, JN Ilkit M et al.Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap.Lancet Microbe. 2023; 4: e470-e480Summary Full Text Full Text PDF PubMed Scopus (0) Google Scholar, 2Berman J Krysan DJ Drug resistance and tolerance in fungi.Nat Rev Microbiol. 2020; 18: 319-331Crossref PubMed Scopus (241) Google Scholar, 3Gow NAR Johnson C Berman J et al.The importance of antimicrobial resistance in medical mycology.Nat Commun. 2022; 135352Crossref PubMed Scopus (41) Google Scholar and C auris4Muñoz JF Gade L Chow NA et al.Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species.Nat Commun. 2018; 95346Crossref Scopus (238) Google Scholar), yet the resistance mechanism has not been identified in C parapsilosis. Our work adds to the relevant knowledge on the C parapsilosis resistance mechanism. We carried out a population genomic study of 113 fluconazole-resistant and 92 non-resistant C parapsilosis clinical isolates collected from 46 hospitals in China. The study revealed only 63 (55·8%) of 113 instances of resistance resulted from well characterised mechanisms (eg, ERG11A395T [51·3%], ERG11A428G [2·7%], or TAC1C1552T [1·8%]), while 50 of (44·2%) 113 of the azole-resistant phenotypes could not be explained by known mechanisms. Copy number variation (CNV) analysis was done to explore potential new resistance mechanisms. We found 14 (12·4%) of 113 isolates had an increased number of ERG11 copies. Two (14·3%) of 14 ERG11 CNV events were attributed to an extra copy of the long arm of chromosome 3 (chr3q, ~609 kb; appendix pp 1–2), which was similar to the mechanism reported in C albicans.2Berman J Krysan DJ Drug resistance and tolerance in fungi.Nat Rev Microbiol. 2020; 18: 319-331Crossref PubMed Scopus (241) Google Scholar, 3Gow NAR Johnson C Berman J et al.The importance of antimicrobial resistance in medical mycology.Nat Commun. 2022; 135352Crossref PubMed Scopus (41) Google Scholar 12 (85·7%) of 14 CNVs were caused by shorter-range amplifications similar to the mechanism reported in C auris,4Muñoz JF Gade L Chow NA et al.Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species.Nat Commun. 2018; 95346Crossref Scopus (238) Google Scholar with copy numbers ranging 5– 12, and size of duplicated segments containing ERG11 gene coding sequences ranging 2·3–12·1 kb within these isolates (appendix pp 1–2). One (7·1%) of 14 resistant isolates with ERG11 CNVs had a A395T mutation. There were six isolates identified from the same hospital, which had identical size of ERG11 duplicated segments (3·4 kb). The genome-wide pairwise single nucleatide polymorphisms analysis showed a high level of genetic similarity between these six isolates (pairwise SNPs ≤330), which suggested a potential nosocomial outbreak (appendix p 2). To extend our evaluation to larger geographical regions, we additionally acquired all whole genome sequencing data of C parapsilosis with fluconazole susceptibility from NCBI public database (n=26, including 18 fluconazole-resistant isolates). ERG11 CNVs were found in seven (38·9%) of 18 of fluconazole-resistant isolates from Portugal, Korea, and Türkiye. Segment aneuploidies of chr3q, containing ERG11A395T gene, were present in two isolates from Portugal. One resistant isolate from Türkiye showed a unique CNV pattern with 6 kb in size and 14 copies. Four isolates from a medical centre in Korea, shared a consistent duplicated segment (6·0 kb, 10–16 copies), which was supposed to be another potential nosocomial outbreak event (pairwise SNPs ≤118; appendix pp 1–2). To our knowledge, this is the first report describing ERG11 CNVs mechanism in fluconazole-resistant C parapsilosis. The CNVs could occur in the form of either segmental aneuploidy or shorter-range amplifications, as have been described in C albicans and C auris, respectively.2Berman J Krysan DJ Drug resistance and tolerance in fungi.Nat Rev Microbiol. 2020; 18: 319-331Crossref PubMed Scopus (241) Google Scholar, 3Gow NAR Johnson C Berman J et al.The importance of antimicrobial resistance in medical mycology.Nat Commun. 2022; 135352Crossref PubMed Scopus (41) Google Scholar, 4Muñoz JF Gade L Chow NA et al.Genomic insights into multidrug-resistance, mating and