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Cited by 20Antifungal resistance and susceptibilityFungal and yeast genetics researchYeasts and Rust Fungi Studies

Ume6-dependent pathways of morphogenesis and biofilm formation in Candida auris

Open access
Louvet, Marine, Li, Jizhou, Brandalise, Danielle, Bachmann, Daniel, Sala de Oyanguren, Francisco, Labes, Danny, Jacquier, Nicolas, Genoud, Christel +4 more·2024·Microbiology Spectrum
DOI 10.1128/spectrum.01531-24PMC PMC11537075
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Abstract

Candida auris is a yeast pathogen causing nosocomial outbreaks of candidemia. Its ability to adhere to inert surfaces and to be transmitted from one patient to another via medical devices is of particular concern. Like other Candida spp., C. auris has the ability to transition from the yeast form to pseudohyphae and to build biofilms. Moreover, some isolates have a unique capacity to form aggregates. These morphogenetic changes may impact virulence. In this study, we demonstrated the role of the transcription factor Ume6 in C. auris morphogenesis. Genetic hyperactivation of Ume6 induced filamentation and aggregation. The Ume6-hyperactivated strain ( UME6 HA ) also exhibited increased adhesion to inert surface and formed biofilms of higher biomass compared to the parental strain. Transcriptomic analyses of UME6 HA revealed enrichment of genes encoding for adhesins, proteins involved in cell wall organization, sterol biosynthesis, and aspartic protease activities. The three most upregulated genes compared to wild-type were those encoding for the agglutin-like sequence adhesin Als4498, the C. auris -specific adhesin Scf1, and the hypha-specific G1 cyclin-related protein Hgc1. The deletion of these genes in the UME6 HA background showed that Ume6 controls filamentation via Hgc1 and aggregation via Als4498 and Scf1. Adhesion to inert surface was essentially triggered by Scf1. However, Als4498 and Hgc1 were also crucial for biofilm formation. Our data show that Ume6 is a universal regulator of C. auris morphogenesis via distinct modulators. IMPORTANCE: C. auris represents a public health threat because of its ability to cause difficult-to-treat infections and hospital outbreaks. The morphogenetic plasticity of C. auris , including its ability to filament, to form aggregates or biofilms on inert surfaces, is important to the fungus for interhuman transmission, skin or catheter colonization, tissue invasion, antifungal resistance, and escape of the host immune system. This work deciphered the importance of Ume6 in the control of distinct pathways involved in filamentation, aggregation, adhesion, and biofilm formation of C. auris . A better understanding of the mechanisms of C. auris morphogenesis may help identify novel antifungal targets.

AI snapshot

Written from the paper’s full text.

TL;DR

Ume6 hyperactivation in *Candida auris* induces filamentation, aggregation, adhesion, and thicker biofilms through distinct downstream effectors. The study maps Ume6-dependent morphogenesis to Hgc1 for pseudohyphae, Als4498 and Scf1 for aggregation, Scf1 for inert-surface adhesion, and Als4498, Scf1, and Hgc1 for biofilm formation.

Key findings

  • Hyperactivated Ume6 (UME6HA) increased pseudohyphae formation from 0.9% in IV.1 to 26.0%, and increased adhesion to polystyrene microspheres from 24.8% to 67.7% (P = 0.0001).
  • RNA-seq of UME6HA showed 384 upregulated and 88 downregulated genes; UME6 itself was upregulated 2,210-fold, and the top overexpressed genes included ALS4498, SCF1, and HGC1 (>100-fold).
  • Deletion in UME6HA showed Ume6 controls pseudohyphae via Hgc1 (pseudohyphae 15.3% in UME6HA/hgc1Δ vs 26.0% in UME6HA), aggregation via Als4498 and Scf1, adhesion mainly via Scf1, and biofilm formation via Als4498, Scf1, and Hgc1.
  • UME6HA biofilms had higher biomass and higher MBEC to amphotericin B (32–64 µg/mL vs 8–16 µg/mL) and micafungin (16–32 µg/mL vs 0.25–0.5 µg/mL), while planktonic MICs were similar; UME6HA did not show a significant virulence difference in the *Galleria mellonella* model.

Methods

  • Generated ume6Δ and UME6HA strains in the *C. auris* IV.1 background using CRISPR-Cas9; UME6HA used PADH1-driven constitutive overexpression plus a C-terminal 3×HA tag.
  • Performed RNA-seq with triplicate samples, GO enrichment, and GSEA against 90 published *C. auris* datasets; validated phenotypes by DIC/SEM, imaging flow cytometry, adhesion flow cytometry, crystal violet biofilm assay, confocal microscopy, antifungal susceptibility testing, and a *Galleria mellonella* virulence assay.
  • Compared strains using unpaired t-tests for most assays and log-rank tests for *Galleria* survival.

Limitations

  • The paper states that no gain-of-function UME6 mutations have been demonstrated in available isolate collections, that the role of Ume6 under real pathogenic conditions remains unclear, and that Ume6-independent pathways remain to be deciphered in clinical isolates.
  • The paper also states that the Ume6-dependent aggregation pathway may be distinct from clade III aggregation and that further analyses are needed in aggregative clinical isolates and other clades.
  • Evident from the text: Ume6 hyperactivation is artificial (PADH1 overexpression plus HA tag), transcriptomics was performed in vitro, virulence was tested only in an insect model, and several assays used limited biological replicates (e.g., technical triplicates and biological duplicates).

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1128/spectrum.01531-24

Cites

67 of 67 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

45 of 68 cited sources checked · 21 supported · 2 flagged · accuracy not yet measured

  • Premisecitation

    Aggregating strains demonstrate higher biofilm-forming capacity.

    “Aggregation seems to play an important role in C. auris biofilm formation, since aggregating strains demonstrated higher biofilm-forming capacity, which was associated with distinct transcriptomic profiles compared to the non-aggregative strains (13, 23, 25, 57).”
    Quote in the paperSubstantial claim2 of 4 sources checked
    • cites [13] Sherry L, Ramage G, Kean R, Borman A, Johnson EM, Richardson MD, Rautemaa-Richardson R. 2017. Biofilm-forming capability of highly virulent, multidrug-resistant Candida auris. Emerg Infect Dis 23: 328– 331. doi: 10.3201/eid2302.161320 28098553 PMC5324806 source

      In The Study (page not provided), the two nonaggregative C. auris strains had biofilm biomass 2.4 and 1.5 times less than C. albicans, while the two aggregative strains had biomass 3.0 and 3.1 times less. The measured aggregative strains therefore formed less biofilm, not more, than the nonaggregative strains. (LLM, conf=0.90)

      Checked by a reasoning model — may be wrong.

      Experimental — accuracy not yet measured
    • cites [23] Singh R, Kaur M, Chakrabarti A, Shankarnarayan SA, Rudramurthy SM. 2019. Biofilm formation by Candida auris isolated from colonising sites and candidemia cases. Mycoses 62: 706– 709. doi: 10.1111/myc.12947 31132181 source
    • cites [25] Brown JL, Delaney C, Short B, Butcher MC, McKloud E, Williams C, Kean R, Ramage G. 2020. Candida auris phenotypic heterogeneity determines pathogenicity in vitro. mSphere 5. doi: 10.1128/mSphere.00371-20 PMC7316489 32581078 source

      The Results (Fig. 1; page not provided) say aggregating isolates tended to form biofilms with greater biomass at 4 and 24 hours, but the group comparisons were not statistically significant. The Results (Fig. 2) also report distinct transcriptomic profiles for one aggregating and one nonaggregating isolate. The claim presents the biomass trend as a demonstrated general difference without that qualification. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [57] Short B, Brown J, Delaney C, Sherry L, Williams C, Ramage G, Kean R. 2019. Candida auris exhibits resilient biofilm characteristics in vitro: implications for environmental persistence. J Hosp Infect 103: 92– 96. doi: 10.1016/j.jhin.2019.06.006 31226270 source
  • Findingown data

    GSEA shows significant overlap between UME6HA upregulated genes and genes upregulated by the in vivo yeast to filament transition.

    “As shown in Fig. S3, the resulting network of data sets showed significant overlap with RNAseq profiles of genes upregulated by the in vivo yeast to filament transition [node “FILAMENT VS YEAST_UP” (20)].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [20] Yue H, Bing J, Zheng Q, Zhang Y, Hu T, Du H, Wang H, Huang G. 2018. Filamentation in Candida auris, an emerging fungal pathogen of humans: passage through the mammalian body induces a heritable phenotypic switch. Emerg Microbes Infect 7: 188. doi: 10.1038/s41426-018-0187-x 30482894 PMC6258701 source
  • Findingown data

    Adhesion to inert surface in UME6HA is essentially triggered by Scf1.

    “Adhesion to inert surface was essentially triggered by Scf1.”
    • Also stated in: § Ume6 controls adhesion to inert surface via Scf1, but Als4498 and Hgc1 are also crucial for biofilm formation · boosted
      “These data confirm the crucial role of Scf1 in adhesion to inert surfaces as recently described (27, 40).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [27] Santana DJ, Anku JAE, Zhao G, Zarnowski R, Johnson CJ, Hautau H, Visser ND, Ibrahim AS, Andes D, Nett JE, Singh S, O’Meara TR. 2023. A Candida auris-specific adhesin, Scf1, governs surface association, colonization, and virulence. Science 381: 1461– 1467. doi: 10.1126/science.adf8972 37769084 PMC11235122 source

      The section “Polymer surface attachment by the adhesin SCF1” reports that deleting SCF1 substantially reduced C. auris adhesion to polystyrene microspheres and restoring it rescued adhesion. That supports Scf1’s role in attachment to an inert surface, but the cited passages do not establish the claim specifically in UME6HA. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [40] Wang TW, Sofras D, Montelongo-Jauregui D, Paiva TO, Carolus H, Dufrêne YF, Alfaifi AA, McCracken C, Bruno VM, Van Dijck P, Jabra-Rizk MA. 2024. Functional redundancy in Candida auris cell surface adhesins crucial for cell-cell interaction and aggregation. bioRxiv: 2024.03.21.586120. doi: 10.1101/2024.03.21.586120 PMC11511831 39455573 source

      The Results section on in vitro biofilm formation reports that deleting SCF1 significantly reduced biofilm formation, while deleting ALS4112 did not; the Methods specify polystyrene plates. This supports a role for Scf1 in biofilm formation on an inert surface, but does not establish that Scf1 essentially triggers initial surface adhesion or show this in UME6HA. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Interpretationcitation

    Scf1 plays a crucial role in adhesion to inert surfaces.

    “These data confirm the crucial role of Scf1 in adhesion to inert surfaces as recently described (27, 40).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [27] Santana DJ, Anku JAE, Zhao G, Zarnowski R, Johnson CJ, Hautau H, Visser ND, Ibrahim AS, Andes D, Nett JE, Singh S, O’Meara TR. 2023. A Candida auris-specific adhesin, Scf1, governs surface association, colonization, and virulence. Science 381: 1461– 1467. doi: 10.1126/science.adf8972 37769084 PMC11235122 source
    • cites [40] Wang TW, Sofras D, Montelongo-Jauregui D, Paiva TO, Carolus H, Dufrêne YF, Alfaifi AA, McCracken C, Bruno VM, Van Dijck P, Jabra-Rizk MA. 2024. Functional redundancy in Candida auris cell surface adhesins crucial for cell-cell interaction and aggregation. bioRxiv: 2024.03.21.586120. doi: 10.1101/2024.03.21.586120 PMC11511831 39455573 source

      The Results section on in vitro biofilm formation reports that deleting SCF1 significantly reduced biofilm formation, and the Methods specify that these assays used polystyrene plates. The Discussion also reports sparse Δscf1 biofilms in catheters. These findings support a role for Scf1 in biofilms on inert surfaces, but the paper identifies its adhesion mechanism as cell–cell adherence; it does not establish that Scf1 is crucial for direct adhesion to the inert surface itself. The indexed copy provides no page numbers for these passages. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
  • Premisecitation

    Non-aggregative variants are more virulent than aggregative variants in Galleria models.

    “Non-aggregative variants were more virulent than aggregative variants in Galleria models (17, 24, 43, 46, 48).”
    Quote in the paperSubstantial claim4 of 5 sources checked
    • cites [17] Borman AM, Szekely A, Johnson EM. 2016. Comparative pathogenicity of United Kingdom isolates of the emerging pathogen Candida auris and other key pathogenic Candida species. mSphere 1: e00189-16. doi: 10.1128/mSphere.00189-16 27547827 PMC4990711 source
    • cites [24] Bing J, Guan Z, Zheng T, Zhang Z, Fan S, Ennis CL, Nobile CJ, Huang G. 2023. Clinical isolates of Candida auris with enhanced adherence and biofilm formation due to genomic amplification of ALS4. PLoS Pathog 19: e1011239. doi: 10.1371/journal.ppat.1011239 36913408 PMC10035925 source
    • cites [43] Fan S, Yue H, Zheng Q, Bing J, Tian S, Chen J, Ennis CL, Nobile CJ, Huang G, Du H. 2021. Filamentous growth is a general feature of Candida auris clinical isolates. Med Mycol 59: 734– 740. doi: 10.1093/mmy/myaa116 33485272 PMC8257410 source
    • cites [46] Garcia-Bustos V, Pemán J, Ruiz-Gaitán A, Cabañero-Navalon MD, Cabanilles-Boronat A, Fernández-Calduch M, Marcilla-Barreda L, Sigona-Giangreco IA, Salavert M, Tormo-Mas MÁ, Ruiz-Saurí A. 2022. Host-pathogen interactions upon Candida auris infection: fungal behaviour and immune response in Galleria mellonella. Emerg Microbes Infect 11: 136– 146. doi: 10.1080/22221751.2021.2017756 34890523 PMC8725852 source
    • cites [48] Garcia-Bustos V, Ruiz-Saurí A, Ruiz-Gaitán A, Sigona-Giangreco IA, Cabañero-Navalon MD, Sabalza-Baztán O, Salavert-Lletí M, Tormo MÁ, Pemán J. 2021. Characterization of the differential pathogenicity of Candida auris in a Galleria mellonella infection model. Microbiol Spectr 9: e0001321. doi: 10.1128/spectrum.00013-21 34106570 PMC8552516 source
  • May combine two claims. 32
  • The quote only partly states this claim. 2
  • Classified as probably not a substantial claim. 21

  • May combine two claims.

    Premisecitation

    Some genes expressed in C. albicans hyphal phase have no orthologs in C. auris or no significant change of expression in different conditions inducing C. auris filamentation.

    “Moreover, some genes expressed in C. albicans hyphal phase have no orthologs in C. auris (e.g., ECE1, HWP1) or no significant change of expression in different conditions inducing C. auris filamentation (e.g., FLO8, EFG1, BRG1, BCR1, EFH1), suggesting distinct pathways between these genotypically distant Candida spp. (20, 37, 47).”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites [20] Yue H, Bing J, Zheng Q, Zhang Y, Hu T, Du H, Wang H, Huang G. 2018. Filamentation in Candida auris, an emerging fungal pathogen of humans: passage through the mammalian body induces a heritable phenotypic switch. Emerg Microbes Infect 7: 188. doi: 10.1038/s41426-018-0187-x 30482894 PMC6258701 source

      The Results section (page not available) says FLO8 was upregulated and EFG1 was downregulated in filamentous C. auris cells, contrary to the claim that they showed no significant expression change. The retrieved passages do not establish whether ECE1 or HWP1 lack C. auris orthologs. (LLM, conf=0.88)

      Checked by a reasoning model — may be wrong.

      Experimental — accuracy not yet measured
    • cites [37] Kim SH, Iyer KR, Pardeshi L, Muñoz JF, Robbins N, Cuomo CA, Wong KH, Cowen LE. 2019. Genetic analysis of Candida auris implicates Hsp90 in morphogenesis and azole tolerance and Cdr1 in azole resistance. mBio 10: e02529-18. doi: 10.1128/mBio.02529-18 30696744 PMC6355988 source

      The Results section (page unavailable) states that C. auris lacks orthologs of HWP1 and ECE1. It also reports that, under Hsp90 inhibition and depletion, its differentially expressed filamentous-growth genes did not overlap with the known C. albicans regulators examined. The copy does not establish the stated expression result for each of FLO8, EFG1, BRG1, BCR1 and EFH1 across different conditions that induce C. auris filamentation. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [47] Kim JS, Lee KT, Lee MH, Cheong E, Bahn YS. 2021. Adenylyl cyclase and protein kinase a play redundant and distinct roles in growth, differentiation, antifungal drug resistance, and pathogenicity of Candida auris. mBio 12: e0272921. doi: 10.1128/mBio.02729-21 34663094 PMC8524339 source

      In Results, under “The role of the cAMP/PKA signaling pathway in the morphological transition of C. auris” (Fig. 2C; page not provided), EFG1 was unaffected by hydroxyurea in nearly all strains, and FLO8 was not induced in the wild type. The paper does not establish that ECE1 or HWP1 lack C. auris orthologs or report expression results for BRG1, BCR1, or EFH1. It tests one filamentation-inducing condition, hydroxyurea, and reports increased FLO8 expression in several mutant strains, so it does not support the broader claim about no change across different conditions. (LLM, conf=0.87)

      Experimental — accuracy not yet measured

  • The quote only partly states this claim.

    Interpretationreasoning

    Conditions favoring the filamentous phase of C. auris, such as blood contact and Hsp90 deprivation, share upregulated genes with UME6HA.

    “Together with other data sets containing genes upregulated in contact with blood cells [node “BLOOD_60 MIN_UP” (36)] and genes upregulated by deprivation of Hsp90 [node “HSP90_TET_UP”, (37)], these conditions have in common that they favor the filamentous phase of C. auris, which is consistent with the morphological effect of UME6HA on C. auris.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [36] Allert S, Schulz D, Kämmer P, Großmann P, Wolf T, Schäuble S, Panagiotou G, Brunke S, Hube B. 2022. From environmental adaptation to host survival: attributes that mediate pathogenicity of Candida auris. Virulence 13: 191– 214. doi: 10.1080/21505594.2022.2026037 35142597 PMC8837256 source

      The Results section on whole-blood infection reports genes upregulated in C. auris at 60 minutes, supporting use of this paper for the blood-response gene set. But the Results section on fungal survival says no switch to hyphal growth was detected in blood, and our copy does not assess overlap with UME6HA-upregulated genes. The separate Hsp90-deprivation data set is cited to another source in the sentence. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [37] Kim SH, Iyer KR, Pardeshi L, Muñoz JF, Robbins N, Cuomo CA, Wong KH, Cowen LE. 2019. Genetic analysis of Candida auris implicates Hsp90 in morphogenesis and azole tolerance and Cdr1 in azole resistance. mBio 10: e02529-18. doi: 10.1128/mBio.02529-18 30696744 PMC6355988 source

  • May combine two claims.

    Premisecitation

    Aggregation is mainly observed among clade III isolates but has also been reported in other clades.

    “Aggregation has been mainly observed among clade III isolates but has also been reported in other clades and can be induced under some in vitro or in vivo conditions (18, 49–51).”
    Quote in the paperNot a substantial claim3 of 4 sources checked
    • cites [18] Szekely A, Borman AM, Johnson EM. 2019. Candida auris isolates of the Southern Asian and South African lineages exhibit different phenotypic and antifungal susceptibility profiles in vitro. J Clin Microbiol 57: e02055-18. doi: 10.1128/JCM.02055-18 30867237 PMC6498034 source
    • cites [49] Pelletier C, Shaw S, Alsayegh S, Brown AJP, Lorenz A. 2024. Candida auris undergoes adhesin-dependent and -independent cellular aggregation. PLoS Pathog 20: e1012076. doi: 10.1371/journal.ppat.1012076 38466738 PMC10957086 source
    • cites [50] Bing J, Guan Z, Zheng T, Ennis CL, Nobile CJ, Chen C, Chu H, Huang G. 2024. Rapid evolution of an adaptive multicellular morphology of Candida auris during systemic infection. Nat Commun 15: 2381. doi: 10.1038/s41467-024-46786-8 38493178 PMC10944540 source

      The Results section on genetic mutations reports aggregative mutants derived from parental strains of different genetic clades, supporting occurrence beyond a single clade. The Results section on aggregate formation also describes testing strains spanning the four major clades. Neither passage says aggregation is mainly observed among clade III isolates, so the claimed predominance is unsupported. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [51] Forgács L, Borman AM, Prépost E, Tóth Z, Kardos G, Kovács R, Szekely A, Nagy F, Kovacs I, Majoros L. 2020. Comparison of in vivo pathogenicity of four Candida auris clades in a neutropenic bloodstream infection murine model. Emerg Microbes Infect 9: 1160– 1169. doi: 10.1080/22221751.2020.1771218 32486923 PMC7448943 source

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    Ume6 is a key regulator of the switch from yeast to hyphal form and of biofilm formation in Candida albicans.

    “Because the zinc cluster transcription factor Ume6 is known to be a key regulator of the switch from yeast to hyphal form and of biofilm formation in C. albicans (28–31), we explored its role in C. auris.”
    Quote in the paperSubstantial claim1 of 4 sources checked
    • cites [28] Banerjee M, Thompson DS, Lazzell A, Carlisle PL, Pierce C, Monteagudo C, López-Ribot JL, Kadosh D. 2008. UME6, a novel filament-specific regulator of Candida albicans hyphal extension and virulence. Mol Biol Cell 19: 1354– 1365. doi: 10.1091/mbc.e07-11-1110 18216277 PMC2291399 source
    • cites [29] Banerjee M, Uppuluri P, Zhao XR, Carlisle PL, Vipulanandan G, Villar CC, López-Ribot JL, Kadosh D. 2013. Expression of UME6, a key regulator of Candida albicans hyphal development, enhances biofilm formation via Hgc1- and Sun41-dependent mechanisms. Eukaryot Cell 12: 224– 232. doi: 10.1128/EC.00163-12 23223035 PMC3571304 source
    • cites [30] Fan Y, He H, Dong Y, Pan H. 2013. Hyphae-specific genes HGC1, ALS3, HWP1, and ECE1 and relevant signaling pathways in Candida albicans. Mycopathologia 176: 329– 335. doi: 10.1007/s11046-013-9684-6 24002103 source
    • cites [31] Uppuluri P, Chaturvedi AK, Srinivasan A, Banerjee M, Ramasubramaniam AK, Köhler JR, Kadosh D, Lopez-Ribot JL. 2010. Dispersion as an important step in the Candida albicans biofilm developmental cycle. PLoS Pathog 6: e1000828. doi: 10.1371/journal.ppat.1000828 20360962 PMC2847914 source

      The Results section identifies UME6 as a regulator important for C. albicans hyphal extension and shows that changing its expression changes biofilm morphology. The paper demonstrates effects on biofilm architecture and dispersion, but does not establish UME6 as a key regulator of biofilm formation itself. Page numbers are unavailable in our copy. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Biofilm formation is a complex process; adhesion to living or inert surfaces represents the first stage, and other steps are required including morphogenetic changes, proliferation, and maturation.

    “Biofilm formation is a complex process. While adhesion to living or inert surfaces represents the first stage, other steps are required including morphogenetic changes, proliferation, and maturation (14).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [14] Malinovská Z, Čonková E, Váczi P. 2023. Biofilm formation in medically important Candida species. J Fungi (Basel) 9: 955. doi: 10.3390/jof9100955 37888211 PMC10607155 source

  • May combine two claims.

    Premisecitation

    PHR1 is upregulated following Hsp90 repression/inhibition, along with SCF1 and other genes of cell surface proteins exhibiting increased expression in UME6HA.

    “PHR1 was also upregulated following Hsp90 repression/inhibition, along with SCF1 and other genes of cell surface proteins exhibiting increased expression in UME6HA (PGA26, RBT4/KRE1) (37).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [37] Kim SH, Iyer KR, Pardeshi L, Muñoz JF, Robbins N, Cuomo CA, Wong KH, Cowen LE. 2019. Genetic analysis of Candida auris implicates Hsp90 in morphogenesis and azole tolerance and Cdr1 in azole resistance. mBio 10: e02529-18. doi: 10.1128/mBio.02529-18 30696744 PMC6355988 source

      The Results section (page not available) reports that PHR1, PGA26, RBT1, and KRE1 were upregulated during C. auris filamentation associated with Hsp90 perturbation. It does not establish that PHR1 increased under both Hsp90 repression and inhibition, and the passages do not support the additional claims about SCF1 or increased expression in UME6HA. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    C. auris displays at least three Als-like, eight Hyr/Iff-like, and one species-specific adhesin (Scf1).

    “C. auris displays at least three Als-like, eight Hyr/Iff-like, and one species-specific adhesin (Scf1) (27, 53–55) (Table S3).”
    Quote in the paperNot a substantial claim3 of 4 sources checked
    • cites [27] Santana DJ, Anku JAE, Zhao G, Zarnowski R, Johnson CJ, Hautau H, Visser ND, Ibrahim AS, Andes D, Nett JE, Singh S, O’Meara TR. 2023. A Candida auris-specific adhesin, Scf1, governs surface association, colonization, and virulence. Science 381: 1461– 1467. doi: 10.1126/science.adf8972 37769084 PMC11235122 source

      In “Polymer surface attachment by the adhesin SCF1” (page not specified), the paper reports twelve genes homologous to the ALS and IFF/HYR adhesin families, but does not give the claimed breakdown of at least three Als-like and eight Hyr/Iff-like genes. The Discussion calls SCF1 a C. auris-specific adhesin; the “adhesive plasticity” section qualifies this by identifying an SCF1 homolog in C. haemulonii and describing reliance on SCF1 for adhesion as specific to C. auris. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [53] Muñoz JF, Welsh RM, Shea T, Batra D, Gade L, Howard D, Rowe LA, Meis JF, Litvintseva AP, Cuomo CA. 2021. Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris. Genetics 218: iyab029. doi: 10.1093/genetics/iyab029 33769478 PMC8128392 source

      The Results section on depleted Hyr/Iff proteins reports eight Hyr/Iff proteins in C. auris. The Discussion identifies several Als-like genes, but the copy does not establish a count of at least three distinct ones. No passage found identifies Scf1 as a species-specific adhesin; the species-specific candidate family discussed in Results is also found in closely related species. Page numbers were not available in the indexed copy. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [54] Singh S, Uppuluri P, Mamouei Z, Alqarihi A, Elhassan H, French S, Lockhart SR, Chiller T, Edwards JE, Ibrahim AS. 2019. The NDV-3A vaccine protects mice from multidrug resistant Candida auris infection. PLoS Pathog 15: e1007460. doi: 10.1371/journal.ppat.1007460 31381597 PMC6695204 source

      The Results section (‘C. auris possesses homologs of C. albicans Als3’; page unavailable) identifies three C. auris proteins homologous to Als3p, supporting the Als-like count. The cited paper does not establish the claimed eight Hyr/Iff-like adhesins or the species-specific adhesin Scf1; those parts of the sentence are not supported by this source. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [55] Smoak RA, Snyder LF, Fassler JS, He BZ. 2023. Parallel expansion and divergence of an adhesin family in pathogenic yeasts. Genetics 223: iyad024. doi: 10.1093/genetics/iyad024 36794645 PMC10319987 source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Filamentation is an important virulence trait of C. albicans, but its pathogenic role in C. auris is less obvious.

    “While filamentation is an important virulence trait of C. albicans, its pathogenic role in C. auris is less obvious (20, 43, 46).”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [20] Yue H, Bing J, Zheng Q, Zhang Y, Hu T, Du H, Wang H, Huang G. 2018. Filamentation in Candida auris, an emerging fungal pathogen of humans: passage through the mammalian body induces a heritable phenotypic switch. Emerg Microbes Infect 7: 188. doi: 10.1038/s41426-018-0187-x 30482894 PMC6258701 source
    • cites [43] Fan S, Yue H, Zheng Q, Bing J, Tian S, Chen J, Ennis CL, Nobile CJ, Huang G, Du H. 2021. Filamentous growth is a general feature of Candida auris clinical isolates. Med Mycol 59: 734– 740. doi: 10.1093/mmy/myaa116 33485272 PMC8257410 source
    • cites [46] Garcia-Bustos V, Pemán J, Ruiz-Gaitán A, Cabañero-Navalon MD, Cabanilles-Boronat A, Fernández-Calduch M, Marcilla-Barreda L, Sigona-Giangreco IA, Salavert M, Tormo-Mas MÁ, Ruiz-Saurí A. 2022. Host-pathogen interactions upon Candida auris infection: fungal behaviour and immune response in Galleria mellonella. Emerg Microbes Infect 11: 136– 146. doi: 10.1080/22221751.2021.2017756 34890523 PMC8725852 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    The gating strategy shown in Fig. S27 was used to separate the cells of interest from out-of-focus cells, debris, and clumps.

    “The gating strategy shown in Fig. S27 was used to separate the cells of interest from the out-of-focus cells, debris, and clumps, as previously reported (64).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [64] McMahon CL, Esqueda M, Yu JJ, Wall G, Romo JA, Vila T, Chaturvedi A, Lopez-Ribot JL, Wormley F, Hung CY. 2023. Development of an imaging flow cytometry method for fungal cytological profiling and its potential application in antifungal drug development. J Fungi (Basel) 9: 722. doi: 10.3390/jof9070722 37504711 PMC10381375 source

  • May combine two claims.

    Premisecitation

    Filamentation of C. auris has a limited impact on virulence, while aggregation has been associated with decreased virulence.

    “This is in line with previous observations showing that filamentation of C. auris has a limited impact on virulence, while aggregation has been associated with decreased virulence (17, 46).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [17] Borman AM, Szekely A, Johnson EM. 2016. Comparative pathogenicity of United Kingdom isolates of the emerging pathogen Candida auris and other key pathogenic Candida species. mSphere 1: e00189-16. doi: 10.1128/mSphere.00189-16 27547827 PMC4990711 source

      The Results and Discussion report that C. auris was highly virulent in Galleria mellonella larvae despite showing no significant filamentation, and that nonaggregating strains were significantly more virulent than aggregate-forming strains (Fig. 4). These observations support the association described, but the paper did not directly test the effect of filamentation on virulence or establish that the findings extend beyond the larval model. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [46] Garcia-Bustos V, Pemán J, Ruiz-Gaitán A, Cabañero-Navalon MD, Cabanilles-Boronat A, Fernández-Calduch M, Marcilla-Barreda L, Sigona-Giangreco IA, Salavert M, Tormo-Mas MÁ, Ruiz-Saurí A. 2022. Host-pathogen interactions upon Candida auris infection: fungal behaviour and immune response in Galleria mellonella. Emerg Microbes Infect 11: 136– 146. doi: 10.1080/22221751.2021.2017756 34890523 PMC8725852 source

      The Discussion describes aggregative C. auris phenotypes as less virulent and observes that they tend to form more pseudohyphae. It says filamentation *might not* be a major pathogenic determinant and *does not seem* as decisive as previously assumed; the claim presents its limited impact on virulence more definitively. Page numbers are not supplied in our copy. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    UME6 is significantly overexpressed in some in vitro filament-inducing conditions but not in vivo after passage through the mammalian body.

    “Regarding C. auris UME6, significant overexpression of this gene was found in some in vitro filament-inducing conditions (e.g., hydroxyurea treatment) but not in vivo after passage through the mammalian body (20, 47).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [20] Yue H, Bing J, Zheng Q, Zhang Y, Hu T, Du H, Wang H, Huang G. 2018. Filamentation in Candida auris, an emerging fungal pathogen of humans: passage through the mammalian body induces a heritable phenotypic switch. Emerg Microbes Infect 7: 188. doi: 10.1038/s41426-018-0187-x 30482894 PMC6258701 source

      The Results section on global gene expression profiles reports differences between yeast and filamentous cells recovered after mammalian passage, but does not identify UME6 or establish its expression level. Searches of our copy for UME6, hydroxyurea treatment, and expression after mammalian passage found no passage addressing the claimed comparison. (LLM, conf=0.72)

      Experimental — accuracy not yet measured
    • cites [47] Kim JS, Lee KT, Lee MH, Cheong E, Bahn YS. 2021. Adenylyl cyclase and protein kinase a play redundant and distinct roles in growth, differentiation, antifungal drug resistance, and pathogenicity of Candida auris. mBio 12: e0272921. doi: 10.1128/mBio.02729-21 34663094 PMC8524339 source

      The Results section on morphological transition reports that hydroxyurea treatment significantly enhanced UME6 expression in wild-type C. auris. The paper mentions filamentous growth after passage through the mammalian body, but does not report UME6 expression after that passage; its murine virulence study does not establish the claimed lack of overexpression in vivo. Page numbers were not available in our copy. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Some C. auris adhesins are upregulated in biofilm conditions.

    “Some of these adhesins were shown to be upregulated in biofilm conditions (26).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [26] Kean R, Delaney C, Sherry L, Borman A, Johnson EM, Richardson MD, Rautemaa-Richardson R, Williams C, Ramage G. 2018. Transcriptome assembly and profiling of Candida auris reveals novel insights into biofilm-mediated resistance. mSphere 3. doi: 10.1128/mSphere.00334-18 PMC6041501 29997121 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    HA tagging of the Ume6 protein was verified by Western blot using a HA tag monoclonal antibody.

    “HA tagging of the Ume6 protein was verified by Western blot using a HA tag monoclonal antibody (Invitrogen, ThermoFisher Scientific, Waltham, MA), as previously described (Fig. S26) (32).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [32] Li J, Aubry L, Brandalise D, Coste AT, Sanglard D, Lamoth F. 2024. Upc2-mediated mechanisms of azole resistance in Candida auris. Microbiol Spectr. doi: 10.1128/spectrum.03526-23 PMC10845950 38206035 source

  • May combine two claims.

    Findingcitation

    Genes involved in filamentous growth (HGC1, DDR48, PHR1) are upregulated in UME6HA and in the filamentous phenotype of C. auris following passage through the mammalian body.

    “For instance, genes involved in filamentous growth (HGC1, DDR48, PHR1) were upregulated in UME6HA and in the filamentous phenotype of C. auris following passage through the mammalian body (20).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [20] Yue H, Bing J, Zheng Q, Zhang Y, Hu T, Du H, Wang H, Huang G. 2018. Filamentation in Candida auris, an emerging fungal pathogen of humans: passage through the mammalian body induces a heritable phenotypic switch. Emerg Microbes Infect 7: 188. doi: 10.1038/s41426-018-0187-x 30482894 PMC6258701 source

      The Results section on global gene expression reports that HGC1 was upregulated in filamentous C. auris cells, and the Results section on mammalian passage reports that passage through mice triggered a filamentous phenotype (page numbers unavailable). Our copy does not report upregulation of DDR48 or PHR1, or mention UME6HA; searches for those terms found no supporting passage. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In C. albicans, Als1 is important for adhesion.

    “In C. albicans, Als1 was found to be important for adhesion (56).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [56] Nobile CJ, Fox EP, Nett JE, Sorrells TR, Mitrovich QM, Hernday AD, Tuch BB, Andes DR, Johnson AD. 2012. A recently evolved transcriptional network controls biofilm development in Candida albicans. Cell 148: 126– 138. doi: 10.1016/j.cell.2011.10.048 22265407 PMC3266547 source

  • May combine two claims.

    Premisecitation

    Scf1 is unique to C. auris and has a different adhesion mechanism compared to other adhesins.

    “Scf1 is unique to C. auris and has a different adhesion mechanism compared to other adhesins (27).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [27] Santana DJ, Anku JAE, Zhao G, Zarnowski R, Johnson CJ, Hautau H, Visser ND, Ibrahim AS, Andes D, Nett JE, Singh S, O’Meara TR. 2023. A Candida auris-specific adhesin, Scf1, governs surface association, colonization, and virulence. Science 381: 1461– 1467. doi: 10.1126/science.adf8972 37769084 PMC11235122 source

      The section “SCF1 and IFF4109 have distinct nonspecific mechanisms” reports that Scf1-mediated adhesion is not dependent on hydrophobicity, supporting the mechanism comparison. However, “C. auris relies on SCF1 for adhesive plasticity” identifies a functional SCF1 homolog in C. haemulonii. Reliance on SCF1 for adhesion is specific to C. auris, but Scf1 itself is not unique to that species. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    The proportions of non-budding, budding, and pseudohyphae cells are 52.1%, 47.0%, and 0.9% for IV.1 and 17.1%, 56.9%, and 26.0% for UME6HA, respectively.

    “The proportions of non-budding cells, budding cells, and pseudohyphae were 52.1%, 47.0%, and 0.9% for IV.1 and 17.1%, 56.9%, and 26.0% for UME6HA, respectively (Fig. 2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    No growth defect or phenotypic alteration was observed in the ume6Δ strain.

    “No growth defect or phenotypic alteration was observed in the ume6Δ strain (Fig. S1A).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    UME6HA exhibits significantly higher expression of 384 genes and lower expression of 88 genes compared to IV.1.

    “UME6HA exhibited significantly higher expression (i.e., ≥2-fold increase and P-value ≤ 0.05 compared to IV.1) and lower expression (i.e., ≥ 2-fold decrease and P-value ≤ 0.05 compared to IV.1) of 384 and 88 genes, respectively (File S1).”
    Quote in the paperSubstantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    Genetic hyperactivation of Ume6 induces filamentation or pseudohyphae formation in C. auris.

    “Genetic hyperactivation of Ume6 induced filamentation and aggregation.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Compared to UME6HA, adhesion is significantly decreased in UME6HA/scf1Δ and slightly increased in UME6HA/als4498Δ, while it is similar in UME6HA/hgc1Δ.

    “Compared to UME6HA, adhesion was significantly decreased in UME6HA/scf1Δ and slightly increased in UME6HA/als4498Δ, while it was similar in UME6HA/hgc1Δ (Fig. 5).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In biofilm conditions, UME6HA exhibits similar MBEC50 to fluconazole compared to IV.1 (16 μg/mL), but higher MBEC to amphotericin B (32-64 μg/mL vs 8-16 μg/mL) and micafungin (16-32 μg/mL vs 0.25-0.5 μg/mL).

    “In biofilm conditions, UME6HA exhibited similar minimal biofilm eradication concentration (MBEC50) to fluconazole compared to IV.1 (16 µg/mL), but higher MBEC to amphotericin B (32–64 µg/mL vs 8–16 µg/mL) and micafungin (16–32 µg/mL vs 0.25–0.5 µg/mL).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Deletion of ALS4498, SCF1, and HGC1 in UME6HA all results in a significant decrease in biofilm formation, which is more pronounced in UME6HA/als4498Δ.

    “The deletion of ALS4498, SCF1, and HGC1 in UME6HA all resulted in a significant decrease in biofilm formation, which was more pronounced in UME6HA/als4498Δ (Fig. 6).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Aggregation in UME6HA is still present in UME6HA/hgc1Δ but not in UME6HA/als4498Δ and UME6HA/scf1Δ.

    “By DIC microscopy and SEM, the aggregation observed in UME6HA was still present in UME6HA/hgc1Δ but not in UME6HA/als4498Δ and UME6HA/scf1Δ (Fig. 1B and C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Compared to UME6HA, UME6HA/als4498Δ and UME6HA/scf1Δ exhibit a higher proportion of longer pseudohyphae (>10 μm), while this proportion is lower in UME6HA/hgc1Δ.

    “When compared to UME6HA, UME6HA/als4498Δ, and UME6HA/scf1Δ exhibited a higher proportion of longer pseudohyphae (>10 µm), while this proportion was lower in UME6HA/hgc1Δ (Fig. S2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The UME6HA colony morphology with irregular and wrinkled borders is conserved in UME6HA/scf1Δ but not in UME6HA/als4498Δ and UME6HA/hgc1Δ.

    “The morphological aspect of the UME6HA colony with irregular and wrinkled borders on solid agar was conserved in UME6HA/scf1Δ but not in UME6HA/als4498Δ and UME6HA/hgc1Δ (Fig. 1A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the first experiment, larvae infected with ume6Δ showed a modest but significant decrease in survival compared to IV.1, which was not reproduced in the second experiment.

    “We observed a modest, but significant, decrease of survival among larvae infected with ume6Δ compared to those infected with IV.1 in the first experiment (Fig. 8A), which was not reproduced in the second experiment (no significant difference, Fig. 8B).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Pseudohyphae formation in UME6HA is conserved in UME6HA/als4498Δ and UME6HA/scf1Δ, while it is abolished in UME6HA/hgc1Δ.

    “The ability of UME6HA to form pseudohyphae was conserved in UME6HA/als4498Δ and UME6HA/scf1Δ, while it was abolished in UME6HA/hgc1Δ (Fig. 1B and C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Compared to UME6HA, the proportion of pseudohyphae is higher in UME6HA/scf1Δ (41.6% vs 26.0%) and UME6HA/als4498Δ (34.0% vs 26.0%), while it is lower in UME6HA/hgc1Δ (15.3% vs 26.0%).

    “Compared to UME6HA, the proportion of pseudohyphae was higher in UME6HA/scf1Δ (41.6% vs 26.0%) and UME6HA/als4498Δ (34.0% vs 26.0%), while it was lower in UME6HA/hgc1Δ (15.3% vs 26.0%) (Fig. 2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Als4498 has a predominant role in biofilm formation, but not in adhesion to inert surfaces.

    “Interestingly, we found that Als4498 had a predominant role in biofilm formation, but not in adhesion to inert surfaces.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Following Ume6 hyperactivation, ALS4498 and SCF1 are drastically overexpressed (>1,000-fold) and HYR3 and IFF9 are overexpressed (10- to 100-fold).

    “Following Ume6 hyperactivation, we observed a drastic overexpression of ALS4498 and SCF1 (>1,000-fold) and, to a lesser extent, of HYR3 and IFF9 (10- to 100-fold), which suggests that these genes can be under the direct control of Ume6.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    ALS4498, SCF1, HYR3, and IFF9 can be under the direct control of Ume6.

    “Following Ume6 hyperactivation, we observed a drastic overexpression of ALS4498 and SCF1 (>1,000-fold) and, to a lesser extent, of HYR3 and IFF9 (10- to 100-fold), which suggests that these genes can be under the direct control of Ume6.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Hgc1 contributes to biofilm formation, possibly by promoting filamentation at the proliferation stage.

    “Hgc1 also contributes to biofilm formation, possibly by promoting filamentation at the proliferation stage.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Als4498 is important in biofilm formation by promoting intercellular adhesion and aggregation rather than adhesion to the inert surface.

    “Therefore, we postulate that Als4498 is important in biofilm formation by promoting intercellular adhesion and aggregation rather than adhesion to the inert surface, as this later mainly relies on Scf1.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Ume6 operates via distinct pathways in the control of morphogenesis in C. auris: aggregation via Als4498 and Scf1, and pseudofilamentation via Hgc1.

    “These results suggest that Ume6 operates via distinct pathways in the control of morphogenesis in C. auris. While its impact on aggregation is mediated via Als4498 and Scf1, its role in pseudofilamentation is mediated via Hgc1.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    C. auris biofilms are distinct from C. albicans biofilms and usually consist of yeast cells with a low amount of extracellular matrix.

    “C. auris biofilms are distinct from that of C. albicans and usually consist of yeast cells with a low amount of extracellular matrix (12).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [12] Khari A, Biswas B, Gangwar G, Thakur A, Puria R. 2023. Candida auris biofilm: a review on model to mechanism conservation. Expert Rev Anti Infect Ther 21: 295– 308. doi: 10.1080/14787210.2023.2179036 36755419 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Adhesion to fluorescent polystyrene microspheres as a readout for adhesion to hydrophobic surfaces can be analyzed by flow cytometry.

    “Adhesion to fluorescent polystyrene microspheres as a readout for adhesion to hydrophobic surfaces can be analyzed by flow cytometry as described previously (61).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [61] Silva-Dias A, Miranda IM, Rocha R, Monteiro-Soares M, Salvador A, Rodrigues AG, Pina-Vaz C. 2012. A novel flow cytometric protocol for assessment of yeast cell adhesion. Cytometry A 81: 265– 270. doi: 10.1002/cyto.a.21170 22076919 source

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Integration of the constructs was verified by PCR.

    “Integration of the constructs was verified by PCR (Fig. S12 to S25).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Data were acquired for at least 25,000 events per sample.

    “Data were acquired for at least 25,000 events/sample.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Events with a bright-field area >1 μm2 and non-saturating pixels were collected to exclude cell debris.

    “Events with a bright-field area >1 µm² (to exclude cell debris) and non-saturating pixels (Raw max pixel values below 4,096) were collected.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The crystal violet biofilm experiment was performed in technical triplicates and biological duplicates for each strain.

    “The experiment was performed in technical triplicates and biological duplicates for each strain.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Ume6 was shown to play a role in C. albicans virulence.

    “Moreover, while Ume6 was shown to play a role in C. albicans virulence (28, 42), we could not reproduce this impact in an insect model of C. auris infection.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [28] Banerjee M, Thompson DS, Lazzell A, Carlisle PL, Pierce C, Monteagudo C, López-Ribot JL, Kadosh D. 2008. UME6, a novel filament-specific regulator of Candida albicans hyphal extension and virulence. Mol Biol Cell 19: 1354– 1365. doi: 10.1091/mbc.e07-11-1110 18216277 PMC2291399 source
    • cites [42] Carlisle PL, Banerjee M, Lazzell A, Monteagudo C, López-Ribot JL, Kadosh D. 2009. Expression levels of a filament-specific transcriptional regulator are sufficient to determine Candida albicans morphology and virulence. Proc Natl Acad Sci U S A 106: 599– 604. doi: 10.1073/pnas.0804061106 19116272 PMC2626749 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    MICs in planktonic conditions were determined according to the CLSI protocol.

    “MICs in planktonic conditions were determined according to the CLSI protocol (41).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [41] 2017. Reference method for broth dilution antifungal susceptibility testing of yeasts, M27. 4th ed. Clinical and Laboratory Standards Institute, Wayne, PA.

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In the flow cytometry protocol, microspheres act as a surface to which yeast cells can adhere, enabling their quantification.

    “In this protocol, microspheres act as a surface to which yeast cells can adhere enabling their quantification.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [61] Silva-Dias A, Miranda IM, Rocha R, Monteiro-Soares M, Salvador A, Rodrigues AG, Pina-Vaz C. 2012. A novel flow cytometric protocol for assessment of yeast cell adhesion. Cytometry A 81: 265– 270. doi: 10.1002/cyto.a.21170 22076919 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    Single color controls for each fluorochrome were acquired to generate the compensation matrix that was applied to each sample prior to analysis.

    “Single color controls for each fluorochrome were acquired to generate the compensation matrix that was applied to each sample prior to analysis (63).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [63] Ortyn WE, Hall BE, George TC, Frost K, Basiji DA, Perry DJ, Zimmerman CA, Coder D, Morrissey PJ. 2006. Sensitivity measurement and compensation in spectral imaging. Cytometry A 69: 852– 862. doi: 10.1002/cyto.a.20306 16969805 source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Antifungal susceptibility testing was performed in biological duplicates and validated if results were similar (± one dilution).

    “Testing was performed in biological duplicates and validated if results were similar (± one dilution).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    RNA quality was assessed on a Fragment Analyzer with RNA quality numbers between 8.3 and 8.6.

    “RNA quality was assessed on Fragment Analyzer (Agilent Technologies, Santa Clara, CA) with RNA quality numbers between 8.3 and 8.6.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Samples were prepared in triplicates for each strain.

    “Samples were prepared in triplicates for each strain.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    MBECs in biofilm conditions were assessed by the XTT reduction assay as previously described, with minor modifications.

    “MBECs in biofilm conditions were assessed by the tetrazolium salt (XTT) reduction assay as previously described (66, 67), with minor modifications.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [66] Melo AS, Bizerra FC, Freymüller E, Arthington-Skaggs BA, Colombo AL. 2011. Biofilm production and evaluation of antifungal susceptibility amongst clinical Candida spp. isolates, including strains of the Candida parapsilosis complex. Med Mycol 49: 253– 262. doi: 10.3109/13693786.2010.530032 21039308 source
    • cites [67] Nett JE, Cain MT, Crawford K, Andes DR. 2011. Optimizing a Candida biofilm microtiter plate model for measurement of antifungal susceptibility by tetrazolium salt assay. J Clin Microbiol 49: 1426– 1433. doi: 10.1128/JCM.02273-10 21227984 PMC3122839 source
49 of 49

  • The paper relies on this without support.

    Transcription factors regulating morphogenesis are still unexplored in Candida auris.

    “However, transcription factors regulating morphogenesis are still unexplored in C. auris.”

  • The paper relies on this without support.

    DyeCycle Green Stain uptake identifies nucleated cells.

    “Cells were delineated based on the uptake of DyeCycle Green Stain, which identifies nucleated cells, characterized by their emission within the green fluorescence spectrum (λem ≈ 488 nm).”

  • The paper relies on this without support.

    Fluorescent microspheres' red fluorescence emission indicates bead binding to yeast cells.

    “Following initial gating on DyeCycle Green-positive events, cells were further analyzed for adherence to fluorescent microspheres characterized by their emission within the red fluorescence spectrum (λem ≈ 645 nm) indicating bead binding.”
3 of 3

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Certain Candida species can transition from yeast forms to filamentous structures, producing true hyphae in species like C. albicans, C. dubliniensis, and C. tropicalis, or pseudohyphae in species such as C. auris and C. parapsilosis.

    “Certain Candida species can transition from yeast forms to filamentous structures, producing true hyphae in species like C. albicans, C. dubliniensis, and C. tropicalis, or pseudohyphae in species such as C. auris and C. parapsilosis96–98.”

    From Distinct echinocandin responses of Candida albicans and Candida auris cell walls revealed by solid-state NMR (2025) · cites this paper as [98]

    The Introduction and Discussion (page numbers unavailable) describe C. auris transitioning to pseudohyphae and refer to true hyphae of C. albicans. The copy does not substantiate the claimed morphology of C. dubliniensis, C. tropicalis, or C. parapsilosis. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Aspect-ratio definition conflicts with classification thresholds

    Minor

    A major/minor axis ratio cannot be less than 1, yet the figure caption assigns budding cells ratios of 0.5-0.8 and pseudohyphae ratios below 0.5. The stated ratio definition and classification thresholds cannot both be correct.

  • Pseudohyphae persist despite being described as abolished

    Minor

    The paper says deleting HGC1 abolished pseudohyphae formation in UME6HA, but its imaging flow cytometry results report 15.3% pseudohyphae in that strain. The measured proportion is lower, not zero.

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. 2017. Reference method for broth dilution antifungal susceptibility testing of yeasts, M27. 4th ed. Clinical and Laboratory Standards Institute, Wayne, PA.

Cited by

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Related

Authors
Louvet, M., Li, J., Brandalise, D., Bachmann, D., Sala de Oyanguren, F., Labes, D., Jacquier, N., Genoud, C., Mucciolo, A., Coste, A. T., Sanglard, D., & Lamoth, F.
Affiliations
  • Centre Hospitalier Universitaire Vaudois (CH)
  • Flow Cytometry Facility, University of Lausanne, Lausanne, Switzerland
  • University of Lausanne (CH)
  • Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
ORCID
Venue
Microbiology Spectrum
Publisher
American Society for Microbiology
Published
2024-11-05
Volume
12
Issue
11
Pages
e0153124-e0153124
ISSN
2165-0497 (ISSN-L)
DOI
10.1128/spectrum.01531-24
PMC
PMC11537075
OpenAlex
W4402643083
Semantic Scholar
a54818c8e51dc6142e2255992657b429be7ef2c7
Cited by
20
References
67
Citations by year
2026: 8 · 2025: 12
FWCI
6.32
Type
journal article
Language
en
Open access
Licence
Locations
  • Microbiology Spectrum (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
  • SERVAL (Université de Lausanne) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • IRIS (submittedVersion, cc-by)
Funders
  • Swiss National Science Foundation (310030_192611)
  • Fondation Santos-Suarez pour la Recherche Médicale
  • Carigest
Topics
  • Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Yeasts and Rust Fungi Studies
Keywords
Candida auris, Ume6, morphogenesis, biofilm formation, filamentation, cell aggregation, transcriptional regulation, virulence factors, antifungal resistance, nosocomial infections, cell wall organization, sterol biosynthesis
MeSH terms
Candida auris, Candidiasis, Fungal Proteins, Humans, Morphogenesis, Transcription Factors, Virulence, Gene Expression Regulation, Fungal, Biofilms

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-20.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-20.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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