The paper by Anton and co-authors describes a new method of diagnostics for skin and nail infections. It is generally well organized and written.

I am concerned that the area of applicability of the assay is poorly defined. If the assay allows to identify Candida albicans, why the title refers to only dermatophyte infections? Yeasts and molds do not cause dermatophytosis (your Ref. 6). Should the title mention onychomycosis / skin and nail infections / superficial fungal infections? Please see Hay 2021 and your Ref. 1 for classification of conditions and etiological agents and come to conclusion what spectrum of diseases can be diagnosed with your approach. Obviously, limiting the taxonomic coverage of high-end assay to just one particular group of infectious agents does not seem attractive.

I checked the correctness of taxonomic identification of fungal cultures. The strain of Epidermophyton floccosum was identified correctly. The sequence AJ000625.1 belongs to Microsporum audouinii. The sequence LC535030.1 does seem to belong to Microsporum, but precise species identity cannot be inferred. My impression is that the sequence has multiple errors. The sequence LC413778.1 belongs to Trichophyton mentagrophytes / T. interdigitale genotype XXIV. The genotypes of the complex deserve attention because most recorded cases of recalcitrant dermatophytosis were associated with Trichophyton mentagrophytes / T. interdigitale genotype VIII, so-called “T. indotineae” (Langfeldt et al. 2022). Recently, this particular dermatophyte attracted attention of the designers of diagnostic assays (Batvandi et al. 2023; Yamada et al. 2023).

Major point (1). Identification of dermatophyte strains should be done at least to the species level. I recommend to obtain new ribosomal ITS region sequence of Microsporum strain MAOA5, deposit the sequence in the database, replace the accession LC535030 in the table with the new one and use in the text exact species name.

Major point (2). The taxonomic coverage of the assay must be broadened. Be it onychomycosis only or fungal skin infections in general, the spectrum of prevalent fungal pathogens is far broader then that one implemented in the assay. For example, see your Ref. 6 for a long list of nondermatophytic filamentous fungi. In the year 2023, an expensive and advanced assay is expected to identify T. mentagrophytes genotype VIII (Jabet et al. 2023), Fusarium (Landreau et al. 2023) and Candida parapsilosis (Faure-Cognet et al. 2016; Youssef et al. 2018) isolates . A very good decision would be to update the spectrum of targets on the basis of recent epidemiological literature. (Lines 260 and 339: Ref. 37 is not an original epidemiological study). Also, I recommend to supplement the panel with a pan-fungal probe. Pay attention to significant diversity of T. mentagrophytes / T. interdigitale ITS region sequences. Will your assay detect all the most prevalent genotypes? Implementation of the point should increase the sensitivity of the assay, as well as usability of its results.

Minor comments

On figure legends, change Dendris to DendrisCHIP®DP. If you are concerned with the appearance of registered sign, slightly enlarge the font. Do not use italics for the “spp” abbreviation and add a point at the end of it. Write “Trichophyton mentagrophytes / T. interdigitale” istead of “Trichophyton mentagrophytes / Trichophyton interdigitale” and “Score (%)” instead of “Score %”. In the caption, describe the method for error calculation. If possible, use vector graphics. In my personal experience, WMF file format worked well in embedding vector art into a DOCX file. For the X axes of different figures, use uniform font orientation.

Make figure captions self-sufficient, so that the content can be understood without reading the main text. It will include writing IC in full.

Table 1. Add a column with strain collection numbers.

Line 59. Usually, "gold-standard" is written without the hyphen.

Line 64 and further in the text. Use light font for reference numbers,

Lines 67-68. Cultural methods allow to track sources of infection. Please see your Ref. [5] for examples and amend the sentence.

Lines 79-80. “In addition, these methods also require technological expertise”. Something like “Some of these methods require technological expertise” would be more appropriate, since for laboratory technicians RT-PCR is a very simple method.

Line 86. “the difficulty of providing the diagnostic results”. Is it possible to be more specific on this point? Precisely what is the difficulty?

Lines 194, 195. Check spaces around equals signs.

Lines 428-429. Please also see the literature on erg1 mutations in Trichophyton.

Batvandi A, Pchelin IM, Kiasat N, Kharazi M, Mohammadi R, Zomorodian K, Rezaei-Matehkolaei A. Time and cost-efficient identification of Trichophyton indotineae. Mycoses. 2023 Jan;66(1):75-81. doi: 10.1111/myc.13530. Epub 2022 Sep 22. PMID: 36114817.

Faure-Cognet O, Fricker-Hidalgo H, Pelloux H, Leccia MT. Superficial Fungal Infections in a French Teaching Hospital in Grenoble Area: Retrospective Study on 5470 Samples from 2001 to 2011. Mycopathologia. 2016 Feb;181(1-2):59-66. doi: 10.1007/s11046-015-9953-7. Epub 2015 Oct 9. PMID: 26452757.

Hay R. Superficial fungal infections. 2021. https://doi.org/10.1016/j.mpmed.2021.08.006

Jabet A, Normand AC, Brun S, Dannaoui E, Bachmeyer C, Piarroux R, Hennequin C, Moreno-Sabater A. Trichophyton indotineae, from epidemiology to therapeutic. J Mycol Med. 2023 Aug;33(3):101383. doi: 10.1016/j.mycmed.2023.101383. Epub 2023 Mar 29. PMID: 37031652.

Landreau A, Simon L, Delaunay P, Pomares C, Hasseine L. Superficial fungal infections in the south of France-is fusariosis the next emergent onychopathy? Med Mycol. 2023 Feb 3;61(2):myad015. doi: 10.1093/mmy/myad015. PMID: 36758968.

Langfeldt A, Gold JAW, Chiller T. Emerging Fungal Infections: from the Fields to the Clinic, Resistant Aspergillus fumigatus and Dermatophyte Species: a One Health Perspective on an Urgent Public Health Problem. Curr Clin Microbiol Rep. 2022;9(4):46-51. doi: 10.1007/s40588-022-00181-3. Epub 2022 Sep 27. PMID: 36188157; PMCID: PMC9512973.

Yamada T, Nojo H, Kano R. Long Amplification PCR (LA-PCR) Detection of Azole Resistant Trichophyton indotineae. Mycopathologia. 2023 Sep 26. doi: 10.1007/s11046-023-00793-3. Epub ahead of print. PMID: 37751125.

Youssef AB, Kallel A, Azaiz Z, Jemel S, Bada N, Chouchen A, Belhadj-Salah N, Fakhfakh N, Belhadj S, Kallel K. Onychomycosis: Which fungal species are involved? Experience of the Laboratory of Parasitology-Mycology of the Rabta Hospital of Tunis. J Mycol Med. 2018 Dec;28(4):651-654. doi: 10.1016/j.mycmed.2018.07.005. Epub 2018 Aug 11. PMID: 30107987.