<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN" "http://jats.nlm.nih.gov/publishing/1.2/JATS-journalpublishing1.dtd"><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" article-type="other" dtd-version="1.2" xml:lang="en">
    <front>
        <journal-meta>
            <journal-id journal-id-type="pmc">F1000Research</journal-id>
            <journal-title-group>
                <journal-title>F1000Research</journal-title>
            </journal-title-group>
            <issn pub-type="epub">2046-1402</issn>
            <publisher>
                <publisher-name>F1000 Research Limited</publisher-name>
                <publisher-loc>London, UK</publisher-loc>
            </publisher>
        </journal-meta>
        <article-meta>
            <article-id pub-id-type="doi">10.12688/f1000research.141657.1</article-id>
            <article-categories>
                <subj-group subj-group-type="heading">
                    <subject>Study Protocol</subject>
                </subj-group>
                <subj-group>
                    <subject>Articles</subject>
                </subj-group>
            </article-categories>
            <title-group>
                <article-title>Study of molecular characterization for diagnosis of chronic and recurrent dermatophytosis</article-title>
                <fn-group content-type="pub-status">
                    <fn>
                        <p>[version 1; peer review: 2 approved with reservations]</p>
                    </fn>
                </fn-group>
            </title-group>
            <contrib-group>
                <contrib contrib-type="author" corresp="yes">
                    <name>
                        <surname>Warghade</surname>
                        <given-names>Aditi</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Conceptualization</role>
                    <role content-type="http://credit.niso.org/">Resources</role>
                    <role content-type="http://credit.niso.org/">Writing &#x2013; Review &amp; Editing</role>
                    <uri content-type="orcid">https://orcid.org/0000-0002-3970-8060</uri>
                    <xref ref-type="corresp" rid="c1">a</xref>
                    <xref ref-type="aff" rid="a1">1</xref>
                </contrib>
                <contrib contrib-type="author" corresp="yes">
                    <name>
                        <surname>Mudey</surname>
                        <given-names>Gargi</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Writing &#x2013; Original Draft Preparation</role>
                    <xref ref-type="corresp" rid="c2">b</xref>
                    <xref ref-type="aff" rid="a1">1</xref>
                </contrib>
                <aff id="a1">
                    <label>1</label>Department of Microbiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, Maharashtra, 442001, India</aff>
            </contrib-group>
            <author-notes>
                <corresp id="c1">
                    <label>a</label>
                    <email xlink:href="mailto:aditiwarghade1@gmail.com">aditiwarghade1@gmail.com</email>
                </corresp>
                <corresp id="c2">
                    <label>b</label>
                    <email xlink:href="mailto:gargi.microbiology@dmiher.edu.in">gargi.microbiology@dmiher.edu.in</email>
                </corresp>
                <fn fn-type="conflict">
                    <p>No competing interests were disclosed.</p>
                </fn>
            </author-notes>
            <pub-date pub-type="epub">
                <day>22</day>
                <month>2</month>
                <year>2024</year>
            </pub-date>
            <pub-date pub-type="collection">
                <year>2024</year>
            </pub-date>
            <volume>13</volume>
            <elocation-id>136</elocation-id>
            <history>
                <date date-type="accepted">
                    <day>18</day>
                    <month>10</month>
                    <year>2023</year>
                </date>
            </history>
            <permissions>
                <copyright-statement>Copyright: &#x00a9; 2024 Warghade A and Mudey G</copyright-statement>
                <copyright-year>2024</copyright-year>
                <license xlink:href="https://creativecommons.org/licenses/by/4.0/">
                    <license-p>This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
                </license>
            </permissions>
            <self-uri content-type="pdf" xlink:href="https://f1000research.com/articles/13-136/pdf"/>
            <abstract>
                <p>Dermatophytes are the keratinophilic fungi which infect humans and is the most recurring type of disease. The high level of transmissibility creates an epidemiological risk and emphasises the significance of these illnesses. However, a growing number of reports describing dermatophytes can cause deep infections in diabetic and immunocompromised patients, by invading deep layers like the dermis and hypodermis. Despite the prevalence and significance of dermatophytes in clinical mycology, it is not always possible to accurately diagnose this specific infection due to its overlapping structures among species of dermatophytes. Since it is difficult to identify species that exhibit weak characteristics in the morphological highlights, identification of the dermatophyte is often relied on its morphological analysis, which is a laborious process and demands skill. The massive shift in genetic variation, the source of infection, and epidemiological research can be discovered using molecular approaches. Therefore, the development of an accurate laboratory test for dermatophyte species identification is essential for the prevention and efficient management of dermatophytoses. One such methodology allows use of PCR technology which has many methods for molecular level characterization which is rapid, efficient, and capable of producing DNA polymorphisms specific to various dermatophyte species based on distinctive band patterns seen by agarose gel electrophoresis. The RAPD-PCR approach will be used in this study protocol to molecularly characterize the dermatophytes for precise speciation of the sample. In addition to improving knowledge of fungal biology and pathology with a focus on adaptive mechanisms to combat difficult conditions from host counteractions, there is a need to improve awareness of the importance of these diseases through accurate epidemiological data. The advantages of molecular approaches for characterizing objects over traditional methods are their sensitivity and specificity.</p>
            </abstract>
            <kwd-group kwd-group-type="author">
                <kwd>Dermatophytosis</kwd>
                <kwd>Molecular</kwd>
                <kwd>Characterisation</kwd>
                <kwd>RAPD-PCR</kwd>
                <kwd>Electrophoresis</kwd>
                <kwd>fungus</kwd>
                <kwd>keratinophilic</kwd>
                <kwd>Conventional</kwd>
            </kwd-group>
            <funding-group>
                <award-group id="fund-1">
                    <funding-source>Datta Meghe Institute of Higher Education and Research, Wardha, India</funding-source>
                </award-group>
                <funding-statement>An intramural grant from the Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha has been received. </funding-statement>
                <funding-statement>
                    <italic>The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</italic>
                </funding-statement>
            </funding-group>
        </article-meta>
    </front>
    <body>
        <sec id="sec1" sec-type="intro">
            <title>Introduction</title>
            <p>Different clinical symptoms caused by dermatophytes range from superficial to subcutaneous affliction, including tinea corporis, tinea capitis, tinea pedis, and tinea unguium.
                <sup>
                    <xref ref-type="bibr" rid="ref1">1</xref>
                </sup> These diseases can range in severity clinically from moderate to severe depending on the host's immune system, the virulence of the strain, and other environmental factors.
                <sup>
                    <xref ref-type="bibr" rid="ref2">2</xref>
                </sup>
                <sup>&#x2013;</sup>
                <sup>
                    <xref ref-type="bibr" rid="ref4">4</xref>
                </sup> Although dermatophytoses harm people throughout, they are more common in tropical regions due to high temperatures and humidity.
                <sup>
                    <xref ref-type="bibr" rid="ref5">5</xref>
                </sup> Age, sex, time of year, socioeconomic and cultural circumstances, and geographic location are all factors that might influence the development of dermatophytosis.
                <sup>
                    <xref ref-type="bibr" rid="ref6">6</xref>
                </sup> Potassium hydroxide (KOH) direct microscopy followed by selective medium culture is the standard procedure for dermatophyte screening in clinical samples. A quick screening technique for fungal structures is microscopy performed directly on clinical specimens, but this method lacks specificity.
                <sup>
                    <xref ref-type="bibr" rid="ref7">7</xref>
                </sup> By using phenotypic techniques, dermatophyte isolates can be classified according to genus or species based on colony characteristics, microscopic assessments, and biochemical tests like growth patterns.
                <sup>
                    <xref ref-type="bibr" rid="ref8">8</xref>
                </sup> Because there are changes from one isolate to another and overlaps in the features of several species, dermatophyte species identification by morphology in cultures may be difficult or imprecise.
                <sup>
                    <xref ref-type="bibr" rid="ref9">9</xref>
                </sup> Molecular-based methods rely on identifying genotypic variations in pathogenic organisms.
                <sup>
                    <xref ref-type="bibr" rid="ref10">10</xref>
                </sup>
                <sup>&#x2013;</sup>
                <sup>
                    <xref ref-type="bibr" rid="ref12">12</xref>
                </sup> Molecular methods are being used to identify dermatophytes since they are more precise than conventional techniques.
                <sup>
                    <xref ref-type="bibr" rid="ref13">13</xref>
                </sup> The development of molecular diagnostics were encouraged by the conventional techniques for identifying dermatophytes which are imprecise and have a delayed diagnostic character. Techniques that permit for both the early and accurate detection of dermatophytosis in order to provide timely antifungal treatment that prevents generic over-the-counter medication.
                <sup>
                    <xref ref-type="bibr" rid="ref14">14</xref>
                </sup> Therefore, it is essential to create more reliable dermatophyte identification techniques.
                <sup>
                    <xref ref-type="bibr" rid="ref15">15</xref>
                </sup> The current study's objective is to utilize RAPD-PCR method to identify and distinguish between the strains of fungi present in clinical isolates that cause chronic recurrent dermatophytosis.</p>
        </sec>
        <sec id="sec2">
            <title>Protocol</title>
            <sec id="sec3">
                <title>Study design</title>
                <p>
                    <italic toggle="yes">Case control study</italic> (observational study). Study participants: 100 participants having skin lesions, hair and nail positive for dermatophytic infection will be included in the study.</p>
            </sec>
            <sec id="sec4">
                <title>Study setting</title>
                <p>
                    <list list-type="bullet">
                        <list-item>
                            <label>&#x2022;</label>
                            <p>Samples (Skin scrapings, hair, nail clipping) will be collected from the patients visiting Dermatology OPD, Acharya Vinoba Bhave Rural Hospital, Sawangi (Meghe), Wardha.</p>
                        </list-item>
                        <list-item>
                            <label>&#x2022;</label>
                            <p>Samples will be processed in the Department of Microbiology, Jawaharlal Nehru Medical College, Sawangi (Meghe), Wardha.</p>
                        </list-item>
                        <list-item>
                            <label>&#x2022;</label>
                            <p>Method of selection of participants:</p>
                            <list list-type="order">
                                <list-item>
                                    <label>1.</label>
                                    <p>Patients having skin lesions will be included for taking the skin scrapings.</p>
                                </list-item>
                                <list-item>
                                    <label>2.</label>
                                    <p>Patients with hair infections positive for fungal infection will be included for hair plucking.</p>
                                </list-item>
                                <list-item>
                                    <label>3.</label>
                                    <p>Patients with nail infection will be considered for nail clippings.</p>
                                </list-item>
                            </list>
                            <p>All the samples will be collected in a black paper and stored in sterile container with proper labeling for further process.</p>
                        </list-item>
                    </list>
                </p>
            </sec>
            <sec id="sec5">
                <title>Eligibility criteria</title>
                <p>Patients having visible lesions and itching, positive for fungal infections are included in the study.</p>
            </sec>
            <sec id="sec6">
                <title>Data management</title>
                <p>Samples will be collected directly from the patients and reports will be obtained from the microbiology laboratory. Data of all patients will be entered in 
                    <ext-link ext-link-type="uri" xlink:href="https://www.microsoft.com/en-gb/microsoft-365/excel">Microsoft Excel</ext-link> taking proper precautions for wrapping the patient identifier information. The final deidentified data will be shared with statistician for further analysis.</p>
            </sec>
            <sec id="sec7">
                <title>Sample size</title>
                <p>Sensitivity formula for calculating the sample size.
                    <disp-formula id="e1">
                        <mml:math display="block">
                            <mml:mi mathvariant="normal">N</mml:mi>
                            <mml:mo>&#x2265;</mml:mo>
                            <mml:msubsup>
                                <mml:mi mathvariant="normal">Z</mml:mi>
                                <mml:munder accentunder="true">
                                    <mml:mrow>
                                        <mml:mn>1</mml:mn>
                                        <mml:mo>&#x2212;</mml:mo>
                                        <mml:mi mathvariant="normal">&#x03b1;</mml:mi>
                                        <mml:mo>/</mml:mo>
                                        <mml:mn>2</mml:mn>
                                    </mml:mrow>
                                    <mml:mo stretchy="true">&#x00af;</mml:mo>
                                </mml:munder>
                                <mml:munder accentunder="true">
                                    <mml:mn>2</mml:mn>
                                    <mml:mo stretchy="true">&#x00af;</mml:mo>
                                </mml:munder>
                            </mml:msubsup>
                            <mml:mfrac>
                                <mml:mrow>
                                    <mml:mtext>Sens</mml:mtext>
                                    <mml:mspace width="0.12em"/>
                                    <mml:mfenced close=")" open="(">
                                        <mml:mrow>
                                            <mml:mn>1</mml:mn>
                                            <mml:mo>&#x2212;</mml:mo>
                                            <mml:mtext>Sens</mml:mtext>
                                        </mml:mrow>
                                    </mml:mfenced>
                                </mml:mrow>
                                <mml:mrow>
                                    <mml:msup>
                                        <mml:mi>d</mml:mi>
                                        <mml:mn>2</mml:mn>
                                    </mml:msup>
                                    <mml:mo>&#x00d7;</mml:mo>
                                    <mml:mo mathvariant="italic">Pr</mml:mo>
                                    <mml:mi mathvariant="italic">ev</mml:mi>
                                </mml:mrow>
                            </mml:mfrac>
                        </mml:math>
                    </disp-formula>
                </p>
                <p>Alpha (&#x03b1;) 0.05</p>
                <p>Estimated sensitivity (Sens) 
                    <underline>0.95</underline>
                </p>
                <p>Prevalence of disease (Prev) 
                    <underline>0.79</underline>
                </p>
                <p>Estimated error (d) 
                    <underline>0.05</underline>
                </p>
                <p>Minimum number of diseases needed: 73</p>
                <p>Minimum total sample size needed: 93</p>
            </sec>
            <sec id="sec8">
                <title>Reagents required</title>
                <p>
                    <list list-type="order">
                        <list-item>
                            <label>1.</label>
                            <p>Culture media Sabouraud Dextrose Agar (SDA)</p>
                        </list-item>
                        <list-item>
                            <label>2.</label>
                            <p>Culture media Sabouraud Chloramphenicol + Cycloheximide Agar</p>
                        </list-item>
                        <list-item>
                            <label>3.</label>
                            <p>Culture media Dermatophyte Agar Base</p>
                        </list-item>
                        <list-item>
                            <label>4.</label>
                            <p>Dermato Supplement</p>
                        </list-item>
                        <list-item>
                            <label>5.</label>
                            <p>Culture Media Corn meal agar</p>
                        </list-item>
                        <list-item>
                            <label>6.</label>
                            <p>Distilled Water</p>
                        </list-item>
                        <list-item>
                            <label>7.</label>
                            <p>Potassium Hydroxide Pellets</p>
                        </list-item>
                        <list-item>
                            <label>8.</label>
                            <p>Normal Saline</p>
                        </list-item>
                        <list-item>
                            <label>9.</label>
                            <p>10% Glycerol</p>
                        </list-item>
                        <list-item>
                            <label>10.</label>
                            <p>Lactophenol Cotton Blue Stain</p>
                        </list-item>
                        <list-item>
                            <label>11.</label>
                            <p>Polyvinyl Alcohol</p>
                        </list-item>
                        <list-item>
                            <label>12.</label>
                            <p>Ethyl Alcohol</p>
                        </list-item>
                        <list-item>
                            <label>13.</label>
                            <p>Sodium Hypochlorite Solution</p>
                        </list-item>
                        <list-item>
                            <label>14.</label>
                            <p>dNTP mix, 40mM</p>
                        </list-item>
                        <list-item>
                            <label>15.</label>
                            <p>Hi-Temp PCR Master mix</p>
                        </list-item>
                        <list-item>
                            <label>16.</label>
                            <p>Primers</p>
                        </list-item>
                        <list-item>
                            <label>17.</label>
                            <p>AllPrep&#x00ae; Fungal DNA isolation kit</p>
                        </list-item>
                        <list-item>
                            <label>18.</label>
                            <p>PCR Block Plates</p>
                        </list-item>
                        <list-item>
                            <label>19.</label>
                            <p>Pipette</p>
                        </list-item>
                        <list-item>
                            <label>20.</label>
                            <p>Pipette tips (10&#x03bc;l, 20&#x03bc;l, 100&#x03bc;l, 1000&#x03bc;l)</p>
                        </list-item>
                        <list-item>
                            <label>21.</label>
                            <p>Microscopic glass slides</p>
                        </list-item>
                        <list-item>
                            <label>22.</label>
                            <p>Coverslip</p>
                        </list-item>
                        <list-item>
                            <label>23.</label>
                            <p>Inoculating loop</p>
                        </list-item>
                        <list-item>
                            <label>24.</label>
                            <p>Teasing needle</p>
                        </list-item>
                        <list-item>
                            <label>25.</label>
                            <p>Petri dishes</p>
                        </list-item>
                        <list-item>
                            <label>26.</label>
                            <p>Forceps</p>
                        </list-item>
                        <list-item>
                            <label>27.</label>
                            <p>Glass Beakers</p>
                        </list-item>
                        <list-item>
                            <label>28.</label>
                            <p>Flasks</p>
                        </list-item>
                        <list-item>
                            <label>29.</label>
                            <p>Glass rod</p>
                        </list-item>
                        <list-item>
                            <label>30.</label>
                            <p>Bunsen Burner</p>
                        </list-item>
                        <list-item>
                            <label>31.</label>
                            <p>Gel electrophoresis chamber</p>
                        </list-item>
                    </list>
                </p>
            </sec>
            <sec id="sec9">
                <title>Instruments required</title>
                <p>
                    <list list-type="order">
                        <list-item>
                            <label>1.</label>
                            <p>Light Microscope</p>
                        </list-item>
                        <list-item>
                            <label>2.</label>
                            <p>Autoclave</p>
                        </list-item>
                        <list-item>
                            <label>3.</label>
                            <p>PCR</p>
                        </list-item>
                        <list-item>
                            <label>4.</label>
                            <p>Biosafety Cabinet</p>
                        </list-item>
                        <list-item>
                            <label>5.</label>
                            <p>Biological Oxygen Demand (BOD) Incubator</p>
                        </list-item>
                        <list-item>
                            <label>6.</label>
                            <p>Electronic Weighing Machine</p>
                        </list-item>
                    </list>
                </p>
            </sec>
            <sec id="sec10">
                <title>Protocol</title>
                <p>
                    <list list-type="alpha-upper">
                        <list-item>
                            <label>A.</label>
                            <p>
                                <underline>Sample collection</underline>
                            </p>
                            <list list-type="order">
                                <list-item>
                                    <label>1.</label>
                                    <p>The area of sample collection will be cleaned with 70% alcohol.</p>
                                </list-item>
                                <list-item>
                                    <label>2.</label>
                                    <p>For skin samples, the lesion will be scraped around the corners using a scalpel blade or glass slide.</p>
                                </list-item>
                                <list-item>
                                    <label>3.</label>
                                    <p>For nail samples, the nail clippings will be collected using a nail cutter in a sterile container</p>
                                </list-item>
                                <list-item>
                                    <label>4.</label>
                                    <p>For hair samples, the hair will be plucked from the shaft of the hair having a lesion.</p>
                                </list-item>
                            </list>
                        </list-item>
                        <list-item>
                            <label>B.</label>
                            <p>
                                <underline>Sample processing</underline>
                            </p>
                            <list list-type="order">
                                <list-item>
                                    <label>1.</label>
                                    <p>The skin scrapings will be dissolved in 10% KOH and nail clippings will be dissolved in 40% KOH for microscopic observation.</p>
                                </list-item>
                                <list-item>
                                    <label>2.</label>
                                    <p>Samples will be inoculated on Dermatophyte Test Medium (DTM) as well as Sabouraud's dextrose agar (SDA) containing chloramphenicol and cycloheximide.</p>
                                </list-item>
                                <list-item>
                                    <label>3.</label>
                                    <p>Samples will be incubated in BOD incubator, for observation of growth on the SDA and DTM slants.</p>
                                </list-item>
                                <list-item>
                                    <label>4.</label>
                                    <p>Lactophenol cotton blue staining and slide culture technique will be used to view morphology and colony characteristics of the samples after growth.</p>
                                </list-item>
                            </list>
                        </list-item>
                        <list-item>
                            <label>C.</label>
                            <p>
                                <underline>Application of RAPD-PCR method for molecular characterization</underline>
                            </p>
                            <list list-type="order">
                                <list-item>
                                    <label>1.</label>
                                    <p>Standardization of molecular assay will be done using the standard strains of Trichophyton (D15P127, CBS 118892, UCMS-IGIB-CI11), Microsporum (ATCC 36299), and laboratory-confirmed strains.</p>
                                </list-item>
                                <list-item>
                                    <label>2.</label>
                                    <p>AllPrep&#x00ae; Fungal DNA isolation kit will be used for DNA isolation from fungal cultures.</p>
                                </list-item>
                                <list-item>
                                    <label>3.</label>
                                    <p>The primer required for the RAPD-PCR reaction will be synthesized by Beacon designer probe/primer designer software from GeneX India Biosciences Velachery, Chennai, Tamil Nadu.</p>
                                </list-item>
                                <list-item>
                                    <label>4.</label>
                                    <p>PCR assay mixture, reaction buffer, dNTPs, each primer set (GACA4) and novel primer (CTGT3), DNA template, using these PCR reaction cycles will be carried out.</p>
                                    <p>(39 cycles)</p>
                                    <list list-type="alpha-lower">
                                        <list-item>
                                            <label>a)</label>
                                            <p>Denaturation at 93&#x00b0; - 1-minute,</p>
                                        </list-item>
                                        <list-item>
                                            <label>b)</label>
                                            <p>Annealing step at 50&#x00b0; -1-minute,</p>
                                        </list-item>
                                        <list-item>
                                            <label>c)</label>
                                            <p>-Extension step at 72&#x00b0;- 1 minute</p>
                                        </list-item>
                                        <list-item>
                                            <label>d)</label>
                                            <p>Final-extension step at 72&#x00b0;- 7 min</p>
                                        </list-item>
                                    </list>
                                </list-item>
                                <list-item>
                                    <label>5.</label>
                                    <p>Final PCR products will be separated in 0.5X (Tris Borate-Ethylene diamine tetraacetic acid) Buffer and 1% Agarose and stained with the Ethidium-Bromide solution and then the image will be obtained.</p>
                                </list-item>
                                <list-item>
                                    <label>6.</label>
                                    <p>Interspecies and intraspecies patterns and polymorphism for known strains will be studied.</p>
                                </list-item>
                            </list>
                        </list-item>
                    </list>
                </p>
            </sec>
            <sec id="sec11">
                <title>Statistical analysis plan</title>
                <p>All the results will be calculated using R version 4.3.2. Patients enrolled in the study sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV) will be resulted from molecular methods used in comparison to the conventional method (gold standard).</p>
                <p>Categorical variable will be summarized by the samples positive for fungal hyphae in KOH and culture on SDA (Sabouraud Dextrose Agar) and Dermatophyte Test Medium (DTM).</p>
                <p>The percentage of agreement (overall, positive, and negative) between the two methods will be calculated using agreement analysis (primary and secondary endpoints), along with the Kappa coefficient, p-value, and 95% confidence interval.</p>
                <p>
                    <bold>Dissemination</bold>
                </p>
                <p>Papers will be presented at relevant conferences and related studies will be published in indexed journals.</p>
            </sec>
            <sec id="sec12">
                <title>Study status</title>
                <p>This research is ongoing. Using previously used primers, we are validating the protocol. The instruments, reagents, enzymes, and primers are set up. Clinical sample collection and processing of the sample by conventional method and standardization of molecular methods for the identification of species is ongoing.</p>
            </sec>
            <sec id="sec13">
                <title>Ethical considerations</title>
                <p>This study has been granted by the ethics committee of Datta Meghe Institute of Higher Education and Research, Sawangi Meghe, Wardha with the approval number: DMIMS (DU)/IEC/2022/851, dated: 05/04/2022.</p>
                <p>Written informed consent will be obtained from the study participants for participation in the study and publication of their data.</p>
            </sec>
        </sec>
        <sec id="sec14" sec-type="discussion">
            <title>Discussion</title>
            <p>Fungal infections in humans are becoming more common, especially in immunocompromised people, which has made them a global public health concern. The course of the disease, which can range from mild cutaneous or subcutaneous infections to invasive, widespread, and potentially fatal infections, is determined by the immunological health of the host.
                <sup>
                    <xref ref-type="bibr" rid="ref16">16</xref>
                </sup> For epidemiological reasons, accurate antifungal treatment prevention of transmission includes exact separation between dermatophytosis and non-dermatophyte, and thorough identification of disease-causing organisms is vital.
                <sup>
                    <xref ref-type="bibr" rid="ref17">17</xref>
                </sup>
                <sup>,</sup>
                <sup>
                    <xref ref-type="bibr" rid="ref18">18</xref>
                </sup> The most reliable approach to diagnose dermatophytosis is through the isolation and identification of dermatophytes from clinical samples. However, it typically takes a long time for the dermatophyte to grow in culture and sporulate, which delays diagnosis. Successful management of dermatophytes depends on prompt diagnosis and correct identification.
                <sup>
                    <xref ref-type="bibr" rid="ref19">19</xref>
                </sup> A study from Sweden by Ovr&#x00e9;n, E 
                <italic toggle="yes">et al.</italic> (2016) stated fluorescent staining method enhances the sensitivity and specificity in direct microscopy from skin, hair and nail samples and found that the specificity = (91.7&#x2013;93.8%), positive predictive value (PPV) = (77.1&#x2013;81.4%) and negative predictive value (NPV) = (83.7&#x2013;89.9%).
                <sup>
                    <xref ref-type="bibr" rid="ref20">20</xref>
                </sup> Molecular methods are available for the characterization of the dermatophyte species namely restriction fragment length polymorphism (RFLP), (random amplified polymorphic DNA (RAPD), gene-specific-PCR,
                <sup>
                    <xref ref-type="bibr" rid="ref21">21</xref>
                </sup>
                <sup>,</sup>
                <sup>
                    <xref ref-type="bibr" rid="ref22">22</xref>
                </sup> chitin synthase encoding gene,
                <sup>
                    <xref ref-type="bibr" rid="ref23">23</xref>
                </sup> DNA hybridization,
                <sup>
                    <xref ref-type="bibr" rid="ref24">24</xref>
                </sup> and sequencing of the internal transcribed spacer region (ITS).
                <sup>
                    <xref ref-type="bibr" rid="ref7">7</xref>
                </sup>
                <sup>,</sup>
                <sup>
                    <xref ref-type="bibr" rid="ref25">25</xref>
                </sup> A study by Li, H. C., Bouchara 
                <italic toggle="yes">et al.</italic> (2007) from the United Kingdom stated the use of oligonucleotide array based on ITS-1 and ITS-2 sequence for identification of 17-dermatophyte species subsequently, hybridization of a series of oligonucleotides (17&#x2013;30mers) digoxigenin-labeled PCR products immobilized on a nylon membrane of the 198 clinical dermal filamentous strains tested and 90 non-targeted strains, the array sensitivity and specificity were 99.5% and 97.8%, respectively.
                <sup>
                    <xref ref-type="bibr" rid="ref26">26</xref>
                </sup> Many molecular methods have made a way for early detection of dermatophytes to the species level. Along with these techniques serological methods have also detected the dermatophyte infection in the studies stated. A study by Higashi, Y 
                <italic toggle="yes">et al</italic>. (2012) from Japan stated that the use of newly developed immunochromatographic strip-test for the diagnosis of dermatophytes found the overall sensitivity and specificity of the immunochromatographic test were 83.5% and 66.7%.
                <sup>
                    <xref ref-type="bibr" rid="ref27">27</xref>
                </sup>
            </p>
        </sec>
    </body>
    <back>
        <sec id="sec17" sec-type="data-availability">
            <title>Data availability</title>
            <p>No data are associated with this article.</p>
        </sec>
        <ack>
            <title>Acknowledgments</title>
            <p>We would like to acknowledge Department of Microbiology, JNMC and Central Research Laboratory (CRL) for their support.</p>
        </ack>
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    <sub-article article-type="reviewer-report" id="report256151">
        <front-stub>
            <article-id pub-id-type="doi">10.5256/f1000research.155121.r256151</article-id>
            <title-group>
                <article-title>Reviewer response for version 1</article-title>
            </title-group>
            <contrib-group>
                <contrib contrib-type="author">
                    <name>
                        <surname>Panda</surname>
                        <given-names>Saumya</given-names>
                    </name>
                    <xref ref-type="aff" rid="r256151a1">1</xref>
                    <role>Referee</role>
                    <uri content-type="orcid">https://orcid.org/0000-0002-8020-0330</uri>
                </contrib>
                <aff id="r256151a1">
                    <label>1</label>Jagannath Gupta Institute of Medical Sciences and Hospital, Kolkata, West Bengal, India</aff>
            </contrib-group>
            <author-notes>
                <fn fn-type="conflict">
                    <p>
                        <bold>Competing interests: </bold>No competing interests were disclosed.</p>
                </fn>
            </author-notes>
            <pub-date pub-type="epub">
                <day>14</day>
                <month>5</month>
                <year>2024</year>
            </pub-date>
            <permissions>
                <copyright-statement>Copyright: &#x00a9; 2024 Panda S</copyright-statement>
                <copyright-year>2024</copyright-year>
                <license xlink:href="https://creativecommons.org/licenses/by/4.0/">
                    <license-p>This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
                </license>
            </permissions>
            <related-article ext-link-type="doi" id="relatedArticleReport256151" related-article-type="peer-reviewed-article" xlink:href="10.12688/f1000research.141657.1"/>
            <custom-meta-group>
                <custom-meta>
                    <meta-name>recommendation</meta-name>
                    <meta-value>approve-with-reservations</meta-value>
                </custom-meta>
            </custom-meta-group>
        </front-stub>
        <body>
            <p>This is an interesting and relevant protocol, given that there is an epidemic of chronic and recurrent dermatophytosis that is currently ongoing in our country as well as in several other countries and regions in the world. However, the protocol suffers from some serious lapses:</p>
            <p> 1.&#x00a0;The protocol is titled as 'Study of molecular characterization for diagnosis of chronic and recurrent dermatophytosis'. However, the sampling methods and selection criteria of the cases do not mention these conditions at all!</p>
            <p> 2. Study design is mentioned as 'case control'. However, there is no description of the control group. The description matches that of a cross-sectional study, which is what it should be.</p>
            <p> 3. In sample size estimation, there is no reference to the prevalence value that has been taken, thus making the whole exercise infructuous.</p>
            <p> 4. The basic rationale of the study has not been mentioned - the current epidemic of recalcitrant dermatophytosis is due to the emergence of a new species called 
                <italic>Trichophyton indotineae</italic>, which is morphologically and culturally indistinguishable from&#x00a0;
                <italic>Trichohyton mentagrophytes</italic>&#x00a0;and&#x00a0;
                <italic>Trichophyton interdigitale.</italic>&#x00a0;Thus its identification requires advanced molecular diagnostics like ITS genotyping or modified MALDI-TOF, which are not frequently available.</p>
            <p>Is the study design appropriate for the research question?</p>
            <p>No</p>
            <p>Is the rationale for, and objectives of, the study clearly described?</p>
            <p>Partly</p>
            <p>Are sufficient details of the methods provided to allow replication by others?</p>
            <p>Yes</p>
            <p>Are the datasets clearly presented in a useable and accessible format?</p>
            <p>Not applicable</p>
            <p>Reviewer Expertise:</p>
            <p>Dermatology</p>
            <p>I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.</p>
        </body>
        <sub-article article-type="response" id="comment11930-256151">
            <front-stub>
                <contrib-group>
                    <contrib contrib-type="author">
                        <name>
                            <surname>Warghade</surname>
                            <given-names>Aditi</given-names>
                        </name>
                        <aff>Department of Microbiology, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha., Wardha, Maharashtra, India</aff>
                    </contrib>
                </contrib-group>
                <author-notes>
                    <fn fn-type="conflict">
                        <p>
                            <bold>Competing interests: </bold>Competing interests-none</p>
                    </fn>
                </author-notes>
                <pub-date pub-type="epub">
                    <day>29</day>
                    <month>6</month>
                    <year>2024</year>
                </pub-date>
            </front-stub>
            <body>
                <p>Respected Madam,</p>
                <p> Thank you for considering our manuscript and suggesting the following changes to be processed for further publication in F1000 research subject to a satisfactory revision as per your suggestions. We have made the changes in our manuscript. Please consider the following changes.</p>
                <p> </p>
                <p> This is an interesting and relevant protocol, given that there is an epidemic of chronic and recurrent dermatophytosis that is currently ongoing in our country as well as in several other countries and regions in the world. However, the protocol suffers from some serious lapses:</p>
                <p> 1.&#x00a0;The protocol is titled as 'Study of molecular characterization for diagnosis of chronic and recurrent dermatophytosis'. However, the sampling methods and selection criteria of the cases do not mention these conditions at all!</p>
                <p> 
                    <bold>Answer</bold>: Thank you for the suggestion mam. We have changed our title to "Diagnosis and Molecular Characterization of Dermatophytosis: An Observational Study". Track changes enabled and highlighted for the same.</p>
                <p> </p>
                <p> 2. Study design is mentioned as 'case-control'. However, there is no description of the control group. The description matches that of a cross-sectional study, which is what it should be.</p>
                <p> 
                    <bold>Answer</bold>: Thank you for the suggestion, mam. We have stated the study design as an observational study as suggested.</p>
                <p> </p>
                <p> 3. In sample size estimation, there is no reference to the prevalence value taken, thus making the whole exercise infructuous.</p>
                <p> 
                    <bold>Answer</bold>: Thank you for the suggestion mam. Mistakenly the study wasn&#x2019;t added in the prevalence section. I have corrected the draft and added the study with Ref no-3 and highlighted the citation as it is not getting added in the reference list in sequence.</p>
                <p> </p>
                <p> 4. The basic rationale of the study has not been mentioned - the current epidemic of recalcitrant dermatophytosis is due to the emergence of a new species called&#x00a0;
                    <italic>Trichophyton indotineae</italic>, which is morphologically and culturally indistinguishable from&#x00a0;
                    <italic>Trichophyton mentagrophytes</italic>&#x00a0;and&#x00a0;
                    <italic>Trichophyton interdigitale.</italic>&#x00a0;Thus its identification requires advanced molecular diagnostics like ITS genotyping or modified MALDI-TOF, which are not frequently available.</p>
                <p> 
                    <bold>Answer</bold>: Thank you for the suggestion, mam. I have added the reference information in the draft and quoted it as Ref no 1&amp;2.</p>
            </body>
        </sub-article>
    </sub-article>
    <sub-article article-type="reviewer-report" id="report251787">
        <front-stub>
            <article-id pub-id-type="doi">10.5256/f1000research.155121.r251787</article-id>
            <title-group>
                <article-title>Reviewer response for version 1</article-title>
            </title-group>
            <contrib-group>
                <contrib contrib-type="author">
                    <name>
                        <surname>Aboul-Ella</surname>
                        <given-names>Hassan</given-names>
                    </name>
                    <xref ref-type="aff" rid="r251787a1">1</xref>
                    <role>Referee</role>
                </contrib>
                <aff id="r251787a1">
                    <label>1</label>Cairo University, Giza, Giza Governorate, Egypt</aff>
            </contrib-group>
            <author-notes>
                <fn fn-type="conflict">
                    <p>
                        <bold>Competing interests: </bold>No competing interests were disclosed.</p>
                </fn>
            </author-notes>
            <pub-date pub-type="epub">
                <day>27</day>
                <month>3</month>
                <year>2024</year>
            </pub-date>
            <permissions>
                <copyright-statement>Copyright: &#x00a9; 2024 Aboul-Ella H</copyright-statement>
                <copyright-year>2024</copyright-year>
                <license xlink:href="https://creativecommons.org/licenses/by/4.0/">
                    <license-p>This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
                </license>
            </permissions>
            <related-article ext-link-type="doi" id="relatedArticleReport251787" related-article-type="peer-reviewed-article" xlink:href="10.12688/f1000research.141657.1"/>
            <custom-meta-group>
                <custom-meta>
                    <meta-name>recommendation</meta-name>
                    <meta-value>approve-with-reservations</meta-value>
                </custom-meta>
            </custom-meta-group>
        </front-stub>
        <body>
            <p>The current work describes a protocol for an observational study through collecting samples from dermatophytes-suffering patients followed by conventional and molecular diagnostic process, the obtained data will be very useful in improving and updating the epidemiological data in this field.&#x00a0; &#x00a0;&#x00a0;</p>
            <p> </p>
            <p> 
                <underline>
                    <bold>General comments</bold>
                </underline>
            </p>
            <p> </p>
            <p> While the&#x00a0;research focuses on an encouraging area of research and addresses an area of study with minimal existing&#x00a0;research, it requires substantial editing of vocabulary in English especially in the following sections; abstract, introduction, and discussion.</p>
            <p> </p>
            <p> 
                <underline>
                    <bold>Specific comments</bold>
                </underline>
            </p>
            <p> </p>
            <p> - The title needs certain modifications to be more representable for the designed study. Therefore, I suggest "Diagnosis and molecular characterization of dermatophytosis: an observational study"</p>
            <p> </p>
            <p> - The abstract, introduction, and methodological protocol sections are well designed, structured, and described.&#x00a0;&#x00a0;</p>
            <p> </p>
            <p> - The discussion is missing certain necessary references to support the flow of the work and the researcher point of view in the following points;</p>
            <p> </p>
            <p> 
                <bold>1)</bold>&#x00a0;The most reliable approach to diagnose dermatophytosis is through the isolation and identification of dermatophytes from clinical samples. However, it typically takes a long time for the dermatophyte to grow in culture and sporulate, which delays diagnosis.&#x00a0;</p>
            <p> - The suggested [Ref 2]
                <bold>&#x00a0;</bold>in which a culture-dependent cross sectional study has been performed on dermatophytosis showing the importance of culture in dermatophytosis diagnosis as well as the extend of to which extend this technique is laborious and time consuming and that will support the researcher point of view.&#x00a0;</p>
            <p> </p>
            <p> 
                <bold>2)</bold>&#x00a0;&#x00a0;Many molecular methods have made a way for early detection of dermatophytes to the species level.</p>
            <p> - The suggested [Ref 3]
                <bold>&#x00a0;</bold>in which a comprehensive&#x00a0;and collective mentioning and illustration of the molecular advancement and molecular diagnostic techniques that is have been developed in the field of dermatophytosis and the extend of the diagnostic level of those techniques and that of course will strongly support the researcher point of view.&#x00a0;</p>
            <p> </p>
            <p> 
                <bold>3)&#x00a0;</bold>A study by Higashi, Y&#x00a0;
                <italic>et al</italic>. (2012) from Japan stated that the use of newly developed immunochromatographic strip-test for the diagnosis of dermatophytes found the overall sensitivity and specificity of the immunochromatographic test were 83.5% and 66.7%.&#x00a0;</p>
            <p> - The suggested [Ref 1]&#x00a0;with all respect of the cited study as Higashi 
                <italic>et al. </italic>2012, study in the field of immunochromatographic diagnosis of dermatophytosis is really a pioneering study in this field but to be more accurate and more updated I suggest adding the suggested reference in addition to the Higashi 
                <italic>et al. </italic>2012, study as the suggested reference represents a newest designed and developed immunochromatographic assay for dermatophytosis diagnosis with a competitive results and certain important production modification over that of Higashi kits.</p>
            <p>Is the study design appropriate for the research question?</p>
            <p>Yes</p>
            <p>Is the rationale for, and objectives of, the study clearly described?</p>
            <p>Yes</p>
            <p>Are sufficient details of the methods provided to allow replication by others?</p>
            <p>Yes</p>
            <p>Are the datasets clearly presented in a useable and accessible format?</p>
            <p>Not applicable</p>
            <p>Reviewer Expertise:</p>
            <p>Mycology, dermatophytosis, and mycological diagnostic techniques are my major research areas</p>
            <p>I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.</p>
        </body>
        <back>
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        <sub-article article-type="response" id="comment11929-251787">
            <front-stub>
                <contrib-group>
                    <contrib contrib-type="author">
                        <name>
                            <surname>Warghade</surname>
                            <given-names>Aditi</given-names>
                        </name>
                        <aff>Department of Microbiology, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha., Wardha, Maharashtra, India</aff>
                    </contrib>
                </contrib-group>
                <author-notes>
                    <fn fn-type="conflict">
                        <p>
                            <bold>Competing interests: </bold>Competing interests-none</p>
                    </fn>
                </author-notes>
                <pub-date pub-type="epub">
                    <day>29</day>
                    <month>6</month>
                    <year>2024</year>
                </pub-date>
            </front-stub>
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                <p>Respected sir,</p>
                <p> Thank you for considering our manuscript and suggesting the following changes to be processed for further publication in F1000 research subject to a satisfactory revision as per your suggestions. We have made the changes in our manuscript as per the suggestions given. Please consider the following changes</p>
                <p> </p>
                <p> The title needs certain modifications to be more representable for the designed study. Therefore, I suggest "Diagnosis and molecular characterization of dermatophytosis: an observational study"</p>
                <p> 
                    <bold>Answer:</bold>
                </p>
                <p> Thank you for the suggestion, sir. I agree with the changes suggested and would like to change the title to "Diagnosis and Molecular Characterization of Dermatophytosis: An Observational Study"</p>
                <p> </p>
                <p> - The abstract, introduction, and methodological protocol sections are well-designed, structured, and described.&#x00a0;&#x00a0;</p>
                <p> - The discussion is missing certain necessary references to support the flow of the work and the researcher's point of view in the following points;</p>
                <p> </p>
                <p> 
                    <bold>1)</bold>&#x00a0;The most reliable approach to diagnose dermatophytosis is through the isolation and identification of dermatophytes from clinical samples. However, it typically takes a long time for the dermatophyte to grow in culture and sporulate, which delays diagnosis.&#x00a0;</p>
                <p> - The suggested [Ref 2]
                    <bold>&#x00a0;</bold>in which a culture-dependent cross-sectional study has been performed on dermatophytosis showing the importance of culture in dermatophytosis diagnosis as well as the extend of to which extend this technique is laborious and time consuming and that will support the researcher point of view.&#x00a0;</p>
                <p> 
                    <bold>Answer:</bold> Thank you for the comment, sir. We have added the suggested reference in the draft, quoted as Ref No-4, and highlighted the citation as it is not getting added in the reference list in sequence.</p>
                <p> </p>
                <p> 
                    <bold>2)</bold>&#x00a0;&#x00a0;Many molecular methods have made a way for early detection of dermatophytes to the species level.</p>
                <p> - The suggested [Ref 3]
                    <bold>&#x00a0;</bold>in which a comprehensive&#x00a0;and collective mentioning and illustration of the molecular advancement and molecular diagnostic techniques that is have been developed in the field of dermatophytosis and the extend of the diagnostic level of those techniques and that of course will strongly support the researcher point of view.&#x00a0;</p>
                <p> 
                    <bold>Answer:</bold> Thank you for the suggestion, sir. We have added the suggested reference in the draft quoted as Ref No- 5, and highlighted the citation as it is not getting added in the reference list in sequence.</p>
                <p> </p>
                <p> 
                    <bold>3)&#x00a0;</bold>A study by Higashi, Y&#x00a0;
                    <italic>et al</italic>. (2012) from Japan stated that the use of newly developed immunochromatographic strip-test for the diagnosis of dermatophytes found the overall sensitivity and specificity of the immunochromatographic test were 83.5% and 66.7%.&#x00a0;</p>
                <p> - The suggested [Ref 1]&#x00a0;with all respect of the cited study as Higashi&#x00a0;
                    <italic>et al.&#x00a0;</italic>2012, study in the field of immunochromatographic diagnosis of dermatophytosis is really a pioneering study in this field but to be more accurate and more updated I suggest adding the suggested reference in addition to the Higashi&#x00a0;
                    <italic>et al.&#x00a0;</italic>2012, study as the suggested reference represents a newest designed and developed immunochromatographic assay for dermatophytosis diagnosis with a competitive results and certain important production modification over that of Higashi kits..</p>
                <p> 
                    <bold>Answer</bold>: Thank you for the suggestion, sir. We have added the suggested reference in our study and quoted it as Ref No-6, and highlighted the citation as it is not getting added in the reference list in sequence.</p>
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