Molecular Techniques and Target Selection for the Identification of Candida spp. in Oral Samples

Round 1

Reviewer 1 Report

This manuscript is interesting and, on the whole, well-written. As the authors are focusing on Candida spp. from oral sources, perhaps a paragraph could be added that describes potential difficulties with oral fluids (e.g. saliva), including recommended methods of nucleic acid purification.

Some other comments:

1. Line 74 - Centers for Disease Control and Prevention (CDC) - U.S. spelling

2. Lines 76-77 - candidaemia (U.K.) or candidemia (U.S.)? Please use consistent spelling.

3. Spelling errors - Line 92 ("opportunistic"), line 93 ("ultimately"), line 95 ("commonly"), line 111 ("candidaemia" - not capitalized), line 157 ("huge").

4. Line 124 - maybe "Conversely" rather than "Consequently" is a better word.  Similarly, in line 125, the word "reliably" is more appropriate than "safely".

5. Line 197 - Kanbe et al. [74]...

6. Lines 353-356 - Illumina is not a new technology; it became mainstream commercially around the same time as pyrosequencing. In contrast to pyrosequencing, Illumina generates shorter sequences but in far greater numbers of sequences, i.e. terabytes of total bp. Perhaps the authors can mention barcoding samples so that many more samples can be processed in one sequencing run.

7. Line 378 - "large amounts of money", not big.

8. Figure 1 - what is the ideal time for generation of results? Perhaps the authors meant to write <2h rather than >2h (longer than 2 hours). A range of time values is suggested to give the reader an idea of how long processing should realistically take.

9. Section 1.3 (Target selection) - could the authors comment or add a paragraph on the value of genomic sequencing in identifying new molecular targets (or genes) for nucleic acid-based techniques? Are there any new candidates for multilocus-based identification?

 

 

Author Response

Please see the attachment

Author Response File: Author Response.docx

Reviewer 2 Report

Dear Authors,

 

I have been invited to review your work entitled “Molecular techniques and target selection for the identification of Candida spp. in oral sample”. I believe it is a work of concern, however there are many major issues that deserve revision for the acceptance of this work to Applied Sciences (MDPI).

 

Please, provide a point-by-point response, highlighting the corrections with a color mark specific for each reviewer.

 

Affiliations

·      Corresponding authors are not indicated. Please, revise.

 

Abstract

·      The abstract exceeds 200 words, a limit stated in the authors' guideline. Please, reduce its length.

·      Grammar check is recommended.

 

Keywords

·      I suggest organizing the keywords alphabetically.

 

Manuscript

·      As indicated in the author guidelines, please indicate the bibliographic references within the same square bracket. For example, change from [1],[2] to [1,2].

·      Since the manuscript refers to the oral environment, I suggest, for completeness, to indicate that changes in the balance of the oral microbiota can lead to some oral important consequences such as periodontitis and peri-implantitis, with some important differences in terms of population of microorganisms (For example, pointing to this bibliographic reference: https://doi.org/10.3390/app12073250 and https://doi.org/10.1002/cre2.635).

·      As stated in the authors guidelines, it is not correct to indicate the chapters present after the introduction with this numbering. Therefore, I suggest naming the chapter "1.1 Epidemiology of Candida infections" to "2. Epidemiology of Candida infections" and so to follow. Clearly if a paragraph can be a subsection of a chapter then I suggest numbering it this way: i.e. "3. Molecular identification of Candida spp." and “3.1 Conventional PCR” ecc.

·      I suggest that chapter titles be indicated in lower case.

·      Correct the indentation of the text in those parts of the manuscript where it is different from the introduction (i.e. in chapter 1.1). The indentation must be the same throughout the text.

·      Correct spaces between paragraphs where different from the introduction (i.e. in chapter 1.1).

·      Check the spaces between words. For example, insert space between optimization and [83].

·      I suggest including a summary table presenting advantages and limitations of the various techniques described.

·      Specify the limitations of this study and future studies.

·      English editing by a native speaker is recommended, spelling and editing errors should be corrected.

 

Thank you for the effort.

Comments for author File: Comments.docx

Author Response

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Author Response File: Author Response.docx

Reviewer 3 Report

Dear Authors

Interesting article for someone who deals with dentistry. You can see that the authors are professionals in their field. But sometimes it would be good to explain the research methods a little more precisely so that they would also be understandable to the dentist, who struggle with patients who have inflammatory conditions on a daily basis. It is such a dear attention to the future.

Especially when translating abbreviations that may be difficult for professionals, but they cause confusion for dentists.

 

Abstract:

Please not use aberration in abstract such PCR or MALDI-MS.  Some people read the abstract at the beginning, if they are not interested, then they do not read the whole article anymore. Let's try to prepare an abstract to be as understandable as possible.

 

Introduction

Line 30

thrush- may instead use one term for inflammation in the oral cavity of Candidosis. Because this is just one tight incident, besides there are red spots, ulcers, etc.

 

Lines 42-44 In two sentences you use Candida 3 times. You can use other terms for bacteria, micro-organisms, etc. English is a rich language with a lot of ambiguous

 

In the case of Candidosis in dentistry, it is worth noting that this applies to a very large number of people using removable , , partial or complete. On their surface, this pathogen collects very quickly. And in the case of poor hygiene, we already have infections throughout the mouth.

Line 165-

 it will be good to describe what ITS2 means, for unfamiliar reader, please

line 176

-Real Time-PCR - it would be great if the authors described in two sentences what RT-PCR is and how it is done. Again, not all are experts, and they would love to learn something new.

Line 235

HaeII , BfaI, NlaIII what do it means?

Line 287

Tm  what do it means?

 

 

Note for later works. If you write reviews, it is good to indicate where the materials were collected, e.g. the PubMed base from 2000-2022. Found e.g. 300 articles by keyword search. For the text it was used 100 articles - PRISMA. This allows the reader to judge your work whether only some of the articles have been viewed or all of them. Because maybe there are others, which are not covered, but contribute a lot to the topic described.

 

good luck with your further research

Author Response

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Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

The authors correctly made all the corrections I suggested. Therefore, the article can be accepted in the present form.