Peer Review History

Original SubmissionAugust 16, 2021
Decision Letter - Saeed El-Ashram, Editor

PONE-D-21-26307Prevalence and distribution of Cryptosporidium spp. among diarrheic calves in the Republic of KoreaPLOS ONE

Dear Dr. Kyoung-Seong Choi,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Nov 20 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Saeed El-Ashram

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at 

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Partly

Reviewer #3: Yes

Reviewer #4: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

Reviewer #4: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear Author,

I can say that I really like the subject of your article.

However, there is some confusion. What is the method by which you specify subtypes? According to which literature did you identify these subtypes?

I have not seen such a method in the literature number 24 that you use on this subject.

You should provide information about this in your article.

Kind regards

Reviewer #2: The current MS presented Cryptospordiosis distribution among calves in ROK. The main issue of this work is the methods in which the authors described it in a briefly way. As PLOS ONE has broad base of readers, so, authors should be mentioned the methods used in something of details. Extraction of DNA from fecal samples needs specific precautions, authors need to mention how they manage these samples, add preservative or not, what about the inhibitors from feces? Also, I can't understand how the authors differentiate between C. ryanae and C. parvum? How did the authors decide that this is C. ryanae and other one is C. bovis then they did sequence and then differentiate between them?

-The introduction needs a paragraph about importance and improvements that were done in the molecular identifications of Cryptosporidium.

- In the discussion the authors need to discusses why the age below 20 days calves are more susceptible to C. parvum?

Reviewer #3: Dear authors,

Thank you for this interesting work.

The manuscript is well written.

Here you are my comments/ remarks for your consideration.

Title

Line2

Should be changed: “Prevalence and distribution pattern of Cryptosporidium spp. among pre-weaned diarrheic calves in the Republic of Korea”

Abstract

L24: Add Cryptosporidium spp. are protozoan parasites that belong to subphylum apicomplexa and cause diarrhea in humans and animals worldwide

L42: Illustrate that family IIa belongs to C. parvum

L45, 46: add the percentage of the rest subtypes that you found .

Key words

L52 Add : spp. to Cryptosporidium,

Materials and Methods

L93-L131 The Materials and Methods should be written in more details.

L110: Why did not you collect an equal number of samples in different age groups ?

Thus you can get more accurate prevalence and actual association between age and Cryptosporidium spp. distribution.

Results and discussion

Results and discussion were written in a good details.

Reviewer #4: Dear Author

This is a generally well written manuscript with minor grammatical errors. Just a few comments or corrections:

1. Correlations are mentioned in the results (line 170) but not described in the statistical analysis.

2. Consider moving the sentence in line 174 to the discussion as it is not a description of the results.

3. Line 216 statement on prevalence of C. ryanae in calves is ambiguous please revise.

4. Line 296 change "sequencing analysis" to "sequence analyses".

5. Line 297 add the word "respectively after the G at the end of the sentence. Line 313 add a recommendation.

Thank you and well done on this work.

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

Reviewer #4: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachments
Attachment
Submitted filename: PONE-D-21-26307_reviewer.pdf
Revision 1

Reviewer #1: Dear Author,

I can say that I really like the subject of your article.

However, there is some confusion. What is the method by which you specify subtypes? According to which literature did you identify these subtypes?

I have not seen such a method in the literature number 24 that you use on this subject.

You should provide information about this in your article.

Kind regards

Response: We are sorry for the confusion and agree with this comment. As the reviewer’s comment, we have provided them. Please see lines 131-133 and 466-468.

Reviewer #2: The current MS presented Cryptospordiosis distribution among calves in ROK. The main issue of this work is the methods in which the authors described it in a briefly way. As PLOS ONE has broad base of readers, so, authors should be mentioned the methods used in something of details. Extraction of DNA from fecal samples needs specific precautions, authors need to mention how they manage these samples, add preservative or not, what about the inhibitors from feces? Also, I can't understand how the authors differentiate between C. ryanae and C. parvum? How did the authors decide that this is C. ryanae and other one is C. bovis then they did sequence and then differentiate between them?

Response: We agree with this comment and understand the reviewer’s concern. Unfortunately, we did not examine oocysts from each feces, because we are not expert in this field. However, we used PCR method to detect Cryptosporidium species. All feces were stored at 4�C without additional treatment of preservation and were used for DNA extraction. We extracted directly DNA from feces using the QIAamp Fast DNA Stool Mini Kit (Qiagen) according to the manufacturer's instructions. We have provided the methods as the reviewer’s suggestion. Please see lines 121-126.

In addition, to detect Cryptosporidium species, we first used the 18S rRNA gene and sequenced all positive samples. By sequencing analysis, samples that yielded positive results for Cryptosporidium spp. were further screened to identify the species using species-specific primers. Positive samples for C. parvum was re-tested using the 60-kDa glycoprotein (gp60) gene to determine its subtype. To differentiate between C. bovis and C. ryanae, amplified sequences were compared and confirmed. According to the results of sequence, two species were different from each other. Please see lines 127-131, and 138-139.

-The introduction needs a paragraph about importance and improvements that were done in the molecular identifications of Cryptosporidium.

Response: In this study, we utilized the partial 18S rRNA gene, not SSU rRNA gene. In general, SSU rRNA gene is based on a nest PCR method. As you know, nested PCR has some problems such as contamination risks owing to multiple rounds of DNA amplification and concomitant DNA manipulation steps. To exclude these problems, we used conventional PCR method which have a short fragment. This method can easily be used to detect Cryptosporidium spp. We have provided them. Please see lines 87-91.

- In the discussion the authors need to discusses why the age below 20 days calves are more susceptible to C. parvum?

Response: We agree with this comment. At this point, we cannot make a conclusion about this, but it could be related to immune system of calves. In addition, it has been reported that C. parvum can be transmitted from cow to calf. Please see lines 219-227.

Reviewer #3: Dear authors,

Thank you for this interesting work.

The manuscript is well written.

Here you are my comments/ remarks for your consideration.

Title

Line2

Should be changed: “Prevalence and distribution pattern of Cryptosporidium spp. among pre-weaned diarrheic calves in the Republic of Korea”

Response: We have changed as the reviewer’s suggestion. Please see lines 2-3.

Abstract

L24: Add Cryptosporidium spp. are protozoan parasites that belong to subphylum apicomplexa and cause diarrhea in humans and animals worldwide

Response: We have modified as the reviewer’s suggestion. Please see lines 22-23.

L42: Illustrate that family IIa belongs to C. parvum

Response: We have modified as the reviewer’s suggestion. Please see lines 39-40.

L45, 46: add the percentage of the rest subtypes that you found .

Response: We have provided as the reviewer’s suggestion. Please see lines 43-45.

Key words

L52 Add : spp. to Cryptosporidium,

Response: We have modified as the reviewer’s suggestion. Please see line 51.

Materials and Methods

L93-L131 The Materials and Methods should be written in more details.

Response: We agree with this comment. As the reviewer’s comment, we have provided them. Please see lines 114-115, 117, 121-133, and 138-140.

L110: Why did not you collect an equal number of samples in different age groups ?

Thus you can get more accurate prevalence and actual association between age and Cryptosporidium spp. distribution.

Response: We understand the reviewer’s concern and agree with this comment. Our lab is focused on calf diarrhea, especially neonates. As you know, calf diarrhea occurs mainly less than 1 month old. Because most of the samples requested to be tested by our lab are under 30-day-old and feces were less in the age group over 30 days of age. For this reason, currently, it is difficult to compare the association between age group and distribution of Cryptosporidium spp. We are going to try to compare the prevalence and association between age and Cryptosporidium spp., if the number of samples is similar in all age groups. Please understand our situation. Thank you for your comment.

Results and discussion

Results and discussion were written in a good details.

Reviewer #4: Dear Author

This is a generally well written manuscript with minor grammatical errors. Just a few comments or corrections:

1. Correlations are mentioned in the results (line 170) but not described in the statistical analysis.

Response: We agree with this comment. We have provided. Please see lines 186-187 and Table 3.

2. Consider moving the sentence in line 174 to the discussion as it is not a description of the results.

Response: We agree with this comment. We have removed it and added in discussion. Please see lines 311-312.

3. Line 216 statement on prevalence of C. ryanae in calves is ambiguous please revise.

Response: We are sorry for the confusion and have revised. Please see lines 236-238.

4. Line 296 change "sequencing analysis" to "sequence analyses".

Response: We have changed as the reviewer’s suggestion. Please see lines 317-318.

5. Line 297 add the word "respectively after the G at the end of the sentence. Line 313 add a recommendation.

Response: We have modified as the reviewer’s suggestion and added some references. Please see line 319 and 335.

Thank you and well done on this work.

Reviewer comment

1. Line 111. No microscopic examination was performed. How did you know for sure that the stools could be infective? Was it a coincidence?

Response: We agree with this comment and understand the reviewer’s concern. We were not able to examine the oocytes because we are not expert in this field. So, we tested all fecal samples for detection of Cryptosporidium infection.

2. Line 114. DNA was extracted from 200 mg. Specify what pretreatment was done to break up the oocyst wall.

Response: We understand the reviewer’s concern. Because we did not test the oocysts and did not perform the step to break up the oocysts wall. To extract DNA, we directly used feces according to the manufacturer’s instructions. Please see lines 114-115, 117, and 121-126.

3. Line 119. As far as I know, C.bovis/ryanae cannot be differentiated with this gene region. Clarification on the primers used should be clarified.

Response: We agree with this comment. We have provided the reference of species-specific primers which we use. Please see line 129.

4. Line 126. Since the base of sequences of C. bovis and C. ryanae are similar, all positive samples of the 18S rRNA were separated by comparing the sequences. Which method or according to which technique was this process done?

Response: We agree with this comment and understand the reviewer’s concern. We first used the 18S rRNA gene to detect Cryptosporidium species and positive samples for Cryptosporidium species by sequencing analysis were screened to identify the four species using species-specific primers. Finally, positive samples for C. bovis/C. ryanae were differentiated by sequence analysis and species was confirmed based on the sequence analysis. According to our results, these two species had differences in nucleotide sequences.

5. Line 142-143. If C. andersoni was not found, please specify.

Response: We have provided. Please see lines 158-159.

Attachments
Attachment
Submitted filename: Response to Reviewers.docx
Decision Letter - Saeed El-Ashram, Editor

Prevalence and distribution pattern of Cryptosporidium spp. among pre-weaned diarrheic calves in the Republic of Korea

PONE-D-21-26307R1

Dear Dr. Kyoung-Seong Choi,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Saeed El-Ashram

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Thank you very much for all of your hard work and dedication. I, the academic editor, welcome your future submissions on behalf of the PLoS ONE editorial members.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

Reviewer #4: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Accept

It can be published in this form

best wishes

Accept

It can be published in this form

best wishes

Reviewer #2: The authors addressed all comments and corrections that recommended by the reviewer. The manuscript could be accepted in this form

Reviewer #3: Dear authors,

Thank you for performing all the modifications i requested in the manuscript.

Well done and good effort.

With my best wishes

Reviewer #4: Dear Authors

Thanks for the thorough revision of the article and addressing all the reviewer comments. The manuscript is reading well and I recommended it to be accepted for publication.

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: Yes: Shawky M Aboelhadid

Reviewer #3: No

Reviewer #4: No

Formally Accepted
Acceptance Letter - Saeed El-Ashram, Editor

PONE-D-21-26307R1

Prevalence and distribution pattern of Cryptosporidium spp. among pre-weaned diarrheic calves in the Republic of Korea

Dear Dr. Choi:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Professor Saeed El-Ashram

Academic Editor

PLOS ONE

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .