Dear Prof. dr. Houf,

Thank you very much for submitting your manuscript "Campylobacter in children under the age of five with diarrhea, backyard farm animals, and companion animals: Occurrence and antibiotic resistance" for consideration at PLOS Neglected Tropical Diseases. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Kirkby D Tickell, MBBS BSc

Academic Editor

PLOS Neglected Tropical Diseases

Elsio Wunder Jr

Section Editor

PLOS Neglected Tropical Diseases

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Reviewer's Responses to Questions

Key Review Criteria Required for Acceptance?

As you describe the new analyses required for acceptance, please consider the following:

Methods

-Are the objectives of the study clearly articulated with a clear testable hypothesis stated?

-Is the study design appropriate to address the stated objectives?

-Is the population clearly described and appropriate for the hypothesis being tested?

-Is the sample size sufficient to ensure adequate power to address the hypothesis being tested?

-Were correct statistical analysis used to support conclusions?

-Are there concerns about ethical or regulatory requirements being met?

Reviewer #1: The goal of this study, to use new methods to quantify Campylobacter in young children experiencing diarrhoeal disease and in animals in Ethiopia is well articulated. The methods seem appropriate to address this objective and the populations which were sampled are well described. However, it is unclear if all animals in the home were sampled or if only a subset were sampled. If the data is available, information about children who were not eligible to participate due to insufficient sample collection would be useful to include as well.

Reviewer #2: Methodologically, the manuscript sounds good to address all the issues mentioned above.

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Results

-Does the analysis presented match the analysis plan?

-Are the results clearly and completely presented?

-Are the figures (Tables, Images) of sufficient quality for clarity?

Reviewer #1: The analysis matches the methods described. The structure of Table 1, with the different sections for occurrence and identification could be more clearly presented, as in the current form the difference between the two sections is not immediately clear. Overall the description of the results is comprehensive. However, in the section on demographic data in children, it is mentioned that there is no association between infection and number of siblings but no additional information is provided in Table 2 or in the text. In Table 5 is is also unclear why these specific sample pairs were selected to be presented. Based on Figure 4, they do not appear to be all instances of these concurrent isolations.

Reviewer #2: The results are nicely presented using figures, graphics, and narrative methods. Both on the document itself and in a separate file, there are a few little problems stated.

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Conclusions

-Are the conclusions supported by the data presented?

-Are the limitations of analysis clearly described?

-Do the authors discuss how these data can be helpful to advance our understanding of the topic under study?

-Is public health relevance addressed?

Reviewer #1: The authors conclude that these results suggest direct animal to human transmission. However, given the cross-sectional nature of this study, concluding transmission instead of simply co-occurrence in both groups is a not supported by the data. In addition, the unmatched AST profiles between animals and children support the possibility of other explanations, which the authors do mention later in the discussion. Discussion of limitations is minimal and could be further expanded upon to include limitations other than those related to molecular methods. The authors discuss their findings in the context of previous work done both in Ethiopia and globally. However, further consideration of reasons for differences in findings beyond culture techniques could be discussed if they exist. In the one study where this is discussed, the differences in methods with regards to who was sampled are significant, which raises the question of the inclusion criteria in other studies which are discussed. Finally, while Campylobacter infection is arguably a One Health issue, and this study makes reference to One Health at several points, this study does not include all three domains of One Health. It does not include environmental samples and includes minimal discussion of the role of the environment in transmission or as an opportunity for intervention.

Reviewer #2: To emphasize the importance of the One Health doctrine, the work approach is relatively new in the study location (Ethiopia).

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Editorial and Data Presentation Modifications?

Use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. If the only modifications needed are minor and/or editorial, you may wish to recommend “Minor Revision” or “Accept”.

Reviewer #1: In the results section on child demographics, reference is made to as group classifications of the Ethiopian Public Health Institute. However, the phrasing of this significant difference is unclear and could be reworded or clarified. The first sentence in the discussion also states that the study presents the spatial distribution of Campylobater. However, while the spatial distribution of sampled households is presented, those that were positive are not delineated.

Reviewer #2: Minor revision.

The detail is organized on a separate file.

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Summary and General Comments

Use this section to provide overall comments, discuss strengths/weaknesses of the study, novelty, significance, general execution and scholarship. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. If requesting major revision, please articulate the new experiments that are needed.

Reviewer #1: In general, this study presents useful information about the burden of Campylobacter in the study region. It's strengths include it's methods and the number of samples, as well as the description of the distribution and characteristic of positive samples. The authors adequately discuss these findings in the context of previous findings. However, the conclusions drawn from the study regarding transmission are ambitious given the cross sectional nature of the study and lack of genetic analysis. The limitations of this study and how it fits into a One Health approach could also be expanded. In addition, there are places where the writing could be reworded to improve clarity.

Reviewer #2: The detail is organized on a separate file.

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Reviewer #1: No

Reviewer #2: No

Figure 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. 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 us at figures@plos.org.

Data Requirements:

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Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

References

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article's retracted status in the References list and also include a citation and full reference for the retraction notice.

Attachments

Attachment

Submitted filename: Reviewer feedback T-PLOS-2024.pdf

Attachment

Submitted filename: PNTD-D-23-01585 -Reviewed 2024.pdf

Dear Prof. dr. Houf,

We are pleased to inform you that your manuscript 'Campylobacter occurrence and antimicrobial resistance profile in under five-year-old diarrheal children, backyard farm animals, and companion pets' has been provisionally accepted for publication in PLOS Neglected Tropical Diseases.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Neglected Tropical Diseases.

Best regards,

Kirkby D Tickell, MBBS BSc

Academic Editor

PLOS Neglected Tropical Diseases

Elsio Wunder Jr

Section Editor

PLOS Neglected Tropical Diseases

***********************************************************

Reviewer's Responses to Questions

Key Review Criteria Required for Acceptance?

As you describe the new analyses required for acceptance, please consider the following:

Methods

-Are the objectives of the study clearly articulated with a clear testable hypothesis stated?

-Is the study design appropriate to address the stated objectives?

-Is the population clearly described and appropriate for the hypothesis being tested?

-Is the sample size sufficient to ensure adequate power to address the hypothesis being tested?

-Were correct statistical analysis used to support conclusions?

-Are there concerns about ethical or regulatory requirements being met?

Reviewer #1: (No Response)

**********

Results

-Does the analysis presented match the analysis plan?

-Are the results clearly and completely presented?

-Are the figures (Tables, Images) of sufficient quality for clarity?

Reviewer #1: (No Response)

**********

Conclusions

-Are the conclusions supported by the data presented?

-Are the limitations of analysis clearly described?

-Do the authors discuss how these data can be helpful to advance our understanding of the topic under study?

-Is public health relevance addressed?

Reviewer #1: (No Response)

**********

Editorial and Data Presentation Modifications?

Use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. If the only modifications needed are minor and/or editorial, you may wish to recommend “Minor Revision” or “Accept”.

Reviewer #1: (No Response)

**********

Summary and General Comments

Use this section to provide overall comments, discuss strengths/weaknesses of the study, novelty, significance, general execution and scholarship. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. If requesting major revision, please articulate the new experiments that are needed.

Reviewer #1: My previously identified concerns have adequately been addressed in this revision.

**********

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