Dear Dr. Debes,

Thank you very much for submitting your manuscript "Prioritizing interventions for cholera control in Kenya, 2015-2020" 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,

Elsio Wunder Jr, D.V.M., Ph.D.

Section 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 reviewer found the objective of the study to be clear. There were a few issues that would improve the readers understanding of the methods. (1) The IDSR definition of suspect cholera (3 or more episodes in 24 hours, age>2) appears to have low specificity. ETEC, Campy, Shigella infections would also cause 3 or more episodes in 24 hours for children and adults. Can the authors provide data supporting the validity of this definition for case detection? Was there a requirement that suspects cases be epidemiologically linked to a laboratory confirmed case? (2) Provide additional information on how the 90th percentile for MAI was chosen. Did you rank all MAI by county and select the 90th percentile value? Provide methods for selecting the persistence cutoff too. (3) For readers unfamiliar with Kenya, it would be helpful to describe the administrative division of the country. What is the number of counties and subcounties and number rural and urban counties/subcounties. How do counties/subcounties differ by population size. It may be helpful to give an example of a county with total number of subcounties. (4) In figures, it was unclear what the denominator was for "Total Annual Incidence Rate." Was this the number of cases or case number per population value (e.g., 100,000 persons)? (5) The authors identified both suspect and confirmed cholera cases. Can the authors provide data on the frequency of laboratory confirmed cases in high incidence areas?

Reviewer #2: (No Response)

Reviewer #3: Methods

All clear.

Line 99: Could you specify who discussions at the MOH were held with e.g. departments? How many people? And what you mean by “logistics for targeting interventions”? I think it is a very important point that targeting is based on the ability and resources available within the country and this may affect the thresholds set by other countries. For instance, Kenya have said 90th percentile but other settings may need to specify higher or lower based on their capacities. If you could go into 1-2 sentences more detail on the decision making, this would be useful.

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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: This reviewer found the analysis and presentation of results to be clear.

Reviewer #2: (No Response)

Reviewer #3: Results

All clear.

Table 1: is there a full list of the sub-counties included in the high, medium and low priority levels? I would find this useful as a planning tool.

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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: This is a very practical study with implications for cholera control in and outside Kenya. The limitations section was adequate. In the limitations section, the authors addressed my concern with the cholera case definition. It would be appropriate to further explore in brief what are the implications for low specificity. The authors should consider a brief discussion on alternative, if any, to this approach to selecting target areas. Are there other approaches that an MoH could consider.

Reviewer #2: (No Response)

Reviewer #3: Although the authors have talked about how counties and sub-counties would be prioritised during 2015-2020, based on the data available, it would be useful to see what the authors consider recommendations going forward. Should these 13 priority areas from 8 counties be prioritised from 2020 onwards? Could the authors add more to the discussion on what the implications are for control measures? Did the authors re-consult the MoH on what this means for Kenya’s cholera strategy?

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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: GADM database was mentioned. In a sentence, clarify what is the GADM. Many readers will not know.

Reviewer #2: (No Response)

Reviewer #3: n/a

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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: This is a very practical study with important implications for cholera control in cholera endemic countries. The reviewer mentioned several methodological issues that should be addressed. Beyond these issues, the author does not have any concerns.

Reviewer #2: (No Response)

Reviewer #3: Overall:

A very interesting paper and analysis of existing data! This paper is a good example of how countries can use their own surveillance systems to prioritise and target cholera control resources.

It would be useful to see recommendations based on this paper included in the discussion. This paper is led by the MoH and it could be an opportunity for them to suggest a plan based on the findings of this paper. Other minor comments below.

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Reviewer #1: No

Reviewer #2: Yes: Aminata P Kilungo

Reviewer #3: Yes: Lauren D'Mello-Guyett

Figure Files:

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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: Prioritizing interventions for cholera control in Kenya 2015-2020_APK Comments.docx

Dear Dr. Debes,

Thank you very much for submitting your manuscript "Prioritizing interventions for cholera control in Kenya, 2015-2020" 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,

Elsio Wunder Jr, D.V.M., Ph.D.

Section Editor

PLOS Neglected Tropical Diseases

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

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:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

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.

Dear Dr. Debes,

We are pleased to inform you that your manuscript 'Prioritizing interventions for cholera control in Kenya, 2015-2020' 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,

Elsio Wunder Jr

Section Editor

PLOS Neglected Tropical Diseases

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