Dear Dr. Omore,

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.

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ACADEMIC EDITOR: As attached document with track

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silas onyango awuor, msc

Academic Editor

PLOS ONE

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Kindly see the attached document with track for your action

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Attachments

Attachment

Submitted filename: PBIDS_Shigella_burden_Main Text_22Jul2025docx.docx

Population-based incidence and antimicrobial susceptibility patterns of shigellosis among children and adults from rural and urban Kenya, 2010-2019

PONE-D-25-40297R1

Dear Dr. Omore,

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.

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Kind regards,

Babak Pakbin

Academic Editor

PLOS One

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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

Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: No

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

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: The manuscript presented to me deals with an important topic. The epidemiology of shigellosis has gradually begun to fall out of focus among European researchers. However, the disease continues to be active in industrially developed regions. The description of the problem and the guidelines for solving gaps are valuable; the manuscript is structured adequately to the topic, provides answers to the questions discussed. Correct statistical methods have been used. I highly appreciate the manuscript and, after the changes made, I propose that it be accepted for publication.

Reviewer #2: The manuscript is technically sound, the statistical methodology is rigorous, and the conclusions are well-supported by the presented data. I recommend this manuscript for publication following some minor revisions primarily concerning data availability protocols and grammatical corrections.

-The methodology is robust and appropriate for the study's epidemiological scope.

Disease Burden: The conclusion that children aged 12-23 months bear the highest burden is clearly supported by the adjusted incidence rates of 1,873/100,000 in Asembo and 2,828/100,000 in Kibera.

Species Distribution: The authors appropriately draw vaccine-related conclusions based on their finding that S. flexneri accounts for approximately two-thirds of the isolates in both settings (61% and 67%).

-Statistical Rigor:

The authors have demonstrated excellent epidemiological rigor by moving beyond crude incidence estimates.

The application of a two-step adjustment to account for the proportion of eligible participants who had stool collected and the proportion who sought out-of-network care is a major strength of this paper.

Calculating the uncertainty around the adjusted incidence using Monte Carlo simulations (10,000 simulations sampling from Poisson and binomial distributions) is a highly sophisticated and appropriate technique to establish 95% Confidence Intervals.

The use of the Mann-Kendall test to assess temporal trends is the correct statistical choice for this data.

-Data Availability:

The current Data Availability Statement notes that KEMRI owns the data, which is available upon reasonable request to the corresponding author. To fully comply with the PLOS Data policy, the authors should not rely solely on a single author as the point of contact.

Recommendation: Please provide a persistent, non-author institutional contact (such as an email address for KEMRI's data access or ethics committee) to ensure long-term data accessibility for future researchers.

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Reviewer #1: Yes: Valeri R Velev

Reviewer #2: Yes: Ismail Yosri Abdelgelel Ismail

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