Please submit your revised manuscript by January 15, 2026. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosntds@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pntd/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

Response to ReviewersRevised Manuscript with Track ChangesManuscript

Shaden Kamhawi

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

orcid.org/0000-0003-4304-636XX

Paul Brindley

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

orcid.org/0000-0003-1765-0002

Journal Requirements:

1) Please provide an Author Summary. This should appear in your manuscript between the Abstract (if applicable) and the Introduction, and should be 150-200 words long. The aim should be to make your findings accessible to a wide audience that includes both scientists and non-scientists. Sample summaries can be found on our website under Submission Guidelines:

https://journals.plos.org/plosntds/s/submission-guidelines#loc-parts-of-a-submission

2) Please upload all main figures as separate Figure files in .tif or .eps format. For more information about how to convert and format your figure files please see our guidelines:

https://journals.plos.org/plosntds/s/figures

3) Please amend your detailed Financial Disclosure statement. This is published with the article. It must therefore be completed in full sentences and contain the exact wording you wish to be published.

1) State the initials, alongside each funding source, of each author to receive each grant. For example: "This work was supported by the National Institutes of Health (####### to AM; ###### to CJ) and the National Science Foundation (###### to AM)."

2) State what role the funders took in the study. If the funders had no role in your study, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

4) Please revise your current Competing Interest statement to the standard "The authors have declared that no competing interests exist."

5) We noted that you have cited tables (1 ,2) , and then tables ( from 5 to 7)  ; however, tables 3 and 4 have not been cited or included in the manuscript. Please re-label and number the tables in a numerical order.

Note: If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

Reviewers' comments:

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 applied methods are consistent with the stated objectives of the study.

Reviewer #2: (No Response)

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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 results correspond to the analysis plan and are sufficiently presented.

Reviewer #2: (No Response)

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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 conclusions are supported by the conducted work and obtained data.

Reviewer #2: (No Response)

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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: (No Response)

Reviewer #2: (No Response)

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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: 1. Overall Evaluation

The manuscript presents an original and relevant study focused on the application of statistical and machine learning models to predict the presence of Salmonella Typhi in wastewater samples from Ghana. The work is methodologically sound, well-structured, and addresses a significant public health issue related to wastewater-based surveillance (WBE). The authors combine classical regression approaches (GLMM, GAM, GEE) with modern non-parametric algorithms (Random Forest, SHAP), providing a comprehensive comparative analysis. The findings confirm the efficiency of non-parametric models and highlight the environmental and seasonal factors influencing S. Typhi persistence.

2. Strengths

- High scientific and practical relevance for WBE systems in endemic regions.

- Thorough data processing and the use of several complementary analytical methods.

- Clear structure, well-presented results, and consistent discussion with literature.

- Good graphical and tabular quality, making the findings easy to interpret.

3. General Recommendations

The manuscript appears complete and well-prepared. To further enhance transparency and reproducibility, it is recommended to:

- Clarify methodological details such as variable selection criteria, model validation parameters, and data partitioning into training/testing subsets.

- Expand the discussion of study limitations, including sample size, seasonality, and potential overfitting concerns given the high accuracy metrics (Accuracy > 0.99).

- Slightly reinforce the interpretation of ecological and biological mechanisms underlying S. Typhi persistence in environmental contexts.

- In the Conclusion, emphasize the potential contribution of the model to practical public health systems (GHSA, WHO GLASS).

4. Significance and Impact

This study has strong potential for application in endemic regions and can serve as a methodological model for similar pathogen monitoring efforts (e.g., Vibrio cholerae, Salmonella Paratyphi). It expands the methodological foundation for early warning systems based on wastewater surveillance and contributes to regional biosecurity capacities.

5. Overall Recommendation

Minor revision. The manuscript is suitable for publication after minor textual and methodological clarifications.

Reviewer #2: (No Response)

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Reviewer #1: No

Reviewer #2: Yes: Manfred Dakorah Asiedu

Figure resubmission:

Reproducibility:--> -->-->To enhance the reproducibility of your results, we recommend that authors of applicable studies deposit 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-->?>

Dear Dr. Twumasi-Ankrah,

We are pleased to inform you that your manuscript 'Statistical Methods for Predicting the Presence of Salmonella Typhi in Wastewater Samples at Asante Akyem Agogo, Ghana.' 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,

Travis J Bourret

Academic Editor

PLOS Neglected Tropical Diseases

Ana LTO Nascimento

Section Editor

PLOS Neglected Tropical Diseases

Shaden Kamhawi

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

orcid.org/0000-0003-4304-636XX

Paul Brindley

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

orcid.org/0000-0003-1765-0002

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