-->PONE-D-26-09918-->-->Multistate Animal-Contact-Related Nontyphoidal Salmonella enterica Outbreaks in the United States, 2009-2022: Network and Machine Learning Analyses of Exposure Sources, Settings, and Serovars-->-->PLOS One

Dear Dr. Varga,

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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: Yes

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

Reviewer #1: Yes

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-->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: No

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-->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

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-->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: Overall comment: The authors conducted a study titled “Multistate Animal-Contact-Related Nontyphoidal Salmonella enterica Outbreaks in the United States, 2009-2022: Network and Machine Learning Analyses of Exposure Sources, Settings, and Serovars” that analyzed animal contact-related non-typhoidal Salmonella (NTS) outbreak data, which was utilized for calculating incidence rate per 10 million population‑years, assessed temporal trends using Join point regression, co‑occurrence network linking, and machine learning classification algorithm, such as a random forest classifier to identify variables most useful for distinguishing outbreak profiles. Overall, the manuscript is well written and provides important information on the burden of multistate NTS outbreaks associated with animal contact. This manuscript addresses an important one-health issue. However, the following comments need to be addressed to improve the manuscript clarity and readability.

Specific comment:

Introduction:

Comment: The author should include a brief introduction about the public health burden of non-typhoidal Salmonella (NTS), including the predominant NTS serovars in the United States.

Comment: The relevance of the study is unclear. The author should clarify why this study findings are important (by addressing the “so what?” question in the introduction section).

Materials and Methods:

Comment: The author should provide a brief description of how animal contact related NTS outbreak surveillance data were collected to help the reader understand the data source, collection, population, and reporting process.

Comment: The author should describe how the surveillance data is assessed, including missing values, value distributions, and duplication, before preparing the analytic dataset for this study.

Comment: Authors should provide a clear case definition of 'animal contact related NTS outbreak' for better understanding by the readers of the paper. Additionally, the author should mention the inclusion criteria for including ‘animal contact related NTS outbreak' events for analysis in this study.

Comment: The author should report the study design in the methods section.

Comment (Line 116): The author should provide a full elaboration of ‘NORS’ before introducing the abbreviation.

Comment (Line 145): Authors should provide a table that displays all explanatory variables (features), along with their categories and types, to enhance reader understanding about the variables of interest in this study.

Comment: The author should provide a logical order of data analysis, with their headings, to test each hypothesis in this study

Comment: The author should specify the version of the Joinpoint Regression (JPR) software used in this study.

Comment (Line 144): What is the reasoning behind exclusively using the random forest model (RF)? How do the authors partition (%) the data into training and testing sets for the RF model? The author should provide this information. Did the author try any alternative classification algorithm (e.g., logistic regression ….) as part of the sensitivity analysis? What form of cross‑validation was used to assess the RF model's performance? The author should specify the R packages used for the RF modeling.

Comment: The author should provide a brief introduction and a rationale for the network analysis and explain why the network is treated as undirected and weighted. Additionally, the author should specify the R packages used in the study's network analysis.

Comment (Line 144): In the RF model section, the author should specify the outcome variable and explain how it is defined. Also, specify the predictor of interest and explain how the predictors were chosen for inclusion in the model.

Comment: It would be helpful if the author included the full R scripts for the RF model and network analyses as supplementary files to help readers and learners understand the analyses.

Results:

Comment (Line 190-192): These sentences should be in the method section, not part of the result section of the manuscript.

Comment (Line 193-194): These sentences should be placed in the discussion section, not in the results section. In the RF model results, the reader can expect to see the RF model performance matrices and the variable importance identified in the RF model (top, second, and third variables) as the strongest predictors of the outcome variable of interest.

Comment (Line 228-232): These sentences are not results; they are part of the discussion. The author should remove this section from the results section and place it in the appropriate section in the discussion.

Discussion

Comment: The author should provide a primary conclusion statement that logically and defensibly draws from the study results.

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Reviewer #1: Yes: Shamim Sarkar

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Attachments

Attachment

Submitted filename: comments and suggestions-PONE-D-26-09918-v3.pdf

Multistate animal-contact-related nontyphoidal Salmonella enterica outbreaks in the United States, 2009-2022: Network and machine learning analyses of exposure sources, settings, and serovars

PONE-D-26-09918R1

Dear Dr. Varga,

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,

Yung-Fu Chang

Academic Editor

PLOS One

Additional Editor Comments (optional):

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: All comments have been addressed

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-->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

**********

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

Reviewer #1: 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

**********

-->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

**********

-->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: (No Response)

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-->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: Yes: Shamim Sarkar

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