-->PONE-D-26-03469-->-->Antibiotics and priority effects determine colonizing resistant Escherichia coli strain assemblages in community settings-->-->PLOS One

Dear Dr. Ng’eno,

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Academic Editor

PLOS One

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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: No

Reviewer #2: Partly

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

Reviewer #1: No

Reviewer #2: 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

Reviewer #2: 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

Reviewer #2: 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: The title indicates that the paper has found priority effects that determine resistant E. coli strains in a community tested. These priority effects are not clear. The data presented are largely correlative, and using modeling. There is value in doing modeling and looking for correlations but whether any novel correlations are found here are not clear. The images of several figures are blurry, but even if they were not blurry, the text does not indicate clear or novel findings.

Some questions I had were:

1. Were the people who fecal samples were taken from asked about their antibiotic usage? If so, a figure connecting the antibiotic use and resistance found would have been useful.

2. Did the authors collect the fecal samples and do the experiments to detect antibiotic resistance or did they get the data from PBIDS and do modeling with the data?

3. Was all of the data from PBIDS?

4. Did the authors do the experiments described in lines 210 to 218 on page 10 or is it from PBIDS?

5. The text regarding Fig 2 does not fully explain the data shown. The correlation between Streptomycin resistant with Sulfamethoxazole, tetracycline, and trimethoprim is not mentioned.

6. Fig 3 – several of the graphs here are described as bimodal. It is not clear how the line on the graph is made and what data it is representing.

7. The relevance of Fig 4 is not clear.

8. In the covariate data from Fig 5, in what context are all of the antibiotics listed on the x-axis? From this figure, relevant covariates are not clear.

9. Fig 6, the relevance of the variance proportion is not clear. The most variance is attributed to the selective section. What is the selective section referring to? What is included in there?

10. The relevance of Figure 7 is not clear. What value does a residual joint species distribution model provide? It is not clear in the text or the figure legend.

Limitations of the study are discussed clearly in the discussion but the relevance to the literature of the study findings are not clear.

Reviewer #2: The manuscript presents an insightful and methodologically sophisticated investigation into the ecological determinants of colonizing antibiotic-resistant Escherichia coli strain assemblages in a community setting. The integration of antibiotic exposure, dispersal processes, and inferred biotic interactions within a joint species distribution modeling framework is commendable and reflects a contemporary, systems-level approach to understanding antimicrobial resistance dynamics.

The study is technically sound, with appropriate use of longitudinal surveillance data, spatially explicit predictors, and Bayesian modeling techniques. The application of the HMSC framework, coupled with convergence diagnostics and complementary analyses (e.g., SparCC correlations and null model simulations), demonstrates a high level of analytical rigor. The findings regarding the roles of antibiotic selection, colonization legacy (priority effects), and dispersal are generally well supported by the data and provide valuable contributions to the field.

However, several aspects warrant careful consideration and clarification:

1. Interpretation of Biotic Interactions:

While the manuscript attributes observed patterns to biotic interactions and positive feedback mechanisms, these inferences are largely indirect, based on residual correlations, bimodality, and background density effects. The authors are encouraged to temper causal language and more explicitly acknowledge the inferential nature of these conclusions.

2. Explained Variance and Model Limitations:

The model explains a relatively modest proportion of variance (~10%), suggesting that important unmeasured factors may influence strain assemblages. This limitation should be more prominently discussed, particularly in relation to the strength and generalizability of the conclusions.

3. Outcome Transformation:

The conversion of resistance proportions into binary presence–absence variables may result in loss of information. The authors may wish to justify this choice more explicitly or discuss its potential implications for sensitivity and interpretation.

4. Spatial Interpolation of Predictors:

The reliance on interpolated antibiotic exposure and background density surfaces introduces potential spatial smoothing biases. A brief discussion of the uncertainty associated with these interpolations would strengthen the methodological transparency.

5. Data Availability:

The data are not fully publicly available and are accessible only upon request and approval due to regulatory constraints. While this is understandable, it limits reproducibility and should be clearly aligned with the journal’s data-sharing policies.

6. Language and Presentation:

The manuscript is generally well written and intelligible; however, minor grammatical inconsistencies, occasional awkward phrasing, and overly long sentences are present. A thorough language edit would improve clarity and readability.

7. Scope and Generalizability:

The study is conducted within a single, highly specific setting. The authors should further emphasize the context-dependent nature of their findings and exercise caution in extrapolating to broader populations.

Despite these limitations, the manuscript addresses an important and timely topic and offers meaningful ecological insights into antimicrobial resistance dynamics. With minor revisions to improve clarity, temper interpretation, and address methodological considerations, the manuscript would be suitable for publication.

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Reviewer #1: No

Reviewer #2: No

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Antibiotics and priority effects shape colonizing resistant Escherichia coli strain assemblages in a community setting

PONE-D-26-03469R1

Dear Dr. Ng’eno,

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.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Muhammad Hussnain Siddique

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

Reviewer #2: 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

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 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

Reviewer #2: Yes

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-->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

Reviewer #2: Yes

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-->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)

Reviewer #2: The manuscript entitled “Antibiotics and priority effects shape colonizing resistant Escherichia coli strain assemblages in a community setting” addresses an important and timely topic concerning antimicrobial resistance ecology in densely populated community settings. The study integrates ecological theory with epidemiological analysis and provides novel insights into the role of antibiotic exposure, dispersal, and priority effects in shaping resistant E. coli assemblages. The manuscript is generally well structured, scientifically relevant, and supported by an extensive dataset. All the concerns were addressed satisfactorily.

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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: No

Reviewer #2: No

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