PONE-D-23-15982Population structure of community-acquired extended-spectrum beta-lactamase producing Escherichia coli and methicillin resistant Staphylococcus aureus in a French region showed no difference between urban and rural areasPLOS ONE

Dear Dr. Biguenet,

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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: Yes

Reviewer #2: Partly

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

Reviewer #1: Yes

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: Yes

Reviewer #2: Yes

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

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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: Antimicrobial resistance is an urgent global public health threat，with high mortality rates due to infections caused by multidrug-resistant bacteria. Understanding the molecular epidemiology of multidrug-resistant bacteria acquired in the community is crucial for effectively preventing and controlling infections caused by these resistant strains.

There are also some major concerns,

1. In line 74, the authors mentioned conducting a prospective multicenter study. It is unclear whether this study underwent ethical review. Moreover, the sampling methods and detailed information regarding the samples have not been specified.

2. In Figure 1, it would be helpful to annotate each circle with specific information to indicate what each circle represents.

3. Do the authors analyze the MLST of the MRSA isolates?

4. Do the authors compare the evolutionary changes of multidrug-resistant bacteria between 2019 and 2021 in the region?

Reviewer #2: Biguenet et al. has performed a population structure/genomic analysis of ESBL producing E. coli and MRSA isolates in France - reporting the prevalence of STs and AMR genes. The authors has also studied the distribution of these characteristics in relation to the region/areas based on population size. In general the study was interesting and important to public health, and the MS was well written. However, the classification of three areas such as urban and rural was quite arbitrary, and not convincing.

Major questions:

1. line 79: population size was not the only factor. other factors such as anthropogenic activities, animal farming, agriculture, or winery would be more relevant to the relationship of isolates under one health approach. So the authors did not know where the patients were from?

2. line 169-170: The association of ESBLs and plasmids was not based on solid methodology, as only short-read sequencing data were used to determine the genetic location of these genes. Multicopy insertion elements may fragment the short-read assemblies into multiple contigs, and reconstruction of ESBL plasmids requires additional experiments, such as long-read sequencing or PCR gap closure.

3. Line 298-304: The lack of clinical data or relevant metadata had weakened the discussion and entire investigation. It was unusual that the origin of these isolates were unknown. Without knowing the source, all the discussion was kind of speculation, even though Ec ST131 tended to be circulated among the communities. Was the study supported by the ethical board?

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Reviewer #1: No

Reviewer #2: No

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Population structure of community-acquired extended-spectrum beta-lactamase producing Escherichia coli and methicillin resistant Staphylococcus aureus in a French region showed no difference between urban and rural areas

PONE-D-23-15982R1

Dear Dr. Biguenet,

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,

Zhi Ruan, Ph.D.

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: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: 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

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

**********

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: All the questions have been addressed in the revised manuscript. An ethical statement has been included in the methods

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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: Tian Jiang

Reviewer #2: No

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