Dear Dr. Perovic,

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Mohamed O Ahmed, Ph.D

Academic Editor

PLOS ONE

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“This study data analysis was made possible with funding received by the Global Antibiotic Research and Development Partnership (GARDP) from the South African Medical Research Council (SAMRC). The authors acknowledge the GERMS-SA team for laboratory and epidemiology-based surveillance and the National Health Laboratory Service Corporate Data Warehouse (CDW) for the data.”

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4. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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

Reviewer #1: No

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. 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: This study was carried out with a sound methodology. It is well discussed in the manuscript.The conclusion is too general. However the conclusion is too general. The authors should rewrite the conclusion to specifically address and justify their findings.

Reviewer #2: Dear Authors, please review my comments and suggestions in the attached document. Additionally, ensure that abbreviations are used consistently and that comma delimiters are applied uniformly in the reporting of results.

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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.

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Reviewer #1: Yes:  Gülsüm İclal Bayhan

Reviewer #2: Yes:  Michelle Lowe

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

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Attachments

Attachment

Submitted filename: PONE-D-24-22805_reviewer_Manuscript_Reviewer comments.pdf

Dear Dr. Perovic,

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.

Please submit your revised manuscript by Feb 28 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Mohamed O Ahmed, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #3: (No Response)

**********

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

Reviewer #3: Yes

**********

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

Reviewer #3: Yes

**********

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

The PLOS Data policy

Reviewer #3: Yes

**********

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

Reviewer #3: Yes

**********

Reviewer #3: The manuscript presents a comprehensive surveillance study of carbapenem-resistant Enterobacterales (CRE) in South Africa from 2015 to 2021. The updated version demonstrates significant improvements addressing most of the reviewers' previous concerns. However, some additional issues should be addressed to further enhance the clarity, rigor, and overall flow of the manuscript.

Abstract and Clarity:

The modifications made to the abstract (lines 31–48) have improved its readability. Ensure that abbreviations (e.g., GNB, CRF) are used consistently across the entire abstract and that all abbreviations are clearly defined upon first use.

The sentence on lines 35–38 ("We aimed to provide a holistic overview...") is now clearer; however, further simplification would improve flow. Consider shortening by merging overlapping ideas.

Introduction:

The revised introduction effectively sets the context. However, some references added (lines 74 and 83) are quite general and may not fully support the specific claims. Ensure they are the most relevant sources.

Methods Section:

The additional clarifications in lines 121–132 improve the description of audit cases. However, the rationale for excluding certain samples could benefit from brief elaboration.

Lines 149–150 ("Viable CRE BSI isolates...") now reference CHARM clearly; this is a welcome improvement.

Results and Figures:

Figures 4A and 4B have been revised as requested, with corrections to italics for "bla" genes and corrected spelling for "KwaZulu-Natal." These changes enhance accuracy.

Check whether additional legends or annotations can further improve figure readability, particularly where percentages are presented alongside totals.

The overall presentation of statistical results is clearer. However, certain segments, such as the resistance trends (lines 354–373), are still slightly dense. Use bullet points where possible to improve readability.

Discussion:

The discussion was refined to address gaps in interpretation. However, ensure that references support each key assertion, especially regarding carbapenemase distribution.

Consider tightening the language in lines 421–427 and 434–438 to reduce redundancy and improve clarity.

Tables and Supplementary Materials:

The tables now include necessary details, but cross-referencing them within the text (e.g., S1–3 Tables) remains crucial for coherence. Double-check for proper placement of in-text citations.

Suggested Minor Edits:

Ensure uniformity in decimal formatting (e.g., percentages).

Confirm spelling consistency (e.g., "sulfonamide" vs. "sulphonamide").

Verify alignment between legends, figures, and main text descriptions.

**********

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 #3: Yes:  Maurizio Sanguinetti

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org

Carbapenem-resistant Enterobacterales among patients with bloodstream infections in South Africa: consolidated surveillance data, 2015-2021

PONE-D-24-22805R2

Dear Dr. Perovic,

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,

Mohamed O Ahmed, Ph.D

Academic Editor

PLOS ONE