Transfer Alert

This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present.

PONE-D-24-33778A Comprehensive Outline of Antimicrobial Resistance, Antibiotic Prescribing, and Antimicrobial Stewardship in South Africa: A Scoping Review ProtocolPLOS ONE

Dear Dr. Ahmed,

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 Nov 21 2024 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.

Please include the following items when submitting your revised manuscript:

• 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,

Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

Academic Editor

PLOS ONE

Journal requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. We note that you have indicated that there are restrictions to data sharing for this study. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions.

Before we proceed with your manuscript, please address the following prompts:

a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., a Research Ethics Committee or Institutional Review Board, etc.). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent.

b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see

https://journals.plos.org/plosone/s/recommended-repositories. You also have the option of uploading the data as Supporting Information files, but we would recommend depositing data directly to a data repository if possible.

We will update your Data Availability statement on your behalf to reflect the information you provide.

3. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process.

4. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript.

5. 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?

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: Partly

Reviewer #2: Yes

Reviewer #3: Partly

**********

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

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: N/A

**********

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: Yes

Reviewer #3: No

**********

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

Reviewer #3: Yes

**********

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: I believe this should be a protocol instead of research article, as I understand that the main article is still currently on and not submitted for publication yet, because most of the work results has not been presented, so you might want to change it from the online submission form or kindly clarify.

Reviewer #2: I appreciate the effort of the authors, just a few concerns about methodology to be addressed:

Methods

Search strategy: Provide the comprehensive search strategy for all databases used.

Study selection: Will any software (such as Rayyan or Covidence) be used for article screening?

Will any reference manager software used for deduplication of articles?A software should be used according to updated JBI Synthesis methodology. Please include these details.

See the following references for guidance

Peters, M. D. J., Marnie, C., Tricco, A. C., Pollock, D., Munn, Z., Alexander, L., McInerney, P., Godfrey, C. M., & Khalil, H. (2020). Updated methodological guidance for the conduct of scoping reviews. JBI Evidence Synthesis, 18(10), 2119–2126. https://doi.org/10.11124/JBIES-20-00167

- Peters, M. D. J., Godfrey, C., McInerney, P., Khalil, H., Larsen, P., Marnie, C., Pollock, D., Tricco, A. C., & Munn, Z. (2022). Best practice guidance and reporting items for the development of scoping review protocols. JBI Evidence Synthesis, 20(4), 953–968. https://doi.org/10.11124/JBIES-21-00242

Reviewer #3: Thank you for the opportunity to review your manuscript. I have provided some recommendations that I hope the authors find helpful.

Introduction

Lines 102-105: A recommendation is to put this information in a paragraph format, as a continuation of line 101.

Methods and analysis

Review question/research question: What is the difference between the review question and the research question? Lines 141-143 outlines the review question, while Lines 151-152 outline the key research question. Please clarify the difference between these two types of questions for the benefit of the reader. Research questions typically tend to be at the end of the introduction or background section. A recommendation is to include the research questions for the scoping review at the end of the introduction section.

Search Strategy: There is a need for more information in the inclusion criteria. Studies published within what timeframe are considered for inclusion in the study? The abstract mentions the consideration of all types of study designs for inclusion in the review. However, the body of the scoping review makes no mention of the study designs considered for inclusion. What specific types of study designs would be included in the review? How would the reviewers manage including data from different types of studies? For example, how would data from quantitative and qualitative studies; as well as data from cross-sectional studies and systematic reviews/meta-analysis be managed and analyzed for reporting?

Boolean terms: Would it be helpful to have a subsection for the Boolean terms used for the search strategy as a follow up to the search strategy section?

Literature screening, data extraction and charting: What platform would be used for screening selected papers? Information about key elements in the data extraction form would look better in a paragraph format, rather than in the numbered format. See Lines 195-199 for reference.

Abbreviations: Cross-check if PRISMA-SCR should be written as PRISMA-SCR or PRISMA-ScR. The formatting of the abbreviations and their respective full meanings do not follow the same format. Format LMIC, PCC, PRISMA-SCR and WHO to follow the same format as AMR. See Lines 205-207 for reference.

Appendix: Cross-check the respective PRISMA-SCR checklists to ensure that the corresponding items have the same correct page numbers.

Thank you for the opportunity to review this manuscript, I hope the authors find the feedback helpful.

**********

6. 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: Abdulhakeem Binhambali

Reviewer #2: Yes: Olubunmi Margaret Ogbodu

Reviewer #3: No

**********

[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. Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: Reviewers comment.docx

Attachment

Submitted filename: Highlighted corrected PONE-D-24-33778_reviewer.pdf

PONE-D-24-33778R1A Comprehensive Outline of Antimicrobial Resistance, Antibiotic Prescribing, and Antimicrobial Stewardship in South Africa: a scoping review protocolPLOS ONE

Dear Dr. Ahmed,

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 Jan 03 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.

Please include the following items when submitting your revised manuscript:

• 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,

Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

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

1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions?

The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field.

Reviewer #1: Yes

Reviewer #3: Yes

**********

2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses?

The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory.

Reviewer #1: Yes

Reviewer #3: Partly

**********

3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable?

Descriptions of methods and materials in the protocol should be reported in sufficient detail for another researcher to reproduce all experiments and analyses. The protocol should describe the appropriate controls, sample size calculations, and replication needed to ensure that the data are robust and reproducible.

Reviewer #1: Yes

Reviewer #3: No

**********

4. Have the authors described where all data underlying the findings will be made available when the study is complete?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception, at the time of publication. 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 #3: No

**********

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 #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics.

You may also provide optional suggestions and comments to authors that they might find helpful in planning their study.

(Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This protocol outlines a scoping review aiming to map the evidence on antimicrobial resistance (AMR), antibiotic prescribing practices, and antimicrobial stewardship (AMS) initiatives within South Africa. It aims to address the current state of AMR awareness, antibiotic prescribing patterns, and the implementation of AMS programs in healthcare settings. While the protocol offers a comprehensive approach, several areas could also benefit from further clarification, improvement, and refinement to strengthen the review's overall quality.

Although, the review addresses a highly pertinent global health issue, especially in low- and middle-income countries (LMICs), like South Africa and the aims and objectives of the review are clearly articulated, with a focus on key aspects of AMR in South Africa, including prescribing practices and stewardship efforts however, the inclusion and exclusion criteria (e.g., “studies published in English”) could be better justified. While it is understandable that language barriers may limit accessibility, non-English studies could offer valuable insights, especially in multilingual settings like a Nation as South Africa. It would be beneficial to include a rationale for this exclusion.

Also, excluding animal and environmental studies might be overly restrictive. Many environmental and veterinary studies contribute to understanding AMR dynamics in healthcare settings, especially in LMICs. The authors should provide a more robust argument for excluding these studies or consider including them for a more holistic perspective.

Reviewer #3: Thank you again for the opportunity to review your manuscript. Some feedback and questions from the previous review were not addressed. I reiterated some content from the previous review that were not addressed and provided additional feedback on the updated version of the manuscript.

Abstract

Line 75: It is important to define abbreviations before they are used. Please define AMR before using it.

Line 79: Define PRISMA before the use of the abbreviation.

Introduction

Line 117: Define AMS before using the abbreviation.

Methods and analysis

Lines 131-147: Previous feedback about review question/research question have not been addressed. There are research/review questions in two sections of the manuscript. What is the difference between the review question and the research question? Please clarify the difference between these two types of questions for the benefit of the reader. What are the author’s thoughts about including all the questions in one section? Research questions typically tend to be at the end of the introduction or background section. A recommendation is to include the review/research questions for the scoping review at the end of the introduction section. The rationale for scoping review section could stay in position as the final part of the introduction section, following which all the questions from lines 131-132 and 146-147 could be presented.

Line 156-164: Search strategy. Previous feedback about the search strategy has not been addressed. There is a need for more information in the inclusion and exclusion criteria. Would the year of publication be part of the search criteria? What specific types of study designs would be included in the scoping review? How would the reviewers manage including data from different types of studies? For example, how would data from quantitative and qualitative studies; as well as data from cross-sectional studies and systematic reviews/meta-analysis be managed and analyzed for reporting?

Line 163-164: Would “healthcare workers” referenced in Line 191, rather than “healthcare” currently included as a Boolean term be used as a Boolean term for the literature search?

A recommendation for smoother flow in reading information in the paper is to include the inclusion and exclusion criteria as well as the identification of relevant studies in the search strategy section. The study selection section can come after this section and lead to the data extraction and charting section.

Previous feedback about the literature screening, data extraction and charting have not been addressed. What tool, application or platform would be used for screening data extraction of the selected papers?

Data extraction and charting

Lines 200-204: Information about key elements in the data extraction form would look better in a paragraph format, rather than in the numbered format.

Thank you again for the opportunity to review your manuscript. I hope the authors find this feedback helpful.

**********

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: ABDULHAKEEM BINHAMBALI

Reviewer #3: No

**********

[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. Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: R1 Reviewers comment.docx

A Comprehensive Outline of Antimicrobial Resistance, Antibiotic Prescribing, and Antimicrobial Stewardship in South Africa: a scoping review protocol

PONE-D-24-33778R2

Dear Dr. Ahmed,

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.

An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Page 10: lines 214-215 - Please replace this sentence "Two reviewers (SA and RA) will be screen titles and abstracts independently, against the predetermined inclusion and exclusion criteria" WITH "Two reviewers (SA and RA) will independently screen titles and abstracts against the predetermined inclusion and exclusion criteria".

Reviewers' comments: