PONE-D-23-38872Protocol for surveillance of antimicrobial-resistant bacteria causing community-acquired urinary tract infections in low-income countriesPLOS ONE

Dear Dr. Majigo,

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We look forward to receiving your revised manuscript.

Kind regards,

Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

Academic Editor

PLOS ONE

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

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When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

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"We thank the Ending Pandemics program, Connecting Organizations for Regional Disease Surveillance (CORDS), and East and Southern Africa regional Technical Working Group members for providing valuable insight. We are grateful for the guidance provided by the Ending Pandemics Team. We gratefully acknowledge the technical and funding support received for developing this protocol from the Fleming Fund Grant provided by the UK Department of Health and Social Care (DHSC) and the Mott MacDonald agent for administering this grant." 

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Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: 

"The Fleming Fund Regional grant number FF49/440, Regional Grants Round 2, funded the development of this protocol. The funder had no involvement in the design and development of the protocol."

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does the manuscript report a protocol which is of utility to the research community and adds value to the published literature?

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the protocol been described in sufficient detail?

To answer this question, please click the link to protocols.io in the Materials and Methods section of the manuscript (if a link has been provided) or consult the step-by-step protocol in the Supporting Information files.

The step-by-step protocol should contain sufficient detail for another researcher to be able to reproduce all experiments and analyses.

Reviewer #1: No

Reviewer #2: No

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3. Does the protocol describe a validated method?

The manuscript must demonstrate that the protocol achieves its intended purpose: either by containing appropriate validation data, or referencing at least one original research article in which the protocol was used to generate data.

Reviewer #1: Yes

Reviewer #2: Yes

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4. If the manuscript contains new data, have the authors made this data 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: N/A

Reviewer #2: N/A

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5. Is the article 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 highlight any specific errors that need correcting in the box below.

Reviewer #1: Yes

Reviewer #2: No: The manuscript will benefit from garamma check

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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: Good to see such critical thinking on ways to improve AMR surveillance, and to reduce its burden on the health care system.

I have comments attched.

Reviewer #2: This document outlines a well-structured protocol for antimicrobial resistance (AMR) surveillance of community-acquired urinary tract infections (UTI). The document clearly defines target populations, enrollment criteria, and surveillance areas. It emphasizes the importance of standardized operating procedures (SOPs) for sample collection, handling, transportation, and laboratory testing. The protocol mentions proficiency testing and internal quality assurance for maintaining data integrity. It highlights the importance of data management, analysis, reporting, and sharing.

There are a few areas needing clarification as follows;

1. WHO has classified Enterobacterales carbapenem-resistant and 3rd generation cephalosporin-resistant as critical priority pathogens – This statement is unclear

2. who are residents of a given surveillance area and passively presenting to a health facility for health care – please clarify what ‘passively’ means in this case

3. In addition, the protocol aligns with WHO AMR surveillance guidelines – Reference required

4. community-acquired urinary tract infections in low-income countries are published on protocols.io. – Do the writers mean low income or low-middle income?

5. Table 1 – Lab tests such ass urinalysis and urine microscopy are not usually regarded as ‘signs’

6. Table 3 – May be rather simplistic as it does not into account intrinsic resistance

7. For urinalysis- Include any caution in specimen preserved with boric acid

8. Isolates should be safely transported monthly to the AMR Reference laboratory for additional tests and storage at -80 OC per country SOP for isolate management – is storage at this temperature possible at district level?

9. The QA for AST does not comply with CLSI as stated in the protocol

Overall, a more comprehensive protocol will allow for seamless implementation.

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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.

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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: Yes: Nubwa Medugu

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Attachments

Attachment

Submitted filename: AMR REVIEW.docx

Protocol for surveillance of antimicrobial-resistant bacteria causing community-acquired urinary tract infections in low-income countries

PONE-D-23-38872R1

Dear Dr. Majigo

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,

Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does the manuscript report a protocol which is of utility to the research community and adds value to the published literature?

Reviewer #1: Yes

Reviewer #2: Yes

**********

2. Has the protocol been described in sufficient detail?

To answer this question, please click the link to protocols.io in the Materials and Methods section of the manuscript (if a link has been provided) or consult the step-by-step protocol in the Supporting Information files.

The step-by-step protocol should contain sufficient detail for another researcher to be able to reproduce all experiments and analyses.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Does the protocol describe a validated method?

The manuscript must demonstrate that the protocol achieves its intended purpose: either by containing appropriate validation data, or referencing at least one original research article in which the protocol was used to generate data.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. If the manuscript contains new data, have the authors made this data 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: N/A

Reviewer #2: N/A

**********

5. Is the article 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 highlight any specific errors that need correcting in the box below.

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: The author made all the corrections that were identified in the last version of the manuscript.

The author should align the references according to the journal standards.

Reviewer #2: I am pleased to recommend acceptance of the revised manuscript titled "Protocol for Surveillance of Antimicrobial-Resistant Bacteria Causing Community-Acquired Urinary Tract Infections in Low-Income Countries." The authors have comprehensively addressed all feedback and suggestions from the reviewers. The protocol offers a clear and well-defined approach for monitoring antimicrobial resistance (AMR) in this critical area for low-income countries.

This study holds significant value as it directly addresses the growing threat of AMR in community-acquired UTIs, a prevalent health concern in these settings. The outlined protocol provides a practical and sustainable approach for resource-limited settings, making it widely applicable.

Given the thorough revisions, the absence of ethical or technical concerns, and the manuscript's potential impact, I strongly recommend acceptance for publication.

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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: Yes: Dr Nubwa Medugu

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