PONE-D-24-29224Diagnosis of neonatal and adult sepsis using a Serum Amyloid A lateral flow test.PLOS ONE

Dear Dr. Doyle,

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.

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ACADEMIC EDITOR:Please address all issues raised by the reviewers. Pay attention to the comments related to the methods section and ensure that the conclusions are an accurate reflection of any new changes made. Please carefully proof-read your manuscript before submitting the revised version.

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Please submit your revised manuscript by Oct 07 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,

Novel N. Chegou, Ph.D

Academic Editor

PLOS ONE

Journal requirements: 1. When submitting your revision, we need you to address these additional requirements. 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. Thank you for stating the following in the Acknowledgments Section of your manuscript: [This work was funded by Science Foundation Ireland (SFI) and Irish Aid (Project codes: 21/FIP/SDG/9917 and 21/FIP/SDG/9917P). Special thanks to all Stakeholders involved across Ireland and Uganda, as well as everyone who participated in sample and data collection including all patients, families, nurses, clinicians and laboratory scientists. The Health Innovation Hub Ireland (HIHI) is acknowledged and thanked for assisting with assessment of NeoSep-SAA at the Mercy University Hospital.]We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 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:  [This work was funded by Science Foundation Ireland (SFI) and Irish Aid (Project codes: 21/FIP/SDG/9917 and 21/FIP/SDG/9917P). Authors initials who obtained funding: SD, PW, NM, FN and MD.The funders played no role in the study design, data collection or analysis, decision to publish or preparation of the manuscript. https://www.sfi.ie/funding/funding-calls/future-innovator-sdg/] Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 3. In the online submission form, you indicated that [The data underlying the results presented in the study are available from the Corresponding Authors.]. All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information.This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons on resubmission and your exemption request will be escalated for approval.  4. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 

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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: I Don't Know

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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?

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: No

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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: Reviewer comments

Manuscript title: Diagnosis of neonatal and adult sepsis using a Serum Amyloid A lateral flow test.

Manuscript number: PONE-D-24-29224

Abstract

1. Page 2, line 35: Author states (AS)…’The difficulty in diagnosing neonatal sepsis……. sepsis-specific biomarkers.’

Reviewer comment (RC): The greatest difficulty is that the ‘Gold Standard’ for diagnosis of sepsis i.e. Blood culture is not always positive even in the presence of true sepsis and the long time it takes for the Blood culture result to be available even with BACTEC/BacTAlert.

A mention of this limitation must be made in the Introduction.

2. Page 2, line 38: AS….’as a superior biomarker for the diagnosis of neonatal sepsis.’

RC: Acute phase reactants can only be used to indicate the probable diagnosis of sepsis or the absence of of sepsis (High NPV) in a neonate with commensurate clinical symptoms and signs. They are not a definitive test for diagnosis of sepsis. Throughout the manuscript, authors have mentioned the role of SAA as a diagnostic test. Even though I do not want to take away the enthusiasm of the research team and the authors, the manuscript must be modified where it is made abundantly clear that SAA is only a novel biomarker for the probable diagnosis of neonatal sepsis.

3. Page 2, line 40: AS…. blood at patient-side….

RC: … at patient bedside….

4. Page 2, line 40: AS….low resource environment…

RC: I suggest that ‘resource constrained’ or ‘resource limited’ be used throughout the manuscript rather than ‘low resource’.

5. Page 2, line 46: AS…..(sensitivity: 37 %)…’.

RC: This sensitivity for CRP was as noted in the study cohort. However, abundant published literature has noted the sensitivity to be in the range as reported for the SAA.

6. Page 2, line 51: AS….SDG 3.2 objectives.

RC: SDG can be expanded for the first time and subsequently can be mentioned as SDG throughout the text.

Introduction

1. The introduction is rambling and requires to be made more focussed.

2. Why did the authors select SAA over Serum Procalcitonin and CRP?

3. Colorimetric card tests are available for CRP, PCT and are very efficiently being used in field out of hospital settings. Then why SAA?

4. In a suspected sepsis patient one would be collecting samples for Complete Blood Counts (CBC) and Blood culture. Thus minimally invasive sampling for SAA wold not be much of a benefit.

5. In most neonatal units in neonates suspected to be having sepsis based on clinical features, antibiotic therapy would be initiated. Are the authors implying that use of SAA can limit starting antibiotics in symptomatic neonates before the results of blood/CSF/ urine culture are available. I think not. Thus the introduction must be about the ability of SAA to help a clinician stop antibiotics early.

6. The hypothesis is not clearly stated.

7. The aim of the study must be stated in the last paragraph of the introduction.

Material & methods

1. Page 6, line 143-145: AS….’up to 66% of patient specimens and donors should have evidence of inflammation to indicate presence of SAA in said test specimens’.

RC: How was this figure of 66% positive patient samples decided?

2. Page 7, line 153: AS…’Suspicion of sepsis….’

RC: See comment Sr no. 2 for Abstract section.

Page 7, line158: AS….’factors represents the reality of assessing neonates…’

RC: This statement is suited in the introduction/discussion section and not in the methods section.

3. Page 6, line 169: AS…..suspected infection…..’.

RC: This has been stated in the sentence and seems like a duplication.

Results

1. Page 12, line 276-277: AS….’sensitivity and specificity of the NeoSep-SAA for diagnosis of neonatal sepsis of 92% (89%, 95%) and 73% (68%, 77%), at 95% CI, respectively’.

RC: The high sensitivity and NPV and lower specificity and PPV indicate towards a role as a screening test for neonatal sepsis.

2. Page 12, line 283: AS….’ Additionally, 78 neonates within the CCG were clinically diagnosed with sepsis (Confirmed Sepsis: CS).’

RC: Confirmed sepsis can only be neonates where Blood/urine/CSF culture yielded growth of a bacteria not likely to be a contaminant. For all other cases the diagnosis can be probable sepsis.

Discussion and conclusion

1. These will have to be modified based on the comments given above.

Reviewer #2: Major

Overall

1. Proofread for grammatical errors, typos, and inconsistencies. Ensure that the language is formal and appropriate for a scientific audience.

Introduction

1. Several sentences are long and complex, making them difficult to follow. Breaking them into shorter sentences can improve readability and clarity.

2. The introduction uses both "per annum" and "annually." Consistency in terminology is essential. Use one term consistently.

3. Ensure that technical terms and jargon are explained clearly for readers who may not be familiar with them.

4. Clearly state the objectives and aims of the study in relation to the problem outlined. This helps in setting up the context for the research.

Methodology:

1. Its too long

2. Define terms and abbreviations when first introduced and ensure they are used consistently. For instance, “SAA” should be defined as “Serum Amyloid A” when first mentioned.

3. Break down long or complex sentences into shorter, clearer ones. This will improve readability and comprehension.

4. The text often repeats phrases or concepts, such as "SAA lateral flow test," which can make the content seem redundant. Recommendation is to streamline repetitive language and consolidate similar information to enhance readability and maintain focus.

5. The text sometimes shifts terminology without clear definition, such as switching between "hospital negative control" and "combined negative controls.Define and consistently use terminology throughout the document. Ensure that all abbreviations and terms are clearly defined upon their first use.

6. Some sentences are overly complex or informal, which can hinder understanding. Phrases like "gives the green light" are less formal and can be replaced with more precise language. Rephrase sentences to be more formal and concise. Break up long sentences into shorter, clearer statements.

Discussion:

1. The discussion is lengthy and contains complex sentences, which may overwhelm readers. Breakdown lengthy sentences into shorter, more digestible parts. Ensure each paragraph conveys a single main idea or argument.

2. Some points are repeated, such as the performance metrics of NeoSep-SAA compared to CRP. Avoid repetition by consolidating similar points and emphasizing unique findings in different sections.

3. The use of technical terms and abbreviations may be difficult for non-specialist readers to understand. Define technical terms and abbreviations upon first use and consider adding a glossary or simplifying explanations where possible.

4. While the discussion includes relevant information, some background details on why the test is needed are not fully fleshed out. Provide more context about the global burden of neonatal sepsis and the limitations of current diagnostic methods to highlight the importance of NeoSep-SAA.

5. While the potential impact of NeoSep-SAA is mentioned, the discussion could better explore its practical applications and limitations.

6. The section on future work is somewhat brief and lacks specific suggestions for further research. Elaborate on potential future studies, including how NeoSep-SAA might be combined with other diagnostic tools or tested in different populations.

Minor

1. Line 55 – spell out UN SDG

2. Line 60 - https://www.unicef.org/uganda/research-and-reports add the reference as well.

3. Line 61-65 – sentence is too long

4. Line 65 – these contribute….. consider these factors contribute

5. Line 67 – ASSURED should be (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free and Deliverable)

6. Line 68 – reference should be like [3,4]

7. Line – 118 - NeoSep-SAA – spell out

8. Line 118 - the URL inclusion is not standard in the body of the text. URLs should be included in the references section or integrated into the text more seamlessly.

9. Line 147 – informed consent……should be in ethics sub heading

10. Line 243 – WHO reference

11. Line 250-252 - sentence is lengthy and could benefit from breaking into two for better readability.

12. Line 299 – not good to start the sentence with an abbreviation

13. Line 316-318 – rephrase if for clarity

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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: Vishal Vishnu Tewari

Reviewer #2: No

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[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.

PONE-D-24-29224R1Diagnosis of neonatal and adult sepsis using a Serum Amyloid A lateral flow test.PLOS ONE

Dear Dr. Doyle,

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 Dec 25 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,

Novel N. Chegou, 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.

Additional Editor Comments:

Please attend to the additional queries from Reviewer no 1

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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: (No Response)

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: I Don't Know

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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: Reviewer comments

Manuscript title: Diagnosis of neonatal and adult sepsis using a Serum Amyloid A lateral flow test.

Manuscript number: PONE-D-24-29224R1

Abstract

1. Page 2, line 38: Author States (AS)….’as a superior biomarker for the diagnosis of neonatal sepsis.’

Reviewer comment (RC): The authors have missed the point which I was trying to make.

The above sentence is required to be framed as …’as a superior biomarker for use in the sepsis screen for neonatal sepsis.’ OR ’….as a superior biomarker for the diagnosis of probable neonatal sepsis.’

Introduction

1. I thank the authors for their clarification of the queries raised.

The authors response to the undermentioned queries no. 2, 3, 4 from the previous review may be added in a concise form in the introduction, material & methods or discussion section.

2. Why did the authors select SAA over Serum Procalcitonin and CRP?

3. Colorimetric card tests are available for CRP, PCT and are very efficiently being used in field out of hospital settings. Then why SAA?

4. In a suspected sepsis patient one would be collecting samples for Complete Blood Counts (CBC) and Blood culture. Thus minimally invasive sampling for SAA wold not be much of a benefit.

Results

The explanation that ‘These 78 neonates were clinically diagnosed with sepsis by clinicians independent of the NeoSep-SAA result.’ Must be adequately be mentioned in the manuscript at a relevant place.

Reviewer #2: Reviewer has addressed all the comments and suggestions from the editor and the reviewers, and I have no additional comments.

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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: Vishal Vishnu Tewari

Reviewer #2: Yes: Sana Mahtab

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[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.

Diagnosis of neonatal and adult sepsis using a Serum Amyloid A lateral flow test.

PONE-D-24-29224R2

Dear Dr. Doyle

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,

Novel Njweipi Chegou, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: