PONE-D-23-07664Peptide barcode of multi drug resistant strains of Neisseria gonorrhoeae isolated from patients in ThailandPLOS ONE

Dear Dr. Arpornsuwan

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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Benjamin M. Liu, MBBS, PhD, D(ABMM), MB(ASCP)

Academic Editor

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: Partly

Reviewer #2: Partly

Reviewer #3: Partly

Reviewer #4: Yes

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

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: N/A

Reviewer #4: 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: No

Reviewer #2: Yes

Reviewer #3: No

Reviewer #4: 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: No

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: 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: Summary : It is a very interesting and relevant topic. Determining the antibiotic susceptibility of Neisseria gonorrhoeae by mass spectrometry(MS) will help in easy and early detection of antibiotic resistance and hence efficient treatment of patients. Identification of biomarkers of resistance is also very useful.

Over all Impression: The study combines two research questions. First, generating the peptide barcodes for the different groups of antibiotic resistant Neisseria gonorrhoeae, secondly discovering the peptide biomarker of the antibiotic resistance by LCMS. The results, data and statistical analysis of both the experiments have not been presented adequately in the manuscript.

Major issues:

1. The result part of the MALDI-TOF peptide barcoding , from line number 203, does not clearly provide clear information and data regarding the differences in the peaks of the spectra of the different antibiotic resistance groups mentioned in the study. The Figure 1 is not clear and does not mention the above information. The statistical analysis and Odd's ratio for the same is not reported.

2. Which test of statistical analysis for the LCMS test has been done? The figures of the of the LCMS tests are not very clear.

Minor issues: I suggest that the authors hire a copy editor.

The manuscript deals with important topics of detection of antibiotic resistance by MALDITOF and discovering peptide biomarker of antibiotic resistance by LCMS. If the authors can provide the aforementioned details, it will be a valuable contribution to the research in antibiotic resistance.

Reviewer #2: 1. Novelty statement should be included, as identified 9 peptides are already known for their function in N. gonorrhoeae.

2. What are the Inclusion and Exclusion criteria?

3. What are the limitations of the study?

4. Why sample size is small?

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Reviewer #3: 1. In the abstract and entire document, the name "Neisseria gonorrhoea" should all be typed in italics

2. Line 39, insert "of" between prevalence and infection.

3. line 56 remove hyphen from the word "de-creased"

4. Line 70, include year for the citation mentioned.

5. Line 96, the initial sentence can be re-written as "Sixty-three of the 91 isolates showed resistance to ........"

6. Line 112 remove hyphen from the word "performed"

7. Change "E test" to "E-test"

8. In section 2.5, I think is will be appropriate to describe or provide more detail on how the different bacterial groups were pooled together.

9. Line 300, use the word "consistent"

10. IMPORTANT COMMENT

There appears to be a significant missing link in the results presented in this study. The results obtained in the MIC determination using the E-test strip is not shown. The authors should present the result and further correlate with the peptidome obtained for the bacterial isolates.

This will provide a further validation of the use of the MALDI-TOF as suggested by the authors.

Reviewer #4: 1. There are some language and grammatical errors throughout the manuscript text that should be corrected.

2. Please define the abbreviations at the first mention of them in the text for example, IRB in line 93; PPNG: in line 97.

3. The data of Table 1 is repeated in the text, so this table could be deleted.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes: Dr. Ayodele Oluwaseun AJAYI

Reviewer #4: Yes: Mohammad Hossein Ahmadi

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PONE-D-23-07664R1Peptide barcode of multi drug resistant strains of Neisseria gonorrhoeae isolated from patients in ThailandPLOS ONE

Dear Dr. Arpornsuwan,

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 Aug 20 2023 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-emailutm_source=authorlettersutm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Benjamin M. Liu, MBBS, PhD, D(ABMM), MB(ASCP)

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. 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

Reviewer #4: 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

Reviewer #4: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #4: 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

Reviewer #4: Yes

**********

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

Reviewer #4: 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: Summary:The issues raised in the previous review have been addressed adequately. The manuscript is also presented in intelligible fashion.

Minor issue:

1.The authors could mention the limitations of the study, the MALDI TOF MS in particular as mentioned in the response to reviewers "However, the specific antibiotic resistance peptides on MALDI-TOF mass spectra are difficult to identify due to their low abundance or high molecular weights"

Reviewer #2: (No Response)

Reviewer #4: The authors have adequately addressed all my comments raised in the previous round of review and I think this manuscript is now acceptable 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: Shivankar Agrawal

Reviewer #4: Yes: Mohammad Hossein Ahmadi

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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.

Peptide barcode of multi drug resistant strains of Neisseria gonorrhoeae isolated from patients in Thailand

PONE-D-23-07664R2

Dear Dr. Arpornsuwan,

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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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,

Benjamin M. Liu, MBBS, PhD, D(ABMM), MB(ASCP)

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: