PONE-D-24-10619Nasopharyngeal Carriage, Antibiotic Susceptibility Patterns, and Associated Factors of Gram-positive Bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest EthiopiaPLOS ONE

Dear Dr. Birhanu,

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 Jun 15 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,

Tebelay Dilnessa, MSc

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. Thank you for submitting the above manuscript to PLOS ONE. During our internal evaluation of the manuscript, we found significant text overlap between your submission and previous work in the [introduction, conclusion, etc.].

We would like to make you aware that copying extracts from previous publications, especially outside the methods section, word-for-word is unacceptable. In addition, the reproduction of text from published reports has implications for the copyright that may apply to the publications.

Please revise the manuscript to rephrase the duplicated text, cite your sources, and provide details as to how the current manuscript advances on previous work. Please note that further consideration is dependent on the submission of a manuscript that addresses these concerns about the overlap in text with published work.

[If the overlap is with the authors’ own works: Moreover, upon submission, authors must confirm that the manuscript, or any related manuscript, is not currently under consideration or accepted elsewhere. If related work has been submitted to PLOS ONE or elsewhere, authors must include a copy with the submitted article. Reviewers will be asked to comment on the overlap between related submissions (http://journals.plos.org/plosone/s/submission-guidelines#loc-related-manuscripts).]

We will carefully review your manuscript upon resubmission and further consideration of the manuscript is dependent on the text overlap being addressed in full. Please ensure that your revision is thorough as failure to address the concerns to our satisfaction may result in your submission not being considered further.

3. Thank you for stating the following in your Competing Interests section:  

"The authors' have no conflict of interest"

Please complete your Competing Interests on the online submission form to state any Competing Interests. If you have no competing interests, please state "The authors have declared that no competing interests exist.", as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now 

 This information should be included in your cover letter; we will change the online submission form on your behalf.

Additional Editor Comments:

• Although what authors are reporting is not a novelty, they must however be commended for their efforts in reporting what is prevailing in their locality
• The email addresses of authors were not needed here in the main manuscript as it appears in the system except the corresponding author.
• Based on PLoS One authors’ guideline, figures must be uploaded separately in tif or other form.

• Line 27: ‘…was conducted from May 1 to August 30, 2023.’ It is better written as, ‘…was conducted from May 1, 2023 to August 30, 2023.’
• Lines 29&30: ‘Bacterial species were identified by biochemical tests.’ It is rewritten better as, ‘Bacterial species were identified by colony morphology, Gram stain and biochemical tests.’
• Lines 31 &32: ‘…… were determined using the cefoxitin disc and D-test, respectively.’ Do you think ‘cefoxitin disc and D-test’ are equivalent terms?  Drug Vs technique?
• Lines 46: Write their long form of the ‘MRSA and MDR’
• The abstract should be re-written and make adjustments based on the comments in the methods and results part that follows.

• Once you have used the long form of the name of the bacterium then you can abbreviate the genus name throughout the body of the paper, except headings and subheadings.
• The objective was not needed. Therefore, remove the objective (lines from 104- 115).

• Line 123: The total population of the town is estimated to be 412,739 by the year 2023 [28]. Here this is misleading as the population of Gondar town is not only 412,739 by 2023. It is expected above 1million. Please revise it.
• A separate subheading is needed as, ‘Study population’
• A separate subheading is needed as, ‘Sample size determination and sampling technique’
• Variables of the study should be removed (lines 140-152).
• Why you missed to include chocolate agar especially for isolation of fastidious organisms like S. peumoniae?
• What is the advantage of doing oxacillin and cefoxitin disc diffusion test concurrently? Can we perform oxacillin susceptibility test by disc diffusion for S. aureus?
• Why you miss to do ‘vancomycin susceptibility testing’, the best drug of choice for MRSA?

• During presenting the result some requires both the numerator and denominator. Similarly, associated factor assessment date requires P- value.
• All table titles should be complete in description, area and period of study.

• Most of the reason for variation mentioned in the discussion part were already intensively described by other authors.

• The conclusion was beyond your scope so revise it based on community/government importance (try to select the most important one).
• Line 479-484: Authors contribution should be removed as the system creates automatically.
• It is better also you follow the manuscript writing protocol for PloS One, especially font size, font type, reference list writing, table and figure preparation and whether figures submitted within the main manuscript or not. Additionally, binomial nomenclature for name of the bacteria was not appropriately followed.

[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

**********

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

Reviewer #1: No

Reviewer #2: Yes

**********

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

**********

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

**********

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: Manuscript Number: PONE-D-24-10619

Manuscript Title: Nasopharyngeal Carriage, Antibiotic Susceptibility Patterns, and Associated Factors of Gram-positive Bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia

Dear editor,

I would like to say thanks for giving the opportunity and the invitation. It was my pleasure to review this scientific paper. I have provided comments, reconditions, and question to the authors below:

Point by Point comments to Authors

1. The main concern of this paper is it lacks novelty. There are many researches in Ethiopia in general and even at University of Gondar Comprehensive Specialized Hospital in particular on the Nasopharyngeal Carriage and Antibiotic Susceptibility Patterns of Gram-positive isolates: (DOI:10.1016/j.pedneo.2013.03.017DOI: 10.1016/j.pedneo.2013.03.017, https://doi.org/10.3390/children4040027, https://doi.org/10.1177/23333928231186687, DOI:10.4172/2332-0877.1000109, DOI: 10.2147/IDR.S385866…..). Thus, it is better to supplement some important issues like genotypic characterizations of the isolates via extended your study time, and the study groups (please include the inpatients).

2. Why you focus only on Gram-positive bacteria? For example Gram negative bacteria like Haemophilus influenzae, Klebsiella pneumoniae, Micrococcus catarrhalis ………. Can induce Nasopharyngeal Carriage

3. What about the viral and the fungal agents? As there are some fungal and viral agents, which cause Nasopharyngeal Carriage (DOI: 10.1186/s41479-021-00088-5, https://pubmed.ncbi.nlm.nih.gov/23798081/)

4. Line number 32. Please convert Epi-Data version 4.6.0.6 to 4.6

5. Line number 43: Please convert risk factors to associated factors

6. In the abstract section, minimize the conclusions and the recommendations and omit recommendation as sub-title in the abstract part.

7. In line number 50, please remove colon (:) in front of the introduction

8. The introduction section needs some modification as it focuses on the scientific background. Hence, it will be grateful if you start from the problem with respect to the WHO and CDC data.

9. Please state the problem and prevalence of nasopharyngeal carriage and drug resistance profiles of the isolates among children in Ethiopia and the study area in figures?

10. Online number 105, please convert general objectives to general objective?

11. Why you excluded under 15 ages Children and those with a history of nasal surgery, respiratory infection, and antibiotics from the study?

12. You have used a single population proportion formula to calculate the sample size. Thus, please write the formula and how to obtained 424 and why you used 50% proportion? I think there are plenty of articles even in your study area.

13. Who analyzed the data? You said a trained laboratory technologist analyzed the data (on line numbers 155 and 156).

14. On line number 238, please change p-value ≤ 0.2 to 0.25

15. Please omit the natural resistance profiles of the isolates (those which have known resistance profile to certain antibiotics). For instance, S. aureus naturally resistant to penicillin, clindamycin, and azithromycin.

16. Online number 305, please covert 257 to text as it comes before the full stop.

17. In the discussion section, please state the scientific justifications to associate factors

18. It is better if you minimize the Conclusions and Recommendations statements as it is so bulky

19. Online 461 and 462, avoid the figure (69.8%) and write as low, intermediate, and high

20. In the authors’ contributions statement, please avoid the bolded letters

21. Please re-write the competing of interest and funding statement

22. There are many too old references in the manuscript (ref 2, 3, 4, 18, 20, 25, 27, 30, 31, 34, 41, 44, 49, 54, 68, 69, 76, 78…..). Hence, please update and replace them.

Question

1. What is the clinical utility and value of your study? In your study, the most frequently identified isolate was S. aureus. However, S. aureus is the known causative agent for Nasopharyngeal Carriage. Moreover, Gram-positive bacteria, including S. aureus, Streptococcus pyogens, and Streptococcus pneumoniae are the cause of Nasopharyngeal Carriage naturally. Thus, what is the importance doing this research?

Reviewer #2: Dear Author,

I wish to acknowledge the author's work entitled: Nasopharyngeal Carriage, Antibiotic Susceptibility Patterns, and Associated Factors of Gram-positive Bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. The results illustrated the carriage state of Gram-positive bacteria among children. Therefore, this study will be useful for the prevention and control of the carriage state of Gram-positive bacteria among children in the study area. The manuscript is more or less in line with the vision, objectives, and instructions of PLoS One. Despite its potential, however, this manuscript contains major errors in data presentation and interpretation, grammatically which need to be corrected.

General comments

1. The study mixes carriage isolates with what are likely to be clinical isolates.

2. Why do you exclude Gram-negative bacteria?

3. Uniform writing is needed for the name of drugs.

4. The use of the English language is poor in certain sections and would require a detailed revision.

Abstract

• Lines 32-34: ‘The data was entered into Epi-Data version 4.6.0.6 and exported to SPSS version 25 for analysis. The adjusted odds ratio at a 95% confidence interval with a P-value of < 0.05 was taken as statistically significant.’ It is better written as The data was entered into Epi-Data version 4.6.0.6 and exported to SPSS version 25 for analysis. Bivariable and multivariable logistic regression analysis was used to identify associated risk factors. The adjusted odds ratio at a 95% confidence interval with a P-value of < 0.05 was taken as statistically significant.’

• The number of isolates with the total is better written together with the percentages. Resistant/susceptible with the total including the percentage also should be used. This works for the whole abstract and results part of the paper. For example, Lines 35 &36: ‘The overall nasopharyngeal carriage of Gram-positive bacteria was 296/424 (69.8%, 95% CI: 65.3–74.0). Of these, S. aureus constitutes 122/424 (28.8%), followed by S. pneumoniae 92/424 (21.7%).’ It is better written as, ‘‘The overall nasopharyngeal carriage of Gram-positive bacteria was 296/424 (69.8%, 95% CI: 65.3–74.0). Of these, S. aureus constitutes 122/424 (28.8%), followed by S. pneumoniae 92/424 (21.7%).’

• Lines 40-43: P- value is needed.

• Line 43: …… risk factors……. It is better written as……. associated factors…….

Introduction

• Once you have used the long form of the name of the bacterium then you can abbreviate the genus name throughout the body of the paper, except headings and subheadings.

Materials and Methods

• Line 53: Remove the word ‘analysis’

• Specimen collection and processing needs to be well written.

• What standard microbiological procedures were employed in specimen collection, isolation, identification susceptibility testing, and throughout the procedure?

• How could you standardize the suspension preparation while performing antimicrobial susceptibility testing?

• What is the advantage of doing cefoxitin disc diffusion over oxacillin disc for susceptibility testing for methicillin (MRSA)?

• Better say, ‘Data analysis’ than ‘Statistical analysis’

• What have you done for children positive for the microorganisms?

Results

• How can you define community-associated methicillin-resistant S. aureus (CA-MRSA)? How can you exclude nosocomial sources?

• What is your base for classifying the age group? Have you associated with possible risks of interest? It is better again to re-group and perform the analysis.

Discussions

• The authors tried to compare their findings with different reports from worldwide. They also better justify the reason for variation among results of different research findings with respect to theirs’ based on actual situations.

Conclusions

• Normally, the conclusion emanates from the research.

**********

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: No

Reviewer #2: 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: Reviwers commnets to PLOS ONE.docx

PONE-D-24-10619R1Nasopharyngeal Carriage, Antibiotic Susceptibility Patterns, and Associated Factors of Gram-positive Bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest EthiopiaPLOS ONE

Dear Dr. Birhanu,

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 Jul 22 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,

Tebelay Dilnessa, MSc

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:

See the reviwer comments and the previous comments, still they require attention.

Follow the binomical nomenclature of bacteria.

[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 #3: (No Response)

**********

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 #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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 #3: 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 #3: 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: Thanks for addressing my concerns,

As much as possible, the authors address and cover my concern.

Reviewer #2: The manuscript titled "Nasopharyngeal Carriage, Antibiotic Susceptibility Patterns, and Associated Factors of Gram-positive Bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia" presents an important study addressing the nasopharyngeal carriage and antibiotic resistance patterns of Gram-positive bacteria in a pediatric population. The study is well-structured, with clear objectives, methodology, and significant findings that contribute to the understanding of antimicrobial resistance in the region. The topic is highly relevant, particularly in the context of increasing antibiotic resistance. The findings provide valuable insights into the prevalence and resistance patterns of Gram-positive bacteria, which are crucial for informing treatment strategies and public health interventions. I have some comments here please find it. Make corrections accordingly.

� Introduction: While the introduction provides a good background, it could benefit from a more detailed discussion on the global and regional implications of antibiotic resistance in Gram-positive bacteria. Including recent statistics (numerical data) on antibiotic resistance trends would strengthen the rationale for the study.

� Delete the objectives part it is stated at the end of the introduction part: lines 104-115

� Methods: This section should be rewritten according to the journal guidelines, as it is too wordy. Please try to condense it to align with the guidelines.

� Results: The results section is well written but try to minimize it by focusing on the objectives. Table 1 should concentrate on socio-demographic characteristics to reduce its size, as the data is also available in Table 5.

� Discussion: The discussion effectively interprets the findings.

� Conclusion: The conclusion concisely summarizes the main findings but as much as possible please categorize your findings i.e. the prevalence data as low/medium/ high. It should also provide more specific recommendations for future research and public health policies based on your findings.

� The general style of the manuscript is fine, but it does not completely follow the standard required by PLOS One Journal. Try to minimize the page of your manuscript to attract the reader by focusing on your main findings.

Reviewer #3: Please, confirm if consent was obtained for both minors and guardians, publication ethics

Please confirm any potential competing interest

**********

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: No

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: Rco to authors. Plose One.docx

Attachment

Submitted filename: review.docx

PONE-D-24-10619R2Nasopharyngeal Carriage, Antibiotic Susceptibility Patterns, and Associated Factors of Gram-positive Bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest EthiopiaPLOS ONE

Dear Dr. Birhanu,

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 18 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,

Tebelay Dilnessa, MSc

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:

• The paper was significantly improved, still requires a critical revision and proofreading.
• Lines 40-43: Correct the following as follows: Staphylococcus aureus was the most prevalent 122/424 (28.8%), followed by Streptococcus pneumoniae 92/424 (21.7%). Methicillin resistance was observed in 19/122 (15.6%) of S. aureus and 3/60 (5%) of coagulase-negative staphylococcus (CoNS) species. Inducible clindamycin resistance was 10/122 (8.2%) in S. aureus and 4/53 (7.5%) in coagulase-negative staphylococcus species.
• Italics the ‘P’ to refer p-value throughout the document.
• The conclusion part of the abstract should contain concrete ideas and should emanate from the result based on your objective.
• Lines 63-65: It is better written as, …………. S. pneumoniae, S. aureus, coagulase-negative staphylococcus species (CoNS), and Streptococcus pyogenes [2, 3].
• Line 84 and 88: Write as, Coagulase-negative staphylococcus species…………..
• Line 119 and 120 :……..…. this study addressed gaps left by prior research by offering data on the carriage of Gram-positive bacteria and their antimicrobial resistance patterns, including inducible……….
• It is preferable to use ‘antimicrobial’ than ‘drug’. For example, line 122 throughout the document. Uniformity is more important.
• Unnecessary space between the heading and subheading should be removed.
• Line 125: The subheading ‘Study design, period, and area’. I recommend you to split into two subheadings as ‘Study area and setting’ and ‘Study design and period’
• Line 135: Gondar town is located 750 km……..
• Line 147: ‘Concisely’ was not the correct word.
• Line 168: Specimen collection and processing
• Line 181, 184: Write the source of the media (manufacturer/city/country) similar to line 191.
• Line 192: …….Gram-positive diplococci…..
• How could you standardize the suspension preparation during performing antimicrobial susceptibility testing?
• In the methods and result part, try to shorten the subheadings. For example, line 272, 279 and 299 can be written as follows, respectively: ‘Prevalence of Gram-positive bacteria’, ‘Antimicrobial susceptibility pattern’ & ‘Inducible clindamycin resistance’
• Line 208: Antimicrobial susceptibility testing
• Line 227 and 228: ……… Results of antimicrobial susceptibility testing………………….
• Line 230: ………….. multidrug resistance (MDR) [ 2]. Additionally, the reference you mentioned (reference 2) for MDR was not the correct reference/ and cannot be the source. It is a cross-reference and replace it by the correct reference.
• Line 257: A letter of permission was obtained from……………
• Line 309: Multi-drug resistance pattern
• Line 324: Associated factors for nasopharyngeal carriage
• 421: The MDR proportion of 69.2%, 40%, 39.1%, and 18.2% were found in the current study for S. aureus,……..
• The conclusion and the recommendation were beyond your scope, so make it specific to your study.
• All tables and figure (s) should be cited in the text, otherwise it/they should be removed.
• Figure 1 should be prepared without description in tif and uploaded. The description should be placed within the text where you cited.

[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 #2: All comments have been addressed

**********

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 #2: Yes

**********

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

Reviewer #2: 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 #2: 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 #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 #2: The study is well-organized with clear objectives, methodology, and findings that are valuable for understanding antimicrobial resistance in the region. The topic is highly pertinent given the rising concern of antibiotic resistance. The results offer important insights into the prevalence and resistance patterns of Gram-positive bacteria, crucial for guiding treatment strategies and public health measures. The authors addressed all my concerns effectively. Thank you.

**********

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 #2: 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.

Nasopharyngeal Carriage, Antimicrobial Susceptibility Patterns, and Associated Factors of Gram-positive Bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia

PONE-D-24-10619R3

Dear Dr. Birhanu,

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,

Tebelay Dilnessa, MSc

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: