Nasopharyngeal Colonization and Antimicrobial Susceptibility of Bacterial Isolates in Children and Young Adults with Acute, Protracted, and Chronic Cough: A Cross-Sectional Bulgarian Study

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,

The Article entitled "Nasopharyngeal colonization and antibiotic susceptibility of bacterial isolates in Bulgarian individuals with acute, protract-ed and chronic cough under 20 years of age" has been carefully reviewed,

This paper deserves attention since it highlights an important topic related to the identification of bacterial colonizers of the Nasopharynx in addition to the susceptibility of these bacteria towards different antibiotics. Authors of this paper aimed to investigate the patterns of nasopharyngeal colonization and antibacterial susceptibility in Isolated bacteria in Bulgarians aged less than 20 years old presenting with different severity cough levels (acute, protracted, and chronic). 

The paper is written in an average English language, the design if the paper is average, also Tables are not very clear for readers.

I think that the paper needs a lot of work before being suitable for publication, here is the list of my comments (Minor and Major ones):

Minor 01: The title is not very suitable for the article, I suggest to replace it by a more suitable one.

Minor 02: I suggest to remove at list 3 keywords from this section.

Minor 03: In the Lines 55-57, You mentioned several infectious agents, but I think that you forgot SARS-CoV-2!!

Minor 04: Tables are not clear at all, Information presented in the table are not clear enough. So please correct it accordinnaly.

Minor 05: In the Whole manuscript, Text must be justified.

Minor 06: In your discussion, I think that it would be an added value, if you talk about recent studies concerning the creation and the discovery of new antibiotics. You can use the following articles as references for this point:

-- Antimicrobial Resistance: A Growing Serious Threat for Global Public Health.

-- Towards new antibiotics classes targeting bacterial metallophore.

 

--  Metals to combat antimicrobial resistance.

Major 01: You mentioned that this paper was waived from the IRB, how it can work to start this work without a scientific approval from the committee, I see this as a big issue in your work.

Major 02: Why did you choose the persons aged less that 20? Why not less than 18??

Best Regards,

Author Response

Dear Authors,

The Article entitled "Nasopharyngeal colonization and antibiotic susceptibility of bacterial isolates in Bulgarian individuals with acute, protract-ed and chronic cough under 20 years of age" has been carefully reviewed,

This paper deserves attention since it highlights an important topic related to the identification of bacterial colonizers of the Nasopharynx in addition to the susceptibility of these bacteria towards different antibiotics. Authors of this paper aimed to investigate the patterns of nasopharyngeal colonization and antibacterial susceptibility in Isolated bacteria in Bulgarians aged less than 20 years old presenting with different severity cough levels (acute, protracted, and chronic).

The paper is written in an average English language, the design if the paper is average, also Tables are not very clear for readers.

I think that the paper needs a lot of work before being suitable for publication, here is the list of my comments (Minor and Major ones):

Authors` reply: We are grateful to the reviewer for their detailed evaluation and constructive feedback. We have addressed all points raised, and the revisions are outlined below.

Minor 01: The title is not very suitable for the article, I suggest to replace it by a more suitable one.

Response: Thank you for the suggestion. We have revised the title to better reflect the study's content. The new title is: Nasopharyngeal Colonization Patterns and Antibiotic Resistance in Children and young adults with Acute, Protracted, and Chronic Cough: A cross-sectional Bulgarian study

Minor 02: I suggest to remove at list 3 keywords from this section.

Response: We have streamlined the keywords section by removing less critical terms to improve focus and conciseness.

Minor 03: In the Lines 55-57, You mentioned several infectious agents, but I think that you forgot SARS-CoV-2!!

Response: We appreciate this observation. SARS-CoV-2 has been added to the list of infectious agents in the specified lines to ensure completeness and relevance. Additionally, we add a proper citation.

Minor 04: Tables are not clear at all, Information presented in the table are not clear enough. So please correct it accordinnaly.

Response: The tables have been reformatted to improve clarity and visual presentation. We ensured the use of descriptive headings, consistent alignment, and structured data for easier interpretation by readers.

Minor 05: In the Whole manuscript, Text must be justified.

Response: Thank you for pointing this out. The entire manuscript text has been justified to ensure uniform formatting and improved readability.

Minor 06: In your discussion, I think that it would be an added value, if you talk about recent studies concerning the creation and the discovery of new antibiotics. You can use the following articles as references for this point:

-- Antimicrobial Resistance: A Growing Serious Threat for Global Public Health.

-- Towards new antibiotics classes targeting bacterial metallophore.

 --  Metals to combat antimicrobial resistance.

Response: We agree that discussing recent advancements in antibiotic discovery adds value to the discussion. Relevant insights from the suggested references have been integrated into the discussion, highlighting emerging approaches to combat antimicrobial resistance.

Major 01: You mentioned that this paper was waived from the IRB, how it can work to start this work without a scientific approval from the committee, I see this as a big issue in your work.

Response: We understand the reviewer’s concern. The study utilized anonymized data obtained from routine clinical diagnostics, which, according to our institutional guidelines, does not require formal IRB approval. However, this waiver was granted following local ethical standards. We have clarified this point in the Methods section for transparency. Nevertheless, all investigated subjects (or their parents/guardians) requested the tests and provided consent for sample collection and testing during purchasing the tests.

Major 02: Why did you choose the persons aged less that 20? Why not less than 18??

Best Regards,

Response: We selected individuals under 20 years of age to encompass the full range of pediatric and adolescent populations plus young adults, presented with prolonged cough and indicated for testing. This aligns with the study objectives and design. This rationale has been added to the manuscript for clarity.

We trust these revisions address the reviewer’s concerns effectively and enhance the manuscript's quality. Please let us know if further clarification or changes are required. Thank you again for your valuable feedback.

Reviewer 2 Report

Comments and Suggestions for Authors

-The manuscript should be revised in regard to language and punctuation 

-Why authors chose the age of 20y as a cutoff of children?

- In abstract, sometimes authors use number of cases and sometimes the percentage

- I recommend including a table (should be table1) for the patients’ characteristics (epidemiologic data, etc)

- Table 4 is not clear and should be restructured.

- Conclusion should include the unique findings and mention that the results are from Belgium.

 

Author Response

-The manuscript should be revised in regard to language and punctuation

Response: We appreciate this observation. The manuscript has been thoroughly reviewed and revised to address language and punctuation issues, ensuring clarity and fluency throughout.

-Why authors chose the age of 20y as a cutoff of children?

Response: We selected individuals under 20 years of age to encompass the full range of pediatric and adolescent populations plus young adults, presented with prolonged cough and indicated for testing. This aligns with the study objectives and design. This rationale has been added to the manuscript for clarity.

- In abstract, sometimes authors use number of cases and sometimes the percentage

Response: Thank you for pointing this out. The use of both the number of cases and percentages in the abstract was intentional and aimed at providing a comprehensive understanding of the data. Absolute numbers were included to convey the scale and real-world relevance of the findings, while percentages were used to facilitate comparisons and highlight proportions within the study population. This combination ensures that the results are both contextually meaningful and easily interpretable for readers. If needed, we can further standardize the presentation for greater consistency.

- I recommend including a table (should be table1) for the patients’ characteristics (epidemiologic data, etc)

Response: Thank you for this suggestion. We have carefully considered including a table summarizing patients’ characteristics. However, we believe that presenting the epidemiologic data directly in the text ensures a more concise and seamless integration with the study's narrative. This approach avoids redundancy and allows readers to follow the flow of the manuscript more effectively. The available data, including demographic and clinical characteristics, is clearly described in the text for clarity and readability. If the inclusion of a table is deemed essential, we are open to revisiting this aspect.

- Table 4 is not clear and should be restructured.

Response: Table 4 has been restructured for improved clarity and readability. We ensured that the data is organized in a more intuitive and visually accessible manner.

- Conclusion should include the unique findings and mention that the results are from Belgium.

Response: The conclusion has been revised to highlight the study's unique findings, including the observed patterns of bacterial colonization and antibiotic resistance. Additionally, we have clarified that the results are based on data from Bulgaria. We reflected that also by altering the title as Reviewer 1 suggested to us.

We trust these revisions adequately address the reviewer’s concerns and enhance the manuscript’s overall quality. Thank you again for your valuable feedback.

Reviewer 3 Report

Comments and Suggestions for Authors

Velikova et al. make an important report on the presence of microorganisms of high importance in respiratory infections in Bulgaria. The structure of the research and references are correct. I recommend publishing it after making comments.

 

Abstract

Remove from the abstract the words (1) Background and aim, (2) Methods, (3) Results, and (4) Conclusion; the text by itself is sufficient.

Line 19, double-spaced.

How was the isolation performed?

It would be convenient to summarize the susceptibility test results instead of indicating the presence of the different bacteria found in the age range.

Reduce the abstract as it contains more than the maximum of 200 words.

 

Introduction

Lines 69-70. Mention some examples of the leading causes indirectly associated with AMR deaths.

Line 84. Include the general period of the years of the investigation.

 

Materials and Methods

Line 95. Remove "We used the following methods:"

The formatting of the Subsubheadings is incorrect, revise and correct.

How were the microorganisms isolated from the samples? Describe the methodology and characteristics considered.

In 2.2.1. Identification of Isolates. Describe briefly the methodology and instrumental conditions.

In 2.2.2. Antimicrobial Susceptibility Testing. What antibiotics were used and why, what concentrations were used, and what brands of suppliers were used?

Rewrite this subheading "2.2.4. We also performed genetic analyses for pertussis and mycoplasma".

Line 111, B. pertussis should be in italics.

 

Results

Lines 128 - 134. It is important to indicate how S, R, and I were calculated for the antibiotics tested.

The format of all tables should be adapted to that of the journal.

Line 143, after "indicating its continued efficacy for ceftriaxone" include "and moxiflacin."

The formatting of the text starting on line 143 is different.

I recommend changing Table 2 to a bar graph.

Line 161. I recommend not using ¼; it is preferable to use the whole word.

Report MIC of Moraxella catarrhalis.

Line 171. Haemophilus influenzae should be italicized.

Table 4 is incorrect in format and structure due to different dimensions. I recommend joining the information in the table (which are three tables) in a figure; perhaps they can use plots such as treemap, heatmap, pie chart, or horizontal bar chart; include the distribution of acute, protracted, and chronic cough in the samples.

It would be interesting to report the number of organisms and which bacteria were MDR.

 

Discussions

Include a discussion about MIC and MDR bacteria.

 

References

Revise the format; eliminate PMCID and PMID from the references that contain it.

Standardize the format of all articles; some are different.

 

Author Response

Velikova et al. make an important report on the presence of microorganisms of high importance in respiratory infections in Bulgaria. The structure of the research and references are correct. I recommend publishing it after making comments.

Response: We are grateful to the reviewer for their detailed feedback and valuable suggestions. We have addressed each comment below and revised the manuscript accordingly.

 

Abstract

Remove from the abstract the words (1) Background and aim, (2) Methods, (3) Results, and (4) Conclusion; the text by itself is sufficient.

Response: Thank you for the suggestion. The headings in the abstract have been removed as recommended, and the text has been reorganized to flow naturally.

 

Line 19, double-spaced.

Response: The spacing on Line 19 has been corrected to ensure consistency throughout the manuscript.

 

How was the isolation performed?

Response: A brief description of the isolation methodology has been added to the Methods section of the abstract for clarity.

 

It would be convenient to summarize the susceptibility test results instead of indicating the presence of the different bacteria found in the age range.

Response: We appreciate this suggestion and understand the intent to streamline the data presentation. However, we believe that indicating the presence of different bacteria across the age range provides critical insights into the study's findings and highlights the variability in colonization patterns. This level of detail is essential to understanding the epidemiological context and its implications for clinical practice. Summarizing the susceptibility results alone would risk losing important nuances related to age-specific trends. That said, we have ensured that the results are presented clearly and concisely in the text while maintaining their relevance. We hope this approach aligns with the reviewer’s expectations. However, if the reviewer insists, we can made further adjustments and revisit this point.

 

Reduce the abstract as it contains more than the maximum of 200 words.

Response: The abstract has been revised and condensed to comply with the 200-word limit, retaining only the most critical details.

 

Introduction

Lines 69-70. Mention some examples of the leading causes indirectly associated with AMR deaths.

Response: Examples of leading causes indirectly associated with AMR deaths, such as secondary bacterial infections in respiratory illnesses and bloodstream infections, have been included in Lines 69-70.

 

Line 84. Include the general period of the years of the investigation.

Response: The general period of the investigation has been specified in Line 84 for clarity.

 

Materials and Methods

Line 95. Remove "We used the following methods:"

Response:The phrase has been removed, and the text flows directly into the description of the methods.

 

The formatting of the Subsubheadings is incorrect, revise and correct.

Response: The formatting of all subsubheadings has been reviewed and corrected to meet the journal’s guidelines.

 

How were the microorganisms isolated from the samples? Describe the methodology and characteristics considered.

Response: A detailed description of the isolation methodology and criteria has been added to the relevant subsection.

 

In 2.2.1. Identification of Isolates. Describe briefly the methodology and instrumental conditions.

Response: The methodology and instrumental conditions for isolate identification have been briefly described.

 

In 2.2.2. Antimicrobial Susceptibility Testing. What antibiotics were used and why, what concentrations were used, and what brands of suppliers were used?

Response: Details of the antibiotics used, their concentrations, and suppliers have been added to Section 2.2.2 to ensure transparency and reproducibility.

 

Rewrite this subheading "2.2.4. We also performed genetic analyses for pertussis and mycoplasma".

Response: The subheading has been rewritten to "Genetic Analyses for B. pertussis and Mycoplasma spp." for clarity and consistency.

 

Line 111, B. pertussis should be in italics.

 Response: B. pertussis has been italicized throughout the manuscript as required.

 

Results

Lines 128 - 134. It is important to indicate how S, R, and I were calculated for the antibiotics tested.

Response: The methodology for calculating S (susceptible), R (resistant), and I (intermediate) categories has been added to the Methdos section for clarity.

 

The format of all tables should be adapted to that of the journal.

Response: All tables have been reformatted to adhere to the journal's guidelines for presentation.

 

Line 143, after "indicating its continued efficacy for ceftriaxone" include "and moxiflacin."

Response: We appreciate that you have spotted this technical mistake, "Moxifloxacin" has been included.

 

The formatting of the text starting on line 143 is different.

Response: The formatting issue has been corrected for consistency.

 

I recommend changing Table 2 to a bar graph.

Response: Thank you for this recommendation. While we understand the potential benefits of visualizing the data in a bar graph, we believe that Table 2 in its current tabular format provides a more comprehensive and precise representation of the data, especially for readers seeking detailed numerical comparisons. The table format allows for easy cross-referencing and retains all critical details without oversimplification. We hope this explanation is satisfactory, but we are open to further discussion if additional adjustments are deemed necessary.

 

Line 161. I recommend not using ¼; it is preferable to use the whole word.

Response: The fraction “¼” has been replaced with “one-quarter” for better readability, thank you for the valuable recommendation.

 

Report MIC of Moraxella catarrhalis.

Response: Thank you for this comment. Unfortunately, our study did not include the determination of MIC values for Moraxella catarrhalis, as the methodology employed focused on disc diffusion testing rather than gradient diffusion or broth microdilution techniques required for MIC determination. We recognize the value of including MIC data in future investigations to provide a more comprehensive assessment of antimicrobial susceptibility.

Line 171. Haemophilus influenzae should be italicized.

Response: Haemophilus influenzae has been italicized throughout the manuscript.

 

Table 4 is incorrect in format and structure due to different dimensions. I recommend joining the information in the table (which are three tables) in a figure; perhaps they can use plots such as treemap, heatmap, pie chart, or horizontal bar chart; include the distribution of acute, protracted, and chronic cough in the samples.

Response: We appreciate the thoughtful suggestion to improve the presentation of Table 4. While we agree that visualization can enhance understanding in some contexts, the detailed and multidimensional nature of the data in Table 4 is best captured in its current tabular format. This format ensures clarity and preserves the granularity needed for accurate interpretation, which might be lost in aggregated visual formats such as treemaps or pie charts. We have, however, reviewed and improved the structure and formatting of Table 4 to enhance its readability and align it more closely with the journal's standards. We hope this addresses the reviewer’s concerns effectively. If further refinements are required, we are happy to revisit this point.

 

It would be interesting to report the number of organisms and which bacteria were MDR.

Response: Thank you for this valuable suggestion. Unfortunately, our study did not include specific analyses to quantify the number of organisms identified as multidrug-resistant (MDR) or classify bacteria accordingly. Our primary focus was on general antimicrobial susceptibility patterns based on the methodologies employed. We acknowledge the importance of such data, highlighting the need for future studies to address MDR prevalence more comprehensively.

 

Discussions

Include a discussion about MIC and MDR bacteria.

Response: A discussion on MIC and MDR bacteria has been added, emphasizing their clinical significance and implications in antimicrobial resistance management. Thank you for the valuable suggestion.

 

References

Revise the format; eliminate PMCID and PMID from the references that contain it.

Standardize the format of all articles; some are different.

Response: PMCID and PMID information have been removed from the references as requested. The references have been standardized according to the journal's guidelines.

 

 

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,

Your revision version of the paper entitled "Nasopharyngeal colonization and antibiotic susceptibility of bacterial isolates in Bulgarian individuals with acute, protracted and chronic cough under 20 years of age" has been carefully reviewed.

The article is suitable for publication in its present form, Thanks to the modifications you made,

I just want to ask you to adjust the style of references (35 mainly).

Best Regards,

Author Response

Dear Authors,

Your revision version of the paper entitled "Nasopharyngeal colonization and antibiotic susceptibility of bacterial isolates in Bulgarian individuals with acute, protracted and chronic cough under 20 years of age" has been carefully reviewed.

The article is suitable for publication in its present form, Thanks to the modifications you made,

I just want to ask you to adjust the style of references (35 mainly).

Best Regards,

 

Authors` reply: Dear Reviewer,

Thank you for your careful review and for your positive evaluation of our revised manuscript. We appreciate your constructive feedback throughout the process.

We have now adjusted the reference style, including Reference 35, to ensure consistency with the journal's guidelines. If needed, we can further revise the references style upon journal request.