Biofilm and Antimicrobial Resistance: Mechanisms, Implications, and Emerging Solutions

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

I think it is a very complete review that describes very well the antibiofilm agents that can be used nowadays.

Author Response

 

I think it is a very complete review that describes very well the antibiofilm agents that can be used nowadays.

Response: Thank you for your comments and appreciation.

Reviewer 2 Report

Comments and Suggestions for Authors

Manuscript "Biofilm and antimicrobial resistance: Mechanisms, implications, and emerging solutions" addresses a highly relevant, current and high-impact topic: biofilms. The manuscript is well written, very well founded and practically ready for publication in the journal. However, some points are noteworthy:

1. The use or not of artificial intelligence tools for producing images and/or writing the text should be mentioned at some point.

2. Which descriptors were used for the active search for articles used in the review? Which years of publication were considered? Some articles can be replaced by newer references. Especially in the use of photodynamic therapy (2019). I suggest the introduction of porphyrins as antimicrobial agents.

3. The figures were created by the authors, ok. They were very well done. However, I have seen something very outdated in other publications. Please cite the source of inspiration.

4. I also suggest a topic with nanoparticles of natural products for the eradication of biofilms.

Author Response

Manuscript "Biofilm and antimicrobial resistance: Mechanisms, implications, and emerging solutions" addresses a highly relevant, current and high-impact topic: biofilms. The manuscript is well written, very well founded and practically ready for publication in the journal. However, some points are noteworthy:

Comment: 1. the use or not of artificial intelligence tools for producing images and/or writing the text should be mentioned at some point.

Response: The artificial tools were not used in writing as well as in generating the figures. Statement has been mentioned in the manuscript

2. Which descriptors were used for the active search for articles used in the review? Which years of publication were considered? Some articles can be replaced by newer references. Especially in the use of photodynamic therapy (2019). I suggest the introduction of porphyrins as antimicrobial agents.

Response: The descriptors are mentioned as keywords. It’s a state of art review on biofilm and antimicrobial resistance that discusses the possible solutions to mitigate the biofilms. It’s not a systematic review. However, we have used the updated information to integrate the article without losing the originality. Recent citations have been added at appropriate places. Introduction of porphyrins have been added. Please refer section 5.1.1 (page no. 7).

Comment: 3. the figures were created by the authors, ok. They were very well done. However, I have seen something very outdated in other publications. Please cite the source of inspiration.

Response: Thank you for your suggestion. The figures has been updated. Please refer figure 1

Comment: 4. I also suggest a topic with nanoparticles of natural products for the eradication of biofilms.

Response: Thank you for your suggestion.We have added a paragraph. Refer 5.2.6 (Page no. 14)

 

Reviewer 3 Report

Comments and Suggestions for Authors

This review manuscript provides a timely and significant contribution to the field of microbial pathogenesis and antimicrobial resistance (AMR). The scope outlined – covering modes of action of current strategies, mechanisms of biofilm-associated drug resistance, and innovative solutions – promises a comprehensive and valuable synthesis of current knowledge. Focusing the review around the EPS as a central therapeutic target provides a clear, novel perspective that could stimulate important future research directions.

It can be accepted after added some references about anti-biofilm compounds with novel  mehcanisms. For examples：1. A red fluorescent small-molecule for visualization of higher-order cyclic dimeric guanosine monophosphate (c-di-GMP) structure in live bacterial cells and real-time monitoring of biofilm formation on biotic and abiotic surfaces. （Sensors and Actuators B: Chemical. 2023, 376, 132992）；2. Discovery and antibacterial study of potential PPK1 inhibitors against uropathogenic E. coli.  (Journal of enzyme inhibition and medicinal chemistry. doi: 10.1080/14756366.2020.1766453. 2020, 35 (1), 1224-1232.）

Author Response

This review manuscript provides a timely and significant contribution to the field of microbial pathogenesis and antimicrobial resistance (AMR). The scope outlined – covering modes of action of current strategies, mechanisms of biofilm-associated drug resistance, and innovative solutions – promises a comprehensive and valuable synthesis of current knowledge. Focusing the review around the EPS as a central therapeutic target provides a clear, novel perspective that could stimulate important future research directions.

Comment: It can be accepted after added some references about anti-biofilm compounds with novel mehcanisms. For examples：1. A red fluorescent small-molecule for visualization of higher-order cyclic dimeric guanosine monophosphate (c-di-GMP) structure in live bacterial cells and real-time monitoring of biofilm formation on biotic and abiotic surfaces. （Sensors and Actuators B: Chemical. 2023, 376, 132992）；2. Discovery and antibacterial study of potential PPK1 inhibitors against uropathogenic E. coli.  (Journal of enzyme inhibition and medicinal chemistry. doi: 10.1080/14756366.2020.1766453. 2020, 35 (1), 1224-1232.

Response: Thank you for your suggestion. The suggested information and references were added in the manuscript. Please refer reference no. 142-143.

 

Reviewer 4 Report

Comments and Suggestions for Authors

  In the manuscript titled Biofilm and antimicrobial resistance: Mechanisms, implications, and emerging solutions. The author explores various modern strategies for controlling biofilms, with a focus on their modes of action, resistance mechanisms, and innovative approaches to finding solutions in this area. This topic has significant clinical implications. The author provides a detailed overview of physical, chemical, and biological methods for antibiofilm treatment, particularly in the section on nanomaterials. However, there are also Many key errors in the manuscript.

Major revision has to be done before this manuscript could be accepted for publication in the Microbiology Research. My main comments are as follow:

1. The abstract mentions, ‘This review interestingly targets the extracellular polymeric matrix as a highly effective strategy’, but no comparative data was provided in the article. It is suggested to supplement this part of the evidence, For example, the efficiency difference compared to QS inhibitors or physical clearance.
2. The classification framework for antibiofilm agents in the article is not scientific. The article states that antibiofilm agents are divided into three categories, but the following text specifically mentions seven categories. It is Suggested that reorganizing the classification scheme.
3. On the page 4 and 5, it is mentioned that ‘how antibiotic resistance is brought about in biofilms is not well understood’ and ‘BAT is expected to incorporate alternate paths’. Directly asserting from 'unclear mechanism' that 'alternative paths exist' lacks bridge evidence.
4. Table 1 defects: ‘Inhibitory concentration’ unclassified MIC/MBIC/BEC. And the strain characteristics (clinical isolates/standard strains; MDR/XDR status) were not specified. Suggest clarifying this section to make the article more scientific and rigorous.
5. No mention of new technology phage antibiotic synergy in biological agents. Can add a new chapter: ‘5.8 Collaborative Therapy Strategy’. For example, there are literature reports that engineering bacteriophages carry β-lactase inhibitors, which increase the efficacy of meropenem on biofilms by 100 times. This section can be added to make the article more complete.
6. Language and Format: the overall language expression is relatively clear, and the structure basically conforms to the format of the paper. But some sentences are not concise enough. Moreover, academic language should be standardized. For example, 'quorum sensing' first appeared without abbreviation 'QS' and ‘extracellular DNA’ is abbreviated as ‘eDNA’ in the main text, but Figure 1 uses ‘exDNA’ instead. Use ‘eDNA’ uniformly throughout the entire manuscript and remove ‘exDNA’.
7. Suggest updating highly cited literature from the past five years (after 2020). The original citations are mostly concentrated before 2023 (as cited in line 938 from 2019), but there have been significant breakthroughs in the field of biofilms in recent years (such as CRISPR interference with QS systems). Suggest supplementing Nat Rev Microbiol or Cell Host Microbe related papers published in 2024.
8. Can merge dispersed mechanism diagrams. Figure 1 (mature biofilm structure) and Figure 2 (developmental stage) can be integrated into a coherent "biofilm lifecycle diagram", marking key nodes of EPS, QS, and drug resistance mechanisms. Suggest using layered color coding to distinguish different components.
9. The reference format is confusing and needs to be proofread again. The format should be standardized according to the requirements of the journal.

Comments on the Quality of English Language

The language quality of this manuscript should be further improved.

Author Response

In the manuscript titled Biofilm and antimicrobial resistance: Mechanisms, implications, and emerging solutions. The author explores various modern strategies for controlling biofilms, with a focus on their modes of action, resistance mechanisms, and innovative approaches to finding solutions in this area. This topic has significant clinical implications. The author provides a detailed overview of physical, chemical, and biological methods for antibiofilm treatment, particularly in the section on nanomaterials. However, there are also many key errors in the manuscript.

Major revision has to be done before this manuscript could be accepted for publication in the Microbiology Research. My main comments are as follow:

 

Comment: The abstract mentions, ‘This review interestingly targets the extracellular polymeric matrix as a highly effective strategy’, but no comparative data was provided in the article. It is suggested to supplement this part of the evidence, For example, the efficiency difference compared to QS inhibitors or physical clearance.

Response: Thank you for suggestion. A paragraph has been added. Please refer section 2. (Page no. 2-3)

Comment: The classification framework for antibiofilm agents in the article is not scientific. The article states that antibiofilm agents are divided into three categories, but the following text specifically mentions seven categories. It is Suggested that reorganizing the classification scheme.

Response: Thanks for pointing out, there are only 3 main categories. We have reorganized the classification scheme.

Explanation: In article only three category are mentioned the first category that is physical factors, 2) chemical agents and 3) biological agents. In first category physical agents are mentioned that are from 5.1.1 to 5.1.7.

Comments: On the page 4 and 5, it is mentioned that ‘how antibiotic resistance is brought about in biofilms is not well understood’ and ‘BAT is expected to incorporate alternate paths’. Directly asserting from 'unclear mechanism' that 'alternative paths exist' lacks bridge evidence.

Response: Thank you for your suggestion. BAT only the possible mechanism which protect the bacteria from the antimicrobial substance. Exact mechanisms were still unknown.

Table 1 defects: ‘Inhibitory concentration’ unclassified MIC/MBIC/BEC. And the strain characteristics (clinical isolates/standard strains; MDR/XDR status) were not specified. Suggest clarifying this section to make the article more scientific and rigorous.

Response: Thank you for your suggestion. Inhibitory concentration has been updated. Please refer Table 1.

Comment: No mention of new technology phage antibiotic synergy in biological agents. Can add a new chapter: ‘5.8 Collaborative Therapy Strategy’. For example, there are literature reports that engineering bacteriophages carry β-lactase inhibitors, which increase the efficacy of meropenem on biofilms by 100 times. This section can be added to make the article more complete.

Response: Thank you for your suggestion. A paragraph has been added. Please refer 5.3.4 (Page n0. 17)

Comment: In conclusion, integrating collaborative therapy approaches such as PAS into the antibiofilm arsenal offers a powerful, multi-targeted strategy. Its inclusion reflects the next frontier in personalized and precision treatment for biofilm-associated infections.

Response: Thank you for your suggestion. A paragraph has been added in conclusion section. Please refer page no. 18-19.

Comment: Language and Format: the overall language expression is relatively clear, and the structure basically conforms to the format of the paper. But some sentences are not concise enough. Moreover, academic language should be standardized. For example, 'quorum sensing' first appeared without abbreviation 'QS' and ‘extracellular DNA’ is abbreviated as ‘eDNA’ in the main text, but Figure 1 uses ‘exDNA’ instead. Use ‘eDNA’ uniformly throughout the entire manuscript and remove ‘exDNA’.

Response: Thank you for your suggestion. The language, punctuation, and spellings are carefully checked and corrected throughout the manuscript.

Comment: Suggest updating highly cited literature from the past five years (after 2020). The original citations are mostly concentrated before 2023 (as cited in line 938 from 2019), but there have been significant breakthroughs in the field of biofilms in recent years (such as CRISPR interference with QS systems). Suggest supplementing Nat Rev Microbial or Cell Host Microbe related papers published in 2024.

Response: Thank you for your suggestion. The references were updated.

Comment: Can merge dispersed mechanism diagrams. Figure 1 (mature biofilm structure) and Figure 2 (developmental stage) can be integrated into a coherent "biofilm lifecycle diagram", marking key nodes of EPS, QS, and drug resistance mechanisms. Suggest using layered color coding to distinguish different components.

Response: Thank you for your suggestion. The figure has been updated. Please refer Figure 1.

Comment: The reference format is confusing and needs to be proofread again. The format should be standardized according to the requirements of the journal.

Response: Thank you for your suggestion. The manuscript has been formatted as per journal guidelines.

 

Reviewer 5 Report

Comments and Suggestions for Authors

Dear colleagues,

the importance of this review should be noted, and despite this, certain edits should be made in the design of the material. Please structure the article, add the necessary sections:

1. Introduction (present)

2. Materials and methods (how and where you searched for and systematized information)

3. Results and their discussion

4. Conclusions

Regards,

Reviewer

Author Response

Comment: The importance of this review should be noted, and despite this, certain edits should be made in the design of the material. Please structure the article, add the necessary sections:

1. Introduction (present)
2. Materials and methods (how and where you searched for and systematized information)
3. Results and their discussion
4. Conclusions

Response: Thank you for your valuable suggestions. The complete manuscript has been thoroughly revised based on the comments provided. All sections have been critically evaluated and improved accordingly, in consultation with all co-authors.

 

Round 2

Reviewer 5 Report

Comments and Suggestions for Authors

Dear colleagues,

I see that you have carefully revised the material, but I still have not seen a section or even a paragraph that would indicate which information search databases you used, on the basis of which keywords you selected information, etc.

Please add the relevant information.

Regards,

Reviewer

Author Response

Comment: Dear colleagues, I see that you have carefully revised the material, but I still have not seen a section or even a paragraph that would indicate which information search databases you used, on the basis of which keywords you selected information, etc. Please add the relevant information.

Response: Thank you for your valuable suggestions. We have added the paragraph describing the required information (Line 71 to 75).