Fermented Foods as a Potential Vehicle of Antimicrobial-Resistant Bacteria and Genes

Round 1

Reviewer 1 Report

The review article under the title (Fermented Foods as a Potential Vehicle of Antimicrobial-Resistant Bacteria and Genes) is important in the field of food safety and has a high impact. The article is well designed and has all the necessary recent knowledge. 

 

Author Response

We appreciate the reviewer's thoughtful analysis of our manuscript and are grateful for the positive feedback. 

Reviewer 2 Report

Vinayamohan et al. discussed the potential of fermented food as a vehicle for antimicrobial resistant bacteria and genes. There are lots of contemporaneous and important information in the article which would be greatly appreciated by the scientific community. As a researcher in the bacteriology and antibiotics area, I have not quite considered the fact that the bacteria used in fermented product could demonstrate such AMR to several antibiotics that are prescribed to treat various bacterial infection. It was very enlightening for me, and I thank the authors for their piece. I find it very alarming that the some of the probiotics that human consumes for benefit have been reported to contain AR genes. Following are some comments that if addressed would be great:

1.       In abstract, for a handful of times, AR was mentioned, I think it would be better to write AR microbes and genes in these places instead. Also, in few places ARG is used without first mentioning that ARG stands for antibiotic resistant genes.

2.       It would be nice to provide the following references for page 2 line 45-46.

·         Duche et al. (2023) Antibiotic resistance in potential probiotic lactic acid bacteria of fermented foods and human origin from Nigeria. BMC Microbiology, 142.

·         Erginkaya et al. (2018) Determination of antibiotic resistance of lactic acid bacteria isolated from traditional Turkish fermented dairy products. Iran J Vet Res 19, 53-56

3.       I think the content of page 2 line 66-67 is not quite right. Fermented foods can potentially transfer these elements to other microorganisms…? Should not it be host? Please check.

4.       Page 3 line 133: It is unclear what is the source of S. caprae.

5.       From table 1 it appears that the fermented food contains genes that are resistant to different antibiotics, do some products also contains antibiotic resistant bacteria as mentioned in the title? It would be nice to clarify that in the article a bit.

6.       I think the symbol for ‘Celsius’ is not correct; can you please double check?

7.       Please include the following as references on page 7 line 310-311:

·         Vemula et al. (2016) Cytoplasmic peptidoglycan intermediate levels in Staphylococcus aureus. Biochimie, 121, 72-78

·         Vemula et al. (2017) Antibiotic Effects on Methicillin-Resistant Staphylococcus aureus Cytoplasmic Peptidoglycan Intermediate Levels and Evidence for Potential Metabolite Level Regulatory Loops. Antimicrobial Agents and Chemotherapy, 61, 6.

8.       I think some of the following references should be discussed and cited in section 5.2. It would be nice if the authors can briefly discuss what the regulatory specifications are (following citations can provide a good guideline) and where most of the marketed probiotics stand:

·         Hoffmann et al. (2014) Probiotics: Achieving a Better Regulatory Fit. Food Drug Law J., 69(2): 237–ii.

·         Venugopalan et al. (2010) Regulatory Oversight and Safety of Probiotic Use. Emerg Infect Dis., 16(11): 1661–1665.

9.       Page 9 line 408: there is a highlight on a word, please remove this during next edit.

Author Response

We appreciate the reviewer's thoughtful analysis of our manuscript. Here are the specific modifications we made as per the reviewer's suggestions.

1. In abstract, for a handful of times, AR was mentioned, I think it would be better to write AR microbes and genes in these places instead. Also, in few places ARG is used without first mentioning that ARG stands for antibiotic resistant genes.                                                                                          Response: Appropriate changes has been made in the manuscript abstract (Lines 10, 12, and 19). ARGs was first explained in Line 48 before being abbreviated.

2. It would be nice to provide the following references for page 2 line 45-46. Duche et al. (2023) Antibiotic resistance in potential probiotic lactic acid bacteria of fermented foods and human origin from Nigeria. BMC Microbiology, 142. Erginkaya et al. (2018) Determination of antibiotic resistance of lactic acid bacteria isolated from traditional Turkish fermented dairy products. Iran J Vet Res 19, 53-56                                                                                                  

Response: The two references has been included (Line 47).  

3. I think the content of page 2 line 66-67 is not quite right. Fermented foods can potentially transfer these elements to other microorganisms…? Should not it be host? Please check.                                                                                                    

Response: The following change has been made in Lines 67-69 as per the reviewer's suggestion "As reservoirs of AR bacteria and ARGs, there is a potential for these elements to be transferred to microorganisms within the host, including pathogens."    

4. Page 3 line 133: It is unclear what is the source of S. caprae.                               Response: the source of S. caprae is Nigerian fermented food which has now been included in line 141.

5. From table 1 it appears that the fermented food contains genes that are resistant to different antibiotics, do some products also contains antibiotic resistant bacteria as mentioned in the title? It would be nice to clarify that in the article a bit.                                                                                                        

Response: The table caption has been changed to "Antibiotic-resistant bacteria in fermented foods and their corresponding phenotypic resistance profile." for more clarity. Line 190-191

6. I think the symbol for ‘Celsius’ is not correct; can you please double check?

Response: The symbol has been changed. Lines 263 and 265

7. Please include the following as references on page 7 line 310-311: Vemula et al. (2016) Cytoplasmic peptidoglycan intermediate levels in Staphylococcus aureus. Biochimie, 121, 72-78. Vemula et al. (2017) Antibiotic Effects on Methicillin-Resistant Staphylococcus aureusCytoplasmic Peptidoglycan Intermediate Levels and Evidence for Potential Metabolite Level Regulatory Loops. Antimicrobial Agents and Chemotherapy, 61, 

Response: Both the references has been included. Line 321.

8. I think some of the following references should be discussed and cited in section 5.2. It would be nice if the authors can briefly discuss what the regulatory specifications are (following citations can provide a good guideline) and where most of the marketed probiotics stand: Hoffmann et al. (2014) Probiotics: Achieving a Better Regulatory Fit. Food Drug Law J., 69(2): 237–ii.Venugopalan et al. (2010) Regulatory Oversight and Safety of Probiotic Use. Emerg Infect Dis., 16(11): 1661–1665.

Response : We thank the reviewer for this comment and for providing the references. Based on this suggestions we have briefly discussed the regulations in lines 397-409 and included both the references.

9. Page 9 line 408: there is a highlight on a word, please remove this during next edit.

Response: The highlight has been removed.

 

Reviewer 3 Report

The manuscript by Vinayamohan et all. present the review about the antibiotic resistance phenomena among bacteria in fermented foods. These results are of potential interest to a broad audience, specifically those involved in food fermentation and microbial safety. The paper is generally well-structured and written. However, I suggest two improvements:

1. Line 79-81, Autors wrote that: “Furthermore, using starter cultures in 79 fermentations resulted in a five-fold higher abundance of ARGs than in spontaneous fermentations.”. It is surprising to me. The European Food Safety Authority developed the concept of qualified presumption of safety (QPS) status which covers also the lack of antibiotic resistance features in microorganisms. In the United States, a similar system works – the GRAS. Therefore, why the starter cultures, which should be well-defined and follow the concepts mentioned above are considered as a reservoir of AR features?

2. Traditional African fermented food is considered to be one of the biggest reservoirs of the AR genes. I suggest mentioning it in Table 1.

 

Author Response

We thank the reviewer for the comments. Here are the specific modifications that we made as per the suggestions.

1.Line 79-81, Autors wrote that: “Furthermore, using starter cultures in 79 fermentations resulted in a five-fold higher abundance of ARGs than in spontaneous fermentations.”. It is surprising to me. The European Food Safety Authority developed the concept of qualified presumption of safety (QPS) status which covers also the lack of antibiotic resistance features in microorganisms. In the United States, a similar system works – the GRAS. Therefore, why the starter cultures, which should be well-defined and follow the concepts mentioned above are considered as a reservoir of AR features?                                                                     Response : The following changes has been made in the manuscript in Line 83-88 for more clarity. "Furthermore, using starter cultures in fermentations resulted in a five-fold higher abundance of ARGs than in spontaneous fermentations [14]. This might seem contradictory given the European Food Safety Authority’s Qualified Presumption of Safety (QPS) status and the United States Generally Recognized as Safe (GRAS) system, which both ensure a lack of AR features in microorganisms. However, this apparent discrepancy can be attributed to the enhanced characterization of starter culture microbes, their associated genomes, and associated ARG profiles which leads to more accurate ARG assignments, rather than an actual increase in AR."

2. Traditional African fermented food is considered to be one of the biggest reservoirs of the AR genes. I suggest mentioning it in Table 1.                                         Response : The following articles were included in Table 1 as per the reviewer's suggestions. 

Ouoba, L.I.I.; Mbozo, A.B.V.; Anyogu, A.; Obioha, P.I.; Lingani-Sawadogo, H.; Sutherland, J.P.; Jespersen, L.; Ghoddusi, H.B. Environmental Heterogeneity of Staphylococcus Species from Alkaline Fermented Foods and Associated Toxins and Antimicrobial Resistance Genetic Elements. Int. J. Food Microbiol. 2019, 311, 108356. 

Obioha, P.I.; Anyogu, A.; Awamaria, B.: Ghoddusi, H.B.: Ouoba, l.I.I. Antimicrobial Resistance of Lactic Acid bacteria from Nono, A Naturally Fermented Milk product.Antibiotics 2023,12, 843