Gallium Resistance in Staphylococcus aureus: Polymorphisms and Morphology Impacting Growth in Metals, Antibiotics and Polyfluorinated Compounds

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

I have reviewed the manuscript “Gallium Resistance in Staphylococcus aureus: Polymorphisms and Morphology and that Impact Growth in Metals, Antibiotics and Polyfluorinated compounds” by Akamu Jude Ewunkem and coauthors carry out an experimental study to evaluate the growth of strains of S. aureus resistant to gallium against metals, antibiotics and polyfluorinated compounds. The study is interesting and with novelty. However, there are some sections that need to be improved.

Abstract:
•    The authors use the terminologies "mutations" and "polymorphisms." Standardize and review the appropriate use of each word throughout the manuscript.

Introduction
•    Line 54: Add reference(s) that support this statement.
Methods
•    Line 114: The reference is not in the required format, nor is it in the list of references.
•    Section 2.5.: Include all substances used in the experiments (i.e. chloramphenicol is missing). Verify and adjust the concentration ranges of the substances used according to the results section and figures.
•    Line 141: Excessive use of self-citations. A single reference should be sufficient.
Results
•    Figure 1: The authors use different ways of writing Gallium (III). (Ga III, gallium-3, ...). I suggest standardizing the writing as much as possible in the figures, legends and throughout the manuscript.
•    Line 178: Correct the reference to the figure.
•    Line 180: The growth in silver is not in the concentration range of 0—750 mg/L. 
•    Line 182: Reference to Table 1 is unnecessary at this point. This table should go in section 3.6.
•    Table 1: The results (number of mutations, type of missense mutation, nonsense, ...) should be reported in better detail. Include a footer to give the meaning of the values in cells under C1-C5 (same for Table 3) and symbols as † and ‡. In accordance with 2.4. should they be G1-G5? Verify.
•    I suggest merging tables 1 and 2.
•    Line 248: adenine phosphoribosyltransferase is repeated.
•    Section 3.6: What is the description of major and minor polymorphisms? Detail.
Discussion:
•    Lines 412-426: Add an additional discussion highlighting the importance and care of verifying the virulence potential in vivo.
•    Lines 427-428: These 13 polymorphisms in both populations must be detailed in results. Was the nucleotide/amino acid change the same? Explain and discuss these findings.
•    Line 435: "were detected in" is duplicated.
•    Lines 460-461: Extend this discussion. Since there are shared mutations between populations, the generation of strains resistant to Polyfluorinated Compounds may be overestimated.
•    Add the limitations of the study and future experiments necessary to corroborate the hypotheses derived from the results.

Author Response

Introduction

• Line 54: Add reference(s) that support this statement.

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

• Methods

  • Line 114: The reference is not in the required format, nor is it in the list of references.
  • Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.
• Section 2.5.: Include all substances used in the experiments (i.e. chloramphenicol is missing). Verify and adjust the concentration ranges of the substances used according to the results section and figures.
• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.
• Line 141: Excessive use of self-citations. A single reference should be sufficient.
• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

Results

•    Figure 1: The authors use different ways of writing Gallium (III). (Ga III, gallium-3, ...). I suggest standardizing the writing as much as possible in the figures, legends and throughout the manuscript.

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

 

• Line 178: Correct the reference to the figure.
• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

 

•  Line 180: The growth in silver is not in the concentration range of 0—750 mg/L.
• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.
• Line 182: Reference to Table 1 is unnecessary at this point. This table should go in section 3.6.
• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.
•  
•  
• Table 1: The results (number of mutations, type of missense mutation, nonsense, ...) should be reported in better detail. Include a footer to give the meaning of the values in cells under C1-C5 (same for Table 3) and symbols as † and ‡. In accordance with 2.4. should they be G1-G5? Verify.

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

I suggest merging tables 1 and 2.

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

Line 248: adenine phosphoribosyltransferase is repeated.

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

Section 3.6: What is the description of major and minor polymorphisms? Detail.

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

 

Reviewer 2 Report

Comments and Suggestions for Authors

In the study of Ewunkem et al., the authors conducted laboratory adaptive experiments with the S. aureus strain ATCC 25923, exposing it to gallium nitrate. The derivative strains demonstrated increasing survival under metals and some antimicrobials. The characterization of derivative strains involved the use of scanning electron microscopy and whole genome sequencing. I am concerned about certain methodological issues.

 Major comments.

Firstly, the workflow of SNP calling and related data in Tables 1 and 3 is not clearly understood. A description of all abbreviations (C1-5-control groups, etc.) should accompany the legend. The data in these tables is unclear. What is the meaning of the values? In section 3.6, authors stated, “To determine the effect of gallium selection on S. aureus genomic variations, we sequenced replicates from each selected population and defined major polymorphism as F>0.4);” however, it is unclear what it means. What is major polymorphism? What is minor polymorphism (L.250)? A clear description should be given. What do the symbols in the tables and colors of SNPs mean? This data is very similar to the output of breseq software (https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing). If this pipeline was used in the current study, it should be added in the M&M section. What are the coordinates in column “Position”? The genomic sequence of Staphylococcus aureus (ATCC 25923)? If so, the NCBI GenBank ID should be provided.

 WGS data. Were the reads and/or contigs deposited in the ENA/NCBI databases?

Section 3.3. Why were only tetracycline and chloramphenicol used in the current study? I would suggest expanding this section with the inclusion of other major antibiotic groups (beta-lactams, vancomycin, gentamicin, etc.). “Typically, metal resistance is known to co-select for antibiotic resistance (Dickinson et al., 2019)….” I don’t find the reference “Dickinson et al., 2019” in the citing studies.           

Section 3.5. I don't see any differences between the three photos. The first photo is actually a cluster of cells; it's difficult to tell the cells apart. Descriptive statistics are needed, indicating the length of the cells, diameter, etc. How were the cells prepared for analysis? Was an overnight inoculum used, or were cells collected from a particular growth phase? In the discussion section, it stated, “After 20 days of selection in Gallium (III) nitrate, to our surprise, resulted in the variation of cell shapes while the control and ancestral cells appeared perfectly spherical.“ More measurements and demonstrative photos are required.

L.402 – 406. It would be interesting to determine if the growth rate of the derivative strains changed. The study should incorporate this relatively simple analysis.

L.427 – 430. For a better understanding and visualization of the results, provide a Venn diagram with SNPs (control vs. treated population).

L.439 – 440. “…lower frequencies.” What this mean?    

Minor comments.

L. 105. “…in a 98-well plate GloMax®-Multi Microplate…” Did the authors mean a 96-well plate? Same for L.106.

L.93.“Staphylococcus aureus (ATCC 25923)” should be removed from this section.

Section 2.4. The scheme of in vitro selection would be advisable for better presentation of the experiment.

In section 3.6, place Table 1 in the proper location.

Table 2. Gene system classification data should be added (KEGG or GO).

L.243. “Table 1 shows polymorphisms in the gallium (III)-resistant populations at day 20.” In the Table 1 data, refer to C1-C5 (control group, not resistant population). The sentence need corrections.

Section 3.6. SNPs and gene descriptions can be shortened because they are given in tables.

Author Response

Firstly, the workflow of SNP calling and related data in Tables 1 and 3 is not clearly understood. A description of all abbreviations (C1-5-control groups, etc.) should accompany the legend. The data in these tables is unclear. What is the meaning of the values? In section 3.6, authors stated, “To determine the effect of gallium selection on S. aureus genomic variations, we sequenced replicates from each selected population and defined major polymorphism as F>0.4);” however, it is unclear what it means. What is major polymorphism? What is minor polymorphism (L.250)? A clear description should be given. What do the symbols in the tables and colors of SNPs mean? This data is very similar to the output of breseq software (https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing). If this pipeline was used in the current study, it should be added in the M&M section. What are the coordinates in column “Position”? The genomic sequence of Staphylococcus aureus (ATCC 25923)? If so, the NCBI GenBank ID should be provided.

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow. We did not use the software you suggested

WGS data. Were the reads and/or contigs deposited in the ENA/NCBI databases?

The data were not deposited in ENA/NCBI. I intend to deposit the data

Section 3.3. Why were only tetracycline and chloramphenicol used in the current study? I would suggest expanding this section with the inclusion of other major antibiotic groups (beta-lactams, vancomycin, gentamicin, etc.). “Typically, metal resistance is known to co-select for antibiotic resistance (Dickinson et al., 2019)….” I don’t find the reference “Dickinson et al., 2019” in the citing studies.      

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow. We did not use the software you suggested. We had use other antibiotics for example, ampicillin, sulfonamide, rifampicin . We saw similar results. Presenting we are testing other antibiotics and metals and hope to publish the data soon

 

Section 3.5. I don't see any differences between the three photos. The first photo is actually a cluster of cells; it's difficult to tell the cells apart. Descriptive statistics are needed, indicating the length of the cells, diameter, etc. How were the cells prepared for analysis? Was an overnight inoculum used, or were cells collected from a particular growth phase? In the discussion section, it stated, “After 20 days of selection in Gallium (III) nitrate, to our surprise, resulted in the variation of cell shapes while the control and ancestral cells appeared perfectly spherical.“ More measurements and demonstrative photos are required.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow. We ancestral cells are clustered because we grew them overnight before the experiments. While the control and treated populations were cultured in the broth for 20 days. We did not measure individual cells because the images have scale bars. Also we can clearly see morphological changes in the   treated cells compared to the control populations.

L.402 – 406. It would be interesting to determine if the growth rate of the derivative strains changed. The study should incorporate this relatively simple analysis.

Thank you for pointing this out. We agree with this comment. The treated population exhibited  superior growth in media only . Our statistical analysis showed the difference in growth was statistically significant. 

L.427 – 430. For a better understanding and visualization of the results, provide a Venn diagram with SNPs (control vs. treated population).

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow. Instead of using a Venn Diagram, we color coded the table 2

L.439 – 440. “…lower frequencies.” What this mean?   

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow. We clearly explained the terms.

Minor comments.

105. 105. “…in a 98-well plate GloMax®-Multi Microplate…” Did the authors mean a 96-well plate? Same for L.106. 

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

L.93.“Staphylococcus aureus (ATCC 25923)” should be removed from this section.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

Section 2.4. The scheme of in vitro selection would be advisable for better presentation of the experiment.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow. Please see table 1.

In section 3.6, place Table 1 in the proper location.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

Table 2. Gene system classification data should be added (KEGG or GO).

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

Table 2. Gene system classification data should be added (KEGG or GO).

Thank you for pointing this out. We agree with this comment. We did not use KEGG or GO. We used tables as seen in our previous papers.

L.243. “Table 1 shows polymorphisms in the gallium (III)-resistant populations at day 20.” In the Table 1 data, refer to C1-C5 (control group, not resistant population). The sentence need corrections.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

Section 3.6. SNPs and gene descriptions can be shortened because they are given in tables.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

 

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript describes the gallium resistance in Staphylococcus aureus and the implications for the treatment of relevant infections.

The manuscript is excellent and can be accepted immediately with no changes at all.

I have marked below some points that require attention and should be corrected before acceptance.

-Please describe the objectives of the study clearly in a separate paragraph.

-Please provide a clear indication of the literature gaps that would be filled through the publication of this report.

-Please describe the details of all purveyors of equipment and consumables.

-Please describe in detail the control procedures employed in this study, preferably in a sub-section on their own.

-Presentation. Grahs 1-4 must be improved, possibly by use of box-and-whisker plots.

-Tables. Please make greater use of tables and reduce length of running text.

-The text in Discussion is boring to read and requires significant improvement, for example a) separate in sub-sections, b) present examples of use of gallium against other bacteria, c) present examples of use of other heavy metals against staphylococci.

-References. The number of references employed is small in relation to the complexity of ideas developed in this manuscript. I foresee that over 100 references are necessary to fully explore the potential of this manuscript.

-Conclusions. Please bring in line with the actual findings of the study and please do not over-extrapolate.

 

In all: excellent manuscript that can be accepted immediately, but in which manuscript also significant improvements can be made to improve the final quality – please make the changes and resubmit, otherwise rejection can be recommended at the next round of evaluation.

 

Recommendation: major revision, improvement, re-evaluation.

Author Response

-Please describe the objectives of the study clearly in a separate paragraph.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

-Please provide a clear indication of the literature gaps that would be filled through the publication of this report.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

-Please describe the details of all purveyors of equipment and consumables.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

Please describe in detail the control procedures employed in this study, preferably in a sub-section on their own.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

-Presentation. Grahs 1-4 must be improved, possibly by use of box-and-whisker plots.

Thank you for pointing this out. We agree with this comment. Since we tested several concentrations we could not have use box-whisker plots.

Tables. Please make greater use of tables and reduce length of running text.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

The text in Discussion is boring to read and requires significant improvement, for example a) separate in sub-sections, b) present examples of use of gallium against other bacteria, c) present examples of use of other heavy metals against staphylococci.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

-References. The number of references employed is small in relation to the complexity of ideas developed in this manuscript. I foresee that over 100 references are necessary to fully explore the potential of this manuscript.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

 

-Conclusions. Please bring in line with the actual findings of the study and please do not over-extrapolate.

Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted in yellow.

 

 

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors have addressed almost all the observations made in the first round of review. The point that still needs to be corrected is the excessive use of self-citations (Refs. 25 to 30).

Author Response

The authors have addressed almost all the observations made in the first round of review. The point that still needs to be corrected is the excessive use of self-citations (Refs. 25 to 30).

• Thank you for pointing this out. We agree with this comment. Therefore, we have  edited  the references highlighted green.

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript is excellent and can be accepted immediately as it is, with no changes at all.

Before final acceptance, I have two points that need attention.
1) The authors should make a good polish of English language throughout the manuscript to correct various small errors and grammatical slips.
2) There are some very relevant references published in the last two months. Can the authors please include them in the manuscript as well? This will bring nicely the number of references in the manuscript to 101, which is a nice, round number.

Overall. One of the best pieces of work produced in the international literature during the last 3-4 recent years. Manuscript worthy of immediate acceptance without changes.
I recommend revision and re-evaluation.

 

Comments on the Quality of English Language

The authors should make a good polish of English language throughout the manuscript to correct various small errors and grammatical slips.

Author Response

1) The authors should make a good polish of English language throughout the manuscript to correct various small errors and grammatical slips.

• Thank you for pointing this out. We agree with this comment. Therefore, reviewed the manuscript and made the changes highlighted green.

There are some very relevant references published in the last two months. Can the authors please include them in the manuscript as well? This will bring nicely the number of references in the manuscript to 101, which is a nice, round number.

• Thank you for pointing this out. We agree with this comment. Therefore, we have  added the references highlighted green