All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
Dear Dr. Rashid and colleagues:
Thanks for re-submitting your manuscript to PeerJ, and for addressing the concerns raised by the reviewers. I now believe that your manuscript is suitable for publication. Congratulations! I look forward to seeing this work in print, and I anticipate it being an important resource for microbiologists working on cholera vaccines. Thanks again for choosing PeerJ to publish such important work.
-joe
# PeerJ Staff Note - this decision was reviewed and approved by Elena Papaleo, a PeerJ Section Editor covering this Section #
It is acceptable. The authors appropriately revised the manuscript based on the reviewers' comments.
It is acceptable.
The findings are valid and robust.
The manuscript is appropriately prepared and revised based on the reviewer's comments.
Dear Dr. Rashid and colleagues:
Thanks for submitting your manuscript to PeerJ. I have now received two independent reviews of your work, and as you will see, the reviewers raised some substantial concerns about the research. Despite this, one reviewer is optimistic about your work and the potential impact it will have on the Vibrio cholera vaccine development. The other reviewer is far less optimistic; thus, your revision will need to convince this reviewer of the significance of your work, perhaps by 1) presenting the paper as a purely in silico approach (especially in the title and abstract) 2) improving the writing and presentation of figures, 3) downplaying the importance of antibiotic resistance, 4) avoiding overstatements about certain virulence mechanisms (try providing solid references for all stated virulence factors), 5) better analyzing your findings in the context of previous reports on such approaches. Importantly, some of these criticisms were also raised by reviewer 1.
Accordingly, I am encouraging you to revise your manuscript taking into account all of the concerns raised by both reviewers. Good luck with your revision, and thanks again for submitting your work to PeerJ.
-joe
Please convert the abstract to the structured version. The authors can refer to the Instructions for Authors (in PeerJ) or the similar published papers.
INTRODUCTION:
The presented evidence (lines 54-61) need to accompany with the relevant information regarding the efficacy/effectiveness of the mentioned interventions (anti-cholera oral formulation and genetically engineered V. Cholera O1 live attenuated Vaccine).
In the 3rd paragraph (lines: 63-70), the authors only indicated to the RV strengths. Authors should also consider the weaknesses of this approach. In addition, it is better to compare the effectiveness of this method with other similar methods or alternatives (traditional vaccine development methods or the others method).
Please consider the related literature on V cholera vaccines (different methods or technologies in according to efficacy, safety, …).
METHODS:
Although the method of this study has been published in one of the authors' previous articles (ref.no. 34), it is better to revise the method section of this article in greater detail in the investigation process.
RESULTS:
I think that it is appropriate.
DISCUSSION:
Unfortunately, the authors have not mentioned the limitations of this study and the directions for future research. It is better to consider the clinical implications based on the investigation findings.
Please convert the abstract to the structured version. The authors can refer to the Instructions for Authors (in PeerJ) or the similar published papers.
In this paper, Rahid, Rehman and Andleeb use a multi-step computational approach to predict peptides that they propose would be useful as antigens for cholera vaccines. There may be some valuable information here, but the authors do not sufficiently contextualize their findings in light of other studies (e.g. see pt 7 below).
Major points
1. Make clear in abstract (and title) that this is bioinformatics paper; i.e. that the screen was purely in silico. Usually, in reverse vaccinology approach, candidate polypeptides are tested for immunogenicity.
2. There is an over-emphasis on the importance of antibiotic resistance; in general antibiotic therapy is an adjunct to re-hydration and not a key issue in cholera.
3. It is not clear how/why the STRING analysis aides in predicting good antigens.
4. The claim that NlpD, OmpU, AcfA and OmpW are “critically important virulence mechanisms in V. cholerae” (line 203-205) is not well-grounded. To the best of my knowledge ompU mutants are not attenuated and acfA mutants exhibit only a modest colonization defect.
5. Additional details are necessary in the figure legends. For example, the legend for figure 2 should include a description of the yellow, blue, and red bars and the polar plot in the middle of each chromosome outline; the legend for figure 5 should list which of the protein structures are predictions and which are actual solved crystal structures, inclusion of any PDB accession codes used would also be helpful; in Figure 6 include a description of the different strains that are used in the multiple sequence alignment.
6. The introduction and perhaps discussion requires a more thorough and up to date description of cholera vaccine research.
7. Some references and discussion of prior studies of V. cholerae antigens; in particular the authors should include a comparison of their findings with those included in J Infect Dis. 2017 Jul 1;216(1):125-134. doi: 10.1093/infdis/jix253.
8. The paper is in need of careful editing for typos and grammatical errors.
Minor points:
Line 36 Non-O1 non)139 serogroups can be choleragenic
Line 37 serotype should be serogroup
see comments above
see comments above
see comments above
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.