https://orcid.org/0000-0002-0738-7557
Peer Review History
| Original SubmissionJune 3, 2021 |
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Dear Prof. Maiden, Thank you very much for submitting your manuscript "Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis" for consideration at PLOS Pathogens. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations. Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. When you are ready to resubmit, please upload the following: [1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out [2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file). Important additional instructions are given below your reviewer comments. Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments. Sincerely, Xavier Nassif Section Editor PLOS Pathogens Xavier Nassif Section Editor PLOS Pathogens Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens *********************** Reviewer Comments (if any, and for reference): Reviewer's Responses to Questions Part I - Summary Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship. Reviewer #1: This manuscript uses genome-wide association studies of a large collection of Neisseria meningitides (Mc) isolates to search for genomic difference between invasive and carriage Mc strains. They identify several polymorphisms that would alter the expression of the factor H binding protein (FHBB). They found association within a few capsule genes, the MDA phage that was previously associated with invasive disease, and several other loci. This manuscript follows that of Spinsanti et al (PloS pathogens published in March 2021) that focused only of fHBP to identify a similar finding about expression and the same mechanistic basis. The authors argue that since their study was finished before the Spinsanti study was published and that they used different methods this should not preclude the publication of this work. I am supportive of this viewpoint since the studies are complementary but I believe the manuscript could be improved. Reviewer #2: This work by Sarah G . Earle et al is focused on bacterial genome-wide association studies of N. meningitidis. The events that lead to meningococcal invasion are still elusive. Here, SGE et al explored the relationship between genetic variation and invasive meningococcal disease in GWAS. In parallel, an independent study was published in PloS Pathogen and dealing with the same set of publicly available data (Spinsanti et al). In contrast to this latter work, SGE et al analysed the data set thoroughly and extracted several interesting associations. Among these, the authors chose to focus on fHbp. This clear and concise manuscript highlights a very important topic and goes much further than Spinsanti et al in terms of GWAS analysis. This in-depth analysis provided interesting results and will be an important addition to the community. This justifies publication in PloS Pathogen. ********** Part II – Major Issues: Key Experiments Required for Acceptance Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions. Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject". Reviewer #1: None Reviewer #2: The experiments on fHbp are well documented, although it is to be regretted that the authors did not address other SNPs and Kmers. Considering the early online publication of Spinsanti et al, I would not suggest further experiments. However, and considering the very short discussion, I would really appreciate that the authors discuss other GWAS association, especially those presented in Fig1: - fba is an important finding. This gene was found to be essential in the blood of mice. However, the authors were only interested in fHbp. Modification of fba sequence may alter its metabolic function. - pilV is an interesting finding since it has been proposed as an adhesin. - mafB was described as par of a toxin-antiToxin system. - lptF is involved in LOS maturation - some genes are involved in RNA an tRNA maturation (gidA, vacB) - trkH may regulate K+ uptake, which may be related to resistance against the host. ********** Part III – Minor Issues: Editorial and Data Presentation Modifications Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. Reviewer #1: 1. The Discussion is very short and does not really compare and contrast between the two studies. This needs to be discussed and they need to go into detail. 2. They mention two other polymorphisms in the Results and show others in Figure 1 but do not mention the others in the Results nor any of these in the Discussion. The strength of this whole genome study relative to the focused Spinsanti paper is the identification of these other loci. They each should be given some attention in the Results and the Discussion. Reviewer #2: - ********** PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: H Steven Seifert Reviewer #2: No Figure Files: While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org. Data Requirements: Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5. Reproducibility: To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols References: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. |
| Revision 1 |
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Dear Prof. Maiden, We are pleased to inform you that your manuscript 'Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis' has been provisionally accepted for publication in PLOS Pathogens. Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests. Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated. IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript. Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS. Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Xavier Nassif Section Editor PLOS Pathogens Xavier Nassif Section Editor PLOS Pathogens Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens *********************************************************** Reviewer Comments (if any, and for reference): |
| Formally Accepted |
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Dear Prof. Maiden, We are delighted to inform you that your manuscript, "Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis," has been formally accepted for publication in PLOS Pathogens. We have now passed your article onto the PLOS Production Department who will complete the rest of the pre-publication process. All authors will receive a confirmation email upon publication. The corresponding author will soon be receiving a typeset proof for review, to ensure errors have not been introduced during production. Please review the PDF proof of your manuscript carefully, as this is the last chance to correct any scientific or type-setting errors. Please note that major changes, or those which affect the scientific understanding of the work, will likely cause delays to the publication date of your manuscript. Note: Proofs for Front Matter articles (Pearls, Reviews, Opinions, etc...) are generated on a different schedule and may not be made available as quickly. Soon after your final files are uploaded, the early version of your manuscript, if you opted to have an early version of your article, will be published online. The date of the early version will be your article's publication date. The final article will be published to the same URL, and all versions of the paper will be accessible to readers. Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens |
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