https://orcid.org/0000-0001-8129-7843
Peer Review History
| Original SubmissionOctober 13, 2020 |
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Dear Dr. Goodman, Thank you very much for submitting your manuscript "Enhanced Biofilm and Extracellular Matrix Production by Chronic Carriage versus Acute Isolates of Salmonella Typhi" 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. The reviewers appreciated the attention to an important topic. 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, Andreas J Baumler Associate Editor PLOS Pathogens Renée Tsolis 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: Devaraj et al. characterize a series of acute and chronic Salmonella Typhi strains, showing that, independent of lineage, the chronic strains tend to make “better” biofilms, consistent with their ability or selection to colonize gall stones. The experiments are generally straight forward, although the results are correlative without any molecular explanation. The paper is more wordy than necessary and could be shortened significantly. My other comments also focus on presentation. Reviewer #2: In this study, Devaraj et al characterize a small collection of S. Typhi isolates to investigate whether strains isolated from chronic or acute typhoid fever exhibit genomic or phenotypic differences that could point towards pathoadaptation. Based on the genome sequence of these isolates, the authors generate a phylogenetic tree; this analysis fails to identify obvious patterns that correlate with disease state (chronic vs acute). The authors then analyze biofilm formation of each strain in vitro. Strains isolated from chronically-infected patients tended to form thicker biofilm and these biofilms contained more extracellular DNA and DNABII proteins. In contrast, no difference in the production of the Vi antigen were noted. Antibodies directed against S. Typhi DNABII proteins disrupted the biofilm and decreased biofilm-associated biomass. Overall, the experiments are well-executed, the manuscript is well-written and easy to follow. All major conclusions are supported by the data. The finding that S. Typhi may adapt during chronic infections to produce more biofilm and thus ensure better gall bladder colonization is novel and exciting. Previous studies have reported effects of anti-DNABII on bacterial biofilms and as such, this concept and technology is not entirely novel. However, this was not known for S. Typhi and is new information. I only have some minor comments regarding the writing and data presentation. ********** 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: None ********** 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. Define DNABII proteins in the abstract 2. Both the introduction and discussion could be shortened significantly without loss of important content. 3. It is not clear that the pulse-field gel experiment adds anything to the paper given the subsequent genome sequencing. 4. Line 198. It would be better to call and label JS698 Ty2. You do this in some figures, but not all. JSG4383 isn’t in the strain table so I can’t see the genotype. I wonder if (line 200) you mean that you repaired or replaced the mutant rpoS allele with wt rather than “complemented” it in trans. 5. Line 233. You don’t really mean that “LPS was absent” versus lack of antigen. Rephrase. Indeed, what do you mean by anti-LPS antibody? If it is anti-O9, for example, you just say so. 6. Line 244. “…also the translated proteins of IHF and HU…” is somewhat awkward. 7. Fig 1. Barely visible in Fig 1A, you demarcate acute and chronic strains with very small red and blue dots and this color scheme is carried through to 2B. You need to make this distinction more obvious by repeating the mark in 2B (larger dots would be nice) or saying it in the legend. …and why not carry it through to 2C? 8. Supp Fig 2. Growths curves need to be plotted with the OD on a log scale. Minor comments: 9. Line 58 individuals 10. Line 60. …chronic carrier state, although not genotypically distinct… 11. Line 119. …immune effectors, and antibiotics… 12. Line 121. …that negatively affect its… 13. Line 124. “…that alter the transcriptional landscape of chronic carriage of Salmonella…” This doesn’t make sense as written. Reviewer #2: Fig. S2: Bacterial growth curve are easier to interpret when plotted on semi-log plot (log of OD, time in linear scale). The exponential growth phase is then clearly identifiable as a linear feature on this type of plot. The doubling time, based on exponential growth, should be calculated and reported. Also, is the growth defect referring to a slower growth rate during exponential phase or a lower recovery (density) in stationary phase? Based on the current plot, it certainly is the latter, but the former is difficult to assess. I recommend that standard bacterial genetics nomenclature should be followed throughout the manuscript. It is a bit unusual to see that wild-type strains are referred to by a number assigned by the investigator. JSG698 and JSG210 should be denoted as Ty2 and 14028S in the manuscript (e.g. line 201 and Fig. 2). Also, if the tviB mutant JSG1213 was previously published by the Popoff group, please provide this reference (maybe PMID: 8574397?). ********** 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: No 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, PLOS recommends that you deposit 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. For instructions see http://journals.plos.org/plospathogens/s/submission-guidelines#loc-materials-and-methods |
| Revision 1 |
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Dear Dr. Goodman, We are pleased to inform you that your manuscript 'Enhanced Biofilm and Extracellular Matrix Production by Chronic Carriage versus Acute Isolates of Salmonella Typhi' 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, Andreas J Baumler Associate Editor PLOS Pathogens Renée Tsolis 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 Dr. Goodman, We are delighted to inform you that your manuscript, "Enhanced Biofilm and Extracellular Matrix Production by Chronic Carriage versus Acute Isolates of Salmonella Typhi," 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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