Peer Review History
Original SubmissionFebruary 19, 2024 |
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PONE-D-24-06332Measuring single-cell susceptibility to antibiotics within monoclonal bacterial populationsPLOS ONE Dear Dr. Aristov, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Apr 27 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
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Please amend your authorship list in your manuscript file to include author Charles N. Baroud. 6. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 7. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The depleting pipeline of antibiotics and the spread of AMR necessitates new tools to classify and study antibiotic activity. In this manuscript, the authors use a previously developed microfluidic droplet-based platform to look at antibiotic susceptibility. Using fluorescent E. coli and ciprofloxacin as the candidate antibiotic they evaluate their platform. Initial experiments were carried out to benchmark the growth of the bacteria in the platform and compared with growth in a 96-well plate format. Image analysis pipelines were subsequently developed to quantitate the bacterial growth from 0h to 24h. Exposure to different concentrations of ciprofloxacin on different chips allows them to define microfluidic MIC which is closer to MBC by conventional assays rather than to the MIC values. They further analyze these data to derive single-cell antibiotic susceptibility profiles and also demonstrate the utility of the platform to document morphological changes upon antibiotic exposure. As the authors themselves present in the introduction, there have been numerous studies that have achieved the goals this study set out to do. So, in terms of novelty this is not an entirely unique technique or device. But the study provides an additional toolset available to the research community to address these issues. The experiments are well-designed and the manuscript written well. Specific comments: - In the abstract the authors state “To date, neither bulk nor single-cell methods are able to link the heterogeneity of single-cell susceptibility to the population-scale response to antibiotics.” This is misleading, as there are several studies which have linked single-cell behavior to populations scale responses – publications from Balaban group, James Collins group, Losick group for example. - Ln 48-49, the authors claim that the link between single-cell measurements and the classical biological measurements has never been explicitly tested. Again this is misleading as all the microfluidic papers on antibiotic susceptibility testing that the authors cite indeed compared the findings with classical biological measurements. - It is not very convincing that this platform is any better than a conventional 96 well plate. Imaging of bacteria in a conventional 96 well plate should be able to accomplish most of the observations obtained on this platform. Especially since in any case the cells at the bottom of the droplet are being imaged. For example, in the study (Zahir T, Camacho R, Vitale R, Ruckebusch C, Hofkens J, Fauvart M, Michiels J. 2019. High-throughput time-resolved morphology screening in bacteria reveals phenotypic responses to antibiotics. Communications Biology 2:1–13.) - The authors show that the microfluidic MIC is similar to the MBC determined by conventional method and not to the MIC. This was the observation with antibiotic ciprofloxacin (which seems to lyse the cells), would they expect a similar finding even with bacteriostatic antibiotics. It would have enriched the manuscript if they could have included analysis of an additional antibiotic (bacteriostatic). - Have the authors accounted for the variable depletion of nutrients in the droplets due to differential seeding densities. Would this effect their observations on antibiotic activity, especially under conditions that the droplet is filled up with bacteria. - The authors claims of looking at time evolution of phenotypes over time is not fully supported as from the movies, it appears the cells are in constant turbulence in the droplet and it would not be feasible to follow the same cell over time/ divisions. - Considering that the platform is an additional resource in the antibiotic susceptibility field, it would be beneficial if the authors could summarize and discuss the advantages and disadvantages of their setup in comparison to other microfluidic devices in the field. - Reference 1 seems incomplete. - Movies S1 and S2 appear to be switched. - Ln 31, ‘By’ should be ‘by’ Reviewer #2: The authors present an interesting piece of scientific research using a droplet-based approach to measure how single E.coli cells can expand to form colonies under antibiotic stress. The authors highlight how their current approach is built upon existing platforms and technologies, and could perhaps discuss more on the novelty of their current approach. The authors should include a section in the Materials and Methods on their statistical analyses used in their research; the statistics used are mentioned in their legends. Overall, the manuscript is well written but there are a few minor corrections: There is an inconsistent use of "µ" throughout. Figure 3b is not described in the legend. There are a few spelling errors (lines: 206, 391, 477, Fig 1 legend). ********** 6. 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 ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment 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. Registration is free. 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 PLOS at figures@plos.org. 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Revision 1 |
Measuring single-cell susceptibility to antibiotics within monoclonal bacterial populations PONE-D-24-06332R1 Dear Dr. Andrey Aristov, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and is accepted for publication. An invoice will be generated. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Vinayak Singh, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-24-06332R1 PLOS ONE Dear Dr. Aristov, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Vinayak Singh Academic Editor PLOS ONE |
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