Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE

Lisa Teichmann; Marcus Wenne; Sam Luitwieler; Gaurav Dugar; Johan Bengtsson-Palme; Benno ter Kuile

doi:10.1371/journal.pone.0312223

Peer Review History

Original SubmissionOctober 3, 2024
28 Nov 2024 Decision Letter - Bashir Sajo Mienda, Editor PONE-D-24-43795Genetic Adaptation to Amoxicillin in Escherichia coli: The Limited Role of dinB and katEPLOS ONE Dear Dr. Kuile, 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 Jan 12 2025 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. 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Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: 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: Dear Author, Thank you for your effort to share your research findings with the scientific community through this manuscript entitled, “Genetic Adaptation to Amoxicillin in Escherichia coli: The Limited Role of dinB and katE” and submitting it for publication in PLOS ONE. I have gone through the manuscript draft and found it quite interesting. The manuscript data is technically sound and supports the conclusions drawn. The description of the experiments conducted indicated that it was rigorously carried out, with appropriate controls, replication, and sample sizes. There is adequate evidence that shows data underlying the findings in manuscript are made fully available and presented in an intelligible fashion and written in standard English. The paper is clear and well-composed. The dataset therein is very useful. There is sufficient justification to affirm the originality of the work, numerical figures of the various analytical factors have been reported with a reasonable degree of accuracy. The objectives of the work as outlined in the introductory part of the manuscript have been reasonably achieved. Thus, the work could be adjudged complete within its limitations. In a nutshell, this is a high-quality manuscript that clarified the contributions of DNA polymerase IV (dinB) and catalase HP2 (katE) genes in E. coli's adaptation to beta-lactam resistance. In particular, the work has established that dinB and katE may not be as critical for beta-lactam adaptation as generally assumed. This could be quite thought-provoking to the scientific community However; I have outlined some comments that could help improve the quality of the manuscript. Comments: 1. Line 155. There may be no need of a hyphen between 5 and minute, also the word ‘minutes’ should be written in the plural form, to make it consistent with the other usage elsewhere in the manuscript. 2. L192. The concentration of the antibiotic used needs to be specified. 3. L196. Specify the concentration of the agarose used 4. L439 - 440 The direct involvement of frdD should be further elaborated to adequately discuss its role based on the findings of this study. ****** 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 ******** [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. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: REVIEW REPORT_PONE-D-24-43795.pdf https://doi.org/10.1371/journal.pone.0312223.r001
Revision 1
10 Dec 2024 Author Response Response to the reviewer PONE-D-24-43795 Teichmann et al.,: Genetic Adaptation to Amoxicillin in Escherichia coli: The Limited Role of dinB and katE Reviewers comments: Thank you for providing me the opportunity to review this manuscript titled, “Genetic Adaptation to Amoxicillin in Escherichia coli: The Limited Role of dinB and katE” for publication in your journal (PLOS ONE). I have gone through the manuscript draft and found it quite interesting. The paper is clear and well-composed. The dataset therein is very useful. There is sufficient justification to affirm the originality of the work, numerical figures of the various analytical factors have been reported with a reasonable degree of accuracy. The objectives of the work as outlined in the introductory part of the manuscript have been reasonably achieved. Thus, the work could be adjudged complete within its limitations. In a nutshell, this is a high-quality manuscript that clarified the contributions of DNA polymerase IV (dinB) and catalase HP2 (katE) genes in E. coli's adaptation to beta-lactam resistance. In particular, the work has established that dinB and katE may not be as critical for beta-lactam adaptation as generally assumed. This could be quite thought-provoking to the scientific community However; I have outlined some comments that could help improve the quality of the manuscript. Comments: 1. Line 155. There may be no need of a hyphen between 5 and minute, also the word ‘minutes’ should be written in the plural form, to make it consistent with the other usage elsewhere in the manuscript. Accepted and corrected accordingly 2. L192. The concentration of the antibiotic used needs to be specified. Accepted and corrected accordingly 3. L196. Specify the concentration of the agarose used Accepted and corrected accordingly 4. L439 - 440 The direct involvement of frdD should be further elaborated to adequately discuss its role based on the findings of this study. Frankly, we found this comments slightly confusing. The Involvement of frdD is extensively discussed in line 414-46. The combined authors came up with the following ideas to address this comment: 1. "Mutations in the frd operon have been described to boost ampC amplification and contribute to beta-lactam resistance”: Here, I guess we could compare the expression of ampC in strains with and without these mutations to add to the data in the cited papers These data turned out very hard to compare, confusing instead of clarifying the issue. 2. "changes in energy availability and cellular redox status, influenced by frdD expression, may affect the efficiency of cell wall synthesis, and by extension, bacterial susceptibility to beta-lactam antibiotics.”: This is a long-shot, but could we look at expression of e.g. cell wall synthesis pathway genes in relation to the frdD expression? If we see an association, I guess that would strengthen this case, but this might be hard as I know energy metabolism is affected by a bunch of different things. This association didn’t materialize either. 3. We already analysed the fumarate reductase/succinate dehydrogenase relationship in detail, so this cannot be expanded. 4. "Superoxide dismutase activity has been linked to antibiotic resistance by activating the stringent response, upregulating efflux pumps, downregulating of the outer membrane porin OmpF, and co-regulation of the multidrug-resistant locus mar”: Do we see these upregulations together with increased frdD levels in our data? Turns out that this is not the case either. 5. "elevated superoxide levels can increase mutagenesis”: We have the transcriptomics data from the final strains. It might be interesting to compare the frdD levels at the mid-point to the number of mutations in the corresponding final evolved strains. However, this may be comparing apples to oranges. Indeed, when this analysis was tried, the outcome was an uninterpretable mess. In short, since the involvement of frdD has already been discussed extensively in the framework oh the literature (lines 414-46), we have decided not to add to that. We hope to have convinced you that this is not out of disrespect for the reviewer or lack of will to make the effort. Attachments Attachment Submitted filename: Teichmann et al., response to the reviewer.docx https://doi.org/10.1371/journal.pone.0312223.r002
29 Dec 2024 Decision Letter - Bashir Sajo Mienda, Editor Genetic Adaptation to Amoxicillin in Escherichia coli: The Limited Role of dinB and katE PONE-D-24-43795R1 Dear Dr. KUILE, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. 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, Bashir Sajo Mienda, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 2. 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know ****** 4. 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: Yes ****** 5. 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 ****** 6. 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: (No Response) ****** 7. 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 ******** https://doi.org/10.1371/journal.pone.0312223.r003
Formally Accepted
7 Jan 2025 Acceptance Letter - Bashir Sajo Mienda, Editor PONE-D-24-43795R1 PLOS ONE Dear Dr. ter Kuile, 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. Bashir Sajo Mienda Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0312223.r004

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