Insights into the novel Enterococcus faecalis phage: A comprehensive genome analysis

Sahar Abed; Mohammad Sholeh; Mahshid Khazani Asforooshani; Morvarid Shafiei; Abdolrazagh Hashemi Shahraki; Shaghayegh Nasr

doi:10.1371/journal.pone.0301292

Peer Review History

Original SubmissionJanuary 30, 2024
21 Feb 2024 Decision Letter - Vinod Kumar Yata, Editor PONE-D-24-03766Insights into the Novel Enterococcus faecalis Phage: A Comprehensive Genome AnalysisPLOS ONE Dear Dr. Shafiei, 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 06 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. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 3. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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. Additional Editor Comments: The manuscript titled "Insights into the Novel Enterococcus faecalis Phage: A Comprehensive Genome Analysis" lays a robust foundation for a promising investigation into phage therapy against antibiotic-resistant E. faecalis. Authors are requested to adhere to the "manuscript body formatting guidelines," with a specific emphasis on modifying the abstract in accordance with the provided guidelines. It is essential to ensure that the revised abstract aligns appropriately with the specified formatting requirements. Authors are kindly urged to resubmit the manuscript after addressing the reviewers' comments. We appreciate your cooperation and anticipate the revised submission to meet the specified formatting guidelines and further enhance the overall quality of the manuscript. [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: Yes ****** 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: Yes 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 overall work is good. Methods and materials results and discussions are represented clearly. I encourage the authors to revise their manuscript and to resubmit it to the journal. This work is technically sound and isolation of phages is very difficult but isolation and charectarisation do it perfectly. Reviewer #2: The research article “Insights into the Novel Enterococcus faecalis Phage: A Comprehensive Genome Analysis” by Abed et al., provides important insights on the bacteriophage SAM-E.f 12 genomic potentials. The abstract is well written however the introduction is poorly cited and the research question and context on importance of bacterial comparative genomics needs to be established. With the minor modifications I believe the manuscript can be accepted for publication in Plos One. The specific comments are as follows. 1. Line 48: enlist the class of antibiotics bacteria E. faecalis known for with appropriate citations. 2. Line 49-51: Citation needed. 3. Methods results are well written and represented. ****** 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: Yes: DSC ******** [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: minor revision.docx https://doi.org/10.1371/journal.pone.0301292.r001
Revision 1
8 Mar 2024 Author Response Reviewer #1: The overall work is good. Methods and materials results and discussions are represented clearly. I encourage the authors to revise their manuscript and to resubmit it to the journal. This work is technically sound and isolation of phages is very difficult but isolation and characterization do it perfectly. Response to reviewer 1: Thank you for your encouraging feedback and constructive comments on our manuscript. We are heartened by your recognition of the clarity of our methods, materials, results, and discussions, as well as your acknowledgment of the technical soundness of our work and the successful isolation and characterization of phages. We will take your encouragement to revise and resubmit our manuscript as an opportunity to further refine our work. We appreciate the support and guidance provided by your feedback, which we believe will enhance the overall quality and impact of our study. Sincerely, Reviewer #2: The research article “Insights into the Novel Enterococcus faecalis Phage: A Comprehensive Genome Analysis” by Abed et al., provides important insights on the bacteriophage SAM-E.f 12 genomic potentials. The abstract is well written however the introduction is poorly cited and the research question and context on importance of bacterial comparative genomics needs to be established. With the minor modifications I believe the manuscript can be accepted for publication in Plos One. Response to reviewer: We have revised the introduction section according your suggestions. The specific comments are as follows. 1. Line 48: enlist the class of antibiotics bacteria E. faecalis known for with appropriate citations. We have updated Line 46-55 to include a list of the classes of antibiotics that Enterococcus faecalis is known to resist, accompanied by appropriate citations to ensure comprehensive support for our statements. 2. Line 49-51: Citation needed. In all introduction section we have now incorporated the necessary citations to fully reference the background information provided in this section, thereby strengthening the manuscript's credibility and scholarly depth. 3. Methods results are well written and represented. We are pleased to hear your positive feedback on the methods and results sections. We believe that the clarity and representation of these sections contribute significantly to the overall quality of our research. We are confident that these revisions address your concerns and enhance the manuscript's suitability for publication in Plos One. We look forward to the possibility of our work being accepted and thank you again for your valuable insights. Sincerely, Reviewer #3: Reviewer comment 1: The overall work is good. Methods and materials results and discussions are represented clearly. Dear Reviewer, Thank you for your positive feedback and constructive comments regarding our manuscript. We are grateful for the encouragement to revise and resubmit our work, and we have meticulously addressed the specific concerns you raised to enhance the clarity and impact of our study. Below, we detail our responses and the amendments made to the manuscript in accordance with your suggestions. Reviewer comment 2: I encourage the authors to revise their manuscript and to resubmit it to the journal. Give the explanation regarding the following comments: • In discussion part please mention supporting results of previous study. Response to reviewer: In response to your request for the inclusion of supporting results from previous studies in our discussion, we have meticulously revised the discussion section to incorporate more substantial evidence and references to prior research. Specifically, we have enriched lines 402-408 and lines 417-425 with additional details, now presented as follows: “We acknowledge the pivotal role of previous studies in laying the groundwork for our research on bacteriophage therapy as a viable alternative to traditional antibiotics. These studies have demonstrated the effectiveness of bacteriophages in not only targeting E. faecalis but also in providing a basis for their application in treating various antibiotic-resistant bacterial infections [27, 28]. The selection of E. faecalis as our primary focus was driven by its alarming resistance to a wide array of antibiotics, including vancomycin, and its significant impact on healthcare systems worldwide.” “The bacteriophage SAM-E.f 12 demonstrated remarkable effectiveness against select isolates of clinical E. faecalis, evidenced by the formation of clear plaques in 70% of the 60 strains tested in the spot assay. This notable specificity, underscored by the lack of lytic activity against E. faecium, highlights SAM-E.f 12's targeted action, especially against vancomycin-resistant E. faecalis strains. Such specificity is crucial for addressing the growing challenge of antibiotic resistance and aligns with the findings of previous research, which have documented the efficacy of specific phages in selectively targeting E. faecalis. This alignment not only corroborates SAM-E.f 12's potential in phage therapy but also reinforces the importance of phage specificity in the development of targeted antibacterial treatments [35, 36].” Reviewer comment 3: • Why you only choose Enterobacter faecalis instead of E. coli? Is there any special characteristics having Enterobacter faecalis? Explain clearly in discussion part. Response to Reviewer Comment 3: To clarify our rationale for selecting Enterococcus faecalis over E. coli, we have thoroughly revised the initial part of the discussion section, specifically lines 383-393, to elucidate our objectives and decision-making process. The revised passage now reads: “E. faecalis, a Gram-positive bacterium, poses a formidable challenge in clinical settings due to its intrinsic resistance to a broad spectrum of antibiotics, including those vital for combatting bacterial infections [1, 2, 25]. This resistance has prompted its inclusion in the World Health Organization's priority pathogen list [26]. This resistance has not only placed E. faecalis on the World Health Organization's priority pathogen list but also highlighted the critical need for innovative therapeutic strategies to combat such resilient bacterial strains. Particularly noteworthy is E. faecalis's resistance to antibiotics like vancomycin, accentuating the exigency to explore alternative treatment modalities [27]. Phage therapy, characterized by a targeted approach, emerges as an advantageous strategy, especially in combating antibiotic-resistant E. faecalis strains, aligning with broader efforts to address antibiotic resistance through innovative antimicrobial exploration [27, 28].” The overall paper is good. I strongly agree this work as a publication. Closing Remarks: We sincerely thank you for your positivity and constructive comments. We believe that these revisions have significantly strengthened our manuscript, making a compelling case for the publication of our work. We look forward to the possibility of our revised manuscript being favorably considered for publication. Warm regards Attachments Attachment Submitted filename: Respond to reviewers.docx https://doi.org/10.1371/journal.pone.0301292.r002
14 Mar 2024 Decision Letter - Vinod Kumar Yata, Editor Insights into the Novel Enterococcus faecalis Phage: A Comprehensive Genome Analysis PONE-D-24-03766R1 Dear Dr. Shafiei, 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 http://www.editorialmanager.com/pone/ 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, Vinod Kumar Yata, PhD Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0301292.r003
Formally Accepted
25 Apr 2024 Acceptance Letter - Vinod Kumar Yata, Editor PONE-D-24-03766R1 PLOS ONE Dear Dr. Shafiei, 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. Vinod Kumar Yata Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0301292.r004

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