Plasmidome of Salmonella enterica serovar Infantis recovered from surface waters in a major agricultural region for leafy greens in California

Beatriz Quiñones; Bertram G. Lee; Ashley Avilés Noriega; Lisa Gorski

doi:10.1371/journal.pone.0316466

Peer Review History

Original SubmissionSeptember 25, 2024
24 Oct 2024 Decision Letter - Mabel Kamweli Aworh, Editor PONE-D-24-42911Plasmidome of Salmonella enterica serovar Infantis recovered from surface waters in a major agricultural region for leafy greens in CaliforniaPLOS ONE Dear Dr. Gorski, 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 Dec 08 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. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. Please note that your Data Availability Statement is currently missing the direct link to access each database (GenBank accession numbers PQ365737-PQ365750). If your manuscript is accepted for publication, you will be asked to provide these details on a very short timeline. We therefore suggest that you provide this information now, though we will not hold up the peer review process if you are unable. 4. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. 5. 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: Thank you for submitting your manuscript. Please address the following revisions to improve the clarity and structure of your paper: <ol><li>Restructure the manuscript: Separate the Results and Discussion sections. The Discussion section should not have any subtitles. In the Discussion, avoid repeating the results; instead, provide an interpretation of your findings, discuss their implications, and compare them with similar studies in the literature. Please do not cite any figures or tables in the Discussion section. The Conclusion section should provide a summary of the key findings from your study without any citations. Please ensure the Conclusion is focused on summarizing the main results and offering recommendations based on your findings. The recommendations should be provided in the final paragraph of the Conclusion section. <li>Limitations: Highlight the key limitations of your study as the final paragraph of the Discussion section. [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: I will first like to congratulate the author for a well researched work he's put foward here, it is really rigorous. I have just few issues as outlined below. Line 152: "Twelve strains were selected for sequence analysis." so, is it twelve strains out of the 34, 14 or the 20. please specify out of which group is the 12 selected from. Lines 206-209: "As further demonstrated in the comparative analysis with the Anvi’o workflow (Fig 1), various homogeneity indexes were determined to measure the variation and frequency of their occurrence in the detected plasmid genes with an index of 1 being the highest value indicating no variation." please specify the indexes tool used for this study. Did you have some limitation in this study? if yes please mention some. Did you have ethical approval for this study? please if yes is better if you include it in. what recommendation can you give based on the findings? include the funding information for this study and possible conflict of interest if any. Reviewer #2: Thank you for the opportunity to review this manuscript. After a thorough reading, I found the manuscript to be well-written, scientifically sound, and free of any significant issues. The research is well-structured, and the conclusions drawn are appropriate based on the presented data. I have no further suggestions or revisions at this time, and I believe this manuscript is ready for publication in its current form. ****** 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: Yes: Umar Muhammad Umar 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. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: PONE-D-24-42911.pdf https://doi.org/10.1371/journal.pone.0316466.r001
Revision 1
13 Nov 2024 Author Response RESPONSES TO EDITOR’S COMMENTS\| MANUSCRIPT ID PONE-D-24-42911: 1. EDITOR’S COMMENT: Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. AUTHORS’ REPLY: The manuscript was formatted according to PLOS ONE’s guidelines. 2. EDITOR’S COMMENT: In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. AUTHORS’ REPLY: In the Material and Methods section (lines 77-80), additional statements were inserted in the revised manuscript to indicate that the present study did not require permits issued for since all of the sampling sites were located on public lands within an approximate 20-mile radius of Salinas, California (USA). No specific permissions were required for sampling on the public lands, and these studies did not involve sampling any endangered or protected species. 3. EDITOR’S COMMENT: Please note that your Data Availability Statement is currently missing the direct link to access each database (GenBank accession numbers PQ365737-PQ365750). AUTHORS’ REPLY: Given that the direct link to the sequences through the BioProject site is unavailable, the Data Availability Statement (lines 157-160) was edited in the revised manuscript by providing an alternate site (https://www.ncbi.nlm.nih.gov/nuccore/) to access the plasmid sequences in the NCBI nucleotide database. 4. EDITOR’S COMMENT: We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. AUTHORS’ REPLY: To address the Editor’s comment, the Material and Methods (lines 90-96) and Results (lines 325-329) sections are now included in the revised manuscript text on the analysis of the in vivo antimicrobial resistance against tetracycline, which was originally mentioned as “data not shown”. 5. EDITOR’S COMMENT: Please review your reference list to ensure that it is complete and correct. AUTHORS’ REPLY: The reference list was reviewed to be complete and correct. 6. EDITOR’S COMMENT Restructure the manuscript. Separate the Results and Discussion sections. The Discussion section should not have any subtitles. In the Discussion, avoid repeating the results; instead, provide an interpretation of your findings, discuss their implications, and compare them with similar studies in the literature. Please do not cite any figures or tables in the Discussion section. The Conclusion section should provide a summary of the key findings from your study without any citations. Please ensure the Conclusion is focused on summarizing the main results and offering recommendations based on your findings. The recommendations should be provided in the final paragraph of the Conclusion section. AUTHORS’ REPLY: The manuscript was extensively revised, and the Results (pages 9-18) and Discussion (pages 18-23) are now in separate sections. The highlights of the present study and recommendations for future analyses have been included in the revised Conclusions section (page 24). 7. EDITOR’S COMMENT: Limitations: Highlight the key limitations of your study as the final paragraph of the Discussion section. AUTHORS’ REPLY: The limitations of the current study were included after the Discussion section (page 24) by stating that the current study has provided fundamental information based on annotated sequence data. Given that only genomic data is provided in this study, additional comparative and functional analyses are thus needed to determine the expression patterns of the identified genes and dissect how their expression contributes to the virulence phenotypes. RESPONSES TO REVIEWER #1’S COMMENTS\| MANUSCRIPT ID PONE-D-24-42911: 1. REVIEWER’S COMMENT: Line 152: "Twelve strains were selected for sequence analysis." so, is it twelve strains out of the 34, 14 or the 20. please specify out of which group is the 12 selected from. AUTHORS’ REPLY: An additional statement was inserted in the revised manuscript text (lines 166-167) to specify that the examined 12 Infantis strains were selected based on the high yield recovery of the detected large plasmids. 2. REVIEWER’S COMMENT: Lines 206-209: "As further demonstrated in the comparative analysis with the Anvi’o workflow (Fig 1), various homogeneity indexes were determined to measure the variation and frequency of their occurrence in the detected plasmid genes with an index of 1 being the highest value indicating no variation." please specify the indexes tool used for this study. AUTHORS’ REPLY: To address the Reviewer #1’s question, the manuscript text was revised (lines 145-148) to indicate that the function in the Anvi’o workflow called “anvi-compute-gene-cluster-homogeneity” was employed to compute the geometric and functional homogeneity indexes, and these indexes provided measures of similarity in the detected plasmid genes with an index of 1 being the highest value to indicate no variation. 3. REVIEWER’S COMMENT: Did you have some limitation in this study? if yes please mention some. AUTHORS’ REPLY: The limitations of the current study were included after the Discussion section (page 24) by stating that the current study has provided fundamental information based on annotated sequence data. Given that only genomic data is provided in this study, additional comparative and functional analyses are thus needed to determine the expression patterns of the identified genes and dissect how their expression contributes to the virulence phenotypes. 4. REVIEWER’S COMMENT: Did you have ethical approval for this study? please if yes is better if you include it in. AUTHORS’ REPLY: In the Material and Methods section (lines 77-80), additional statements were inserted in the revised manuscript to indicate that the present study did not require permits issued for since all of the sampling sites were located on public lands within an approximate 20-mile radius of Salinas, California (USA). No specific permissions were required for sampling on the public lands, and these studies did not involve sampling any endangered or protected species 5. REVIEWER’S COMMENT: What recommendation can you give based on the findings? AUTHORS’ REPLY: Recommendations on the directions of future studies based on the results obtained in the present study are included in the Conclusions section (page 24). Recent report have documented that leafy greens have been previously a vehicle of foodborne illness, and surface waters can be a potential a route of transmission of bacterial pathogens. Therefore, subsequent phenotypical studies are aimed at further categorizing the virulence potential as well as the environmental fitness, adaptability and persistence of the examined S. Infantis strains, recovered from this important agricultural region for fresh produce. 6. REVIEWER’S COMMENT: Include the funding information for this study and possible conflict of interest if any. AUTHORS’ REPLY: As indicated in the author guidelines for Plos One, the funding information and conflict of interest needed to be uploaded separately from the manuscript text by using the journal submission site. Attachments Attachment Submitted filename: Responses to Comments.docx https://doi.org/10.1371/journal.pone.0316466.r002
22 Nov 2024 Decision Letter - Mabel Kamweli Aworh, Editor PONE-D-24-42911R1Plasmidome of Salmonella enterica serovar Infantis recovered from surface waters in a major agricultural region for leafy greens in CaliforniaPLOS ONE Dear Dr. Gorski, 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 06 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. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN Academic Editor PLOS ONE Journal Requirements: 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 : Thank you for addressing the previous comments. While your revisions are appreciated, there are still areas that require improvement to align the manuscript with journal standards: <ol><li>Restructure the Manuscript In the Discussion section, avoid repeating the results. Focus on interpreting your findings, discussing their implications, and comparing them with existing studies in the literature. <li>Results Section Remove all citations from the Results section. The Results should strictly state the findings, supported by accompanying tables and figures. Cite tables and figures as appropriate, but do not provide explanations or cite literature in this section. Specifically, citations found in lines 214 and 252–398 of the tracked manuscript version must be removed. <li>Discussion Section Revise the Discussion section to include explanations, implications of findings, and comparisons with relevant literature. Do not restate the results in this section. <li>Other Issues Delete the phrase "see Materials and Methods" from line 245 in the tracked manuscript. Please make these revisions and resubmit the manuscript for further evaluation. Let us know if you have any questions or require additional clarification. [Note: HTML markup is below. Please do not edit.] [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. https://doi.org/10.1371/journal.pone.0316466.r003
Revision 2
9 Dec 2024 Author Response 1. Restructure the Manuscript o In the Discussion section, avoid repeating the results. Focus on interpreting your findings, discussing their implications, and comparing them with existing studies in the literature. • The Results and Discussion sections were edited. Results were removed from the Discussion, references were removed from Results. 2. Results Section o Remove all citations from the Results section. The Results should strictly state the findings, supported by accompanying tables and figures. Cite tables and figures as appropriate, but do not provide explanations or cite literature in this section. • Citations were removed from the Results section. o Specifically, citations found in lines 214 and 252–398 of the tracked manuscript version must be removed. • Citations were removed from the results section. 3. Discussion Section o Revise the Discussion section to include explanations, implications of findings, and comparisons with relevant literature. Do not restate the results in this section. • The Results and Discussion sections were edited. Results were removed from the Discussion, references were removed from Results. 4. Other Issues o Delete the phrase "see Materials and Methods" from line 245 in the tracked manuscript. • This phrase was deleted. Attachments Attachment Submitted filename: Answers to 2nd Review Comments.docx https://doi.org/10.1371/journal.pone.0316466.r004
12 Dec 2024 Decision Letter - Mabel Kamweli Aworh, Editor Plasmidome of Salmonella enterica serovar Infantis recovered from surface waters in a major agricultural region for leafy greens in California PONE-D-24-42911R2 Dear Dr. Gorski, 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, Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0316466.r005
Formally Accepted
13 Dec 2024 Acceptance Letter - Mabel Kamweli Aworh, Editor PONE-D-24-42911R2 PLOS ONE Dear Dr. Gorski, 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. Mabel Kamweli Aworh Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0316466.r006

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