Assessing the mechanisms of multi-drug resistant non-typhoidal Salmonella (NTS) serovars isolated from layer chicken farms in Nigeria

Idowu Oluwabunmi Fagbamila; Elena Ramon; Antonia A. Lettini; Maryam Muhammad; Alessandra Longo; Keti Antonello; Mabel K. Aworh; Jacob K. P. Kwaga; Paul A. Abdu; Jarleth U. Umoh; Junaidu A. Kabir; Antonia Ricci; Lisa Barco

doi:10.1371/journal.pone.0290754

Peer Review History

Original SubmissionMarch 17, 2023
29 Jun 2023 Decision Letter - Nabi Jomehzadeh, Editor PONE-D-23-07992ASSESSING THE MECHANISMS OF MULTI-DRUG RESISTANT NON-TYPHOIDAL SALMONELLA (NTS) SEROVARS FROM LAYER CHICKEN FARMS IN NIGERIAPLOS ONE Dear Dr. Fagbamila, 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 Aug 13 2023 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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Additional Editor Comments: We have received the reports from our advisors on your manuscript, "ASSESSING THE MECHANISMS OF MULTI-DRUG RESISTANT NON-TYPHOIDAL SALMONELLA (NTS) SEROVARS FROM LAYER CHICKEN FARMS IN NIGERIA," submitted to "PloS One." Based on the advice received, I feel your manuscript could be reconsidered for publication should you be prepared to incorporate changes, as suggested by reviewers. [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: A paragraph on the Salmonella spp. as a public health importance is suggested to be incorporated in the introduction section. There are some anomalies in reference writing in the text. It is suggested to follow the journal style properly. Reviewer #2: Authors of the manuscript (PONE-D-23-07992) determines the MDR profiles of 200 NTS serovars and determine the mechanisms of resistance by different approaches. The research design and methodologies are acceptable and the data presentation and manuscript write-up are very good. The research findings/results might have significant values in determining AMR control strategies. Authors may consider few points to improve the manuscript further. Minor Comments 1. Title of the manuscript may be rephrased as below to make it more meaningful: ASSESSING THE MECHANISMS OF MULTI-DRUG RESISTANCE IN NON-TYPHOIDAL SALMONELLA (NTS) SEROVARS ISOLATED FROM LAYER CHICKEN FARMS IN NIGERIA 2. Authors used 200 isolates of NTS serovars from their previous study and determined their MDR profiles and mechanisms of MDR. Though they referred to their previous work and mentioned the criteria they followed to select 200 isolates, it might be good to include a table (might be a supplementary table) to describe the isolates based on the frequency, serovars, geographical and sample type distribution to help the readers. 3. In conclusion section, authors may describe their key findings shortly within few syntaxes followed by their concluding remarks/ recommendations. ****** 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: Dr. Md. Masudur Rahman ******** [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: Reviewer comments_Siddiky.docx Attachment Submitted filename: Reviewer Comments.docx https://doi.org/10.1371/journal.pone.0290754.r001
Revision 1
9 Aug 2023 Author Response Response to Editor comments 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. 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 Response: The manuscript has been reviewed accordingly. 2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://gutpathogens.biomedcentral.com/articles/10.1186/s13099-015-0063-3 https://www.frontiersin.org/articles/10.3389/fmicb.2015.00602/full https://www.liebertpub.com/doi/10.1089/fpd.2007.0090 In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. Response: This has been corrected and can be seen in the manuscript with track changes 3. We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service. Whilst you may use any professional scientific editing service of your choice, PLOS has partnered with both American Journal Experts (AJE) and Editage to provide discounted services to PLOS authors. Both organizations have experience helping authors meet PLOS guidelines and can provide language editing, translation, manuscript formatting, and figure formatting to ensure your manuscript meets our submission guidelines. To take advantage of our partnership with AJE, visit the AJE website (http://learn.aje.com/plos/) for a 15% discount off AJE services. To take advantage of our partnership with Editage, visit the Editage website (www.editage.com) and enter referral code PLOSEDIT for a 15% discount off Editage services. If the PLOS editorial team finds any language issues in text that either AJE or Editage has edited, the service provider will re-edit the text for free. Upon resubmission, please provide the following: The name of the colleague or the details of the professional service that edited your manuscriptA copy of your manuscript showing your changes by either highlighting them or using track changes (uploaded as a supporting information file) A clean copy of the edited manuscript (uploaded as the new manuscript file)” Response: This has been corrected and can be seen in the manuscript with track changes. A clean copy of the edited manuscript has also been attached. The colleagues that edited the manuscript are Dr. Mabel Ahwor and Lisa Barco 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: The research was funded by the Federal government through the competitive agricultural research grant scheme (CARGS). We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: The author(s) received no specific funding for this work. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Response: This section has been removed and rightly placed under acknowledgement 5. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. Response: A section on ethical consideration inserted under the Method section. 6. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. Response: Gel images of both the PCR and PFGE has been placed in the supplementary file 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. Response: Reference section has been reviewed and corrected using Mendeley Response to reviewers’ comment Reviewer 1 Reviewer #1: A paragraph on the Salmonella spp. as a public health importance is suggested to be incorporated in the introduction section. Response: A paragraph on the public health importance of Salmonella has been added. 2. There are some anomalies in reference writing in the text. It is suggested to follow the journal style properly. Response: Reference section has been reviewed and corrected using Mendeley Reviewer 2 Title of the manuscript may be rephrased as below to make it more meaningful: ASSESSING THE MECHANISMS OF MULTI-DRUG RESISTANCE IN NON-TYPHOIDAL SALMONELLA (NTS) SEROVARS ISOLATED FROM LAYER CHICKEN FARMS IN NIGERIA Response: Correction effected as suggested by reviewer. i.e the word ISOLATED was inserted after SEROVARS Authors used 200 isolates of NTS serovars from their previous study and determined their MDR profiles and mechanisms of MDR. Though they referred to their previous work and mentioned the criteria they followed to select 200 isolates, it might be good to include a table (might be a supplementary table) to describe the isolates based on the frequency, serovars, geographical and sample type distribution to help the readers. Response: I have attached extracted tables from previous paper (Fagbamila et al., 2017) as a supplementary document to guide the readers (See also the supplementary files S1). In conclusion section, authors may describe their key findings shortly within few syntaxes followed by their concluding remarks/ recommendations. Response: A sentence on the Key findings has been inserted in the first paragraph of the ‘Conclusion Section’ Attachments Attachment Submitted filename: Response to Editor comments 2.docx https://doi.org/10.1371/journal.pone.0290754.r002
15 Aug 2023 Decision Letter - Nabi Jomehzadeh, Editor ASSESSING THE MECHANISMS OF MULTI-DRUG RESISTANT NON-TYPHOIDAL SALMONELLA (NTS) SEROVARS ISOLATED FROM LAYER CHICKEN FARMS IN NIGERIA PONE-D-23-07992R1 Dear Dr. Fagbamila, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Nabi Jomehzadeh, Ph.D (Assistant Professor) Academic Editor PLOS ONE Additional Editor Comments (optional): After reviewing the responses to the reviewers' comments, the amendments were accepted Reviewers' comments: https://doi.org/10.1371/journal.pone.0290754.r003
Formally Accepted
21 Aug 2023 Acceptance Letter - Nabi Jomehzadeh, Editor PONE-D-23-07992R1 ASSESSING THE MECHANISMS OF MULTI-DRUG RESISTANT NON-TYPHOIDAL SALMONELLA (NTS) SEROVARS ISOLATED FROM LAYER CHICKEN FARMS IN NIGERIA Dear Dr. Fagbamila: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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. Nabi Jomehzadeh Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0290754.r004

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