Evaluation of high-resolution melt curve analysis for rapid differentiation of Campylobacter hepaticus from other species in birds

Petrina Young; Pol Tarce; Sadhana Adhikary; Joanne Connolly; Tim Crawshaw; Seyed A. Ghorashi

doi:10.1371/journal.pone.0251328

Peer Review History

Original SubmissionJanuary 4, 2021
31 Mar 2021 Decision Letter - Iddya Karunasagar, Editor PONE-D-21-00269 Evaluation of high-resolution melt curve analysis for rapid differentiation of Campylobacter hepaticus from other species in birds PLOS ONE Dear Dr. Ghorashi, 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. The authors need to present evidence of specificity of the assay and time taken along with addressing other reviewer comments. Please submit your revised manuscript by May 14 2021 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. 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Please revise considering all reviewer comments point by point. Journal Requirements: When submitting your revision, we need you to address these additional requirements. 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 In your Methods section, please provide additional details regarding the chicken and wild birds, including the number and species, used in your study and ensure you have described the source. For more information regarding PLOS' policy on materials sharing and reporting, see https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-materials. In your Methods section, please provide additional information regarding the permits you obtained for the work. 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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. [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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A ****** 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 ****** 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 ****** 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: PONE-D-21-00269: Evaluation of high-resolution melt curve analysis for rapid differentiation of Campylobacter hepaticus from other species in birds The study evaluated high-resolution melt curve analysis to differentiate Campylobacter hepaticus from Campylobacter coli and Campylobacter jejuni. However, the authors have not conducted any other method comparison study to call the overall method “rapid.” Therefore, this rapid differentiation can be changed or removed or else should add about facts on time duration and justify accordingly. The study does not include any experiment to find out the specificity of the assay. Also, the inclusion of other Campylobacter species and different related genus is important to assess the possibility of false-positive results. In conclusion, “….rapid and sensitive diagnostic tool….” This can be rephrased or possibly soften appropriately Change the figure no. to maintain the order Lines 204-205: Rephrase this sentence ****** 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. https://doi.org/10.1371/journal.pone.0251328.r001
Revision 1
7 Apr 2021 Author Response Academic Editor Dear Prof. Iddya Karunasagar, Thank you for your correspondence on 1st April 2021, regarding our manuscript Re: PONE-D-21-00269 (Evaluation of high-resolution melt curve analysis for rapid differentiation of Campylobacter hepaticus from other species in birds). We are delighted that the manuscript is received well by the reviewers and we thank them for their constructive comments. We have answered reviewers’ comments and carefully revised our manuscript based on the reviewers’ feedback. The revisions in the manuscript are highlighted in track changes. We have also provided detailed responses to reviewers’ comments and concerns in a point-by-point manner, with their comments in red font. We also provided gel image as Supporting Information File. We appreciate your time and effort during the evaluation process of our manuscript, and we look forward to hearing your editorial decision. Kind regards Seyed Ali Ghorashi Journal Requirements: When submitting your revision, we need you to address these additional requirements. 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 The manuscript was re-formatted based on PLOS ONE’s style. 2. In your Methods section, please provide additional details regarding the chicken and wild birds, including the number and species, used in your study and ensure you have described the source. For more information regarding PLOS' policy on materials sharing and reporting, see https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-materials. Required information including the number of tested chickens, wild birds, species and location of collected samples were added to the text lines 87-90. 3. 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. The institutional permit for sample collection was added in the text lines 84-86. 4. 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. Gel image was provided as supporting information (S1 Fig) and the rest of figures were re-numbered accordingly. 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. Done. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. Done. 6. 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. The related phrase was removed from the text (line 179-180). ________________________________________ 5. Review Comments to the Author Reviewer #1: PONE-D-21-00269: Evaluation of high-resolution melt curve analysis for rapid differentiation of Campylobacter hepaticus from other species in birds The study evaluated high-resolution melt curve analysis to differentiate Campylobacter hepaticus from Campylobacter coli and Campylobacter jejuni. However, the authors have not conducted any other method comparison study to call the overall method “rapid.” Therefore, this rapid differentiation can be changed or removed or else should add about facts on time duration and justify accordingly. To address this comment, additional text has been added to the discussion lines 245-249 and 253-256 and provided references that compared the time required to complete PCR-HRM with PCR gel electrophoresis (Thomsen et al., 2012 and Sarker et al., 2014) that confirms PCR-HRM is rapid when compared with PCR gel electrophoresis. The study does not include any experiment to find out the specificity of the assay. Also, the inclusion of other Campylobacter species and different related genus is important to assess the possibility of false-positive results. To evaluate the specificity of the assay, DNA was extracted from seven bacterial strains of genetically similar genera (Klebsiella, Pseudomonas, Enterobacter, Staphylococcus, streptococci, E. coli and Pasteurella) and tested in PCR-HRM to address this comment. This is now added to the text in lines 154-157 and 215-218 of new version of manuscript. In conclusion, “….rapid and sensitive diagnostic tool….” This can be rephrased or possibly soften appropriately This comment is addressed above (first comment). Change the figure no. to maintain the order One figure (gel image- Fig 4) was provided as supporting information file and the rest of figures were re-numbered accordingly to maintain the order in the text. Lines 204-205: Rephrase this sentence To address this comment, the sentence was revised in lines 211-212 of new version of manuscript. ________________________________________ Attachments Attachment Submitted filename: Response to reviewers Comments.docx https://doi.org/10.1371/journal.pone.0251328.r002
26 Apr 2021 Decision Letter - Iddya Karunasagar, Editor Evaluation of high-resolution melt curve analysis for rapid differentiation of Campylobacter hepaticus from other species in birds PONE-D-21-00269R1 Dear Dr. Ghorashi, 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, Iddya Karunasagar Academic Editor PLOS ONE Additional Editor Comments (optional): The authors have addressed the reviewer comments satisfactorily. 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: N/A ****** 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.0251328.r003
Formally Accepted
3 May 2021 Acceptance Letter - Iddya Karunasagar, Editor PONE-D-21-00269R1 Evaluation of high-resolution melt curve analysis for rapid differentiation of Campylobacter hepaticus from other species in birds Dear Dr. Ghorashi: 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. Iddya Karunasagar Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0251328.r004

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