Rapid detection of methicillin-resistant Staphylococcus aureus in positive blood-cultures by recombinase polymerase amplification combined with lateral flow strip

Arpasiri Srisrattakarn; Pimchanok Panpru; Patcharaporn Tippayawat; Aroonwadee Chanawong; Ratree Tavichakorntrakool; Jureerut Daduang; Lumyai Wonglakorn; Aroonlug Lulitanond

doi:10.1371/journal.pone.0270686

Peer Review History

Original SubmissionFebruary 20, 2022
26 May 2022 Decision Letter - Dwij Raj Bhatta, Editor PONE-D-22-05183Rapid detection of methicillin-resistant Staphylococcus aureus in positive blood-cultures by recombinase polymerase amplification combined with lateral flow stripPLOS ONE Dear Dr. Lulitanond, 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 Jul 10 2022 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, Dwij Raj Bhatta, PhD Academic Editor PLOS ONE 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 2. 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 3. 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. 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 (if provided): Manuscript requires corrections as pointed out but by reviewers! Please give justification: as in method section 56 isolates (26 S. aureus and 30 non-S. aureus) collected but in Table 1, there are total 60 isolates. Please check which one is correct. 2) why isolates other then S. aureus and MRSA are listed and studied? is it relevant to the title of the manuscript? study is related to S. aureus and MRSA only? [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: I Don't Know ****** 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 authors described the sensitivity and specificity of RPA assay for the detection of methicillin resistant Staphylococcus aureus. The manuscript has been well written. It can accepted for publication. Reviewer #2: The manuscript is well written and findings are important in rapid detection of MRSA from blood culture. However, some changes are suggested 1) In Material and method section it is mentioned that, 56 isolates (26 S. aureus and 30 non-S. aureus) collected but in Table 1, there are total 60 isolates. Please check which one is correct. 2) Organism other than S. aureus and MRSA are listed. As per the title of the manuscript, study is related to S. aureus and MRSA only. ****** 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: Megha Raj Banjara Reviewer #2: Yes:** Dharm Raj Bhatta [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-22-05183.docx https://doi.org/10.1371/journal.pone.0270686.r001
Revision 1
14 Jun 2022 Author Response June 1, 2022 Dear Editor, Manuscript ID: PONE-D-22-05183 Title: Rapid detection of methicillin-resistant Staphylococcus aureus in positive blood-cultures by recombinase polymerase amplification combined with lateral flow strip Thank you very much for valuable comments and for giving us an opportunity to revise our manuscript. We have responses to all the issues raised by the editor and reviewers as in the following and use the "Track Changes" function in Microsoft Word of the revised manuscript. We would be grateful if you would consider our revised manuscript for publication. Yours sincerely, Aroonlug Lulitanond Corresponding author The response to editor’s and reviewer’s comments 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 Response: We have already checked PLOS ONE style as suggested. Our manuscript was prepared accordingly the PLOS ONE style. 2. 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: Our manuscript provided the original images for all gel data reported in our submission. We already checked the policy and the journal’s other requirements for blot/gel reporting and figure preparation as suggested. We have confirmed that our figures adhere to the guidelines. Our blot/gel image data are not in Supporting Information or posted at a public data repository. 3. 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. 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: The phrases “data not shown” in our manuscript were removed as suggested. The data are not a core part of the research. We have already checked carefully reference list and confirmed that it is complete and correct. Additional Editor Comments (if provided): 1. Manuscript requires corrections as pointed out but by reviewers! Please give justification: as in method section 56 isolates (26 S. aureus and 30 non-S. aureus) collected but in Table 1, there are total 60 isolates. Please check which one is correct. Response: We have already checked as suggested. The 56 isolates (26 S. aureus and 30 non-S. aureus) were used for evaluating the performance of the chosen primer set on the RPA-AGE test for detection of MRSA colonies (S1 Table) whereas the 60 samples were clinical blood-culture bottles from a routine laboratory in hospital which were used for evaluating the performance of RPA-LF test (Table 1). So, we have specified this point in lines 86-88, 90-94, and 126-128. 2) why isolates other than S. aureus and MRSA are listed and studied? is it relevant to the title of the manuscript? study is related to S. aureus and MRSA only? Response: The title of the manuscript is related to S. aureus and MRSA only because we want to develop the RPA assay for the detection of nuc and mecA genes to diagnose S. aureus and its methicillin-resistance status. The organisms other than S. aureus and MRSA are included for testing the specificity of the developed RPA method. A positive result must be generated only with S. aureus and MRSA strains, but not with the other organisms. We have added this matter in lines 98-99. Reviewers' comments: Responses to Reviewer's 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 Response: Thank you very much. ________________________________________ 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know Response: Thank you very much. We have described the sensitivity and specificity (statistical analysis) of RPA assay for the detection of methicillin resistant Staphylococcus aureus. ________________________________________ 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 Response: Thank you very much. ________________________________________ 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 Response: Thank you very much. ________________________________________ 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 authors described the sensitivity and specificity of RPA assay for the detection of methicillin resistant Staphylococcus aureus. The manuscript has been well written. It can accepted for publication. Response: Thank you very much for accepting our manuscript for publication. Reviewer #2: The manuscript is well written and findings are important in rapid detection of MRSA from blood culture. However, some changes are suggested 1) In Material and method section it is mentioned that, 56 isolates (26 S. aureus and 30 non-S. aureus) collected but in Table 1, there are total 60 isolates. Please check which one is correct. Response: We have already checked as suggested. The 56 isolates (26 S. aureus and 30 non-S. aureus) were used for evaluating the performance of the chosen primer set on the RPA-AGE test for detection of MRSA colonies (S1 Table) whereas the 60 samples were clinical blood-culture bottles from a routine laboratory in hospital which were used for evaluating the performance of RPA-LF test (Table 1). So, we have specified this point in lines 86-88, 90-94, and 126-128. 2) Organism other than S. aureus and MRSA are listed. As per the title of the manuscript, study is related to S. aureus and MRSA only. Response: The title of the manuscript is related to S. aureus and MRSA only because we would like to develop the RPA assay for the detection of nuc and mecA genes to diagnose S. aureus and its methicillin-resistance status. The organisms other than S. aureus and MRSA are included for testing the specificity of the developed RPA method. A positive result must be generated only with S. aureus and MRSA strains, but not with the other organisms. We have added this matter in lines 98-99.________________________________________ 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: Megha Raj Banjara Reviewer #2: Yes: Dharm Raj Bhatta Response: Thank you very much. Attachments Attachment Submitted filename: Response to Reviewers_PONE-D-22-05183.pdf https://doi.org/10.1371/journal.pone.0270686.r002
16 Jun 2022 Decision Letter - Dwij Raj Bhatta, Editor Rapid detection of methicillin-resistant Staphylococcus aureus in positive blood-cultures by recombinase polymerase amplification combined with lateral flow strip PONE-D-22-05183R1 Dear Dr. Lulitanond, 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, Dwij Raj Bhatta, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0270686.r003
Formally Accepted
22 Jun 2022 Acceptance Letter - Dwij Raj Bhatta, Editor PONE-D-22-05183R1 Rapid detection of methicillin-resistant Staphylococcus aureus in positive blood-cultures by recombinase polymerase amplification combined with lateral flow strip Dear Dr. Lulitanond: 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 Professor Dwij Raj Bhatta Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0270686.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .