Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020

Nina Van Goethem; An Van Den Bossche; Pieter-Jan Ceyssens; Adrien Lajot; Wim Coucke; Kris Vernelen; Nancy H. C. Roosens; Sigrid C. J. De Keersmaecker; Dieter Van Cauteren; Wesley Mattheus

doi:10.1371/journal.pone.0256820

Peer Review History

Original SubmissionJuly 1, 2021
10 Aug 2021 Decision Letter - Iddya Karunasagar, Editor PONE-D-21-21282 Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020 PLOS ONE Dear Dr. Van Goethem, 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 clarify what is meant by more than 100% coverage and other points raised by the reviewers. Please submit your revised manuscript by Sep 24 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. 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: http://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, Iddya Karunasagar 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. 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. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 3. 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. Additional Editor Comments: The reviewers have made very important comments. Clarification is needed on what is meant by greater than 100%. Please revise considering all the reviewer comments. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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: No ****** 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: Can you explain, and perhaps provide an example in the methods, for how a laboratory can have >100% coverage? [see this in the discussion - wonder if helpful to mention in the methods or as you report that some did - can simply say parenthetically something like. XX labs had coverage greater than 100% (because they reported fewer cases in the survey than the number reported to NRC).] It is said that you removed cases with missing info (line 230) but those should still be included in the n_1 and n_2 shouldn't they? Or at least you should provide what the estimated coverage is when you include them as a lower bound of coverage. Seems that would be 15350 cases with coverage of 80%. It is still very high. The data availability statement should be written in the format that the journal requests. There are clearly issues of personal identifiability, etc., and it should be clearer where to get the data. Overall the text is written in excellent English but there are several small issues and I doubt that I capture them all here. The paper could benefit from a reading by a native English speaking editor. Line 69 - suggest "voluntarily" vs. "voluntary" Line 101 - suggest "previously" vs. "previous" Line 114 - suggest "ranges" vs. "ranged" and if inculsive of 2016 and 2020 would suggest from 2016 to 2020 Line 121 - is capitalization all correct? Line 126 - from a patient who was part of Line 172 - Number of Salmonella Line 177 - suggest "annual" vs. "annuals" Line 196 - "send" instead of "sent" Line 221 - suggest "indicated they used culture" there and elsewhere as appropriate Line 224 - suggest "except one indicated they sent all" Line 257 - unsure of use of "towards" here Line 279-280 - and allowed us to confidently estimate Line 289 - suggest "compared" vs. "compare" ******** 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.0256820.r001
Revision 1
16 Aug 2021 Author Response Authors’ response to reviews Title: Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020 Authors: N. Van Goethem A. Van Den Bossche P.-J. Ceyssens A. Lajot W. Coucke K. Vernelen N.H.C. Roosens S.C.J. De Keersmaecker D. Van Cauteren W. Mattheus Version : 1 Date : 16 August 2021 Authors' response: Thank you very much for considering our manuscript. We thank the reviewer and editorial staff for their valuable review. We carefully went through the constructive reviews provided by the peer reviewer and editor and have revised the manuscript accordingly. We have outlined our responses point by point to the reviewer’s comments. The line numbers presented here correspond to those in the final version (with track changes) of the manuscript. Reviewer 1: Can you explain, and perhaps provide an example in the methods, for how a laboratory can have >100% coverage? [see this in the discussion - wonder if helpful to mention in the methods or as you report that some did - can simply say parenthetically something like. XX labs had coverage greater than 100% (because they reported fewer cases in the survey than the number reported to NRC).] Authors’ response: We thank the reviewer for this comment. In addition to the clarifications that were already provided in the discussion section (L304-309), we have added the following clarifications to the methods section (L150-152): “A laboratory can have >100% coverage when they report fewer cases in the survey than the number of isolates from unique cases sent to the NRC.” Accordingly, we added the following to the results section as suggested (L226-227): “A total of 18 laboratories had a coverage greater than 100% (because they reported fewer cases in the survey than the number reported to the NRC).” Reviewer 1: It is said that you removed cases with missing info (line 230) but those should still be included in the n_1 and n_2 shouldn't they? Or at least you should provide what the estimated coverage is when you include them as a lower bound of coverage. Seems that would be 15350 cases with coverage of 80%. It is still very high. Authors’ response: We thank the reviewer for this comment. As we do not know whether there is a match between the NRC and SNL database for the cases with missing info, we did exclude them from the main analysis. However, we do agree that it might provide a ‘lower bound’ of coverage. Therefore, we have added the following to the results section (L251-254): “When taking into account the cases with missing date of birth, gender, or postal code, the estimated total number of cases was 13,350 (95% CI: 15,172-15,528) and the coverage of the NRC and SNL network were estimated to be 80% (12,316/15,350) (95% CI: 80-81%) and 31% (4,822/15,350) (95% CI: 31-32%), respectively.” Reviewer 1: The data availability statement should be written in the format that the journal requests. There are clearly issues of personal identifiability, etc., and it should be clearer where to get the data. Authors’ response: We thank the reviewer for this remark. We have now included all relevant data underlying the results in the Supporting information. The underlying data on Salmonella epidemiology in Belgium as presented in Fig 1 and Fig 2, is contained in S1 Table and S2 Table, respectively. The laboratory survey results aggregated per laboratory (anonymized), including the number of Salmonella cases reported in the survey, the number of Salmonella isolates from unique cases sent to the National Reference Center (NRC), the method of diagnosis used, the reasons for sending isolates to the NRC, and the serotypes sent to the NRC, are presented in S3 Table. The stool reimbursement data, used to calculate the positivity rate and to estimate the number of Salmonella diagnoses for laboratories that did not participate in the survey, are presented per RIZIV number (anonymized) in S4 Table. Finally, the numbers per year underlying the capture-recapture analyses are presented in S5 Table. Reviewer 1: Overall the text is written in excellent English but there are several small issues and I doubt that I capture them all here. The paper could benefit from a reading by a native English speaking editor. Line 69 - suggest "voluntarily" vs. "voluntary" Line 101 - suggest "previously" vs. "previous" Line 114 - suggest "ranges" vs. "ranged" and if inculsive of 2016 and 2020 would suggest from 2016 to 2020 Line 121 - is capitalization all correct? Line 126 - from a patient who was part of Line 172 - Number of Salmonella Line 177 - suggest "annual" vs. "annuals" Line 196 - "send" instead of "sent" Line 221 - suggest "indicated they used culture" there and elsewhere as appropriate Line 224 - suggest "except one indicated they sent all" Line 257 - unsure of use of "towards" here Line 279-280 - and allowed us to confidently estimate Line 289 - suggest "compared" vs. "compare" Authors’ response: We thank the reviewer for these kind words and the valuable suggestions and corrections. We have adapted all suggestions and corrections in the manuscript accordingly. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0256820.r002
17 Aug 2021 Decision Letter - Iddya Karunasagar, Editor Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020 PONE-D-21-21282R1 Dear Dr. Van Goethem, 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): All reviewer comments have been addressed. 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: Yes ****** 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.0256820.r003
Formally Accepted
19 Aug 2021 Acceptance Letter - Iddya Karunasagar, Editor PONE-D-21-21282R1 Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020 Dear Dr. Van Goethem: 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.0256820.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 .