Peer Review History
Original SubmissionOctober 5, 2020 |
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PONE-D-20-31236 Incidence and risk factors of C. trachomatis and N. gonorrhoeae among young women from the Western Cape, South Africa: the EVRI study PLOS ONE Dear Dr. Jongen, 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 pay specific attention to clarifying the methodological issues raised by the reviewers with regards to bias, definitions, and careful interpretation of the data in the absence of data of partner notification, ToC, etc. ============================== Please submit your revised manuscript by Jan 03 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:
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Dr. Sudenga (K07 CA225404) was supported by the National Cancer Institute." i) We note that one or more of the authors is affiliated with the funding organization, indicating the funder may have had some role in the design, data collection, analysis or preparation of your manuscript for publication; in other words, the funder played an indirect role through the participation of the co-authors. If the funding organization did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and/or research materials, please review your statements relating to the author contributions, and ensure you have specifically and accurately indicated the role(s) that these authors had in your study in the Author Contributions section of the online submission form. Please make any necessary amendments directly within this section of the online submission form. 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Please note that we cannot proceed with consideration of your article until this information has been declared. Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests 5. 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 delete it from any other section. 6. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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 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: The manuscript by Jongen et al. deals with the important topic of high prevalence and incidence rates of STIs among young women in South Africa. Syndromic management remains the main approach to STI care in South Africa, but studies like this highlight the urgent need to move to a diagnostic care approach. The authors describe a high burden of STIs in this cohort, and describe risk factors for incident infections. These results for the incidence analysis need to be interpreted with caution as no test of cure was conducted as part of the study to definitely exclude persistent infection. Overall the manuscript adds to the growing literature of STIs in South Africa, but I suggest that the authors expand the methods section to provide more clarity on potential bias in data collection and interpretation. Major Comments 1. The potential bias with calculating a STI incidence rate have not been adequately addressed in the manuscript. This is notoriously difficult to measure, because it is often difficult to establish whether treatment was actually taken (here it appears to be self-reported), and STIs are often persistent rather than recurrent (due to lack of treatment or treatment resistant STIs). For example, a main finding in this study is that baseline CT infection predicts incident CT. However, some of these infections may not have been treated adequately at baseline (and the study did not include a test of cure). 2. The process of providing results to participants is poorly described. How long after the test were participants informed. How many were reached, and how many accepted/ refused treatment? Furthermore, was treatment offered to partners, or contact cards distributed? 3. The issue of using reusable urine cups in 102 participants, and then retesting those participants after 2 months is not clear at all. The authors state that the results were the same, but how is this possible? Were these participants not treated at baseline? Or did they start the analysis at 2-month instead of baseline for these participants? This is a potential bias in the results and is only superficially described in the methods section. In the results section (NG section) the authors then provide a p-value for the comparison, but the number and effect size is not clear. 4. How was the questionnaire administered and demographic and behavioural data gathered? What were the potential bias with the administration of the questionnaire? Please add this to the methods section. It is briefly mentioned in the limitation section of the discussion, but not in the methods section. 5. There is very little information about partners, partner notification services and partner therapy uptake. Also, the conclusion should probably highlight this as a gap in the STI care cascade. 6. Supplementary Figure 1, the flow diagram, is key to understanding the study, and should be included in the main text of the study instead of supplementary materials. Minor Comments Abstract l.43 suggest to add laboratory assay name to abstract l.58 suggest say ‘the majority of’ rather than ‘all’ women. For example, some may not have a partner or have no sex. Introduction l.72 suggest change organism names to italics. Methods l.111 – 145 expand on how reusable cups were cleaned, and how the authors went about evaluating the validity of these results. How exactly did the comparison with the 2-month visit samples take place, and what were the findings? l.116 How many participants refused treatment? l.133 Where was the Anyplex stationed? In a central laboratory? What were the results turnaround times? Results The questionnaire results should be presented with more caution. For example, line 168, suggest to add ‘reported’ to receive education… l.191 Not clear whether these women were not treated at baseline (see major comment). l.229 The authors present a p-value, saying that there was no difference between baseline and 2-months. There should be an effect size, and further explanation to clarify this to the reader. It almost seems like the authors are confused by the retesting of the 102 participants themselves. Discussion l.260 As mentioned above, several of these infections may not have been cleared in the first place. l.266 Suggest adding the need for better partner services and screening. L.275 I agree with the authors that the overwhelming risk factor in this setting is young age. l.284 ‘Tablet based questionnaires’ – this should be added to the methods as part of the expansion on the information on the questionnaire implementation. l.288 ‘treatment failure’ or person not taking the treatment in the first place? Conclusion L.293 suggest adding ‘the majority’ instead of ‘all’ Reviewer #2: The paper has some interesting points. Can you please include a definition for incident STI infections. There was no mention of partner testing so it is unclear if these were re-infections or new infections. There is no data on previous pregnancies ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). 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Revision 1 |
PONE-D-20-31236R1 Incidence and risk factors of C. trachomatis and N. gonorrhoeae among young women from the Western Cape, South Africa: the EVRI study PLOS ONE Dear Dr. Jongen, 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 Apr 12 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:
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 We look forward to receiving your revised manuscript. Kind regards, Remco PH Peters, MD, PhD, DLSHTM 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. [Note: HTML markup is below. Please do not edit.] 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 #3: (No Response) ********** 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 #3: Partly ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: No ********** 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 #3: No ********** 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 #3: 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 #3: I thought this was an interesting analysis that is worthwhile. As the authors note, these data arise from a trial and it's hard to grasp whether these data can be representative of a wider population. Usually, the answer with trials is no. I feel the authors used appropriate language and noted this in the limitations. I reviewed the design and methods. Overall, this looked good, but I had a few comments below for the authors with the aim of trying to improve the statistical methods. 1. (lines 147-148) I didn't completely understand why participants lost to follow up were excluded. If you are doing a person-time calculation, then you could include everyone for the amount of time for which data are available. 2. (lines 149-151) With the uncertainty of the infection time, an interval censored survival analysis could be implemented. That type of model is specifically designed for such situations and could potentially better handle the lost to follow up. 3. (lines 162-164) If you don't utilize my prior comment, my understanding is that you've modeled the rates of events per 100 person-years. I suggest trying to model the number of incident infections instead of the rates with the person years as an offset. This is a more natural way to model this since the rates can sometimes follow some very strange distributions and have odd outliers. I think you can stick with the Poisson distribution if you like because I'm guessing the outcome will still be zeros and ones. Often, because the mean and variance are the same parameter in Poisson, that can be a very poor assumption in regression models and switching to quasipossion or negative binomial model is a better option. Though, I don't think you need that here, though I would also try to include a robust variance estimate to make sure the confidence intervals are appropriate 4. (lines 164-167) I have a few comments about the variable selection procedures utilized here. Were those variables with p < 0.20 in unvariable models the ones that are forced into the model? Otherwise, it's unclear why both bivariate screening (lines 164-5) and backward selection (lines 166-7) are used. Though, the larger problem is, with the sample sizes you have, stepwise variable selection procedures (backward included) usually do not do a good job of finding the most appropriate model (e.g., https://doi.org/10.1002/sim.3943). Stepwise procedures and any p-value based selection have quite a bit of evidence suggesting that they are poor at selecting the appropriate variables. For a decent summary, see the link above. Generally, it's better to select based on more robust criteria, especially measures which assess the fit of the model, such as BIC, or, better yet, a shrinkage-based estimator such as lasso or lars. 5. (Table 1) Given the sporadic missing data, did you consider using multiple imputation or some other method to try to handle the missing data? 6. (line 267) Since there is no word count and electronic supplements are acceptable, there is really no reason for analyses to not be reported that are important enough to be mentioned in the manuscript. Please include these analyses somewhere. ********** 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 #3: 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. |
Revision 2 |
Incidence and risk factors of C. trachomatis and N. gonorrhoeae among young women from the Western Cape, South Africa: the EVRI study PONE-D-20-31236R2 Dear Dr. Jongen, 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, Remco PH Peters, MD, PhD, DLSHTM Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-20-31236R2 Incidence and risk factors of C. trachomatis and N. gonorrhoeae among young women from the Western Cape, South Africa: the EVRI study Dear Dr. Jongen: 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 Prof Remco PH Peters Academic Editor PLOS ONE |
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