https://orcid.org/0000-0002-3652-5517
Peer Review History
| Original SubmissionDecember 19, 2023 |
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PONE-D-23-41647Nasopharyngeal carriage of Streptococcus pneumoniae among Brazilian children: interplay with viral co-infectionPLOS ONE Dear Dr. Pizzutti, 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 May 02 2024 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: 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, Baochuan Lin, Ph.D. 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 2. 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. Additional Editor Comments: While your paper addresses an interesting question, the reviewers stated several concerns about the presentation as well as the readability of the manuscript and did not recommend publication in its present form. In particular, reviewers voice a number of concerns regarding the data analysis, and these comments need to be addressed carefully. Please see reviewers’ insightful comments below. Personally, at a more detailed level, I find the authors should take care on how the data was calculated, for example, the prevalence of microorganism detection should based on the final number included (n=224) for analysis not the original number (n=230). In addition, the quality of the language needs to be improved. Please have a fluent, preferably native, English-language speaker thoroughly copyedit your manuscript for language usage, spelling, and grammar. [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 Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes Reviewer #3: 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: No Reviewer #3: 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: No Reviewer #2: No Reviewer #3: 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 present an interesting investigation into pneumococcal carriage and detection of respiratory viruses. Abstract: Line 26: I suggest something like ‘prerequisite’ rather than ‘compulsory’ Lines 27-28: This sentence starts by discussing the relationship between carriage and infection, but then goes on to say that the study includes asymptomatic children – which is indicative of lack of infection. This should be rephrased for clarity Lines 42-43: from the text in the abstract, it is not clear how this work contributes to the understanding ‘between these agents and their implications for disease’ – there is no evidence of associations with virus or co-infection and outcomes? Methods: Line 91: What determines a ‘satisfactory’ NP swab? Line 111: superscript the ‘TM’ on the magmax kit (it is the trademark symbol, not an abbreviation of the kit itself). Results: The start of this section would benefit from a little more introduction of the enrolled study population characteristics. Line 155: ‘females’ instead of ‘girls. Line 188: seasonality can be tested/controlled for in a multivariate analysis – this should be checked – as should they other demographic features as well as pathogen detection. Here, you can then also look at household size, school attendance etc, Table 1: it is currently not clear, when reporting significance, what the comparator is. A more robust statistical analysis of this data is required and would strength the data in the field on the associations between demographics and pathogen detection as well as the interplay between pneumococcus and viruses within these groups. Discussion: Did the study team record the density of pneumococcus growth on culture plate? This could be used to look for an association between density and virus type. The paper would benefit from more discussion of hBOV since this is a more novel finding – the discussion on HRV could be condensed – the different studies could be summarized more succinctly. It could be useful to report the Ct values of the virus qPCR detection – if they are low viral loads (high Ct values) this would suggest either a resolving or historic infection (which I commend the authors for recognizing in the text!) so less clinically relevant. If any are higher viral loads (lower Ct) this would suggest more active infection and would be more interesting. Reviewer #2: Major - The manuscript needs to be reviewed for English language. - The data statement indicates that data are available within the manuscript but only aggregate are provided and not individual-level data. - Study design – this is a cohort study with a cross-sectional analysis and cohort analysis. It should not be described as a cross-sectional cohort study. - Methods – more details are needed to understand who is in the study and interpret the results: o It looks like all children in the city were eligible – how were they recruited and were siblings allowed/enrolled. If siblings were allowed, then how was that accounted for in the analysis? (it’s not clear in Table 1 if ‘more than one child in the same household’ refers to enrolled in the study or just present) o The children were considered ‘healthy’ and are called ‘asymptomatic’ throughout the manuscript. They were excluded if they had been diagnosed with ARI or hospitalized the week before. It does not appear that they were excluded if they had respiratory symptoms before (not medically attended) or at the visit. If they were excluded then this should be stated. If they were not excluded, then it should be reported in table 1 how many were symptomatic before or at the visit and the participants should not be referred to as ‘asymptomatic’. I would also remove them from the cohort analysis since they already have symptoms or model incidence to account for this. o The cohort analysis relies on medical records for the outcome. The authors state that they checked 15 different health systems, which seems comprehensive but without knowing this area it is hard to understand if this represents all of the health systems that they could have checked or only a subset. If it’s only a subset, then the completeness of the outcome ascertainment is called into question and it’s not clear if the lack of association is due to misclassification. o The cohort analysis is a univariable analysis. Are there other important factors that affect healthcare seeking (e.g., SES) that may have differed between groups that should be accounted for? As few variables are presented in Table 1, it is hard to know. o Respiratory sample collection and testing – provide brief methods (e.g., broth enrichment) so the reader can know what was done in this study without reviewing another protocol. o Statistical analysis – the authors state that the sample size was determined based on a desired confidence interval. However, no confidence intervals are presented. Is there another paper from this study that should be cited in the Methods where the primary outcome (prevalence of PNC) is reported? o Discussion: � Paragraph starting on line 201: Suggest refocusing to discuss that the study is consistent about an association between PNC and viruses. There was an association with hRV but it was also the most common virus detected. Similar trends were observed for all other viruses except hBOV, but with smaller sample sizes which likely contributed to the lack of statistical significance. � Paragraph starting online 219: since this is the major finding, I suggest expanding the discussion unpack a little more what you measured for both exposure and outcome: • You only measured a subset of viruses and did not measure some major respiratory viruses (e.g., influenza, seasonal coronaviruses) • It’s also not clear with PCR what you measured given that children were 'asymptomatic' – did you measure past infection or did you measure recent infection and the healthcare visits in the next 14 days were for the respiratory viral infection? Was this the right window for detecting pneumococcal infection after a viral infection? • The outcome was medically attended visits and not just respiratory symptoms, which indicates a level of severity of the infection. Minor - Throughout the manuscript be consistent in the number of decimals presented and how numbers are presented (period vs. comma). - Introduction, line 75: the authors state that they considered the increase in infectious disease severity when pathogens interact. This should be rephrased to more accurately reflect what was done. - Methods o line 92: fix typo – ‘health’ professionals o Line 95: remove double period - Results o Line 150: suggest starting out by reporting the % with respiratory viruses by PNC status and providing p-value an then going into co-occurrence. o Line 158: ‘hRV alone + co-detection’ = ‘total’ in the table. Suggest using ‘total (alone + co-detection)’ for ease of reading text. o Line 165: suggest starting by reporting the overall % that required medical care within 14 days. o Line 165: the authors indicate ‘co-occurrence was the most frequent factor among the 43 children who needed medical care’ but this is not what is shown in the table and incidence of medical care in this group was among the lowest. Please re-phrase. - Figure 1 o It looks like no children were excluded for having an ARI – is that correct? Seems odd given detection of viruses. o Box ‘refused to collect or sign ICF’ has an asterix – what is it for? o Fix typo in box ‘children included’ - Table1 o Header row (culture isolation …) is unnecessary and can be deleted o Clarify that PNC and respiratory virus detection columns are ‘only’ o Footnote 2 – clarify that this is ‘at least one dose’ o Footnote 4 is not necessary o Mean (SD) is presented for age – confirm that age was normally distributed; if not, then median (IQR) would be more appropriate. - Table 2 o Title should be changed as it does not only include children with PNC o Rows need to be aligned o Footnotes 2 and 3 are not necessary - Table 3 o Suggested title: incidence of medical appointments 14 days after specimen collection among children, by colonization and respiratory virus detection o As you are presenting incidence (row percents), the ‘no’ column is unnecessary (may cause confusion to include as Table 2 is similarly structured and presents column percents) - Table 4 o Delete header row (culture isolation…) - it is not necessary o Change first section results row to ‘Any documented clinical symptoms within 14 days’ o Change second section results row to ‘Any diagnosis within 14 days’ - S2 Table 1: o Make it clearer what the top row ‘medical records’ refers to and that you are presenting row percents. The rest of the table presents column percents. o Suggest changing ’14 days of medical care’ to ‘medical care within 14 days’ o For the individual symptoms, the percents in the ‘total’ column don’t match what is reported in table 4. - S2 Table 2 – expand the footnote to indicate the test that yielded the p-value and what comparison is being made. Reviewer #3: It is a very interesting article and there are very few articles in Latin America. Some suggestions Line 150: It is not clear what is meant by "The prevalence of microorganism detection found in the children was...", it is suggested to use prevalence of respiratory viruses was... Line 152: "As shown in Table 1, children who tested positive for viral infection, with or without coexisting pneumococcus, were younger (34 vs. 40 months; p = 0.001)." Not displayed in table 1 The lack or shortage of studies in Latin America could be included in the discussion. Line 240-243 The high sensitivity of PCR is not a limitation, but the difficulty of interpreting the presence of viruses is. Line 225 and 245 There is talk of high vaccination coverage; vaccination coverage could be included in the introduction in Brazil and in the state where the study is carried out. ********** 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: No Reviewer #3: Yes: María Eugenia León ********** [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 1 |
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PONE-D-23-41647R1Nasopharyngeal carriage of Streptococcus pneumoniae among Brazilian children: interplay with viral co-infectionPLOS ONE Dear Dr. Pizzutti, 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. Referees still have concerns with the revised manuscript. One referee does not think the explanation and revision improved the quality of the paper to the publishable standard of the journal, and the other referee also has several issues with the current revision. Please see reviewers' insightful comments below. Please submit your revised manuscript by Jul 26 2024 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: 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, Baochuan Lin, Ph.D. Academic Editor PLOS ONE [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 #1: (No Response) Reviewer #2: (No Response) Reviewer #3: 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: Partly Reviewer #2: Yes Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes Reviewer #3: 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 Reviewer #2: Yes Reviewer #3: 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: No Reviewer #2: Yes 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 #1: Abstract, Results, lines 39-41: please consider rephrasing this as it isn’t quite clear what differences were tested for. Abstract line 46: it is still not clear to me how these findings enhance our understanding of the relationship between these potentially pathogenic agents. There have been many other reports on the association between pneumococcus and respiratory pathogens so the authors should add additional detail to highlight was is novel about this. Introduction – PNC and IPD are introduced twice. Please review the text – the introduction should also be reviewed to improve the flow of the messaging. Methods/Results – were siblings controlled for in the analyses? Results – please include a discussion of the demographic details of the 229 children enrolled that is presented in the table – at least highlight if there are any major differences between demographic groups. Please reference to the table in this section too. Results/Conclusion – with such a high frequency of samples generating high Ct values for virus (30-35), this is most likely historic infection as the authors recognize and may not represent active infection – it is perhaps evidence of prior infection which could be skewing associations or why there isn’t higher density of pneumococcus at those sampling moments. Did you look into any association between virus and pneumococcus Ct value? Reviewer #2: In general, the authors were very responsive to the comments and the manuscript reads much better. However, there are still a few issues to address with some of the new analyses. Major comments: Abstract – line 31 (of tracked version): the design should NOT be listed as a cross-sectional cohort study. This was a cohort study an cross-sectional analysis performed at baseline and a longitudinal analysis conducted with the FU data. Methods – line 85: same comment – change to cohort study. Methods – line 91: the authors now indicate that siblings were included but not what proportion of participants involved sibling pairs and therefore how many households are represented. If a large number of siblings were in fact enrolled, then there is clustering in the study population and this should be accounted for in the prevalence estimates and analyses. Methods – lines 133-135: The multinomial regression needs to better described – what were the categories, what was the reference group, how were covariates selected for inclusion, etc. Methods – line 136: the authors indicate that they used Bonferroni tests to adjust for multiple comparison but then indicate that a p<0.05 was considered statistically significant. What, if any, multiple comparisons were adjusted for and what Bonferroni-corrected p-value was considered statistically significant? Results – line 157: the authors indicated in their response that they provided a confidence interval for the prevalence but it does not appear to be included. Discussion – lines 249-259: the new paragraph about hBOV is somewhat confusing: - Line 249 – does the presence of SPN as the only pathogen present refer to findings in MEF? - Line 251 – add period after ‘identified’ - Line 251 – the sentence reads as if the children are acting as antagonists – please revise - Line 252 – the sentence suggests protection of pneumococcus in the absence of hBOV. Don't your results suggest the opposite, that there is protection from SPN when hBOV is present? but only when it is present alone? - Line 253 – what migration is referred to here? Migration to MEF? - Line 259 – provide references for the well-known relationship with co-infection and increased risk of severe SPN disease Table 1: the authors have a category called ‘self-report ethnicity’. I believe this should be ‘self-reported race’ instead. They also have an option for ‘Yellow/Indian’, which is not a term generally used – consider ‘Indigenous’ instead. Table 2: For the p-value, it is unclear what the comparison is. Is it <30/35 vs. >30/35? if so, then the % with each symptom in the reference group needs to be shown in the table in order to interpret the results. For example, sore throat is associated with RNV<35 with 5.3% having sore throat, but is that a higher or lower % than observed in those with RNV>35? Minor comments: Abstract – line 37 & Results – line 157: change to 49.3% (one decimal place). Methods – line 131-132: change ‘qualitative’ to ‘categorical’ and ‘quantitative’ to ‘continuous’ Results – line 157: add ‘of’ and ‘was’ (the prevalence OF pneumococcal carriage WAS…) Results – line 159: italicize S. pneumoniae Discussion – line 210: 47.2% in the table Discussion – line 212: change ‘findings’ to ‘symptoms’ Discussion – line 224: INF and PIV are introduced as new abbreviations – spell out first Discussion – line 268: suggest tempering language and using ‘may have prevented development of diseases’ Table 4 – suggest combining with Table 5 Table 5 – it is interesting that there isn't complete overlap in the “any documented clinical symptoms’ category and having a medical appt in Table 4. What accounts for the discrepancy? S2 Table 1 – the current column (microorganisms) reporting n (%) for each covariate is not interpretable without the corresponding column for ‘no pathogen detected’. S2 Table 2: - Be consistent in the number of decimals presented in this table - Remove the % in the top row labeled ‘medical records’ – these are row percents while the of the table presents column percents and it is confusing. - There is a footnote outlining tests conducted and ‘* p<0.05 significant’, but it’s not clear if any comparisons are being made in this table and nothing is significant. If there are comparisons being made, please outline what they are and what the reference group is. S2 Table 3: While the authors have indicated the statistical test being conducted, it’s still not clear what comparison is being made. For example, there is an asterix on RSV for Fall – is this comparing the distribution of seasons between those that are RSV+ and RSV-? If so, this is only interpretable if we have the distribution for the RSV- group. Reviewer #3: (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 Reviewer #2: No 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 |
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PONE-D-23-41647R2Nasopharyngeal carriage of Streptococcus pneumoniae among Brazilian children: interplay with viral co-infectionPLOS ONE Dear Dr. Pizzutti, 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. Both reviewers agreed that the revised manuscript showed significant improvement, however, there are still concerns raised by the reviewers and these issues need to be addressed carefully. Personally, I also found several issues that need to be addressed (please see specific comments below). In addition, the quality of the language still needs to be improved. There are quite a few awkward and confusing sentences, typos throughout the manuscript. 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. Specific comments:
2. Line 126: Change “described” to “, as described” 3. Line 141 – 144: This is an awkward run on sentence which need rephrasing for clarity. 4. Line 151: If 6 were excluded, this should be 223. In figure 1, 5 were excluded, which would be 224. Please make sure that the numbers are consistent throughout the manuscript. 5. Line 160 – 161: Change “… for and respiratory viruses 49.3% (113/229, CI95%: 42.9% - 55.8%).” To “…and 49.3% (113/229, CI95%: 42.9% - 55.8%) for respiratory viruses.” 6. Line 163: Delete “for both S. pneumoniae and any virus” 7. Table 1: Please include Female number for ease of reading. 8. Line 172: Change “associated with co-occurrence” to “associated with higher rate of co-occurrence” 9. Line 181 – 183: This is an awkward sentence, please rephrase for clarity. 10. Table 3: Do the authors of the information of co-detection of viruses? It maybe helpful to have more details instead of just total number, for example hRV + ADV or hRV + RSV? 11. Line 204: Change “demonstrate” to “revealed” 12. Line 206 – 207: This is an awkward sentence, not sure what the authors wish to convey. 13. Line 220: Not sure the significance and/or relevance of this sentence. Please clarify. 14. Line 256: This sentence missed a period at the end. 15. Line 256 – 257: This sentence needs rephrasing for clarity. Please submit your revised manuscript by Oct 12 2024 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 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, Baochuan Lin, Ph.D. 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 #1: (No Response) Reviewer #2: (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 #1: Yes Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: 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 Reviewer #2: 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 Reviewer #2: 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: I commend the authors for the work they have put in to further update their manuscript. I only have a couple more comments: I believe line 38 where it is talking about respiratory viruses in carriers is also missing a ‘versus non-carriers’. The ‘versus non-carriers’ could move from line 39 to 38 to introduce this comparison and carry that through the subsequent comparisons. It is still not entirely clear how the results enhance our understanding (line 47). That sentence could since the authors have added a new sentence about the study after that. Line 165 – it is not clear in the text to what the p-value represents. Reviewer #2: The authors have adequately addressed most comments. There are two outstanding comments: Table 2: while the authors have clarified that they performed the analysis using two different cutoffs, the table only presents one of the proportions from the comparison being made. Presumably, the comparison being made and referenced by the p-value is the % symptomatic with virus <30 (or <35) compared to the % symptomatic with virus >=30 (or >=35). Given that only RNV is significant at ct<35, I suggest presenting the comparison of <35 vs. >=35 in Table 2 and creating a supplemental table to show the results for <30 vs. >=30 and just refer to the results being consistent at this lower ct cutoff in the text. Also, combine the first two footnotes (e.g., * p<0.05 significant by chi-square or Fisher’s exact test) – the same should be done for Table 1 as well. Methods - line 138-141: Can the authors clarify if the age comparison using the Kruskal-Wallis was followed by post-hoc Dunn’s test with Bonferroni adjustment. The sentences should be clarified to indicate what was done (e.g., The association between pneumococcal carriage and age was conducted using a Kruskal-Wallis test and followed with post-hoc Dunn’s pairwise tests and Bonferroni correction. The association of pneumococcal carriage and demographic data other than age, symptoms,…). Additional minor comments: Abstract – line 31 (tracked version): modify sentence to indicate 229 nasopharyngeal samples collected from children aged 18-59 months at baseline were included. Methods – line 88-101: modify sentence in line 88 to delete ‘and cross-sectional analysis’. Modify line 98 to indicate ‘at enrollment, health professionals trained for the study collected a nasopharyngeal specimen and conducted structure…..’. Methods – line 127-129: move new text to Statistical Analysis section and describe this analysis (chi-square or Fisher’s exact test). Methods – line 141-144: revise the sentence regarding multinomial regression for English (e.g., The multinomial logistic regression included four outcome categories including ‘agent identified’ (reference group), ‘pneumococcal carriage only’, ‘ respiratory virus detection only’, and ‘co-occurrence’. Exposure variables included age in months, male sex, does not sleep alone, season, and any illness symptoms at enrollment.) Methods – line 135: add abbreviation for confidence level (CI) as it is used in the results. Results – line 135: clarify that it is ‘PNC prevalence at enrollment’ Results – line 164: fix grammar leading to prevalence for respiratory viruses Results – line 165: a p-value is provided for the % with respiratory viruses among those with PNC but it is not interpretable unless the % among those without PNC is provided – either remove or provide the % (e.g., p=0.033 compared to X% among those without PNC). Results – line 166: italicize S. pneumoniae Discussion – line 261 – put back in the period after ‘hBOV alone’. References - italicize S. pneumoniae throughout ********** 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 Reviewer #2: 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 3 |
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PONE-D-23-41647R3Nasopharyngeal carriage of Streptococcus pneumoniae among Brazilian children: interplay with viral co-infectionPLOS ONE Dear Dr. Pizzutti, 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 revised manuscript showed significant improvement, however, the reviewer still have one issue that need to be addressed. In addition, on line 71, I suggest that you change "there information..." to "the information..." Please submit your revised manuscript by Dec 20 2024 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 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, Baochuan Lin, Ph.D. 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 #2: (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 #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: 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 #2: 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 #2: 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 #2: I thank the authors for addressing the comments. The manuscript is greatly improved. I have just one remaining comment regarding Table 2 that should be addressed before the manuscript can be accepted. The authors present two cutoffs (which is fine) but do not present the comparison group (which I believe is >35 for both for both cutoffs). Without presenting the results for >35, it is not possible to interpret the % provided. For example, 5.3% of RNV with >35 have a sore throat, but what is that being compared to? is that higher or lower than among those with >35? A column for >35 should be added for each pathogen. ********** 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 #2: 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 4 |
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Nasopharyngeal carriage of Streptococcus pneumoniae among Brazilian children: interplay with viral co-infection PONE-D-23-41647R4 Dear Dr. Kauana Pizzutti, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Jairam Meena, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): 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 #2: 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 #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: 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 #2: 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 #2: 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 #2: No further comments - the authors have addressed all comments and I am happy to approve for publication. ********** 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 #2: No ********** |
| Formally Accepted |
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PONE-D-23-41647R4 PLOS ONE Dear Dr. Pizzutti, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Jairam Meena Academic Editor PLOS ONE |
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