Invasive pneumococcal disease in Latin America and the Caribbean: Serotype distribution, disease burden, and impact of vaccination. A systematic review and meta-analysis

Ariel Bardach; Silvina Ruvinsky; M. Carolina Palermo; Tomás Alconada; M. Macarena Sandoval; Martín E. Brizuela; Eugenia Ramirez Wierzbicki; Joaquín Cantos; Paula Gagetti; Agustín Ciapponi

doi:10.1371/journal.pone.0304978

Peer Review History

Original SubmissionSeptember 24, 2023
19 Jan 2024 Decision Letter - Anirudh K. Singh, Editor PONE-D-23-31108Invasive pneumococcal disease in Latin America and the Caribbean: serotype distribution, disease burden, and impact of vaccination. A systematic review and meta-analysisPLOS ONE Dear Dr. Bardach, 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 Mar 04 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. 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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. Thank you for stating the following financial disclosure: “Pfizer Independent Grant 76436251” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 3. Please include a separate caption for each figure in your manuscript 4. 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: Yes Reviewer #2: No Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: I Don't Know ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes 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: Yes Reviewer #2: Yes 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 study's strengths lie in its diverse coverage of S. pneumoniae aspects across multiple countries and healthcare facilities. However, the study transparently addresses limitations related to sample selection, size, and outcome measurement, acknowledging potential bias risks in data assessment. In summary, the study provides valuable insights into pneumococcal serotype distribution in Latin American IPD. While acknowledging the positive impact of PCVs in reducing vaccine serotypes, it underscores the ongoing challenge of serotype replacement. The study's call for continuous surveillance to monitor serotype distribution changes and address the persisting disease burden is well-founded, making it a pertinent contribution to the field. Reviewer #2: The authors present a comprehensive secondary analysis taking in the analysed data out come of various reports published in period of time. The analysis might be helpful provided the data taken to be rigorous and analysed on various statistical parameters. -Please discuss the outcome of the study in detail incorporating molecular mechanisms based on those studies have had reported. -Please move table 1 to supplementary section. -Think about more suitable representation of table 2 and 3, you can think of segmentation of these respective figures. -Discuss a little about he analysis algorithms that you are following. -A structured discussion incorporating above suggestion will present your views more appropriately. Reviewer #3: The review is important for the field and the countries included in this review are not well studied. I would recommend the authors to refine the manuscript to target larger audience. These references should be referred to express the key findings of a systematic review and meta-analysis. DOI: 10.1016/j.tmaid.2018.05.016 DOI: 10.1016/S2214-109X(16)30306-0 I have few other comments which are as follows: Abstract: • Line 35: “death hospitalization” can be replaced with death after hospitalization or similar. • Line 36: correct serotypes IPD to serotyped IPD. • Line 37: the first line of the result should be shifted to the method section. Or should be reworded to say that 155 studies were screened etc. • Line 38: if invasive diseases mean IPD, then it IPD should be used consistently. • Include some result about the overall incidences in different age groups and the few key findings. • Line 42: specify countries from the LAC region. Introduction: • Line 52: use some other word instead of sterile materials. • Line 55-56: The sentence should be reworded for better clarity. • Line 65: Include the full form of SIREVA. • Line 70: The sentence needs to be reworded to say that that serotypes of the vaccines have been reduced in the population due to vaccine 7/10/13 implantation. The methodology looks elaborate and well written which needs to be checked by the experts in the field of meta-analysis. Results: • Table 1: The outcomes column should be populated more to include serotypes, incidences etc. Discussion: • Line 316: Used the abbreviation IPD consistently. • Line 334-336: Highlight some key finding from the worldwide study. • Line 347: Write the region name or use LAC consistently. • The conclusion should be in line with the title of the review. ****** 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: 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.0304978.r001
Revision 1
16 Feb 2024 Author Response Response to Reviewers: 2. Thank you for stating the following financial disclosure: “Pfizer Independent Grant 76436251” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. Thanks, we already rephrased it in the manuscript and it was modified and highlighted in the cover letter. 3. Please include a separate caption for each figure in your manuscript Done 4. 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. All file captions were added at the end and updated in the manuscript. Reviewer #1: The study's strengths lie in its diverse coverage of S. pneumoniae aspects across multiple countries and healthcare facilities. However, the study transparently addresses limitations related to sample selection, size, and outcome measurement, acknowledging potential bias risks in data assessment. In summary, the study provides valuable insights into pneumococcal serotype distribution in Latin American IPD. While acknowledging the positive impact of PCVs in reducing vaccine serotypes, it underscores the ongoing challenge of serotype replacement. The study's call for continuous surveillance to monitor serotype distribution changes and address the persisting disease burden is well-founded, making it a pertinent contribution to the field. Many thanks for your review. Reviewer #2: The authors present a comprehensive secondary analysis taking in the analyzed data outcome of various reports published in a period of time. The analysis might be helpful provided the data taken to be rigorous and analyzed on various statistical parameters. -Please discuss the outcome of the study in detail incorporating molecular mechanisms based on those studies that have been reported. Molecular methods were not described in detail because this is not one of the objectives of the present work, which describes mostly the epidemiology of serotypes in the region. In addition, only a handful of the studies included this detail. -Please move table 1 to supplementary section. Thank you for your comment. However, the group of authors considers that Table 1 summarizes well the main characteristics of the evidence identified for the region and is the initial type of table for any epidemiological systematic review. As such, we feel it should be included in the main body of the manuscript. Sacrificing this content detracts from the value of the work. -Think about a more suitable representation of table 2 and 3, you can think of segmentation of these respective figures. Thank you for your comment. Table 2 shows the detailed results of proportion meta-analyses of the distribution of vaccine serotypes by condition in LAC, by five-year period, age groups, and countries. In the opinion of the authors' group, it was a very thoughtful and difficult table to produce, and we think it is very informative. We feel it does not require further revamping, as relevant categories have already segmented information. Table 3 shows the Case fatality rate according to type of IPD and sub-analysis by 5-year period, age, and country. This important health outcome accounts for the virulence of circulating serotypes in invasive pneumococcal disease and allows compatibility with other regions. We believe it adds real value to the study. -Discuss a little about the analysis algorithms that you are following. Thank you. We are following the PRISMA statement algorithm for systematic reviews (cited in the text), including the study flowchart (Fig 1), generated by the Covidence Software, as explained in the manuscript. The search algorithm is also explained in the Methods section. -A structured discussion incorporating the above suggestion will present your views more appropriately. Thank you. Several changes have been introduced to improve the structure and readability. Reviewer #3: The review is important for the field and the countries included in this review are not well studied. I would recommend the authors to refine the manuscript to target a larger audience. These references should be referred to express the key findings of a systematic review and meta-analysis. DOI: 10.1016/j.tmaid.2018.05.016 DOI: 10.1016/S2214-109X(16)30306-0 Thanks for your suggestion. We incorporated both references in the introduction section and were highlighted in the references. I have few other comments which are as follows: Abstract: • Line 35: “death hospitalization” can be replaced with death after hospitalization or similar. Done • Line 36: correct serotypes IPD to serotyped IPD. Done • Line 37: the first line of the result should be shifted to the method section. Or should be reworded to say that 155 studies were screened etc. Done • Line 38: if invasive diseases mean IPD, then it IPD should be used consistently. Modified. The same acronym is used throughout the manuscript. • Include some results about the overall incidences in different age groups and the few key findings. This is described in the text, in lines 235-243 and S3 Table and Figure 2. • Line 42: specify countries from the LAC region. All countries of Latin America and the Caribbean were included, as defined by the United Nations Introduction: • Line 52: use some other word instead of sterile materials. Modified • Line 55-56: The sentence should be reworded for better clarity. Done • Line 65: Include the full form of SIREVA. The Spanish meaning was clarified. • Line 70: The sentence needs to be reworded to say that serotypes of the vaccines have been reduced in the population due to vaccine 7/10/13 implantation. Done The methodology looks elaborate and well written which needs to be checked by the experts in the field of meta-analysis. Thanks Results: • Table 1: The outcomes column should be populated more to include serotypes, incidences etc. Thank you. Table 1 is a summary table of the overall type of available evidence in the region. Vaccine serotypes in LAC evidence are meta-analyzed and further summarized in Table 2. Incidence meta-analyses conducted are described in the text (lines 235-247) of Results. The author's group feels that including such information in Table 1 would make it even larger and redundant. Discussion: • Line 316: Used the abbreviation IPD consistently. Done • Line 334-336: Highlight some key findings from the worldwide study. Done. To clarify a paragraph was added as follows: The main findings of this review were that after the introduction of PCVs, a considerable proportion of childhood IPD was caused by non-PCV13 serotypes and, among the vaccine serotypes, 19A was the most frequently identified in different regions of the world. • Line 347: Write the region name or use LAC consistently. LAC was consistently placed in the manuscript. • The conclusion should be in line with the title of the review. Thanks, we re-wrote the conclusions to be more in line with the title. Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0304978.r002
25 Mar 2024 Decision Letter - Anirudh K. Singh, Editor PONE-D-23-31108R1Invasive pneumococcal disease in Latin America and the Caribbean: serotype distribution, disease burden, and impact of vaccination. A systematic review and meta-analysisPLOS ONE Dear Dr. Bardach, 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 follow reviewer# 2 suggestion to move Table 1 to supplementary information. Please read PlosOne policy on reference/citations. I am not sure you can cite a study/abstract/poster if it is not availabe in the public domain. Please submit your revised manuscript by May 09 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Anirudh K. Singh, 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. Additional Editor Comments: Please follow reviewer# 2 suggestion to move Table 1 to supplementary information. Please read PlosOne policy on reference/citations. I am not sure you can cite a study/abstract/poster if it is not availabe in the public domain. [Note: HTML markup is below. Please do not edit.] [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.0304978.r003
Revision 2
28 Mar 2024 Author Response Response to Reviewers R2: Please follow reviewer# 2 suggestion to move Table 1 to supplementary information. Thank you. Done Please read PlosOne policy on reference/citations. I am not sure you can cite a study/abstract/poster if it is not availabe in the public domain. Thank you, we added more information and links to these 3 references: Benitez JD, Martinez ME, Specht MH von, Gerlach E, Gonzalez CA, Grenon SL. Epidemiology and risk factors for invasive pneumococcal disease in pediatrics. Descriptive, postvaccinal study. Epidemiología y factores de riesgo de enfermedad invasiva neumocócica en pediatría Estudio descriptivo, postvacunal. Revista de ciencia y tecnologia 2017; 4–10. Available: http://ri.conicet.gov.ar/handle/11336/177141 Accessed May 5th 2023 Agudelo CI, Sanabria OM, Ovalle MV, Castaneda E. Laboratory surveillance of Streptococcus pneumoniae serotypes from infected children aged less than 5 years: 1994-2000. Biomédica 2001;21(2): 193–199. Agudelo I, Diaz LP, Sanabria MO, Ovalle VM, Castaneda E, Rosa Gallego C, et al. Laboratory surveillance of Streptococcus pneumoniae isolated by invasive processes in the population older than 5 years, 1998-2001. Vigilancia por el laboratorio de Streptococcus pneumoniae aislado de procesos invasores en población mayor de 5 años, 1998-2001. 2002;7: 177–183. https://www.cabidigitallibrary.org/doi/full/10.5555/20023161394 Accessed May 5th 2023 Attachments Attachment Submitted filename: Response to reviewers R2.docx https://doi.org/10.1371/journal.pone.0304978.r004
9 Apr 2024 Decision Letter - Anirudh K. Singh, Editor Invasive pneumococcal disease in Latin America and the Caribbean: serotype distribution, disease burden, and impact of vaccination. A systematic review and meta-analysis PONE-D-23-31108R2 Dear Dr. Bardach, 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, Anirudh K. Singh, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0304978.r005
Formally Accepted
28 May 2024 Acceptance Letter - Anirudh K. Singh, Editor PONE-D-23-31108R2 PLOS ONE Dear Dr. Bardach, 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. Anirudh K. Singh Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0304978.r006

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