Peer Review History
| Original SubmissionAugust 10, 2021 |
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PONE-D-21-25854Pertussis immunisation in infancy and atopic outcomes: A protocol for a population-based cohort study using linked administrative dataPLOS ONE Dear Dr. Pérez Chacón1, 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. ============================== ACADEMIC EDITOR: Please insert comments here and delete this placeholder text when finished. Be sure to:
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Kind regards, Lucinda Shen, Staff Editor on behalf of Daniela Flavia Hozbor 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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 (if provided): [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions? The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field. Reviewer #1: Yes Reviewer #2: Yes ********** 2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses? The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory. Reviewer #1: Yes Reviewer #2: Yes ********** 3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable? Reviewer #1: Yes Reviewer #2: Yes ********** 4. Have the authors described where all data underlying the findings will be made available when the study is complete? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception, at the time of publication. 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 and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics. You may also provide optional suggestions and comments to authors that they might find helpful in planning their study. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This seems a straightforward retrospective cohort study that has the potential to answer an important question. I like the design and would like to commend the authors for considering this study. Its use of retrospective data is a major advantage and will hopefully get to useful answers quickly and relatively cheaply. I do have a few minor questions and comments for the authors to consider: Lines 55-56: Although this is not core to the protocol, it is important to note that Yeung’s modelling study actually indicates that significant inequities persist with the poorest countries carrying the brunt of both pertussis morbidity and death. The EPI as a framework has been great but deal less with capacity that increases access to vaccines although other access programs were later leveraged on it (e.g. GAVI). Line 65: ‘more or less stochastic’ – I did smile a bit at the wording because being a disciple of C.S Lewis I would have gone for the simple ‘random’, in part because statisticians tend to technically use ‘stochastic’ to technically refer to deliberately created randomness. Lines 80-82: I think it is important to note that a decrease in asthma hospitalisations should not be read to imply a decrease in asthma as there has been a significant improvement over time in managing asthma in ways that reduce severe exacerbations. What would be useful would be to know the prevalence over the period. Still I understand why this is mentioned here given the anticipated outcome. Lines 89: Is that food-induced or just anaphylaxis in general? Line 105: Did the period of shortage eliminate wP from the schedule or did it just reduce the number of wP doses in the schedule? Line 113: ‘primed with wP’: It may be important to note that in ‘pertussis cycles’, the word ‘prime’ has been used both to refer to the first dose of the vaccine given (a child who gets a single dose of wP as first dose but received aP for the balance of the schedule would thus have been wP primed) as well as the completing of a 3-dose primary schedule. This may be important here as the study may need to take this distinction into consideration in the context of ‘mixed’ vaccination. Lines 168-172: Will this require a need to consider stratifying by or adjusting for aP type? wP seems simple enough as there was only one manufacturer over the period under review. Pertussis vaccines, even if same ‘type’ differ with respect to how they are manufactured, adjuvants used, constituted, etc., All these have an in impact on immunogenicity and efficacy. Line 199: ‘hospitalisations for asthma before 5 years old will be disregarded’ : I am reading this to mean that they will not count as an outcome rather than that they will be ignored. Age at onset of asthma, and number of previous hospitalisations have been known to be important predictors of future need for hospitalisation. So, am I hoping that the authors intend to note this if as a minimum to consider it as a potential confounder that may require some adjusting for. Having said that, and having read the reasons for excluding events before 5 years of age, I cannot figure out why disregarding this period is sensible if the data were available especially given the introduction section that shows an increase in allergic reaction in younger children. Why would it not be more reasonable to rather have to rather stratify the outcomes by the ages of the cohort? As such I would assume that the second reason given, that of lack of data before 2001 would be the only defensible reason in my opinion. Table 2. ‘Index of Relative Socio-economic Advantage and Disadvantage’: Will that be at the time of vaccination, start of time under evaluation (5 years) or at the time of outcome? Or does it not matter? Lines 275-284 + Figures 2. This may be just my understanding of the design that leads to this comment on the descriptions of this Lexis diagram. In this design, a cohort would be defined by exposure and that exposure occurs in infancy, quite close to birth. Does that then not mean that each child enters the cohort at the verifiable time of exposure, even if assessed time at risk of outcome is only entered after 5 years? Or does the lack of data alluded to before affect this understanding? Finally, while I do appreciate the fact that the authors have spent some time on bias as the major concern, I would have liked to see a distinct reflective section on ‘Limitations’ to acknowledge other potential limitations, even if briefly. Are there not other limitations? What about confounding for example. I absolutely like the fact that the authors have chosen to use DAGs to decide on potential factors, but even the chosen model is determined and limited by causal assumptions made. For example, some may argue that admissions before 5 years of age as predictor of further admissions are missing from the model; should genetic predisposition and parental asthma be two independent variables, etc. Reviewer #2: The burden of IgE-mediated food allergy in Australian born children is reported to be among the highest globally. This illness shares risk factors and frequently coexists with asthma, one of the most common noncommunicable diseases of childhood. Findings from a case-control study suggest that compared to immunisation with acellular pertussis vaccine, early priming of infants with whole-cell pertussis vaccine may be associated with a lower risk of subsequent IgE-mediated food allergy. The authors propose a protocol for a population-based cohort study using linked administrative. The observational design will use administrative data to assess the hazard of hospital admission and emergency department presentation for allergic diseases in a birth cohort of children born in Australia during the transition from using wP to aP priming vaccine doses. The authors describe the methods to compare a birth cohort of children vaccinated with a first dose of wP versus aP with respect to the time to a first or recurrent tertiary care encounter for acute exacerbations of asthma and other atopic diseases. The strengths and limitations of this study are clearly identified and described in detail. I suggest that authors mention how the results obtained in this study would be complemented with those obtained from the OPTIMUM study (Perez Chacon G, Estcourt MJ, Totterdell J, et al. OPTIMUM study protocol: an adaptive randomised controlled trial of a mixed whole-cell/acellular pertussis vaccine schedule. BMJ Open 2020;10:e042838. doi:10.1136/ bmjopen-2020-042838) ********** 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: Yes: Rudzani Muloiwa 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/. 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| Revision 1 |
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Pertussis immunisation in infancy and atopic outcomes: A protocol for a population-based cohort study using linked administrative data PONE-D-21-25854R1 Dear Dr. Gladymar Pérez Chacón, 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, Daniela Flavia Hozbor Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions? The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field. Reviewer #1: Yes ********** 2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses? The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory. Reviewer #1: Yes ********** 3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable? Reviewer #1: Yes ********** 4. Have the authors described where all data underlying the findings will be made available when the study is complete? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception, at the time of publication. The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics. You may also provide optional suggestions and comments to authors that they might find helpful in planning their study. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Thank you for meaningfully engaging with my comments - all really made as suggestions to the authors to improve what I had already indicated was a solid manuscript. I have no further comments to make. ********** 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: Yes: Rudzani Muloiwa |
| Formally Accepted |
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PONE-D-21-25854R1 Pertussis immunisation in infancy and atopic outcomes: A protocol for a population-based cohort study using linked administrative data Dear Dr. Pérez Chacón: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Daniela Flavia Hozbor Academic Editor PLOS ONE |
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