Factors associated with community acquired severe pneumonia among under five children in Dhaka, Bangladesh: A case control analysis

Sabiha Nasrin; Md. Tariqujjaman; Marufa Sultana; Rifat A. Zaman; Shahjahan Ali; Mohammod J. Chisti; Abu S. G. Faruque; Tahmeed Ahmed; George J. Fuchs; Niklaus Gyr; Nur H. Alam

doi:10.1371/journal.pone.0265871

Peer Review History

Original SubmissionFebruary 24, 2021
3 Nov 2021 Decision Letter - Dario Ummarino, PhD, Editor PONE-D-21-06226Factors associated with community acquired severe pneumonia among under five children in Dhaka, Bangladesh: A case control studyPLOS ONE Dear Dr. Faruque, 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 manuscript has been evaluated by two reviewers, and their comments are available below. The reviewers have raised a number of concerns that need attention. In particular, reviewer #1 has raised several points regarding the statistical analysis and the general reporting of the methodology, including a specific request to follow the STROBE guidelines. Could you please revise the manuscript to carefully address the concerns raised? Please submit your revised manuscript by Dec 17 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: 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, Dario Ummarino, Ph.D. Senior 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf [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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Abstract: 'annual incidence' in line 22 and 'each year' on line 23 are a repetition. Introduction - since you are reporting absolute incidences, it would be useful to also indicate the global change in the population of the children referred to in line 49 (i.e. the denominator for those incidences). - would it be accurate to use 'non-severe pneumonia' to refer to what you currently call 'pneumonia'; for example, in line 70: "we analysed a large dataset of children with severe and non-severe pneumonia..." and in line 71/72: "... factors associated with severe pneumonia compared to non-severe pneumonia." Methods - please report the methods according to STROBE guidelines for case-control studies (see https://www.equator-network.org/wp-content/uploads/2015/10/STROBE_checklist_v4_case-control.pdf). - there doesn't seem to be any value on the chi-squared tests, Mann-Whitney tests or t-tests listed in line 175 given your intention to conduct univariable regression models as described in line 177. Results - linked to the last comment in methods (above), the results described in line 246 relating to unadjusted regression analysis would be expected to be identical to those of the univariate test p-values in Table 1. I would recommend that you keep table 1 purely descriptive with no hypothesis tests of the differences between the two groups and p-values, as this is what table 2 explores. - in table 2, you should report a single likelihood ratio p-value or global wald test for multicategorical variables such as wealth index and received care, not the individual wald test p-values comparing each category to the reference category as currently done. It is that single p-value that should be used to assess evidence of association with the whole variable. For example, you report that received care was no longer associated with the outcome after adjusting for other variables, but this is unlikely to be correct based on a single global test (as described above). Reviewer #2: The presence of crepitation indicating alveolar involvement is part of the clinical diagnosis of pneumonia. It is possible that its absence in the control group may have occurred due to differential diagnoses of other respiratory diseases. I suggest removing the presence of crepitation as a risk factor. Regarding size, it can be as the authors did, although in our opinion it would be more appropriate to respect the case-control (1:1 ratio) study design and the cases and controls had the same number of participants. ****** 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: Yes:** Eduardo Jorge da Fonseca Lima [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.0265871.r001
Revision 1
11 Dec 2021 Author Response Reviewer #1: Comment: Abstract: 'annual incidence' in line 22 and 'each year' on line 23 are a repetition. Response: Thank you very much for spotting this. We have deleted “each year” from line 24 as suggested. Comment: Introduction - since you are reporting absolute incidences, it would be useful to also indicate the global change in the population of the children referred to in line 49 (i.e. the denominator for those incidences). Response: Thank you so much for the suggestion. We have edited line 49, it now reads “Implementation of feasible and effective interventions has reduced under-five pneumonia death substantially from 13·6 per 1000 livebirths in 2000 to 6·6 per 1000 livebirths in 2015” (line 61). Comment: - would it be accurate to use 'non-severe pneumonia' to refer to what you currently call 'pneumonia'; for example, in line 70: "we analysed a large dataset of children with severe and non-severe pneumonia..." and in line 71/72: "... factors associated with severe pneumonia compared to non-severe pneumonia." Response: We appreciate and accept your suggestion. We have replaced all “non-severe pneumonia” term to “pneumonia” (line 112, 258). Comment: Methods - please report the methods according to STROBE guidelines for case-control studies (see https://www.equator-network.org/wp-content/uploads/2015/10/STROBE_checklist_v4_case-control.pdf). Comment: Thank you so much for the excellent suggestion. Please find the STROBE table below. We have mentioned the line numbers where the information was specified in the manuscript. Find the full checklist in "Reviewers Response" document, but a summary is given below: Title and abstract Line 1 and 19 Background/rationale Lines 50-80 Objectives Lines 82-86 Study design Lines 105-112 Setting Lines 95-101 Participants Lines 134-157 Outcomes, exposures: Lines 195-223 Data sources Lines 105-112 Study size Lines 111-112 Statistical methods Lines 181-193 Results Line 230 (Fig 1.) Descriptive data Lines 245-250;Table 1. Outcome data Lines 258-264 Comment: - there doesn't seem to be any value on the chi-squared tests, Mann-Whitney tests or t-tests listed in line 175 given your intention to conduct univariable regression models as described in line 177. Response: Thank you for your comment. To get the p-values in table 1, We used the chi-squared tests, Mann-Whitney tests, or t-tests. However, as per your other suggestion, we are keeping Table 1 pure descriptive, so, we have deleted the line from data analysis section. Comment: Results - linked to the last comment in methods (above), the results described in line 246 relating to unadjusted regression analysis would be expected to be identical to those of the univariate test p-values in Table 1. I would recommend that you keep table 1 purely descriptive with no hypothesis tests of the differences between the two groups and p-values, as this is what table 2 explores. Response: Authors agree with the suggestion. We have edited Table 1 and kept it purely descriptive as per your valuable suggestion. (Line 245). Comment: - in table 2, you should report a single likelihood ratio p-value or global wald test for multicategorical variables such as wealth index and received care, not the individual wald test p-values comparing each category to the reference category as currently done. It is that single p-value that should be used to assess evidence of association with the whole variable. For example, you report that received care was no longer associated with the outcome after adjusting for other variables, but this is unlikely to be correct based on a single global test (as described above). Response: We appreciate your suggestion. We re-analyzed the data according to your suggestion and presented a single likelihood ratio p-value for the categorical variables (wealth index, received care). (Line 258). Reviewer #2: Comment: The presence of crepitation indicating alveolar involvement is part of the clinical diagnosis of pneumonia. It is possible that its absence in the control group may have occurred due to differential diagnoses of other respiratory diseases. I suggest removing the presence of crepitation as a risk factor. Response: Thank you so much for your advice. We have re-analyzed the data by removing the crepitation variable as a risk factor from the multivariable model that you have suggested (Line 258). Comment: Regarding size, it can be as the authors did, although in our opinion it would be more appropriate to respect the case-control (1:1 ratio) study design and the cases and controls had the same number of participants Response: Thank you so much for your suggestion. We did the secondary data analysis with all the available samples in the study. The study sample size was determined based on the original study objective. Children presenting to study clinics were assessed and those diagnosed as severe pneumonia, N=1963, and pneumonia, N=904 were included in this analysis. We kept these total estimated sample sizes and analyzed the data accordingly. Therefore, we have deleted the sample size section from the manuscript as it appeared to be unnecessary. Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0265871.r002
14 Feb 2022 Decision Letter - Tanya Doherty, Editor PONE-D-21-06226R1Factors associated with community acquired severe pneumonia among under-five children in Dhaka, Bangladesh: A case control analysisPLOS ONE Dear Dr. Faruque, 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 address the remaining comments from reviewer 1 regarding operational definitions. Please also remove reference to crepitation in the conclusion of the abstract. I think there does still need to be a section on sampling in your methods where you describe how the final sample was obtained and clarifying that you included all eligible children. Please submit your revised manuscript by Mar 31 2022 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, Tanya Doherty, PhD 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: 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: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) ****** 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: (No Response) ****** 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 Response) ****** 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: Please edit 'operational definitions' paragraph in lines 118 to 124 as follows for clarity: "Pneumonia was defined as a history of cough or difficult breathing and lower chest wall in-drawing or age-specific fast breathing (≥50 and ≥40 breaths/minute for 2–11 month-olds and 12–59 month-olds respectively) without any danger signs [13,14]. Severe pneumonia was defined as pneumonia with at least one of the following danger signs: central cyanosis or hypoxemia (oxygen saturation < 90% measured by pulse oximeter), severe respiratory distress (e.g. grunting, very severe chest in-drawing), inability to breastfeed or drink, lethargy or unconscious, and convulsion." ****** 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 [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.0265871.r003
Revision 2
1 Mar 2022 Author Response Comments from the Academic Editor: Comments: Please address the remaining comments from reviewer 1 regarding operational definitions. Please also remove reference to crepitation in the conclusion of the abstract. I think there does still need to be a section on sampling in your methods where you describe how the final sample was obtained and clarifying that you included all eligible children. Response: Thank you so much for your kind review and valuable suggestions. As suggested, we have edited the ‘operational definitions’ as per reviewer 1’s suggestion in lines 126-133. We have removed ‘crepitation’ in the conclusion of the abstract (line 50). We appreciate your suggestion on adding a section on sampling in method section. We have added and now it reads, “Sample size:The secondary data analysis was done with the available samples in the study. Children presenting to study clinics were assessed and those diagnosed as severe pneumonia, N=1963, and pneumonia, N=904 were included in this analysis” in lines 116-119. Reviewer #1: Comment: Reviewer #1: Please edit 'operational definitions' paragraph in lines 118 to 124 as follows for clarity: "Pneumonia was defined as a history of cough or difficult breathing and lower chest wall in-drawing or age-specific fast breathing (≥50 and ≥40 breaths/minute for 2–11 month-olds and 12–59 month-olds respectively) without any danger signs [13,14]. Severe pneumonia was defined as pneumonia with at least one of the following danger signs: central cyanosis or hypoxemia (oxygen saturation < 90% measured by pulse oximeter), severe respiratory distress (e.g. grunting, very severe chest in-drawing), inability to breastfeed or drink, lethargy or unconscious, or convulsion." Response: We appreciate and accept your suggestion. We have edited the ‘operational definitions’ paragraph in lines 126 to 133 as per your suggestion for clarity. Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0265871.r004
10 Mar 2022 Decision Letter - Tanya Doherty, Editor Factors associated with community acquired severe pneumonia among under-five children in Dhaka, Bangladesh: A case control analysis PONE-D-21-06226R2 Dear Dr. Faruque, 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, Tanya Doherty, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0265871.r005
Formally Accepted
14 Mar 2022 Acceptance Letter - Tanya Doherty, Editor PONE-D-21-06226R2 Factors associated with community acquired severe pneumonia among under five children in Dhaka, Bangladesh: A case control analysis Dear Dr. Faruque: 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 Professor Tanya Doherty Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0265871.r006

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .