https://orcid.org/0000-0002-6630-5742
Peer Review History
| Original SubmissionJune 21, 2021 |
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PONE-D-21-20289 Treatment outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective study. PLOS ONE Dear Dr. Rahimi, 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. Note that I am send this request for revision before sending the manuscript out for review in that there are things that must be addressed before a review can be done. The first and most important is that a definition of acute bacterial meningitis must be provided. Second, there is a description of CSF findings but only with a range given that includes WBCs as low as 5 and neutrophil counts as low as 0 or lymphocytes up to 100. What is the reason for believing that these were bacterial (or were not TB)? It may still be difficult to publish in view of the lack of microbiologic data but at least this will improve the chance. On another note, the sample size calculation appears to be irrelevant to the study being reported. Please submit your revised manuscript by Aug 27 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. 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, Rodney D Adam Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements.
https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and [Note: HTML markup is below. Please do not edit.] Reviewers' comments: [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-21-20289R1Treatment outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective study.PLOS ONE Dear Dr. Rahimi, 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 do a careful response to the reviews and include your point by point response to the items raised. Please submit your revised manuscript by Oct 24 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: 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, Rodney D Adam Academic Editor PLOS ONE Journal Requirements: 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. 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: Partly Reviewer #2: No ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: No ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #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: Abstract Line 25: Background – no need to say handicap as this is covered by the term morbidity Introduction - Reference number 3 is not useful to this paper as it is from 1993 and treatment and outcomes have improved much since then - Line 59: remove “three most common bacteria” - Lines 59 – 61: the information included from reference no. 4 is outdated and has been replaced with a newer Lancet study (GBD 2016 Meningitis Collaborators. Global, regional, and national burden of meningitis, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Neurol. 2018 Dec;17(12):1061-1082) - Consider including some data from the region (as local data is not available) Methodology - Lines 83 – 85: need to indicate which data was collected from the questionnaire and to whom were these questionnaires administered. Also, indicate which data was abstracted from patient files. - How was vaccination status assessed? - Line 95: define what treatment outcomes your study is looking at - Line 96: describe the factors that you will include in assessing this objective - Line 99: who made the diagnosis of ABM and how was it made i.e. primary clinician Or study investigator? If made by clinician please provide some detail on how the clinicians in the facility make this diagnosis? is made in this facility). If by study investigator, explain at what point and how this was done. - Lines 103 & 104: how were the diagnoses of TBM and encephalitis made and confirmed; Note that CSF findings from table 5 suggest that patients might have had TBM and viral meningitis/encephalitis - Line 105: why were patients with a history of parenteral broad-spectrum antibiotics use before admission excluded from the study? Also define which antibiotics were included in this category - Line 110: instead of sample size calculation, power calculation can be done and they can be used to demonstrate the minimum detectable difference with different sample sizes. - Line 128 – 133: The definition of ABM – not clear why this has been included – this should be covered under line 99 and has been addressed above. Results: - Consider providing the flow of study participants – i.e. how many patients were excluded by each criteria indicated in lines 103 - 106 - The results of variables with outliers should include median (IQR) e.g. age, duration, CSF cell count, differentials etc. - The overall presentation of results in tables 1 and 6 should be done in a logical and more meaningful manner. Consider reducing the number of tables and assign variables to the appropriate table i.e. o Table 1 : baseline demographic and social characteristics including vaccination data (can have both categorical and continuous data) o Table 2: clinical presentation o Table 3: lab findings including CSF findings o Table 4: treatment and outcome findings - There is no need to include the total row for each variable under all tables (a single N at the top should suffice) and also there is no need to include the total number in the write-up of the results, just the number and percent suffices e.g. no need for 138/339 (58.8%) for male gender. - De-clutter the tables – there are too many variables being presented and not all are necessary; consider dropping e.g. number in the same room, no. of <5 in the same room, age of starting breastfeeding, birth order, twins, mode of delivery etc - Dexamethasone therapy, Duration of admission (LOS), no of days of iv ceftriaxone and no. of days of iv ampicillin should be in the treatment & outcome table (not in table 1) - Also consider presenting antibiotic data as one variable i.e. duration of anti-meningitic antibiotics - Some variables presented in the results are not clear and should be defined either in the methodology section or as a footnote in the tables e.g. income categories, breastfeeding, bottle feeding; - The symptoms and signs variables should also be defined in terms of, at what point were they obtained i.e. at admission, or at any point in their stay - Age categories – consider having an additional category for above 12 years - Weight and height should be presented as wt for age and ht for age - Vaccination variables: Why have the HiB and PCV vaccinations been combined into a single variable? - Comorbidity variable: This variable needs to be defined and categorized as either acute or chronic; the acute conditions are most likely concurrent infections; need to reconsider how this data has been presented. Moreover, the acute concurrent infections should be in the clinical presentations table while the chronic underlying co-morbidities should be in the baseline characteristics table - Table with lab results should include units e.g. TLC, platelets, WBC in CSF - Results write-up should include the most relevant information from the tables and to the overall objective e.g. o Lines 156-158 should include something on next stiffness or headaches o Lines 162-163: should include information on CSF white cell count and differential results - Consider excluding the patients that were self-discharged from the treatment & outcome table as they could not be assessed for complications and outcomes - Table 7: o Current table 7 analysis is testing for factors associated with survival not mortality: redo this table and assess for mortality across all variables and should indicate the reference categories against each variable, as this has also not been done in a uniform manner o The values presented for the OR and p-value for living in over-crowded areas is incorrect, needs to be redone; also reconsider using this variable as 99.2% of participants were living in the crowded areas (>5). o This table does not need the total number in each row as well (total N at the top is good enough) o De-clutter this table similar to the suggestion for table 1 and 2 above o Consider not testing for complications as a factor associated with mortality. Most complications assessed in this study are likely assessed at discharge or at recovery. Also, death can be considered as a complication of ABM. o Assess acute and chronic co-morbidities separately Discussion - Case Fatality Rate – exclude the number who were self-discharged - The references given for the proportions of case fatality and complication from the various countries should also include the populations in which these studies were done as they are not all the same e.g. some are in infants, others in children under 5 and others across all pediatric age groups - Lines 240 – Should read: …will have incremental effects in reducing the global burden… - As mentioned above, living in crowded areas has been incorrectly included Conclusion: - Line 274: incorrect conclusion: your study does not prove the cost-effectiveness of vaccination - Lines 275-276: not sure how the assessment of outcomes and factors was hindered by unavailability of culture confirmed cases Reviewer #2: August 28, 2021 PLOS ONE Manuscript ID: PONE-D-21-20289R1 Title: Treatment outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective study Thank you for the opportunity to review this interesting manuscript. The authors conducted a prospective observational cohort study of 393 children <18 years of age with acute bacterial meningitis (ABM) at Mirwais Regional Hospital in Afghanistan from February 2020 through January 2021. The sociodemographic components reflected many patients coming from low-income families living in overcrowded households in rural areas and with incomplete childhood vaccination programmes. The in-hospital mortality was 17.6% and adjusted analyses suggested not having received vaccination for Hib or PCV, living in overcrowded houses, complications during admission, and lack of adjunctive dexamethasone as poor prognostic factors. The authors should be commended for performing an important study during very difficult and challenging circumstances. The scientific community definitely needs more data from developing countries. However, the methodology can still be improved in several ways which I believe would strengthen the impact and credibility of the data substantially. Major concerns: 1. Abstract. Conclusion. Although there is no doubt that Hib and PCV vaccinations prevent ABM, the provided data do not document a protective effect of Hib or PCV vaccinations on incidence of ABM in children in Afghanistan. This would require a comparison of risk of ABM among vaccinated and unvaccinated children. So, the conclusion that their findings prove the value does not seem to be justified in this dataset. However, they can/should still encourage more widespread implementation of the vaccinations, which makes sense. Please comment. 2. It is my overall impression from the provided methods and the discussion, that they examine in-hospital mortality as primary outcome, which should be clearly specified throughout the abstract and manuscript. Of note, this is not the same as ‘case-fatality rate’ which is also used once in the discussion. Please correct if I understand your study correctly. 3. ‘Comorbidities’ usually denote pre-existing conditions such as diabetes mellitus, arterial hypertension etc. Suggest changing to ‘predisposing’ or ‘concomitant’ infection throughout the manuscript. 4. The authors conducted a prospective observational cohort study. How were the data retrieved, personal interview or medical record review? 5. There are no missing values at all, which seems almost impossible. Especially since some patients were up to 15 years old and the parents may not remember for how long the child was breastfed, length of bottle-feeding etc (which is also likely to be irrelevant in adolescents). Another example is presence of headache which is 100% complete but many cases were babies who are very unlikely to be able to account for presence of headache or not. Were families and relatives contacted to complete all variables and what if they couldn’t be reached? Please comment. 6. Please specify how you categorized socio-economic status and income into e.g. low, middle, and high-income families? 7. Please describe who retrieved the study data or performed the interviews (single or multiple authors)? 8. Table 4. Is it symptoms and signs at admission or in total during course of illness? The proportion with seizures seems extremely high (95%). History of seizures or observed? Misclassification? Please comment? 9. Co-infections and complications, e.g. in Table 6. Some patients were likely to have had several co-infections (e.g. otitis media and pneumonia) or complications (seizures and cerebral palsy). Please account for this in the data provided. 10. Table 7. Please show the reference used for each crude (and adjusted) odds ratio, i.e. male sex in analyses of sex as prognostic factor etc. Minor suggestions: 1. Title. Suggest adding ‘cohort study’ to ‘a prospective study’. 2. Abstract. Suggest specifying ‘complications’. 3. Abstract. The results suggest ‘not administering Hib and PCV vaccines’ was a poor prognostic factor. Would it not be more accurate to write ‘no Hib or PCV vaccines’ since I assume that they refer to children receiving childhood vaccinations before falling ill? 4. Please clarify in the methods which diagnostic methods were available in your setting, e.g. microscopy of CSF but no culture etc. 5. Suggest to simply put in ‘Not applicable’ under sample size calculations. 6. Line 141-143 is a bit unclear to me. Please clarify. 7. Please define ‘coma’ in your study. 8. Suggest to also include differences in study populations and definitions of ABM as a reason for differences in mortality across studies. 9. Line 177 onwards you should delete “%” after the 95% confidence interval and the p-value does not add any information, e.g.: “crude odds ratio [COR] 0.1, 95% CI 0.0-0.1%, and p-value <0.001). 10. The crude odds ratio for coma for in-hospital mortality is currently 0.1 (95% CI 0.0-0.1), which is clearly reversed? 11. Please also check that you have the right reference level in adjusted odds ratios in Table 8, e.g. for adjunctive dexamethasone currently reads as an AOR of 6.2 for in-hospital mortality? 12. Line 234-237. The sentences are a bit unclear with different numbers? 13. Line 242. Overcrowded houses are likely a risk factor for contracting ABM, but your study examines the prognosis after falling ill with ABM. However, it may be a proxy for poverty and a general poor health and thereby an adverse prognostic factor? 14. Line 275. This should be moved to limitations instead of in the conclusions. Best of luck to the authors. ********** 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: Yes: Jacob Bodilsen [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-21-20289R2Treatment outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective study.PLOS ONE Dear Dr. Rahimi, 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. All the reviewer comments should be addressed in your revision. Please submit your revised manuscript by Dec 09 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If 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, Rodney D Adam 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) ********** 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 ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #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. 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: Overall ,the authors have done a great job in improving their manuscript. They must be commended for taking their time in addressing each and every single issue that had been raised and have done so with great detail. Nevertheless, there are still some issues that need to be addressed and these are listed below: 1. Line 1 - Consider removing "Treatment" from the title: the study's primary objective was to report on mortality and not treatment 2. Line 25 - drop "still". 2. Line 33 - drop "by". 3. Line 44 - drop "not giving". 4. Line 45 - drop "no" and combine HiB and PCV vaccine. (This is according to your analysis since you assumed both Hib and PCV were given but this is a significant flaw in your study - refer to comment 11 below) 5. Lines 49 - 50 - Conclusion should be based on your study findings while acknowledging limitaitons. Your study cannot conclude that "ministry of public health should increae coverage". Consider rewording this statement along the lines of "...increasing vaccine coverage can potentially reduce the risk of death from ABM in children in Afghanistan..." 6. Lines 62 - 68: move these sentences ("In 2016.." to "respectively[5]") to the next paragraph. 7. Line 81: Add "The" before "Afghanistan". 8. Line 85: Add "The" before "main". 9. Lines 92-93: Author needs to specify which variables were obtained from interviewing parents/guardians and which ones were obtained by abstraction from clinical records. 10. Lines 96-98: AS mentioned above, indicate which of the above variables were based on physician documentation in clinical records. 11. Lines 102-103: How did authors determine whether patients had received both Hib and PCV vaccines? Even though given at the same age, it is possible that some might have missed one or the other. Also, note according to lines 82-83 PCV-13 was introduced 4 years after Hib, therefore it is not correct to assume that because a child received a vaccine at 6, 10 or 14 weeks they received the Hib and PCV-13. Also, can you please explain how you accounted for those who did not complete vaccination series e.g. if they only received 1 or 2 doses. 12. Line 107: Add "were" before willing. 13. Lines 111-112: Drop these lines; not required in a manuscript 14. Line 114: Drop "treatment" 15. Line 117: Consider dropping "risk" 16. Line 118: Add "children with" before "ABM" and drop "patients". 17. Lines 120-124: Is the WHO criteria used by said pediatricians in their routine practice or were they instructed to apply these during study period? 18. Line 121: consider dropping "expert" 19. Line 125: Drop "Both male and female" 20. Lines 128-131: Need to explain who made this diagnosis. Was it the attending paediatrician? or was this determined by study investigators? Also what is the name of this score? Is this score used in routine practice or was this specifically used during the study period? 21. Lines 132-1314 Need to explain who made this diagnosis. Was it the attending paediatrician? or was this determined by study investigators? Also is the criteria used in routine practice or was this specifically used during the study period? 22. Line 138: It is not clear why macrolides were excluded from this study? Macrolides are unlikely to have an effect on CNS infections. 23. Lines 170-171: Move the sentence on adjunctive dexa therapy to the paragraph of table 4 i.e. Lines 197-201 24. Line 176 (Table 1): Move the row of age(mean) to the row with the age categories. Also present the median(IQR) for age as it is unlikely you have a normal distribution. 25. Line 185 (Table 2): Headache - in the methods section please explain why the N for headaches is less than the total. Explain that it was limited to those whom headache could be assessed. 26. Line 185 (Table 2): No. of concurrent infections - consider dropping this row. This does not add much value to the study and it is extremely unusual to have two or more true infections besides meningitis. 27. Line 186: Coma should be defined using clinical criteria i.e. based on GCS or AVPU scale 28. Line 194 (Table 3): What was the N for this table? 29. Line 197-199: Move the lines of concurrent infections to the write up of Table 1 (from lines 161-172) 30. Line 203 (Table 4): Exclude the self-discharged group entirely from this table. All the variables in this table are dependent on the patient being admitted and therefore cannot be included here. The exclusion of self-discharged group from this part of the analysis should be stated in the methodology. 31. Line 203 (Table 4): Drop the number of complications from this tables; not as important or of any value to the study. 32. Line 207: Drop "main" and add "significantly" before "associated". 33. Line 215 (Table 5): The reference groups indicated here are mostly not correct. E.g. check Age, PCV, Hib, Vomitting, irritability. 34. Line 215 (Table 5): The percentages presented for the survived and died groups for each row should be the proportions based on row totals and not column totals. E.g. Age <5 survived 129 (82.7%) died (17.3%), Age >=5 survived (74.5%) died (25.5%). 35. Line 226 (Table 6): There is no need to present the numbers of patients who survived or died in each row. It might be better to include a column of the Crude OR in this table, as this allows to compare the crude and adjusted at the same instance. 36. Line 238-239: Consider dropping the Canada study, as the age of the study population is not the same 37. Line 240-243: Consider dropping the UK & Ireland, France, and Taiwan study, as the as the age of the study population is not the same. 38. Line 247: Consider dropping the Saudi Arabia study as the age is also not the same 39. Line 252-254: Is there a reference to this statement? 40. Line 270: change from "is declined" to "has declined" 41. Line 282: drop "is" before "may" ********** 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: Adeel A Shah [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-21-20289R3Treatment outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective study.PLOS ONE Dear Dr. Rahimi, 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 major issues now are related to grammar in addition to a few other items that need attention. I would strongly urge you to have a native English speaker review the manuscript English usage in order to facilitate the publication of this manuscript. Please submit your revised manuscript by Jan 20 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:
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, Rodney D Adam 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) ********** 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 ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ********** 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. 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 have done a good job in addressing the previous comments and the quality of the manuscript is greatly improved. There are some minor issues that have been noted at this time and these need to be addressed so as to improve the readability and coherence of the manuscript: 1. Lines 39-42: rewrite this sentence - "Concurrent infections..."; has logical and grammatical errors 2. Lines 47-48: consider removing the sentence "The coverage of PCV and Hib...", can be incorporated with the sentence in line 49 - "Increasing vaccine coverage..." 3. Line 56: change from "the case fatality" to "a case fatality" 4. Line 57: rewrite to "7% and a risk of neurological..." 5. Line 72: use number formatting for the figures presented i.e. 63,001; 16,335; 7,302 and 6,907 6. Lines 83-84: rewrite the sentence from "Unfortunately, there is currently..." to "Currently, there is no published data on the outcome of ABM in children in Afghanistan and the factors associated with poor outcomes." 7. Line 85: remove the word "treatment" and also reword "outcome of ABM patients.." to "outcome of ABM in children..." 8. Line 91: should read "during a 12-month period" 9. Line 109: Change to Study design and participants, then move the study design and period to be part of this section 10. Lines 92-108: this should be under a section called "Study procedures" and should come after the Study design and participants section 11. Lines 147-148: remove this section altogether; no added value of having this presented in the manuscript. 12. Line 173: Median of 4.8 seems incorrect i.e. median is usually a whole number or half of two whole numbers e.g. 4.5 if the median lies between 4 and 5; please check again how you calculated this, as 4.8 would be more of mean than median. 12. Line 173: 207 (52.7%) children under age 5, this is discrepant with the data presented in table 1 - please check 13. Line 182: Table 1: - median (IQR) - present the IQR as a range i.e. the 25th and 75th centile figures rather than the actual value of the range e.g. for age it would be median (IQR) - 4.5(2.5-7); (please do this wherever IQR is presented i.e. Table 3) - consider combining HiB and PCV as one category - since you mentioned in your previous response that you confirmed everyone who received HiB also received PCV. (also do this for all the other tables where you present Hib and PCV data i.e. Tables 5 and 6) 14. Lines 184 - 185: some of the footnotes not relevant to this table e.g. cm, CSF, mg/dl, kg 15. Line 200: you refer to mean +/- SD while in the table it is median (IQR); please confirm which it is and correct accordingly 16. Line 236: Table 6 - please re-look at the adjusted OR for purple rash, this seems to be an error which is most likely due to coding; this kind of dramatic reversal cannot be explained by the other variables in the model. 17. Line 244: drop "living in over-crowded houses, presence of complications" as this was not assessed in the univariate analysis. 18. Line 247: "change from in-hospital mortality rate" to "in-hospital case fatality" and also correct spelling of "Compared" 19. Line 255: consider dropping "huge" 20. Lines 259-261: consider dropping this entire sentence: "The in-hospital mortality...better treatment". This is because you have dealt with the self-discharge group in the outcome analysis and the 21.5% fatality was of the group that did not include the self-discharged group. 21. Line 305: change from "mortality rate" to "case fatality" 22. Line 307: drop "living in over-crowded houses, presence of complications" as this was not assessed in the univariate analysis. 23. Line 313: UNICEF should be in all caps. ********** 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: Adeel Ahmad Shah [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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PONE-D-21-20289R4Outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective observational cohort study.PLOS ONE Dear Dr. Rahimi, 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. I have gone through the reviewer comments and responses and have a number of issues that must still be addressed. The authors must remember that there is no copy editor so the manuscript must be ready to go when approved. The major substantive issue remaining is the CSF white count. What lab method was used? If it was the hemocytometer, mononuclear cells are lumped together (rather than a specific reference to lymphocytes). Thus, the percent of neutrophils and mononuclears should add up to 100%. That does not appear to be the case for the data shown in Table 3. It is also highly unusual for acute bacterial meningitis to have a mononuclear predominance as the data in Table 3 suggest; uncommon enough to require re-evaluation of the presumptive diagnosis of bacterial meningitis. The follow up is not available for the 72 who “discharged themselves” from the hospital. I assume that means that the parents removed them against medical advice. Is anything known about their outcome? Especially, how many were removed because the parents thought they were dying? Line 30: “of” after total is missing. Also, median has been used instead of mean Line 58: a citation is needed at the end of the first sentence Line 156: the 0C did not come through correctly on my version of the pdf Line 158: eliminate the space before the comma Please submit your revised manuscript by Mar 19 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:
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, Rodney D Adam 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: [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 5 |
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PONE-D-21-20289R5Outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective observational cohort study.PLOS ONE Dear Dr. Rahimi, 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. Thank you for your revision. There are still two issues that should be covered before publication:1. The fact that 72 of the children were critical ill when brought home by their parents means that the mortality rate may have been much higher than the stated 21.5%. If all of these died, the mortality would have actually been 35.9%. It would be appropriate to raise this possibility at the beginning of the discussion where the mortality rate is discussed.2. I am surprised by the high percent of CSFs with a mononuclear predominance (25%). Is it possible that some of these were actually tuberculous meningitis? That possibility should also be raised in the discussion. Please submit your revised manuscript by Apr 14 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:
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, Rodney D Adam 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: [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 6 |
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Outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective observational cohort study. PONE-D-21-20289R6 Dear Dr. Rahimi, 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, Rodney D Adam Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-21-20289R6 Outcome of acute bacterial meningitis among children in Kandahar, Afghanistan: A prospective observational cohort study. Dear Dr. Rahimi: 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. Rodney D Adam Academic Editor PLOS ONE |
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