Prevalence of bacteriologically confirmed pulmonary tuberculosis and associated risk factors: A community survey in Thirvallur District, south India

Chandra Kumar Dolla; Bhaskaran Dhanaraj; Padmapriyadarsini Chandrasekaran; Sriram Selvaraj; Pradeep Aravindan Menon; Kannan Thiruvengadam; Rajendran Krishnan; Rajesh Mondal; Muniyandi Malaisamy; Srinivasa B. Marinaik; Lakshmi Murali; Srikanth Prasad Tripathy

doi:10.1371/journal.pone.0247245

Peer Review History

Original SubmissionJune 5, 2020
6 Aug 2020 Decision Letter - Frederick Quinn, Editor PONE-D-20-16942 Prevalence of bacteriologically confirmed pulmonary tuberculosis and associated risk factors: A community survey in Thirvallur District, south India PLOS ONE Dear Dr. Kumar, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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Currently, your Funding Statement reads as follows: [The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.] 5. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: No ****** 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: Review of ms # PONE-D-20-16942 submitted to PLOS ONE by Kumar et. Al. Tuberculosis remains one of the major respiratory diseases in southeast asia including the Indian subcontinent and a variety of environmental factors and co-morbidities determine not only the pathology of TB but also success of TB treatment. In this manuscript, Kumar et. al provide a summary of active TB surveillance done in the south Indian Thiruvallur district. Community based surveillance targeting ~69,000 individuals >15y of age included screening for pulmonary TB using sputum samples and chest X-rays. The authors also collected demographical information as well as smoking, alcohol consumption and established correlation with a positive TB outcome. Their data shows a decreasing trend of TB prevalence in this sample set supporting the efficacy of the national strategic plan for TB containment. The study conclusions support previous data on TB incidence and correlation with comorbidities and behavioural traits (tobacco and /or alcohol consumption). Thus, while not novel, the data show the efficacy of the TB NSP and underscore the need for continuing TB surveillance and research. The major critique of the manuscript is there are a lot of typographical errors in the manuscript and these need to be corrected to improve readership. ****** 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 [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.0247245.r001
Revision 1
5 Oct 2020 Author Response Reviewers comments 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. Tuberculosis remains one of the major respiratory diseases in south East Asia including the Indian subcontinent and a variety of environmental factors and co-morbidities determine not only the pathology of TB but also success of TB treatment. In this manuscript, Kumar et. al provide a summary of active TB surveillance done in the south Indian Thiruvallur district. Community based surveillance targeting ~69,000 individuals >15y of age included screening for pulmonary TB using sputum samples and chest X-rays. The authors also collected demographical information as well as smoking, alcohol consumption and established correlation with a positive TB outcome. Their data shows a decreasing trend of TB prevalence in this sample set supporting the efficacy of the national strategic plan for TB containment. The study conclusions support previous data on TB incidence and correlation with comorbidities and behavioural traits (tobacco and /or alcohol consumption). Thus, while not novel, the data show the efficacy of the TB NSP and underscore the need for continuing TB surveillance and research. The major critique of the manuscript is there are a lot of typographical errors in the manuscript and these need to be corrected to improve readership. Reply to Reviewers comments Thank you for the appreciation on our work and comments. We are submitting the revised version of the manuscript entitled “Prevalence of bacteriologically confirmed pulmonary tuberculosis and associated risk factors: A community survey in Thirvallur District, south India”. As suggested by reviewer we carefully checked and English corrections made in the manuscript with track changes. I hope this revised version of the manuscript is most suitable for publication. I am very happy to provide any more details and further clarifications. https://doi.org/10.1371/journal.pone.0247245.r002
4 Jan 2021 Decision Letter - Frederick Quinn, Editor PONE-D-20-16942R1 Prevalence of bacteriologically confirmed pulmonary tuberculosis and associated risk factors: A community survey in Thirvallur District, south India PLOS ONE Dear Dr. Kumar, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript. If you will need significantly more time 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Frederick Quinn Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #2: (No Response) ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2: Partly ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #2: In this manuscript, Dolla et al. summarized an epidemiology study on active pulmonary tuberculosis (PTB) at Tiruvallure district via cluster sampling method. The authors defined PTB according to positive smear test or bacterial culture test. Out of 62494 screened population, the authors determined a PTB prevalence rate as 307 per million population. The authors further reported positive correlation between PTB with decreased BMI, smoking, diabetes and elder population. The study overall is convincing, however the authors need to address the following issues: (1) The BCG vaccination does not have protection judged by a p value of 0.792. Can the authors comment on the possible reasons? (2) The authors applied p value test to justify the statistical significance between 2 groups. However, the authors need to specify the mathematical method and type-II error for statistical power design, which they leveraged to justify their statistics with a smaller sample size compared to the original one. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0247245.r003
Revision 2
15 Jan 2021 Author Response Thank you for this valid question. We would like to clarify that it was documented that the protective efficacy of BCG was effective for children protecting from the severe forms of TB. Reference: Subramani R, Datta M, Swaminathan S. Does effect of BCG vaccine decrease with time since vaccination and increase tuberculin skin test reaction? Indian J Tuberc 2015; 62(4): 226-9. The authors applied p value test to justify the statistical significance between 2 groups. However, the authors need to specify the mathematical method and type-II error for statistical power design, which they leveraged to justify their statistics with a smaller sample size compared to the original one. We used a univariate and multivariate logistic regression model to look for any association between TB and risk factors such as age, gender, BMI, diabetes, hypertension, history of TB tobacco smoking, alcohol consumption and cooking fuel used in the household. We made use of the algorithm suggested by Van Wijngaarden-Dekker-Brent algorithm (Brent, 1973) to test the statistical power of the regression models which are more than 80% as required to ensure the statistical significance. Attachments Attachment Submitted filename: Reply to reviewers comments 2.docx https://doi.org/10.1371/journal.pone.0247245.r004
4 Feb 2021 Decision Letter - Frederick Quinn, Editor Prevalence of bacteriologically confirmed pulmonary tuberculosis and associated risk factors: A community survey in Thirvallur District, south India PONE-D-20-16942R2 Dear Dr. Kumar, 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, Frederick Quinn Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0247245.r005
Formally Accepted
24 Sep 2021 Acceptance Letter - Frederick Quinn, Editor PONE-D-20-16942R2 Prevalence of bacteriologically confirmed pulmonary tuberculosis and associated risk factors: A community survey in Thirvallur District, south India Dear Dr. Dolla: 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. Frederick Quinn Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0247245.r006

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