Intrinsic and extrinsic factors associated with sputum characteristics of presumed tuberculosis patients

Fred Orina; Moses Mwangi; Hellen Meme; Benson Kitole; Evans Amukoye

doi:10.1371/journal.pone.0227107

Peer Review History

Original SubmissionSeptember 10, 2019
8 Oct 2019 Decision Letter - HASNAIN SEYED EHTESHAM, Editor PONE-D-19-25295 Intrinsic and extrinsic factors associated with sputum characteristics of presumed tuberculosis patients PLOS ONE Dear Dr. Orina, 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. We would appreciate receiving your revised manuscript by Nov 22 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. 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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: The manuscript does not fulfill the merit of the journal as it lacks novelty and provide any significant finding that is already not published. Moreover several lacunae were identified regarding studying sputum characteristics, sample consistency analysis, mentioning references at appropriate places, type of culture method used, whether Direct Vs Indirect AFB staining process used, which ICT tests was used. Due to major limitations in the manuscript it is found unsuitable for consideration. Reviewer #2: Manuscript Number: PONE-D-19-25295 Manuscript Title: Intrinsic and extrinsic factors associated with sputum characteristics of presumed tuberculosis patients Review: 1. There is discrepancy in explaining the extrinsic & intrinsic factors in the Statistical analysis section. The authors defined intrinsic factors as those related to the subject and extrinsic factors as those related to the environment (Outside the body of the subjects). Then why did the authors classify 'clinical findings' as extrinsic factors? b) There is error in Table 5, " If yes, the medication (n=70)": the responses do not add up to 70. c) The study deduces that "other means of transport" and "50-75% knowledge of TB transmission" among other factors responsible for good sputum production, but does not discuss the probable reasons due to which these factors effect the sputum production. d) The paper is well written. However, the significance and outcome of the study is not clear and it does not provide any new information and knowledge. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0227107.r001
Revision 1
2 Dec 2019 Author Response Response to reviewers 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: Partly Reviewer #2: No Response: Thank you for this observation we have re-written the conclusion section to match the data presented 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No The statistical analysis was done from univariate analysis bivariate analysis and multivariate analysis. We think these can draw deduction on the factors that affect sputum production. We are open for any more suggestions and further discussions 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 We wish to indicate that we have updated the data on supporting information. 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 Response: Thank you for the observation 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The manuscript does not fulfill the merit of the journal as it lacks novelty and provide any significant finding that is already not published. Response: We wish to indicate that A few studies have been involved in elucidating the quality of sputum from tuberculosis patients through macroscopic and microscopic characterization while others have correlated the sputum quality and detection of tuberculosis using conventional methods or highly advanced molecular techniques. However, NO studies to the best of our knowledge have linked sputum quality and patient related factors or factors that predisposes individual to tuberculosis. We believe the information generated is new. Moreover several lacunae were identified regarding studying sputum characteristics, sample consistency analysis, mentioning references at appropriate places, type of culture method used, whether Direct Vs Indirect AFB staining process used, which ICT tests was used. Response: Than you for the review. We have update the methodology section and included the missing sections including the culture method used and quality control sections. We however wish to clarify that we did not use direct or indirect AFB methods in this study since we used liquid culture for detection of cases. We believe culture is more sensitive that AFB staining methods in detection of TB cases. We have also updated the methods section and indicate the use of capilia as the ICT used Reviewer #2: Manuscript Number: PONE-D-19-25295 Manuscript Title: Intrinsic and extrinsic factors associated with sputum characteristics of presumed tuberculosis patients Review: 1. There is discrepancy in explaining the extrinsic & intrinsic factors in the Statistical analysis section. The authors defined intrinsic factors as those related to the subject and extrinsic factors as those related to the environment (Outside the body of the subjects). Then why did the authors classify 'clinical findings' as extrinsic factors? Response: Thank you for this observation we have revised and appropriately classified clinical findings as part of intrinsic factors. b) There is error in Table 5, " If yes, the medication (n=70)": the responses do not add up to 70. Response: Thank you for this observation, we have revised table 5 and responses add up. c) The study deduces that "other means of transport" and "50-75% knowledge of TB transmission" among other factors responsible for good sputum production, but does not discuss the probable reasons due to which these factors effect the sputum production. Response: We have reviewed the discussion section and deduced the probable reasons d) The paper is well written. However, the significance and outcome of the study is not clear and it does not provide any new information and knowledge. Thank you for the observation. We have reviewed our conclusions to show significance of the outcome. we believe to the best of our knowledge that we have linked sputum quality and patient related factors or factors that predisposes individual to tuberculosis. We believe the information generated is new. https://doi.org/10.1371/journal.pone.0227107.r002
13 Dec 2019 Decision Letter - HASNAIN SEYED EHTESHAM, Editor Intrinsic and extrinsic factors associated with sputum characteristics of presumed tuberculosis patients PONE-D-19-25295R1 Dear Dr. Orina, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, HASNAIN SEYED EHTESHAM Academic Editor PLOS ONE Additional Editor Comments (optional): I have gone through the Author’s response to reviewers comment and the revised manuscript. The Authors have revised the manuscript and appropriately classified clinical findings and these have now been included. Table 5 has been revised completely. In summary, the revised version represents a novel study linking sputum quality and patient related factors to tuberculosis which have not been described so far. I recommend the revised version of this manuscript for publication. Reviewers' comments: https://doi.org/10.1371/journal.pone.0227107.r003
Formally Accepted
17 Dec 2019 Acceptance Letter - HASNAIN SEYED EHTESHAM, Editor PONE-D-19-25295R1 Intrinsic and extrinsic factors associated with sputum characteristics of presumed tuberculosis patients Dear Dr. Orina: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Prof HASNAIN SEYED EHTESHAM Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0227107.r004

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