PONE-D-20-38732

Epidemiology of Mycobacterium tuberculosis and factors associated with strain clustering and lineage predominance around urban and peri-urban settings in Ethiopia.

PLOS ONE

Dear Dr. Adane,

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.

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We look forward to receiving your revised manuscript.

Kind regards,

Md Jamal Uddin

Academic Editor

PLOS ONE

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Please see attached pdf file to see the comments from editor.

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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: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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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

Reviewer #2: Yes

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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

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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 submitted by Taye et al. entitled "Epidemiology of Mycobacterium tuberculosis and factors associated with strain clustering and lineage predominance around urban and peri-urban settings in Ethiopia" is well written, technically sound and scientifically important to proper management of M. tuberculosis in Ethopia. But I have few minor comments, which should address before final acceptance of the manuscript.

1. At end of the title there is a punctuation (.) which have to delete

2. In the abstract authors time to time used abbreviation (PTB, TBLN, SITVIT2, SIT) which is difficult to understand by the general reader. Thus, an elaboration should include.

3. In the Methods of the abstract authors mentioned that they have collected the sample from four different regions in Ethiopia were recruited in the year 2016 and 2017. But why they have publishing this result after 3 years. Need an explanation for that because within this time period lineage of microorganism may change. In addition, it is prescribed to mention the exclusion and inclusion criteria of TB patients recruitment.

4. From the title its clear that authors wanted to find out epidemiology and factors associated with strain clustering and lineage predominance but in the introduction they failed to good use of literature review. They should clearly include what are the possible factors that can be associate and with brief introduction of underlying mechanism. For example, they found that L3 M. tuberculosis strains were more likely to be associated with TBLN and TB-HIV co-infection, but what is the possible mechanism of this association and co-infection. Why M. tuberculosis (bacteria) have association with HIV (virus).

5. For ethical consideration, need to add reference no. of the ethical clearance

6. In the result section, if (optional) the sequencing data of all strains in different geographic region of Ethiopia is available, a phylogenetic tree can represent the closeness of the strains and also better understanding of lineage.

6. In the discussion, authors need elaborate on what are the underlying factors that contributed to prevail more TB in the urban than rural area.

7. In the discussion (Line 275-276), author mentioned unique pattern considered to have resulted from reactivation of latent infection. But what about adaptation of those strains with environment and genetical changes (mutation/polymorphisms)?

Reviewer #2: It is my pleasure to review such a well written manuscript. The data were rigorously analyzed. It involved a great deal of work and dedication to complete this work and it is clearly visible. However, I would like to ask one question to the authors and that would be on sample size calculation. I could not find any clear description on how the investigators arrived at the sample size used in this analysis. The purposive selection of sites coupled with lack of information on sample size calculation makes it difficult to accept the results of such rigorous analysis and also puts the question of generalizability forward. Are these analyses generalizable to the whole community or the regions? We do not know and this information is vital to the analysis. I am sure the authors will be able to answer the question. If it is an exploratory study and the sample size calculation was not done rigorously. I would request the authors to include this information in the limitations section explicitly to make the readers aware of the fact. I congratulate the authors for their hard work and look forward to see their response. Thanks!

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Reviewer #1: Yes: Prof. Dr. Mohammad Jakir Hosen

Reviewer #2: Yes: SHAHRIAR AHMED

[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.

Attachments

Attachment

Submitted filename: PONE-D-20-38732.pdf_Comments by editor..pdf

PONE-D-20-38732R1

Epidemiology of Mycobacterium tuberculosis lineages and strain clustering within urban and peri-urban settings in Ethiopia

PLOS ONE

Dear Dr. Adane,

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.

As requested by academic editor, in online supplements, the author did not provide all necessary software codes, including detailed model fitting criteria, particularly for hierarchical (multi-level) logistic regression. In this case, the author must provide such information, and if such information is not provided, the manuscript will not be considered for further steps.

Please keep the conclusion and recommendations separate. First, provide possible recommendations including clinical implications based on your key findings, and then provide conclusions, which are your article's take-home message.

In the abstract, AOR and CI needs to elaborate first.

Please avoid using older references and instead try to use more recent and relevant ones.

Please submit your revised manuscript by 20 June 2021. 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: 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,

Md Jamal Uddin

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments (if provided):

Thank you for improving the manuscript as requested by reviewers and editor. Still several things need to improve.

As requested by academic editor, in online supplements, the author did not provide all necessary software codes, including detailed model fitting criteria, particularly for hierarchical (multi-level) logistic regression. In this case, the author must provide such information, and if such information is not provided, the manuscript will not be considered for further steps.

Please keep the conclusion and recommendations separate. First, provide possible recommendations including clinical implications based on your key findings, and then provide conclusions, which are your article's take-home message.

In the abstract, AOR and CI needs to elaborate first.

Please avoid using older references and instead try to use more recent and relevant ones.

[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

Reviewer #2: All comments have been addressed

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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: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

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 #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: Current form of manuscript is better than before, novel work, new findings, research and publication ethics strictly maintained, strongly recommended for acceptance.

Reviewer #2: Thank you for addressing the comments. I am satisfied with the responses and the revisions. This is an important piece of work and I feel proud to be associated with this. Best of luck!

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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: Prof. Dr. Mohammad Jakir Hosen

Reviewer #2: Yes: SHAHRIAR AHMED

[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.

Epidemiology of Mycobacterium tuberculosis lineages and strain clustering within urban and peri-urban settings in Ethiopia

PONE-D-20-38732R2

Dear Dr. Adane,

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.

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Kind regards,

Md Jamal Uddin

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: