PONE-D-21-10883

Intestinal parasitic infections and associated factors among street dwellers and prison inmates: A systematic review and meta-analysis

PLOS ONE

Dear Dr. Feleke,

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.

More details needed on methodologies and statistics. If the steps of meta-analysis have not been followed, there is need to rework on the data following appropriate methods suggested by the reviewer.

Please submit your revised manuscript by Aug 05 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: 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,

Iddya Karunasagar

Academic Editor

PLOS ONE

Additional Editor Comments:

The reviewers have suggested very important points regarding methodology, which need further clarification and explanation. Please revise considering the reviewer comments.

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Please confirm that you have included all items recommended in the PRISMA checklist including:

-    the full electronic search strategy used to identify studies with all search terms and limits for at least one database.

-    an explanation for why the search inclusion dates began in 2000

-      the date that the search was last conducted

-    a Supplemental file of the results of the individual components of the quality assessment, not just the overall score, for each study included.

-    See https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1000100#pmed-1000100-t003 for guidance on reporting.

Thank you.

3. For more information on PLOS ONE's expectations for statistical reporting, please see https://journals.plos.org/plosone/s/submission-guidelines.#loc-statistical-reporting. Please update your Methods and Results sections accordingly.

4. Thank you for stating the following in the Acknowledgments Section of your manuscript:

"We express our gratefulness to Addis Ababa University for all necessary supports."

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

"The authors received no specific funding for this work.2"

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

6. We note that this manuscript is a systematic review or meta-analysis; our author guidelines therefore require that you use PRISMA guidance to help improve reporting quality of this type of study. Please upload copies of the completed PRISMA checklist as Supporting Information with a file name “PRISMA checklist”.

[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: Partly

Reviewer #2: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

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: No

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 combination of prison inmate and street dwellers lacks rationale as they live in different environment and thus have different risk to parasitic infection. The inclusion of only a handful of papers is not fully justified and does not show the important information and existence of novel information. The finding of nail fingers as risk factor need more clarification as well as other potential factors.

Reviewer #2: I will focus on methods and reporting.

Major

1) Publication bias tests and plots only relevant if you have >10 studies otherwise underpowered to detect much and tend to lead to conclusions that are not justified http://www.ncbi.nlm.nih.gov/pubmed/11106885. If you don’t have enough studies to assess you should discuss this as a major limitation. Even with 10 or 20 studies it is very difficult to visually assess. If you have 20 or more studies it is a considerable strength. Rephrase the methods section to reflect that and also note that publication bias is only relevant in the context of an intervention (i.e. when you look at factors) and not prevalence.

2) The methodological description on the examination of factors is poor and does not provide enough detail (or clearly list the factors). what weighting is used in those models and what models (inverse variance DerSimoniam-Laird, Mantel-Haenszel etc).

3) Meta-analyses of proportions (prevalence) are a bit more complicated since transformations are needed to account for the 0 and 100% limits. Step 1: transformation; step 2: meta-analysis method using standard approach (i.e. inverse variance DerSimonian-Laird); step 3: back-transformation to percentages and plotting. One approach is logit transformation, which is explained in a different context here: http://www.bmj.com/content/352/bmj.i1114. However, a double arcsine transformation is the norm (http://jech.bmj.com/content/early/2013/08/20/jech-2013-203104). The method is implemented in the Stata module metaan http://www.stata-journal.com/article.html?article=st0201. Alternatively you can manually perform using the command you used (I suspect metan, although not referenced). Also see metaprop.

4) Report the confidence intervals for I^2 (calculated using heterogi or metaan in Stata) as argued in http://www.ncbi.nlm.nih.gov/pubmed/17974687. A simple formula exists in the seminal 2002 Higgins paper that proposed I^2.

5) Regarding heterogeneity estimates, all these estimates are very likely off, especially for small meta-analyses, and you should be wary about homogeneity assumptions http://www.ncbi.nlm.nih.gov/pubmed/23922860. So I am not surprised that in the smaller meta-analyses you fail to identify heterogeneity, which very likely exists. Ideally, you would want to check that the findings stand even if you assume high levels of undetected heterogeneity (implemented in Stata metaan) but if not at the very least you need to discuss as a limitation. Personally, I feel that detecting heterogeneity is a good thing since at least it can be incorporated in the model, and I’d pick that any time over a false homogeneity assumption.

Minor

1) Abstract: NOS needs to be defined.

2) Stata not STATA (not an acronym).

3) Cochrane Q is a test

4) Some language corrections are needed (minor).

5) Abstract: the methods need to be described, model used (random effects), what predictors examined, how was heterogeneity assessed etc.

6) don't report results in your methods section. Say, for example, "we decided a priori that if large heterogeneity was observed we would conduct sensitivity analyses".

7) "Furthermore, sensitivity analysis was done to observe the level of heterogeneity" not clear what that means.

8) Year may be worth considering in bias assessment, especially if you don't have enough studies for a formal test: http://www.ncbi.nlm.nih.gov/pubmed/25988604. With newer studies we would be more confident.

9) Reference the commands you used in Stata.

10) How was the random-effect model implemented, i.e. how was heterogeneity estimated? There are numerous ways to do so. Did they use the standard DerSimonian-Laird method? If so, please state so. Also there are better performing methods, for example please see https://www.ncbi.nlm.nih.gov/pubmed/28815652 (or http://www.ncbi.nlm.nih.gov/pubmed/23922860) and the metaan command in Stata where these are implemented (https://www.stata-journal.com/article.html?article=st0201).

11) Did you have to use any continuity corrections or is the outcome not that rare? better to be clear either way.

12) Cochran Q (i.e. chi-square) is notoriously underpowered to detect heterogeneity, especially for small meta-analyses http://www.ncbi.nlm.nih.gov/pubmed/9595615. I would not use

**********

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.]

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.

Intestinal parasitic infections and associated factors among street dwellers and prison inmates: A systematic review and meta-analysis

PONE-D-21-10883R1

Dear Dr. Feleke,

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,

Iddya Karunasagar

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

All reviewer comments have been addressed.

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: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

**********

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: I am not ecstatic about the changes made to the paper in response to my previous comments and I don't really understand why the authors struggle to report confidence intervals for I^2 when a formula exists (And I pointed it out to them) and there are user-written commands in Stata that compute it. The fact most studies do not report it does not mean that is good practice.

**********

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