PGPH-D-21-00728

Pooling sputum for Xpert MTB/RIF and Xpert Ultra testing during the Covid-19 pandemic in Lao People's Democratic Republic

PLOS Global Public Health

Dear Dr. Iem,

Thank you for submitting your manuscript to PLOS Global Public Health. After careful consideration, we feel that it has merit but does not fully meet PLOS Global Public Health’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 by Dec 17 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 globalpubhealth@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pgph/ 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 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'.

Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

We look forward to receiving your revised manuscript.

Kind regards,

Miguel Angel Garcia-Bereguiain, PhD

Academic Editor

PLOS Global Public Health

Journal Requirements:

1. Thank you for stating "Informed consent and ethical waivers were obtained from the National TB Control Center of Lao PDR and the Liverpool School of Tropical Medicine Research Ethics Committee, UK (Ethical waiver 20-037)." Please clarify whether these ethics committees specifically approved your research, or whether they waived the need for ethics approval and the reason why approval was waived. 

In addition, please provide additional details regarding participant consent. In your Methods, please ensure that you have specified:

 - whether consent was obtained from participants

 - whether consent was informed 

 - what type of consent you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). 

 - if your study included minors, state whether you obtained consent from parents or guardians. 

 - if the need for consent was waived by the ethics committee, please include this information.

2. We do not publish any copyright or trademark symbols that usually accompany proprietary names, eg (R), (C), or TM  (e.g. next to drug or reagent names). Therefore please remove all instances of trademark/copyright symbols throughout the text, including Xpert® on reference 29.

3. Please amend your detailed Financial Disclosure statement. This is published with the article, therefore should be completed in full sentences and contain the exact wording you wish to be published.

i). State the initials, alongside each funding source, of each author to receive each grant.

ii). State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”

4. In the online submission form, you indicated that "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable requests for guideline development and systematic reviews."

All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information.

This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons by return email and your exemption request will be escalated to the editor for approval. Your exemption request will be handled independently and will not hold up the peer review process, but will need to be resolved should your manuscript be accepted for publication. One of the Editorial team will then be in touch if there are any issues.

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):

Dear Dr Iem,

After reading your manuscript and the comments made by the 3 reviewers, I believe that your work is potentially suitable for publication. However, some concerns and comments have been made by some of the reviewers. Please, address those comments and improve the manuscript accordingly and submit the revise version of the manuscript and a letter addressing a point by point answers to reviewers.

Sincerely

Miguel Angel Garcia Bereguiain, PhD.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does this manuscript meet PLOS Global Public Health’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS Global Public Health 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

Reviewer #3: 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 paper is very interesting and the researchers have clearly described their methods and statistical analysis. They have written the results in a very descriptive way and provided sound arguments on the discussion section.

Reviewer #2: Manuscript complies PLOS Global Public Health publication criteria and statistical analysis are appropiate for the type of study that was performed. Proper use of English that communicates easily the findings in the study.

Reviewer #3: This paper is well-written overall. The topic is very applicable in the current pandemic situation, and the conclusions are strongly supported by the data presented. I have only minor suggestions to improve the comprehension and impact.

1. General comment throughout the text: report the n/N, followed by the percent. Example, in line 41: 70/70 (100% sensitivity).

2. Paragraph starting on line 57: include more background on Xpert, Ultra, and RIF-resistance. Note that smear microscopy does not include detection of drug resistance.

3. Paragraph starting on line 67: include the prevalence of drug resistance in Lao.

4. Explain earlier in the text how if any pool tested positive, the four individual samples would need to be re-tested. This is only mentioned in the Results (line 213).

5. Add more detail to Figure 1, such as the sample volumes going to pooled vs individual testing.

6. In Table 1, there are differences in demographic and Xpert results between the two groups (2020 and 2021 surveys). Have you tested whether these are significant? Was there any difference in the populations tested between years? Xpert Ultra is more sensitive, which would explain some of the differences. But would not explain why the proportion of male/female MTB detected would switch?

7. Please report n/N (%) consistently throughout the Results section.

8. Add a legend for Figure 2, including labelling the colors used for different groups.

9. The findings for how many additional patients could be tested with the pooling method are very strong, and suggest emphasizing this point more. Could also state it as 620-715 (60-70%) additional TB patients could be tested with the same cost of resources. And could even take it one step further and apply that to closing the country-wide testing gap if the data is available.

10. Now that Xpert Ultra is available, will the standard Xpert MTB/RIF cartridges still be used in Lao? May be good to mention in the Discussion.

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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.

Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public.

For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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[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.

PGPH-D-21-00728R1

Pooling sputum for Xpert MTB/RIF and Xpert Ultra testing during the Covid-19 pandemic in Lao People's Democratic Republic

PLOS Global Public Health

Dear Dr Iem,

The manuscript has been substantially improved following reviewers and editorial comments. However, I realized than some minor comments made by reviewer 1 were not addressed on your response letter.

In my response letter, those comments did not show up as the were uploaded as a word file. Alhtough I believe you could access this file in the submission system, please find below those comments.

There are very minor comments so simply addressed them prior to final acceptance of your manuscript.

And sorry for this inconvenience.

Please submit your revised manuscript by Jan 24 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 globalpubhealth@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pgph/ 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 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'.

Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

We look forward to receiving your revised manuscript.

Kind regards,

Miguel Angel Garcia-Bereguiain, PhD

Academic Editor

PLOS Global Public Health

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):

Dear Dr Iem,

The manuscript has been substantially improved following reviewers and editorial comments. However, I realized than some minor comments made by reviewer 1 were not addressed on your response letter. On my response letter, those comments did not show up as the were uploaded as a word file. Alhtough I believe you could access this file in the submission system, please find below those comments. There are very minor comments so simply addressed them prior to final acceptance of your manuscript. And sorry for this inconvinience.

Reviewer’s comments

Line 92- please indicate the individuals as adults (as the study was done in adults)

Line 139-why did you need ethical waiver because the usual way is to ask for informed consent for each individual during enrolment to the study?

Line 145-46-the sentence mentioning that males are likely to be xpert positive than females, does it have any explanation? and p<0.1 . I don’t think it is worth to mention unless there is some possible explanation or at least statistically significant( p value usually used is <0.05 to say statistically significant).

Line 157- Table 1 -please indicate the lowest age group in the range.

268-270 The sentence “which may be attributed to the increased manipulation of samples resulting in an increased risk of contamination and labelling errors and these varying results may reflect the competency and dedicated time available of laboratory staff for sample processing.”

How did you reach to this argument? Was it stated by the studies as their limitation?

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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.

Pooling sputum for Xpert MTB/RIF and Xpert Ultra testing during the Covid-19 pandemic in Lao People's Democratic Republic

PGPH-D-21-00728R2

Dear Dr. Iem,

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 https://www.editorialmanager.com/pgph/ 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 globalpubhealth@plos.org.

Kind regards,

Miguel Angel Garcia-Bereguiain, PhD

Academic Editor

PLOS Global Public Health