Comparison of tests done, and tuberculosis cases detected by Xpert® MTB/RIF and Xpert® MTB/RIF-Ultra in Uganda

Michael Kakinda; Didas Tugumisirize; Abdunoor Nyombi; Marvin Mugisha; Stavia Turyahabwe; Simon Walusimbi; Joseph K. B. Matovu

doi:10.1371/journal.pone.0275960

Peer Review History

Original SubmissionNovember 2, 2020
14 Jan 2021 Decision Letter - Shampa Anupurba, Editor PONE-D-20-34522 Comparison of tests done and Tuberculosis cases detected by Xpert® MTB/RIF and Xpert® MTB/RIF-Ultra in Uganda PLOS ONE Dear Dr. Kakinda, 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 by Feb 28 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 We look forward to receiving your revised manuscript. Kind regards, Shampa Anupurba, MD Academic Editor PLOS ONE Additional Editor Comments: In this manuscript Xpert MTB/RIF has been compared with Xpert MTB/RIF Ultra by including the data from 112 sites during two different time periods.Although it has been concluded that there was no significant difference in test performance and overall detection of DS-TB and RR-TB, the study could have highlighted the difference between smear positive and negative samples. Secondly,it would have been interesting to note whether there were more cases from any particular extra pulmonary sample.There have been studies which have shown that sensitivity and specificity varied according to the type of sample.Thirdly, the performance of Xpert MTB/RIF ultra in paediatric age group could have been shown. Minor corrections Line 75- The sentence could be completed after 'Jan2012' Line 110- Rifampicin resistant TB should be RR-TB 4th and 5th lines under 'Comparison between Xpert® MTB/RIF and Xpert® MTB/RIF Ultra'- MDR-TB to be replaced by RR-TB. Also, in Table 2, MDR-TB to be replaced by RR-TB. 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. 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Furthermore, information should be provided about the issue of “trace positive samples” by Ultra. In addition to detection of the single-copy rpoB gene for the simultaneous diagnosis of TB and rifampicin resistance, Ultra includes two new and more sensitive PCR assays that target the multicopy IS6110 and IS1081 genes to improve M.tuberculosis detection in paucibacillary samples. Information about RIF-R is not available in IS6110 or IS1081 positive and rpoB negative samples are categorised as “trace” by Ultra. Thus MDR-TB cases can be missed among the “trace” positive samples. For these samples, information about drug resistance can only be provided by culture. Therefore, when comparing the two methods, it is important to have this information. Minor comments: Mycobacterium Tuberculosis should be written as Mycobacterium tuberculosis The sentence in the last paragraph of discussion should be corrected “This study was not with limitations….” ****** 6. 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Revision 1
16 Jul 2022 Author Response POINT-BY-POINT RESPONSE TO THE EDITOR’S AND THE REVIEWERS’ COMMENTS Response to the Editor’s comments In this manuscript Xpert MTB/RIF has been compared with Xpert MTB/RIF Ultra by including the data from 112 sites during two different periods. Although it has been concluded that there was no significant difference in test performance and overall detection of DS-TB and RR-TB, the study could have highlighted the difference between smear positive and negative samples. Secondly, it would have been interesting to note whether there were more cases from any extrapulmonary sample. There have been studies that have shown that sensitivity and specificity varied according to the type of sample. Thirdly, the performance of Xpert MTB/RIF ultra in the pediatric age group could have been shown. We thank the editor for this comment since it is fundamental to why the Xpert MTB/RIF was introduced. The authors have tried to accommodate the comment in the limitations section since it is not routine to have a culture for all Sputum TB samples. Unless they are Rifampicin Resistant Indeterminate. The same applies to the extra-pulmonary versus the pulmonary samples, the former samples are likely to be negligible. So, there are unlikely to change the overall results. Line 75- The sentence could be completed after 'Jan2012' We have made this correction. Line 110- Rifampicin resistant TB should be RR-TB This correction has been made. 4th and 5th lines under 'Comparison between Xpert® MTB/RIF and Xpert® MTB/RIF Ultra'- MDR-TB to be replaced by RR-TB. Also, in Table 2, MDR-TB is to be replaced by RR-TB. This correction has been made, see lines 4 and 5 and Table 2. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. Response: We have revised our manuscript to ensure that the level 1 headings are 18 pt font, while level two headings are 16 pt font and level 3 are 14 pt font. They are all in bold and we have capitalized only the first word of the heading, the first word of the sub-heading and any proper nouns and genus names. The rest of the text is 12 pt font. Supplementary information files have been renamed following the PLOS ONE’s style requirements. 2. We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service. Whilst you may use any professional scientific editing service of your choice, PLOS has partnered with both American Journal Experts (AJE) and Editage to provide discounted services to PLOS authors. 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Could you please provide further details on why your study is exempt from the need for approval and confirmation from your institutional review board or research ethics committee (e.g., in the form of a letter or email correspondence) that ethics review was not necessary for this study? Please include a copy of the correspondence as an "Other" file. We have made changes for the ethical approval section. I have attached a letter from the Operational Research and Ethics Review Committee of the National Tuberculosis and Leprosy Program of Uganda. The authors had previously got the approval to use the data and publish it but, it had not been written. However, we got a copy and will attach it under others. 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. 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Response: The following statement should be included in the online submission system: “The authors have declared that no competing interests exist”. 7. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Response: The following statement has been used to meet the ‘Data availability’ requirements of the journal: “All relevant data are within the paper and its Supporting Information files” Response to Reviewer’s comments Comment: Furthermore, information should be provided about the issue of “trace positive samples” by Ultra. In addition to detection of the single-copy rpoB gene for the simultaneous diagnosis of TB and rifampicin resistance, Ultra includes two new and more sensitive PCR assays that target the multicopy IS6110 and IS1081 genes to improve M.tuberculosis detection in paucibacillary samples. Information about RIF-R is not available in IS6110 or IS1081 positive and rpoB negative samples are categorized as “trace” by Ultra. Thus MDR-TB cases can be missed among the “trace” positive samples. For these samples, information about drug resistance can only be provided by culture. Therefore, when comparing the two methods, it is important to have this information. We have acknowledged the shortcomings of not having the data for culture and we have included it in the study limitations. However, in the literature despite the changes in the targets on IS6110 and IS1081 genes, there wasn’t a significant change in the detection of Rifampicin Resistant Cases. Comment: Mycobacterium Tuberculosis should be written as Mycobacterium tuberculosis We thank the reviewer for this comment, and this has been revised. Comment:The sentence in the last paragraph of the discussion should be corrected “This study was not with limitations….” We thank the reviewer for this comment. The authors have corrected this to “…This study was not without limitations”… Attachments Attachment Submitted filename: Response to reviewers PONE-D-20-34522R1.doc https://doi.org/10.1371/journal.pone.0275960.r002
12 Sep 2022 Decision Letter - Shampa Anupurba, Editor PONE-D-20-34522R1Comparison of tests done and Tuberculosis cases detected by Xpert® MTB/RIF and Xpert® MTB/RIF-Ultra in UgandaPLOS ONE Dear Dr. Kakinda, 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. The manuscript has been revised satisfactorily. However, there are two minor corrections Line 58- 'Tuberculosis' to be replaced by 'tuberculosis' Line 137- 'got' to be replaced by 'obtained' Please submit your revised manuscript by Oct 27 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 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: https://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, Shampa Anupurba, MD 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. [Note: HTML markup is below. Please do not edit.] 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. https://doi.org/10.1371/journal.pone.0275960.r003
Revision 2
15 Sep 2022 Author Response POINT-BY-POINT RESPONSE TO THE EDITOR’S AND THE REVIEWERS’ COMMENTS Response to the Editor’s Comments The manuscript has been revised satisfactorily. However, there are two minor corrections Line 58- 'Tuberculosis' to be replaced by 'tuberculosis' We do thank the editor for this observation. We have made this correction. Line 137- 'got' to be replaced by 'obtained We have made this correction. Attachments Attachment Submitted filename: Response to reviewers PONE-D-20-34522R2.doc https://doi.org/10.1371/journal.pone.0275960.r004
27 Sep 2022 Decision Letter - Shampa Anupurba, Editor Comparison of tests done and Tuberculosis cases detected by Xpert® MTB/RIF and Xpert® MTB/RIF-Ultra in Uganda PONE-D-20-34522R2 Dear Dr. Kakinda, 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, Shampa Anupurba, MD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0275960.r005
Formally Accepted
29 Sep 2022 Acceptance Letter - Shampa Anupurba, Editor PONE-D-20-34522R2 Comparison of tests done, and Tuberculosis cases detected by Xpert® MTB/RIF and Xpert® MTB/RIF-Ultra in Uganda Dear Dr. Kakinda: 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. Shampa Anupurba Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0275960.r006

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