Pyrazinamide resistance in rifampicin discordant tuberculosis

Nomonde Ritta Mvelase; Ravesh Singh; Khine Swe Swe-Han; Koleka Patience Mlisana

doi:10.1371/journal.pone.0274688

Peer Review History

Original SubmissionJune 9, 2022
21 Jul 2022 Decision Letter - Frederick Quinn, Editor PONE-D-22-16671Pyrazinamide resistance in rifampicin discordant tuberculosisPLOS ONE Dear Dr. Mvelase, 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. If you will need significantly more time 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. 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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 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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: 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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: GENERAL Highly relevant contribution to the field of MDRTB. Recent guidelines on the treatment of MDRTB (WHO, 2020) recommended that pyrazinamide only be considered for inclusion in drug regimens if susceptibility to the drug has been shown. Pyrazinamide is a highly effective anti-TB agent and its use would be preferred. The hypothesis in this paper is that isolates resistant to rifampicin by genotypic assay but susceptible to the drug by phenotypic assay (discordant) have a high probability for susceptibility to pyrazinamide (and also to isoniazid). Therefore, the baseline rifampicin profile has major implication for selecting an appropriate treatment regimen that also includes pyrazinamide, especially where DST for the latter agent is not available. It is, therefore, useful to define categories of MDRTB patients where pyrazinamide resistance is likely to be low and its use might be recommended as standard of care. MAJOR COMMENT The study investigated pyrazinamide resistance in 80 isolates classified as discordant on rifampicin gDST-pDST results. In these isolates, the pDST of rifampicin was determined using 7H10 medium and a rifampicin critical concentration of 1 ug/ml. In a 2021 technical report on critical concentrations for drug susceptibility testing of isoniazid and the rifamycins (rifampicin, rifabutin and rifapentine), the World Health Organization recommended lowering the CC of rifampicin in 7H10 and MGIT grown cultures to 0.5 ug/ml. The authors need to elaborate on the implications of this change, if applied to their dataset, on the rationale for the study as stated in the last paragraph of the Introduction. How many of the 80 isolates would still be considered discordant if the revised CC is applied? Do the conclusions for the study hold for isolates regarded as discordant under the revised breakpoint, i.e would the probabilities for association with isoniazid and/or pyrazinamide susceptibility remain unaltered? Are there any high-confidence rpoB mutations in discordant isolates by the revised definition that would predict pyrazinamide susceptibility? The above additional perspective is to be provided as an expansion of the existing narrative, not necessarily as a replacement of the study results and conclusions as presented. MINOR COMMENT The prevalence of pyrazinamide resistance in MDRTB isolates in South Africa is high, as emphasised by the authors. Reference 24 (Ismail, et al. 2018) is quoted in the context of prevalence of rpoB mutations in a national survey. A general perspective on the magnitude of pyrazinamide resistance would be useful in stating the importance of the current work. Does the same reference provide an estimate of the level of pyrazinamide resistance? By comparison, the 2008 paper by Mphahlele, et al., DOI: 10.1128/JCM.00973-08, would be useful, also for insight into the genomics of MDRTB isolates at the time. ****** 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 ******** [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.0274688.r001
Revision 1
11 Aug 2022 Author Response Thank you for the opportunity to submit our revised manuscript for further consideration. We appreciate the insightful comments given by the reviewer and we believe that the revised manuscript is of a much better quality. We have addressed each of the comments in the rebuttal letter plus we have also incorporated changes recommended by the reviewer into the manuscript. Response to reviewer 1 comments: MAJOR COMMENT The study investigated pyrazinamide resistance in 80 isolates classified as discordant on rifampicin gDST-pDST results. In these isolates, the pDST of rifampicin was determined using 7H10 medium and a rifampicin critical concentration of 1 ug/ml. In a 2021 technical report on critical concentrations for drug susceptibility testing of isoniazid and the rifamycins (rifampicin, rifabutin and rifapentine), the World Health Organization recommended lowering the CC of rifampicin in 7H10 and MGIT grown cultures to 0.5 ug/ml. The authors need to elaborate on the implications of this change, if applied to their dataset, on the rationale for the study as stated in the last paragraph of the Introduction. How many of the 80 isolates would still be considered discordant if the revised CC is applied? Do the conclusions for the study hold for isolates regarded as discordant under the revised breakpoint, i.e would the probabilities for association with isoniazid and/or pyrazinamide susceptibility remain unaltered? Are there any high-confidence rpoB mutations in discordant isolates by the revised definition that would predict pyrazinamide susceptibility? The above additional perspective is to be provided as an expansion of the existing narrative, not necessarily as a replacement of the study results and conclusions as presented. Response: Thank you for this comment. The WHO lowering of rifampicin critical concentration (CC) actually strengthens our findings of low pyrazinamide prevalence in rifampicin discordant TB. 45% of the discordant isolates remain discordant after the revision of the CC. Of the six pyrazinamide resistant isolates, only one occurred within this group of isolates, the other five are amongst those who would be considered rifampicin resistant (Rifampicin MIC of >0.5 µg/mL. This means pyrazinamide resistance is even lower in rifampicin discordant TB than originally thought. We have included this information in the description of our M. tuberculosis isolates under the methods section as well as the results section. Additionally, we have expanded our discussion to include the effect of the change on our findings. The specific rifampicin mutations were not helpful in predicting pyrazinamide resistance, probably due to small number of PZA resistant isolates. MINOR COMMENT The prevalence of pyrazinamide resistance in MDRTB isolates in South Africa is high, as emphasised by the authors. Reference 24 (Ismail, et al. 2018) is quoted in the context of prevalence of rpoB mutations in a national survey. A general perspective on the magnitude of pyrazinamide resistance would be useful in stating the importance of the current work. Does the same reference provide an estimate of the level of pyrazinamide resistance? By comparison, the 2008 paper by Mphahlele, et al., DOI: 10.1128/JCM.00973-08, would be useful, also for insight into the genomics of MDRTB isolates at the time. Response: We have also expanded our discussion of pyrazinamide resistance to include this information (paragraph 3 on discussion). Although pyrazinamide resistance is high among drug resistant TB isolates in South Africa, it is much lower in drug susceptible TB. In Ismail’s paper, the overall pyrazinamide resistance was only 3.7%. Attachments Attachment Submitted filename: Response to reviewers comments_Plos One 2022.docx https://doi.org/10.1371/journal.pone.0274688.r002
2 Sep 2022 Decision Letter - Frederick Quinn, Editor Pyrazinamide resistance in rifampicin discordant tuberculosis PONE-D-22-16671R1 Dear Dr. Mvelase, 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, Frederick Quinn Academic Editor PLOS ONE Additional Editor Comments (optional): 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: The authors have responded positively to previous recommendations, especially as far as the Major comment raised is concerned. The manuscript now contains additional considerations of the study outcome in the light of recent changes in international recommendations for the rifampicin breakpoint in liquid media. Minor comments by the reviewer have also been adequately addressed. There are no additional clarifications or amendments required. ****** 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: No ******** https://doi.org/10.1371/journal.pone.0274688.r003
Formally Accepted
12 Sep 2022 Acceptance Letter - Frederick Quinn, Editor PONE-D-22-16671R1 Pyrazinamide resistance in rifampicin discordant tuberculosis Dear Dr. Mvelase: 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. Frederick Quinn Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0274688.r004

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