Peer Review History
| Original SubmissionJune 11, 2020 |
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PONE-D-20-17903 Sequence variation and immunogenicity of the Mycoplasma genitalium MgpB and MgpC adherence proteins during persistent infection of men with non-gonococcal urethritis PLOS ONE Dear Dr. Wood, Thank you for submitting your manuscript to PLOS ONE. I want to apologize for the delay- finding reviewers was challenging this summer. 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 Oct 12 2020 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:
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In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. [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 Reviewer #2: Yes Reviewer #3: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: N/A ********** 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 Reviewer #3: 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 Reviewer #2: Yes Reviewer #3: 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 manuscript by Wood and colleagues reports on the sequence variation of two highly variable adhesion related proteins of the STI pathogen, Mycoplasma genitalium. This species uses rampant recombination between variant sequences to shuffle new coding sequences into a single expression locus. Although the main features of the process have been known for a while, this study documents variation seen isolates from four persistently colonized men. Overall the data are quite clear cut, although it was no unambiguously clear, how much of the MgpB variation was previously reported in reference 27 (please see below) Specific Points 1. Introduction. Since there are a number of different protein names used for MgpB and MgpC, it would be informative to include these in parentheses the first time the proteins are introduced (e.g. L57; for example include MG numbers and P110 etc). 2. L68 The term MgPars is introduced here, without any information provided about their nature. 3. L70 It is not clear how recombination mediated antigenic variation and the “exchange of large regions of mgpBC with single or multiple MgPars” i.e. phase variation, are actually different processes. Is it the length of the region shuffled? In which case this third mechanism of phase variation would seem to be one extreme end of the antigenic variation recombination spectrum. This distinction was unclear when I read it. 4. L71 It is not clear how recA (the primary mechanism for these phenomena) can generate point mutations (L70) unless some of the MgPars carry such isolated mutations. 5. L83. This might be interpreted that immune selection is causing the variation directly, whereas presumably it is the driver of selecting against the previous antigenic epitopes. 6. L134. Please include the name of the PCR polymerase (hi fidelity? ) and the typical number of cycles that were necessary to amplify the variable regions. These points are important when trying to assess the sequence variation obtained. 7. L30 and L135. As you read the methods, there are day numbers that seem discrepant. On L30, DNA is prepared from co-cultured cells after day 7, 14, 21, 28 but then on L135 the templates are from three or 10 weeks. 8. L147. The authors state that the conserved regions of mgpB for these isolates were reported in ref 27. Table S3 from that paper seems to include variable regions also, so it is not 100% clear what was reported before and what is new (in regards to variable sequences in MgpB). 9. L189 and ref 37. How many different strain types are known? And how many different strains can have the same “strain type”? Although it is possible that the strain typing shows that a “single strain across all time points” was present, it does not categorically prove that. It would be more accurate to state that only a single strain type was detected. Also L352 “with a single persistent strain type…”? 10. Most of the sequence analysis comes from clones of PCR products obtained from co-cultured cells and uses the 3 week DNA prep. Was insufficient DNA recoverable at earlier times (the methods indicate that day 7 and day 14 DNA preps were made, but these were not characterized)? What was the rationale for this? 11. Is the recombination reciprocal and do the authors have data from any of the MgPar sites? Minor points 1. L47 Should “Chlamydia” be italicized? 2. L99 versus L121. There is variable hyphenation usage in “co-culture”. Please use one style throughout. 3. L119, L124, L132, L137. Please provide ECL and pCR2.1 supplier details and check to see if company locations are required for ATCC, Epicentre and PCR enzyme (see point 6 above) 4. Figure 2-indicate what he “Rb” refers to in the legend. 5. L402 i.e. (should this be italicized)? 6. L416 should “in silico” be italicized? Reviewer #2: The main goal of the study from Wood et al., is to determine the extent of sequence variation in the MgpB and MgpC over time in men persistently infected with Mycoplasma genitalium. MgpB and MgpC are adherence proteins, which are immunodominant targets of host antibodies. The work extends previous studies (analyzing mostly a single variable region or with other limitations) carried out by some of the coauthors and by other groups. The methodology used and the analysis performed in the present work seem appropriated and the conclusions consistent. However, the amount of patients used (four) in the study is maybe a bit too small and the novelty of results limited. It would be nice to indicate at some point in the text the alternative nomenclature of P140 and P110 for MgpB and MgpC, respectively. In the work the analysis is performed in parallel for MgpB and MgpC, except for the mapping of the variant amino acids onto the protein structure that is only done for MgpC. Since some weeks ago the structure of MgpB was published and it is now also available. In my opinion the mapping of variants should now also be done for MgpB and included in this work. Reviewer #3: In this manuscript, Wood and colleagues examine the generation of sequence variation within the main adhesins of M. genitalium during persistent infection. This variation is intended to modify/replace the antigenic regions of the MgpB and MgpC adhesins to avoid host antibody recognition. In contrast to previous studies, where the analysis was limited to a single region or a low number of cloned sequences, the current report addresses sequence variation in all four variable regions of the mgpBC expression site and analyze multiple clones. Therefore, the present study provides a more complete picture of the diversity and complexity of MgpB and MgpC variation over time. The topic of study is critical to understand persistence of M. genitalium in the genital tract and the authors have wide experience investigating sequence variation in this pathogen. Overall, the results are well-presented and are easy to follow, so I do not have specific comments on this regard. However, in my opinion, there are a few questions regarding the study design that would need to be clarified: 1) To identify sequence variants (L134-141 and L207-217), the authors use PCR amplification, followed by cloning and Sanger sequencing of multiple plasmids (around 75). The number of individual clones analyzed seems sufficient to obtain a representative view of the predominant sequence variants present at each time point. However, clone selection is always a matter of concern. Therefore, could Next Generation Sequencing technology have been used to analyze the different PCR amplicons? If so, do the authors think that the use of NGS could impact or improve the results presented in this study? Could the use of NGS benefit future studies addressing sequence variation of Mge during persistent infection? 2) The Mge isolates analyzed were recovered by co-culture of processed patient urine with Vero cells (L120-133). The possible impact of co-culture with Vero cells (three or more weeks) on sequence variation is also matter of concern (L272-282). In this regard, could this step introduce some bias in the sequence variants identified? For example, selecting for adhesin variants with increased adherence capacity or some other feature important for in vitro survival. Therefore, was this co-culture strictly necessary? Can DNA from Mge be extracted/sequenced directly from a patient sample (for example the urine pellets after centrifugation)? In addition, why was only culture supernatants used to isolate DNA (L131)? I do not have experience isolating Mge clinical strains but, shouldn’t the bacteria be attached to Vero cells? 3) The current study seems appropriate to determine the extent of sequence variation in the adhesin genes over time in men with NGU persistently infected with Mge (L174). However, the relationship between the observed changes and antigenic variation, and the impact on antibody recognition in less apparent. In this sense, all evidences are indirect. Even if amino acid changes localize (in general) to regions predicted as epitopes, no direct evidence is provided that these changes effectively avoid antibody recognition. Therefore, all conclusions on this regard must be limited and presented as a possibility rather than a fact. To establish a solid relationship between sequence variation and antibody recognition, direct evidence is required. For example, for each particular Mge isolate, is it possible to test if patient serum from Visit 1 is less or non-reactive against MgpB or MgpC variants predominantly expressed at Visit 3? To test this, can the Mge strains expressing the adhesin variants predominant at Visit 3 be isolated and used as template (whole cell lysates) for western blotting analysis using sera from Visit 1? Alternatively, is it possible to generate Mge mutants expressing these new variants that could be analyzed by western blotting instead of G37 whole cell lysates? Moreover, could the predominant variants (MgpB/MgpC) identified at Visit 3 be expressed as recombinant proteins (heterologous expression) and used to demonstrate loss of recognition by serum from Visit 1? Minor points: Why are Figure legends embedded within the manuscript? L64 “is affected by two mechanisms”: rather than two mechanisms, I think antigenic and phase variation are two processes or even purposes. L99 “Among the four”. New paragraph. L135 “three (or ten weeks)”. When ten? L207-217. This is Methods rather than Results? L224 “consistent with immune selection against specific epitopes”. Could sequence variation have other purposes? Perhaps not all sequence changes are aimed to avoid immune system recognition and are negatively/positively selected by other forces with different purposes. L226 “the predominant sequence”. Are “predominant sequences” much more abundant than other sequences in each sample? Can the authors show the % of identification of the predominant sequence for each isolate and time point? Were mixtures often identified (other than for patient 43 Visit 1)? ********** 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 Reviewer #3: 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. |
| Revision 1 |
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Sequence variation and immunogenicity of the Mycoplasma genitalium MgpB and MgpC adherence proteins during persistent infection of men with non-gonococcal urethritis PONE-D-20-17903R1 Dear Dr. Wood, 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, Catherine A. Brissette, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-20-17903R1 Sequence variation and immunogenicity of the Mycoplasma genitalium MgpB and MgpC adherence proteins during persistent infection of men with non-gonococcal urethritis Dear Dr. Wood: 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. Catherine A. Brissette Academic Editor PLOS ONE |
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