Antibody activities in hyperimmune plasma against the Rhodococcus equi virulence -associated protein A or poly-N-acetyl glucosamine are associated with protection of foals against rhodococcal pneumonia

Susanne K. Kahn; Colette Cywes-Bentley; Glenn P. Blodgett; Nathan M. Canaday; Carly E. Turner-Garcia; Mariana Vinacur; Sophia C. Cortez-Ramirez; Patrick J. Sutter; Sarah C. Meyer; Angela I. Bordin; Daniel R. Vlock; Gerald B. Pier; Noah D. Cohen

doi:10.1371/journal.pone.0250133

Peer Review History

Original SubmissionMarch 25, 2021
11 Jun 2021 Decision Letter - Ashlesh K Murthy, Editor PONE-D-21-09880 Antibody Activities in Hyperimmune Plasma Against the Rhodococcus equi Virulence -Associated Protein A or Poly-N-Acetyl Glucosamine are Associated with Protection of Foals Against Rhodococcal Pneumonia PLOS ONE Dear Dr. Cohen, 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 expert reviewers appreciate the new findings of the study. However, a number of clarifications are sought regarding methodology and interpretation. The response to these is important to further determine the suitability of this manuscript for publication. I urge you to address these issues, should you submit a revised version of manuscript. 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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. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. Thank you for stating the following in the Competing Interests section: "I have read the journal's policy and the authors of this manuscript have the following competing interests: Gerald B. Pier (GBP) is an inventor of intellectual properties [human monoclonal antibody to PNAG and PNAG vaccines] that are licensed by Brigham and Women’s Hospital to Alopexx Vaccine, LLC, an entity in which GBP also holds equity. As an inventor of intellectual properties, GBP also has the right to receive a share of licensing-related income (royalties, fees) through Brigham and Women’s Hospital from Alopexx Vaccine, LLC. GBP’s interests were reviewed and are managed by the Brigham and Women’s Hospital and Partners Health care in accordance with their conflict of interest policies. Colette Cywes-Bentley (CC-B) is an inventor of intellectual properties [use of human monoclonal antibody to PNAG and use of PNAG vaccines] that are licensed by Brigham and Women’s Hospital to Alopexx Vaccine, LLC. As an inventor of intellectual properties, CC-B also has the right to receive a share of licensing-related income (royalties, fees) through Brigham and Women’s Hospital from Alopexx Vaccine, LLC. Daniel R. Vlock is the Chief Executive Officer of ALOPEXX Vaccines and owns the rights to the PNAG vaccine. Dr. Vlock had no role in the design or analysis of the study. SC Meyer and PJ Sutter work for MG Biologics that produced the plasma and thus might have potential earnings; however, they had no part in the design or analysis of the study." We note that one or more of the authors are employed by a commercial company: 36666 Ranch, Lazy E Ranch, Mg Biologics, Inc, Alopexx Inc. 3.1. Please provide an amended Funding Statement declaring this commercial affiliation, as well as a statement regarding the Role of Funders in your study. If the funding organization did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and/or research materials, please review your statements relating to the author contributions, and ensure you have specifically and accurately indicated the role(s) that these authors had in your study. You can update author roles in the Author Contributions section of the online submission form. 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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: The manuscript entitled, “Antibody Activities in Hyperimmune Plasma Against the Rhodococcus equi Virulence -Associated Protein A or Poly-N-Acetyl Glucosamine are Associated with Protection of Foals Against Rhodococcal Pneumonia” aims to assess the impact of two types of hyperimmune plasma on the clinical and subclinical incidence of Rhodococcal pneumonia in foals. My comments are as follows, 1. Do these farms historically use plasma as a preventative measure? 2. Who was responsible for allocating foals to the treatment groups? Was allocation sequence concealed from the person assigning foal to treatment groups? Were any demographics on the foals recorded? 3. Who was responsible for thoracic ultrasound examinations? Who administered the plasma? Were any complications noted following administration of either type of plasma? 4. What was the standard treatment protocol for subclinical/clinical cases? 5. Line -234 how was data that was obtained from this foal before it was lost handled? Was it excluded from the analysis? 6. Line 284 – does the percentage of foals that developed pneumonia reflect those that developed clinical and subclinical pneumonia? Please clarify in the main text and the figure legend. 7. Figure 4: assuming each dot represents an individual animal for Farm B, I count 10 data points for this that developed pneumonia, whereas the text says 9. Please clarify. 8. Figures 7 and 8, please consider labeling the Y-axis. 9. Did all the foals that developed clinical or subclinical survive? Was there any difference in survival for those treated with PNAG HIP vs. RE HIP? 10. Can you please describe the roles of the authors affiliated with Mg Biologics and Alopexx Inc. in the study design, excitation, analysis, and manuscript preparation? Was the plasma provided as gift from these companies? ****** 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: Yes:** Brina Lopez [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.0250133.r001
Revision 1
21 Jun 2021 Author Response June 12, 2021 Prof. Ashlesh K. Murthy Academic Editor PLoS One Subject: Revision of manuscript entitled, “Antibody Activities in Hyperimmune Plasma Against the Rhodococcus equi Virulence -Associated Protein A or Poly-N-Acetyl Glucosamine are Associated with Protection of Foals Against Rhodococcal Pneumonia” Dear Dr. Murthy: Thank you for your electronic message dated June 11, 2021 about the above-referenced manuscript. I also thank the reviewers who carefully considered our report. My coauthors and I have revised the report on the basis of the reviewer’s comments that were provided to us. Below, we detail how each point raised by the reviewer was addressed in the revised report. The revised report with marked changes and an unmarked manuscript will be uploaded to the PLoS One website along with this response letter. Comments from Reviewer 1: 1. Do these farms historically use plasma as a preventative measure? AUTHORS’ RESPONSE: We thank the reviewer for pointing out this important omission. The manuscript has been revised to indicate that both farms historically used R. equi hyperimmune plasma transfusion to control R. equi pneumonia. 2. Who was responsible for allocating foals to the treatment groups? Was allocation sequence concealed from the person assigning foal to treatment groups? Were any demographics on the foals recorded? AUTHORS’ RESPONSE: We thank the reviewer for raising more great points. Allocation of treatment was made by investigators at Texas A&M University. In the fall of 2018, each farm provided a list of the eligible mares at the farm ordered by expected breeding date. These mares were randomly assigned in a balanced manner to either plasma 0 or 1. The randomly assigned list was provided to the veterinarians at the farm. Because the true foaling date did not always match the expected foaling date, the order of treatment was further randomized by nature. We arrived at this system based on internal discussions with investigators and statisticians and farm personnel. The manuscript has been revised to clarify who was responsible for the treatment allocation and that those administering plasma were aware of which foal was assigned to which plasma. We have also revised the report to indicate which additional data (including sex of the Quarter Horse foals) were collected for each foal. 3. Who was responsible for thoracic ultrasound examinations? Who administered the plasma? Were any complications noted following administration of either type of plasma? AUTHORS’ RESPONSE: The manuscript has been revised to indicate that thoracic ultrasonography was performed by the farm veterinarians (Drs. Blodgett, Canaday, and Turner). The manuscript also has been revised to indicate that plasma transfusion was performed by veterinary technical staff or veterinarians at the farm. The manuscript has been revised to indicate that no adverse effects were noted among transfused foals. We thank the reviewer for prompting us to address each of these important points. 4. What was the standard treatment protocol for subclinical/clinical cases? AUTHORS’ RESPONSE: The standard antimicrobial treatment at both farms was a macrolide with or without combination with rifampin. The manuscript has been revised to include these details for each farm. 5. Line -234 how was data that was obtained from this foal before it was lost handled? Was it excluded from the analysis? AUTHORS’ RESPONSE: We apologize for the ambiguity. The manuscript has been revised to clarify that the data from this foal were excluded from analysis. 6. Line 284 – does the percentage of foals that developed pneumonia reflect those that developed clinical and subclinical pneumonia? Please clarify in the main text and the figure legend. AUTHORS’ RESPONSE: We apologize for the ambiguity. The manuscript has been revised to clarify that the percentage of foals includes those with clinical pneumonia (Farm A) and subclinical pneumonia (Farm B). 7. Figure 4: assuming each dot represents an individual animal for Farm B, I count 10 data points for this that developed pneumonia, whereas the text says 9. Please clarify. AUTHORS’ RESPONSE: We apologize for the confusion. The extra point was actually an artifact from the same symbol being used to indicate an outlier as was used to reflect individual foals (i.e., an extra dot was added to indicate that foal’s value was an outlier). The figure was revised to correct this problem. 8. Figures 7 and 8, please consider labeling the Y-axis. AUTHORS’ RESPONSE: The Y axis has been labelled in revised Figures 7 and 8. 9. Did all the foals that developed clinical or subclinical survive? Was there any difference in survival for those treated with PNAG HIP vs. RE HIP? AUTHORS’ RESPONSE: We have revised the manuscript to indicate that no study foals died of pneumonia caused by R. equi. The third paragraph from the end of the Discussion indicates that there was no significant difference in protection between the 2 plasma products; however, these results should be interpreted with caution because the study was not designed to test this hypothesis. 10. Can you please describe the roles of the authors affiliated with Mg Biologics and Alopexx Inc. in the study design, excitation, analysis, and manuscript preparation? Was the plasma provided as gift from these companies? AUTHORS’ RESPONSE: Thank you for these comments. The editor also has asked that this be addressed in the Funding Statement and Competing Interest Statements. Neither Mg Biologics nor Alopexx played a role in the design, execution, analysis, or manuscript preparation for this study EXCEPT that Mg Biologics agreed to make labels masking the plasma identity and to not break the code for the plasma until data collection was completed. Vaccine to hyperimmunize donors against PNAG was provided as a gift by ALOPEXX, Inc. The plasma was purchased by the farms from Mg Biologics. Again, we thank you and the reviewer for taking the time to carefully consider our report. Please let us know if you have any additional questions or concerns regarding the revised manuscript. Sincerely, Noah D. Cohen Attachments Attachment Submitted filename: Response Letter PLoS One June 14_2021.pdf https://doi.org/10.1371/journal.pone.0250133.r002
16 Aug 2021 Decision Letter - Ashlesh K Murthy, Editor Antibody Activities in Hyperimmune Plasma Against the Rhodococcus equi Virulence -Associated Protein A or Poly-N-Acetyl Glucosamine are Associated with Protection of Foals Against Rhodococcal Pneumonia PONE-D-21-09880R1 Dear Dr. Cohen, 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, Ashlesh K Murthy, M.D., Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0250133.r003
Formally Accepted
18 Aug 2021 Acceptance Letter - Ashlesh K Murthy, Editor PONE-D-21-09880R1 Antibody Activities in Hyperimmune Plasma Against the <i>Rhodococcus equi<i/> Virulence -Associated Protein A or Poly-<i>N<i/>-Acetyl Glucosamine are Associated with Protection of Foals Against Rhodococcal Pneumonia Dear Dr. Cohen: 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 Ashlesh K Murthy Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0250133.r004

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