Rapid pathogen identification and antimicrobial susceptibility testing in in vitro endophthalmitis with matrix assisted laser desorption-ionization Time-of-Flight Mass Spectrometry and VITEK 2 without prior culture

Lindsay Y. Chun; Laura Dolle-Molle; Cindy Bethel; Rose C. Dimitroyannis; Blake L. Williams; Sidney A. Schechet; Seenu M. Hariprasad; Dominique Missiakas; Olaf Schneewind; Kathleen G. Beavis; Dimitra Skondra

doi:10.1371/journal.pone.0227071

Peer Review History

Original SubmissionSeptember 16, 2019
21 Oct 2019 Decision Letter - Demetrios G. Vavvas, Editor PONE-D-19-26072 Rapid Pathogen Identification and Antimicrobial Susceptibility Testing in in vitro Endophthalmitis with Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry and VITEK 2 without Prior Culture PLOS ONE Dear Dr. Skondra, 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. This is an exciting new study and idea. both reviewers find it so as well. There are some minor issues that can easily be addressed and we would welcome the revised version. We would appreciate receiving your revised manuscript by Dec 05 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols 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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Demetrios G. Vavvas Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 ****** 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: Thank you for submitting your research work to PLOS One. I find this article very interesting. Congratulations on the excellent work of the entire team and on the well-written manuscript. Despite its limitations, I agree that this technology can become a powerful tool for rapid identification of pathogens in patients with endophthalmitis. There is a typo: p.6 the word Design (currently is DEISGN). Thank you. Reviewer #2: This is a very interesting study but would recommend the following modifications: 1. Please modify the last sentence of the first paragraph of Introduction, which states that 23-35% of eyes affected by endophthalmitis are left with no light perception. This very high rate of NLP visual outcome may be true for bleb-related endophthalmitis (the reference the authors give), but this is not true for other common types of endophthalmitis such as post-cataract endophthalmitis. Visual outcome is highly associated with pathogen; in coagulase-negative endophthalmitis - the major pathogen of post-cataract endophthalmitis -- NLP vision is very rare (<4%). 2. Please add a discussion of this study versus a similar one (not listed in Reference list) published in 2017 by Song Z, et al. "Using MALDI-TOF MS to test Staphylococcus aureus-infected vitreous". Mol Vis. 2017; 23: 407–415. The Song study used porcine eyes injected with S. aureus and directly tested the resulting infected vitreous with MALDI-TOF, so is similar in some regards to the present study -- results may in fact be complimentary. Also, the current study mentions a MALDI-TOF result in a patient with culture-negative endophthalmitis (ref 33), and the Song 2017 study mentions results from 2 patients with culture-positive endophthalmitis in which MALDI-TOF and standard culture yielded the same organism identification. This also may be worth noting. ****** 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 [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 to be viewed.] 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. 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Revision 1
29 Nov 2019 Author Response Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 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 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 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: Thank you for submitting your research work to PLOS One. I find this article very interesting. Congratulations on the excellent work of the entire team and on the well-written manuscript. Despite its limitations, I agree that this technology can become a powerful tool for rapid identification of pathogens in patients with endophthalmitis. There is a typo: p.6 the word Design (currently is DEISGN). Thank you; we have edited the typo. Reviewer #2: This is a very interesting study but would recommend the following modifications: 1. Please modify the last sentence of the first paragraph of Introduction, which states that 23-35% of eyes affected by endophthalmitis are left with no light perception. This very high rate of NLP visual outcome may be true for bleb-related endophthalmitis (the reference the authors give), but this is not true for other common types of endophthalmitis such as post-cataract endophthalmitis. Visual outcome is highly associated with pathogen; in coagulase-negative endophthalmitis - the major pathogen of post-cataract endophthalmitis -- NLP vision is very rare (<4%). Thank you; this sentence has been modified to state: “Depending on the causative pathogen and pathophysiology, infectious endophthalmitis can lead to poor visual outcomes in the affected eye; for example, the incidence of no light perception ranges from 23% to 35% in bleb-related endophthalmitis(3,4).” 2. Please add a discussion of this study versus a similar one (not listed in Reference list) published in 2017 by Song Z, et al. "Using MALDI-TOF MS to test Staphylococcus aureus-infected vitreous". Mol Vis. 2017; 23: 407–415. The Song study used porcine eyes injected with S. aureus and directly tested the resulting infected vitreous with MALDI-TOF, so is similar in some regards to the present study -- results may in fact be complimentary. Also, the current study mentions a MALDI-TOF result in a patient with culture-negative endophthalmitis (ref 33), and the Song 2017 study mentions results from 2 patients with culture-positive endophthalmitis in which MALDI-TOF and standard culture yielded the same organism identification. This also may be worth noting. The discussion has been modified to state: “Another group previously reported on the implementation of MALDI-TOF MS in identifying a strain of S. aureus from in-vitro and ex-vivo models of endophthalmitis with porcine eyes, and in identifying the causative organisms in culture-positive human endophthalmitis samples, (34). However, we aimed to anticipate the extrapolation of our methods to potential clinical scenarios, and we thus optimized our methodology to require relatively minimal steps in sample preparation, clearly delineate the parameters and materials we employed, and help establish a range of minimum time needed for organism identification with MALDI-TOF MS. Although the previously reported findings on the direct analysis of samples with MALDI-TOF MS support our study, a wider breadth of organisms including other bacteria, mycobacteria, fungi, and polymicrobial infections should also be investigated with MALDI-TOF MS.” 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 Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0227071.r002
12 Dec 2019 Decision Letter - Demetrios G. Vavvas, Editor Rapid Pathogen Identification and Antimicrobial Susceptibility Testing in in vitro Endophthalmitis with Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry and VITEK 2 without Prior Culture PONE-D-19-26072R1 Dear Dr. Skondra, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Demetrios G. Vavvas 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 #2: 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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: I Don't Know ****** 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 #2: 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 #2: 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 #2: (No Response) ****** 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 #2: No https://doi.org/10.1371/journal.pone.0227071.r003
Formally Accepted
17 Dec 2019 Acceptance Letter - Demetrios G. Vavvas, Editor PONE-D-19-26072R1 Rapid Pathogen Identification and Antimicrobial Susceptibility Testing in in vitro Endophthalmitis with Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry and VITEK 2 without Prior Culture Dear Dr. Skondra: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Demetrios G. Vavvas Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0227071.r004

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