Usefulness of the MALDI-TOF MS technology with membrane filter protocol for the rapid identification of microorganisms in perioperative drainage fluids of hepatobiliary pancreatic surgery

Kazuyuki Sogawa; Shigetsugu Takano; Takayuki Ishige; Hideyuki Yoshitomi; Shingo Kagawa; Katsunori Furukawa; Tsukasa Takayashiki; Satoshi Kuboki; Fumio Nomura; Masayuki Ohtsuka

doi:10.1371/journal.pone.0246002

Peer Review History

Original SubmissionJuly 27, 2020
18 Nov 2020 Decision Letter - Massimiliano Galdiero, Editor PONE-D-20-20446 Usefulness of the MALDI-TOF MS technology with membrane filter protocol for the rapid identification of microorganisms in perioperative drainage fluids of hepatobiliary pancreatic surgery. PLOS ONE Dear Dr. Takano 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 Jan 02 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. 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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, Massimiliano Galdiero, M.D., Ph.D. Academic Editor PLOS ONE Journal Requirements: Additional Editor Comments (if provided): [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 ****** 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: Very interesting and innovative study, well performed, with accuracy and precision. I have only minor comments: - I recommend to slightly reformulate, in the abstract, the methods paragraph, in order to include a sentence about the tests made to evaluate the LOD of Rapid BACpro with/without filtration - In the result chapter, please report the details about the identification rates also for cultures with 2 different bacterial species, and report how the MALDI-TOF MS detected both species from the direct sample (in all cases, were both species identified by MALDI? how did you realized, from the MALDI ID result, that two different species were present?) - In the discussion chapter, please discuss the performance of MALDI-TOF MS in monomicrobial and polymicrobial samples. - Please replace BioTyper with Biotyper, and add mention "Bruker Daltonik" as "Bruker Daltonik GmbH, Bremen, Germany) - Please mention that one of the limitation of the study is that the presence of anaerobes has not been investigated (since the plates were incubated only in aerobic environment) - the 38 culture-negative samples could actually be positive for the presence of anaerobes. Reviewer #2: The manuscript "Usefulness of the MALDI-TOF MS technology with membrane filter protocol for the rapid identification of microorganisms in perioperative drainage fluids of hepatobiliary pancreatic surgery" by Kazuyuki Sogawa et al. describes a novel approach to identify microbes directly from clinical specimen by MALDI-TOF mass spectrometry. The Authors modified the protocol using a novel commercial system BACpro for increasing the sensitivity of detected bacteria. Generally, the use of clinical specimen for direct identification of bacteria is challenging. Currently used methods (e.g., commercially available SepsiTyper) are usually time-consuming with limited outputs. The Authors show another approach which could provide reliable data within short turnaround time. The study is sufficiently designed and the manuscript is well written. In the Discussion, limits of the study are also provided. I have some minor comments to the text only: - Page 7, Line 5: The Authors can avoid the use of "(on average)" as the time difference is probably meaningless; - Page 8, Lines 7-10: It is not necessary to specify MWs of proteins included in commercial calibration standard; - Page 8, Lines 14-15: Similarly, description of automatic spectra processing can be avoided; - Page 10, Line 16: Please use capital "R" for Gram-negative and Gram-positive; - Page 11, Lines 19-20: Please reformulate "The gold standard for microorganism identification is to culture bacterial colonies on agar plates" as the culture is only prerequisite for identification of microbes. - Page 11, Lines 20-21: MALDI-TOF MS was not originally developed for identification of microbes. Please reformulate. - Page 12, Line 20: "for bacterial purification" - I am very sorry to say, but I do not understand this sentence; - Page 12, Lines 22-24: Microarrays are not routinely used in diagnostic laboratories. If I am not correct, please add the reference; Page 13, Lines 9-12: If MALDI-TOF MS is used for identification of bacteria from culture, the process can take shorter (24 h) time. Please correct. ****** 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: Miriam Cordovana, Bruker Daltonik, GmbH Reviewer #2: Yes:** Jaroslav Hrabak [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.0246002.r001
Revision 1
3 Dec 2020 Author Response Thank the academic editor and two reviewers so much for taking your precious time to evaluate and improve our manuscripts and giving us the precious comments. Reviewer #1: - I recommend to slightly reformulate, in the abstract, the methods paragraph, in order to include a sentence about the tests made to evaluate the LOD of Rapid BACpro with/without filtration. [Authors' reply] We appreciate the reviewer’s suggestion. We added the sentence, “The levels of detail of rapid BACpro® pretreatment with or without filtration were also evaluated for the accuracy of bacterial identification.” in the section of Abstract of the revised manuscript. - In the result chapter, please report the details about the identification rates also for cultures with 2 different bacterial species, and report how the MALDI-TOF MS detected both species from the direct sample (in all cases, were both species identified by MALDI? how did you realized, from the MALDI ID result, that two different species were present?) [Authors' reply] We appreciate the reviewer’s meaningful suggestion. We added the sentence, “In two-colony morphology samples in which both species were identified, the presence of a mixed culture was recognized by the Sepsityper module software.” in the section of Result of the revised manuscript. - In the discussion chapter, please discuss the performance of MALDI-TOF MS in monomicrobial and polymicrobial samples. [Authors' reply] We appreciate the reviewer’s helpful comment. We added the sentence, “For the identification of monomicrobial and polymicrobial samples using MLDI-TOF MS, the Sepsityper module which we utilized also includes a novel functionality where an alert is generated automatically for mixed samples [17].” in the section of Discussion of the revised manuscript. We also added the article “17. Scohy A, Noël A, Boeras A, Brassinne L, Laurent T et al. Evaluation of the Bruker MBT Sepsityper IVD module for the identification of polymicrobial blood cultures with MALDI-TOF MS. Eur J Clin Microbiol Infect Dis 2018;37:2145–2152.” in the reference of the revised manuscript. - Please replace BioTyper with Biotyper, and add mention "Bruker Daltonik" as "Bruker Daltonik GmbH, Bremen, Germany) [Authors' reply] As the reviewer‘s suggestion, we amended “BioTyper” to “Biotyper”, and "Bruker Daltonics" to "Bruker Daltonik" in the revised manuscript. - Please mention that one of the limitation of the study is that the presence of anaerobes has not been investigated (since the plates were incubated only in aerobic environment) - the 38 culture-negative samples could actually be positive for the presence of anaerobes. [Authors' reply] We appreciate the reviewer’s comment. We added the limitation indicated above in the revised manuscript. Reviewer #2: - Page 7, Line 5: The Authors can avoid the use of "(on average)" as the time difference is probably meaningless; [Authors' reply] We appreciate the reviewer’s comment. We deleted the part "(on average)" in the revised manuscript. - Page 8, Lines 7-10: It is not necessary to specify MWs of proteins included in commercial calibration standard; [Authors' reply] As the reviewer’s helpful suggestion, we deleted the part indicated above in the revised manuscript. - Page 8, Lines 14-15: Similarly, description of automatic spectra processing can be avoided; [Authors' reply] As the reviewer’s helpful suggestion, we also deleted the part indicated above in the revised manuscript. - Page 10, Line 16: Please use capital "R" for Gram-negative and Gram-positive; [Authors' reply] We amended “gram-negative and gram-positive “ to “Gram-negative and Gram-positive” in the revised manuscript. - Page 11, Lines 19-20: Please reformulate "The gold standard for microorganism identification is to culture bacterial colonies on agar plates" as the culture is only prerequisite for identification of microbes. [Authors' reply] As the reviewer’s suggestion, the sentence was amended to “Identification of microorganisms is primarily undertaken by the culture of bacterial colonies on agar plates.” in the revised manuscript. - Page 11, Lines 20-21: MALDI-TOF MS was not originally developed for identification of microbes. Please reformulate. [Authors' reply] We agree with the comment. We reformulated the sentence “The MALDI-TOF MS system has been developed for bacterial identification in bacterial colonies.” in the revised manuscript. - Page 12, Line 20: "for bacterial purification" - I am very sorry to say, but I do not understand this sentence; [Authors' reply] We appreciate the comment. In order to avoid confusion, we amended “ for bacterial purification” to “ for bacterial identification” in the revised manuscript. - Page 12, Lines 22-24: Microarrays are not routinely used in diagnostic laboratories. If I am not correct, please add the reference; [Authors' reply] We deleted “Microarrays” in the revised manuscript. - Page 13, Lines 9-12: If MALDI-TOF MS is used for identification of bacteria from culture, the process can take shorter (24 h) time. Please correct. [Authors' reply] We added the sentence “MALDI-TOF MS can take shorter time of process for identification of bacteria from culture in 24 hours.” in the revised manuscript. Attachments Attachment Submitted filename: PONE-Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0246002.r002
12 Jan 2021 Decision Letter - Massimiliano Galdiero, Editor Usefulness of the MALDI-TOF MS technology with membrane filter protocol for the rapid identification of microorganisms in perioperative drainage fluids of hepatobiliary pancreatic surgery. PONE-D-20-20446R1 Dear Dr. Takano, 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, Massimiliano Galdiero, M.D., Ph.D. 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: N/A ****** 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 addressed my comments and followed my suggestions, delivering a new version of the manuscript which requires no more corrections, from my point of view. I recommend the publication of the manuscript in the current format. ****** 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.0246002.r003
Formally Accepted
14 Jan 2021 Acceptance Letter - Massimiliano Galdiero, Editor PONE-D-20-20446R1 Usefulness of the MALDI-TOF MS technology with membrane filter protocol for the rapid identification of microorganisms in perioperative drainage fluids of hepatobiliary pancreatic surgery. Dear Dr. Takano: 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 Prof. Massimiliano Galdiero Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0246002.r004

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