Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Denise van Hout; Tess D. Verschuuren; Patricia C. J. Bruijning-Verhagen; Thijs Bosch; Anita C. Schürch; Rob J. L. Willems; Marc J. M. Bonten; Jan A. J. W. Kluytmans

doi:10.1371/journal.pone.0227604

Peer Review History

Original SubmissionOctober 28, 2019
13 Dec 2019 Decision Letter - Jose Melo-Cristino, Editor PONE-D-19-29528 Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content PLOS ONE Dear Mrs. van Hout, 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. I am sorry for the delay with the revision process but it was not easy to find available expert reviewers. The manuscript is very good but please submit a revised version that addresses all the points raised by the two reviewers. Furthermore, I agree that the manuscript is long. Please be more concise and provide clear explanations. We would appreciate receiving your revised manuscript by Jan 27 2020 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, Jose Melo-Cristino, M.D., Ph.D. 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 [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: I Don't Know ****** 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: This is a well-designed, and overall well performed study. Lots of data that have been obtained here, and Tables and Figures and well thought in order to make the whole set easy to understand and analyse. I would suggest to include S1, S2 and S3 in the main manuscript rather than as Supplements, but this is a detail somehow. What is missing on my opinion to provide the reader all the tools to analyse those data in term of population structure distribution are some words about the links between ST. Indeed it is essential to figure out whether a so-called ST73 for instance is phylogenetically close or by contrast very different from an ST131. This would mean completely different things as you may guess. The part dealing with virulence factors might be very much reduced on my opinion. In fact, the entire manuscript would benefit from signifiant shortening, and to condense it would surely make it more attractive to the reader. Reviewer #2: The manuscript describes a molecular and serologic epidemiological study of E. coli isolates from bacteremia ESBL and non- ESBL producers. The manuscript is well written, and despite not showing results completelly new, is interesting to a scientific reader and add more data on the epidemiology of E. coli recovered from blood samples. The molecular study is very complete and WGS was used for analysing the genome of the isolates. I just have a few remarks: Line 276: some VG scores were similar, not completelly different (lines 250-59) Line 309: It is well known that usually in E. coli there is an inversion in resistance genes versus virulence genes, mostly in UPEC (see Johnson et al papers). The exception is ST131, the most well studied ST right now. So, this is not a novelty. Minor comment: Introduction, authors repeat consecutively references (1-4) from lines 62 until 69. Not necessary. ****** 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. 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0227604.r001
Revision 1
16 Dec 2019 Author Response Dear Dr. José Melo-Cristino, We sincerely thank the reviewers for their valuable time to evaluate this manuscript. The paper has been modified in response to the comments and suggestions. All changes are highlighted in the revised document in yellow. Furthermore, the manuscript was shortened by 651 words (20%). In the following we address all comments point by point. The response letter has also been submitted as a seperate PDF document. Yours sincerely, Denise van Hout Response to Reviewer #1: This is a well-designed, and overall well performed study. Lots of data that have been obtained here, and Tables and Figures and well thought in order to make the whole set easy to understand and analyse. Response: We would sincerely like to thank the reviewer for the time taken to critically appraise this manuscript and the input to further improve the manuscript. In the following we will address the comments point by point. I would suggest to include S1, S2 and S3 in the main manuscript rather than as Supplements, but this is a detail somehow. Reply: Thank you for this suggestion. We have indeed considered to move some of the figures from the Supplement in to the main manuscript, given they provide additional illustrative information. However, given the manuscript is very data-dense, including 4 figures and 2 tables already, we are afraid addition of more figures might be a bit too much. We would therefore like to request the reviewer to keep the figures in the supplementary material. What is missing on my opinion to provide the reader all the tools to analyse those data in term of population structure distribution are some words about the links between ST. Indeed it is essential to figure out whether a so-called ST73 for instance is phylogenetically close or by contrast very different from an ST131. This would mean completely different things as you may guess. Reply: Thank you for this comment. We indeed agree with the reviewer that the manuscript indeed lacked guidance on how to interpret the results of the different ST distributions. We have therefore added a comment to the Methods section that includes a short explanation of the MLST scheme (lines 101-102 of the revised manuscript) and have added a short comment to the Discussion section about the known phylogenetic relationship between ST73 and ST131, see lines 238-239 of the revised manuscript. The part dealing with virulence factors might be very much reduced on my opinion. In fact, the entire manuscript would benefit from signifiant shortening, and to condense it would surely make it more attractive to the reader. Reply: We agree with the reviewer that the part on virulence genes was too elaborate and have therefore shortened this paragraph by almost half (lines 209-216 of the revised manuscript). Furthermore, the rest of the manuscript was also shortened (by 20%), as suggested by the reviewer and the academic editor (mainly in the introduction, methods and in the description of results on resistance gene and VG content). Response to Reviewer #2: The manuscript describes a molecular and serologic epidemiological study of E. coli isolates from bacteremia ESBL and non- ESBL producers. The manuscript is well written, and despite not showing results completelly new, is interesting to a scientific reader and add more data on the epidemiology of E. coli recovered from blood samples. The molecular study is very complete and WGS was used for analysing the genome of the isolates. Reply: We would like to thank the reviewer for the time and we sincerely appreciate the careful reading of our manuscript. In the following we respond to the comments point by point. I just have a few remarks: Line 276: some VG scores were similar, not completelly different (lines 250-59) Reply: Thank you for this comment. The reviewer is right to point out that when assessing epidemiological subgroups, most of the VG scores were not significantly different between groups. These analyses were stratified on ESBL-positivity, thus were performed for non-ESBL-Ec and ESBL-Ec separately. We would like to point out that the statement made in line 276 however (line 233 of the revised manuscript), does not refer to the epidemiological subgroups, but refers to the overall significant difference in VG score that was found between non-ESBL-Ec and ESBL-Ec isolates, as provided in lines 211-212 of the revised manuscript. The paragraph on VG scores has been shortened and hopefully is now more clear to the reader. Line 309: It is well known that usually in E. coli there is an inversion in resistance genes versus virulence genes, mostly in UPEC (see Johnson et al papers). The exception is ST131, the most well studied ST right now. So, this is not a novelty. Reply: We thank the reviewer for this comment; we agree that the paragraph did not appropriately reflect current literature and have revised it accordingly. This also included referencing of additional papers, among which important papers performed by Johnson et al., Vila et al. and Velasco et al. (lines 267-273 of the revised manuscript). Minor comment: Introduction, authors repeat consecutively references (1-4) from lines 62 until 69. Not necessary. Reply: Thank you for this suggestion, the changed were made as suggested by the reviewer. Attachments Attachment Submitted filename: Response to reviewers.pdf https://doi.org/10.1371/journal.pone.0227604.r002
20 Dec 2019 Decision Letter - Jose Melo-Cristino, Editor PONE-D-19-29528R1 Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content PLOS ONE Dear Mrs. van Hout, 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. In Table 2, after some serotypes, you have indicated (%), as it is indicated after the value of N in the top of both vertical rows. Can you clarify the mention of (%) in some serotypes? We would appreciate receiving your revised manuscript by Feb 03 2020 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, Jose Melo-Cristino, M.D., Ph.D. Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] [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. 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0227604.r003
Revision 2
20 Dec 2019 Author Response Table 2 was edited in reply to the comments of the editor. https://doi.org/10.1371/journal.pone.0227604.r004
26 Dec 2019 Decision Letter - Jose Melo-Cristino, Editor Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content PONE-D-19-29528R2 Dear Dr. van Hout, 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, Jose Melo-Cristino, M.D., Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0227604.r005
Formally Accepted
31 Dec 2019 Acceptance Letter - Jose Melo-Cristino, Editor PONE-D-19-29528R2 Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content Dear Dr. van Hout: 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 Prof. Jose Melo-Cristino Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0227604.r006

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .