Five millennia of Bartonella quintana bacteraemia

Ba-Hoang-Anh Mai; Rémi Barbieri; Thomas Chenal; Dominique Castex; Richard Jonvel; Davide Tanasi; Patrice Georges-Zimmermann; Olivier Dutour; David Peressinotto; Coralie Demangeot; Michel Drancourt; Gérard Aboudharam

doi:10.1371/journal.pone.0239526

Peer Review History

Original SubmissionMarch 15, 2020
23 Apr 2020 Decision Letter - David Caramelli, Editor PONE-D-20-07460 Five millennia of Bartonella quintana bacteremia. PLOS ONE Dear Dr. Aboudharam, 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. We would appreciate receiving your revised manuscript by Jun 07 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, David Caramelli, Ph.D Academic Editor PLOS ONE Journal requirements: When submitting your revision, we need you to address these additional requirements: 1. 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.plosone.org/attachments/PLOSOne_formatting_sample_main_body.pdf and http://www.plosone.org/attachments/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for including the following ethics statement on the submission details page: 'all the teeth studied, we were provided by their scientific managers having the full liberty to conducted microbiology studies. This kind of sample is not restricted by any regulation in force and only requires the authorization of the scientific manager (all granted as co-authors)' Please also include this information in the ethics statement in the Methods section of your manuscript. 3. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files 4. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 5. Thank you for stating the following in the Acknowledgments Section of your manuscript: "This work was supported by the French Government under the Investissements d’avenir (Investments for the Future) program managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research), [reference: Méditerranée Infection 10-IAHU-03]. This work was supported by Région Le Sud (Provence Alpes Côte d’Azur) and European funding [FEDER BIOTK]." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "The author(s) received no specific funding for this work." 6. We note you have included a table to which you do not refer in the text of your manuscript. Please ensure that you refer to Table 1-3 in your text; if accepted, production will need this reference to link the reader to the Table. 7. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files 8. Please upload a copy of Supporting Information Table S1-S3 which you refer to in your text on page 5. 9. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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: Partly Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A 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: No Reviewer #2: No ****** 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: No Reviewer #2: No ****** 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: I have genuinely appreciated the spirit of the paper and the original data presented by the authors of this manuscript. The topic of B. quintana infection is interesting and the genetic data derived from ancient samples can help science reconstruct the evolutionary history of this pathogen, its interaction with the human species and its global impact on humankind's health. However, there are some issues that the authors should carefully consider and work on: 1. the English of the manuscript is generally week, with several expressions and collocations typically seen in other languages. In addition, the names of pathogens are not consistently written in italics throughout the manuscript. The manuscript should be read by a native speaker; 2- the tone of the manuscript is often too assertive e.g. "the results reported here are authentic"; 3- the general clinical aspects of B. quintana infection should also be presented in the "Introduction" section, as much as the fact that presence of the pathogen does not implicate a severe clinical manifestation. Furthermore, the historical part on the first description of trench fever should be discussed more at length, with a focus on the overall impact on soldiers' health, as much as its interplay with the subsequent Spanish flu pandemic (they are correct in touching co-morbidities later on in the manuscript); 4- talking of comorbidities, the authors should endeavour to speculate more in depth on the potential health consequences on the analyzed individuals; 5- the comparison between infection in soldiers and civilians is interesting but mostly "artificial" because this disease was considered a "military disease" at the very beginning of its recorded history only due to the (special) circumstances under which it was originally described, but there is no real reason to think that poor hygiene conditions are an exclusive characteristic of military life. Way more interesting would be to examine the demographic information for each site, e.g. male/female ratio, distribution according to age range, living standards, diet, detected co-morbidities; 6- in the article, the authors also touch upon the topic of animal infection and zoonotic transmission to the human species, which is indeed a very good point. Further details should be given for the ancient populations analyzed in this study; 7- with reference to the St. Lucia Catacomb (Syracuse, Sicily), from the scientific perspective and that of science communication, I find it controversial that on 8th April 2019 an article (https://www.lasicilia.it/gallery/sicilians/234328/davide-tanasi-l-archeologo-che-dagli-stati-uniti-svela-la-sicilia-antica.html) appeared in the Italian-language press where directly quoted statements were made about the presence in two individuals of "febbre del legionario" - possibly referred to "Legionnaires' disease"?, a completely different disease caused by Legionella pneumophila - while in this manuscript it is written that only 1/28 citizens tested positive. Are we talking about the same sample(s) presented in this paper or something published elsewhere/unpublished? If we are talking about the same sample(s), has something changed in the lab data in the meantime? Interestingly, in that press report, a correlation was made between poor diet and disease (exactly what I mentioned in point #5). Why has this not been investigated further in the official scientific publication? Reviewer #2: It is an interesting manuscript which shows, however, some relevant lacunae. A. In the abstract the last sentence is not clear: are the Author/s talking about their findings or findings in this area in general? Please clarify this point. B. Insufficient demographic data are provided for each site in the supplementary material (6 out of 9 sites have no anthropological data). I also suggest to use this data in the context of a lengthier discussion in the main manuscript. C. The manuscript lacks information about the skeletons and teeth that were examined: for example table 1 should also contain more details about the samples, not only how many and whether they tested positive. In order to better assess the quality of the analyzed sample, I would like to know which specific tooth, from which side, if it is monoradicular or pluriradicular and also the sex and age at death of the skeletons considered. Or you can provide another table with this information. This nice genetic result, to achieve a higher value, should be better related to a proper and exhaustive demographic or, at least when not possible, anthropological discussion. An addition like this would increase the quality of the manuscript. D. Do the Author/s have any data on the dietary conditions of these ancient individuals? Literary or archaeological or isotope analyses. E. In the discussion (page 5), the Author/s write "free of traumatic lesions": can the Author/s better clarify this point? Are the Author/s talking about the absence of pathologies like caries or calculus and also tooth fractures? F. The English of the manuscript shows some impurities: a check by a native speaker would be a good option. ****** 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.0239526.r001
Revision 1
24 Jun 2020 Author Response Dear Editor, Please find enclosed the revised version of our manuscript PONE-D-20-07460 entitled “Five millennia of Bartonella quintana bacteremia” along with the answers of the authors to the reviewers’remarks. Please note that all the authors agreed on the addition of David Peressinotto, and Coralie Demangeot as additional co-authors which now contribution helped to answer some reviewers’ comments. 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'. 1. 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.plosone.org/attachments/PLOSOne_formatting_sample_main_body.pdf and http://www.plosone.org/attachments/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for including the following ethics statement on the submission details page: 'all the teeth studied, we were provided by their scientific managers having the full liberty to conducted microbiology studies. This kind of sample is not restricted by any regulation in force and only requires the authorization of the scientific manager (all granted as co-authors)' Please also include this information in the ethics statement in the Methods section of your manuscript. Authors’answer: we included this information (lines 75-78) 3. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files 4. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 5. Thank you for stating the following in the Acknowledgments Section of your manuscript: "This work was supported by the French Government under the Investissements d’avenir (Investments for the Future) program managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research), [reference: Méditerranée Infection 10-IAHU-03]. This work was supported by Région Le Sud (Provence Alpes Côte d’Azur) and European funding [FEDER BIOTK]." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "The author(s) received no specific funding for this work." Authors’answer: The text has been corrected accordingly and the appropriate section has been completed in the website. 6. We note you have included a table to which you do not refer in the text of your manuscript. Please ensure that you refer to Table 1-3 in your text; if accepted, production will need this reference to link the reader to the Table. Authors’answer: The authors corrected mislabelling of Tables, all the three Tables are now cited in the text (Lines 121-125). 7. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files Authors’answer: Corrected accordingly 8. Please upload a copy of Supporting Information Table S1-S3 which you refer to in your text on page 5. Authors’answer: The authors corrected mislabelling of Tables, there are NO supplementary Tables. 9. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. Authors’answer: Corrected accordingly, line 78 in the text (S1 Text) and Supporting Information, line 323-324 Reviewer's Responses to Questions Comments to the Author Reviewer #1: I have genuinely appreciated the spirit of the paper and the original data presented by the authors of this manuscript. The topic of B. quintana infection is interesting and the genetic data derived from ancient samples can help science reconstruct the evolutionary history of this pathogen, its interaction with the human species and its global impact on humankind's health. However, there are some issues that the authors should carefully consider and work on: 1. the English of the manuscript is generally week, with several expressions and collocations typically seen in other languages. In addition, the names of pathogens are not consistently written in italics throughout the manuscript. The manuscript should be read by a native speaker; Authors’answer: The revised version of the manuscript has been corrected by professionals (Certificate enclosed). 2- the tone of the manuscript is often too assertive e.g. "the results reported here are authentic"; Authors’answer: The revised version of the manuscript has been corrected by professionals who took this appreciation (which is just incomprehensible for French authors) into consideration (Certificate enclosed). 3- the general clinical aspects of B. quintana infection should also be presented in the "Introduction" section, as much as the fact that presence of the pathogen does not implicate a severe clinical manifestation. Furthermore, the historical part on the first description of trench fever should be discussed more at length, with a focus on the overall impact on soldiers' health, as much as its interplay with the subsequent Spanish flu pandemic (they are correct in touching co-morbidities later on in the manuscript); Authors’answer: - The clinical manifestations of infection presented in the Introduction section are now expanded as proposed by the reviewer (Lines 55-58). - The authors do not agree with the following remark of the reviewer that B. quintana infection is a mild one. The authors are now reporting on mortality rates which clearly indicate that B. quintana infection is indeed a life-threatening infection (Lines 52-55). - The authors carefully checked that no report issued regarding B. quintana and Spanish flu (see reference [2,3], line 211-213). 4- talking of comorbidities, the authors should endeavour to speculate more in depth on the potential health consequences on the analyzed individuals; Authors’answer: The authors thanks the reviewer to give the opportunity to discuss this interesting aspect (Lines 139-142). 5- the comparison between infection in soldiers and civilians is interesting but mostly "artificial" because this disease was considered a "military disease" at the very beginning of its recorded history only due to the (special) circumstances under which it was originally described, but there is no real reason to think that poor hygiene conditions are an exclusive characteristic of military life. Way more interesting would be to examine the demographic information for each site, e.g. male/female ratio, distribution according to age range, living standards, diet, detected co-morbidities; Authors’answer: Indeed, one output of the present study was to demonstrate an absence of significant difference between civil and military populations; hence suggesting the absence of differences in terms of cloth hygiene (Lines 180-182). 6- in the article, the authors also touch upon the topic of animal infection and zoonotic transmission to the human species, which is indeed a very good point. Further details should be given for the ancient populations analyzed in this study; Authors’answer: The authors just not have any data regarding contacts with animals in any of the buried populations here reported. 7- with reference to the St. Lucia Catacomb (Syracuse, Sicily), from the scientific perspective and that of science communication, I find it controversial that on 8th April 2019 an article (https://www.lasicilia.it/gallery/sicilians/234328/davide-tanasi-l-archeologo-che-dagli-stati-uniti-svela-la-sicilia-antica.html) appeared in the Italian-language press where directly quoted statements were made about the presence in two individuals of "febbre del legionario" - possibly referred to "Legionnaires' disease"?, a completely different disease caused by Legionella pneumophila - while in this manuscript it is written that only 1/28 citizens tested positive. Are we talking about the same sample(s) presented in this paper or something published elsewhere/unpublished? If we are talking about the same sample(s), has something changed in the lab data in the meantime? Interestingly, in that press report, a correlation was made between poor diet and disease (exactly what I mentioned in point #5). Why has this not been investigated further in the official scientific publication? Authors’answer: - The reviewer is perfectly right to point to the possibility of co-infection with Bartonella quintana in ancient populations, and this interesting point is now emphasized in the revised version of the manuscript (Lines 139-142). - Then, to the best of the authors knowledge, co-infections with Bartonella quintana are with other lice-borne pathogens including Yersinia pestis, Rickettsia prowazekii; this point is now clarified in the revised version of the manuscript (Lines 139-142). - Then, to the best of the authors knowledge, Legionella pneumophila is NOT known to be a lice-borne pathogen; but rather a water-borne pathogen currently transmitted by aerosols of contaminated water. - Therefore, there was no particular reason to test for the hypothesis of Legionella pneumophila rather than any other hypothesis. - At last, the “La Sicilia” paper referred to by the reviewer, is clearly grey literature which cannot be incorporated nor discussed as a reference in the present work to be published in PLoS ONE. - The authors did not test for Legionella pneumophila but rather for Bartonella quintana; the 1/28 individual in Table 1 is referring to Bartonella quintana, not at all to Legionella pneumophila. Reviewer #2: It is an interesting manuscript which shows, however, some relevant lacunae. A. In the abstract the last sentence is not clear: are the Author/s talking about their findings or findings in this area in general? Please clarify this point. Authors’answer: The reviewer is perfectly right and this sentence was deleted from the revised version. B. Insufficient demographic data are provided for each site in the supplementary material (6 out of 9 sites have no anthropological data). I also suggest to use this data in the context of a lengthier discussion in the main manuscript. Authors’answer: The reviewer is right but no further demographic data were available in the reasonable time for revising this manuscript. C. The manuscript lacks information about the skeletons and teeth that were examined: for example table 1 should also contain more details about the samples, not only how many and whether they tested positive. In order to better assess the quality of the analyzed sample, I would like to know which specific tooth, from which side, if it is monoradicular or pluriradicular and also the sex and age at death of the skeletons considered. Or you can provide another table with this information. This nice genetic result, to achieve a higher value, should be better related to a proper and exhaustive demographic or, at least when not possible, anthropological discussion. An addition like this would increase the quality of the manuscript. Authors’answer: The reviewer is right but no further demographic data were available in the reasonable time for revising this manuscript. D. Do the Author/s have any data on the dietary conditions of these ancient individuals? Literary or archaeological or isotope analyses. Authors’answer: The reviewer is right but no further demographic data were available in the reasonable time for revising this manuscript. E. In the discussion (page 5), the Author/s write "free of traumatic lesions": can the Author/s better clarify this point? Are the Author/s talking about the absence of pathologies like caries or calculus and also tooth fractures? Authors’answer: The reviewer is perfectly right, this point is clarified both in the Discussion section (Lines 128-130). F. The English of the manuscript shows some impurities: a check by a native speaker would be a good option. Authors’answer: The revised version of the manuscript has been corrected by professionals (Certificate enclosed). 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. As the authors answered all the Editor and Reviewers’ remarks and corrected the manuscript accordingly, they hope that this revised version will be accepted for publication in PLoS ONE. Sincerely, Dr. Gérard ABOUDHARAM, Corresponding author. Attachments Attachment Submitted filename: Plos One answers.docx https://doi.org/10.1371/journal.pone.0239526.r002
11 Aug 2020 Decision Letter - David Caramelli, Editor PONE-D-20-07460R1 Five millennia of Bartonella quintana bacteremia. PLOS ONE Dear Dr. Aboudharam, 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 minor point highlighted by one referee that are reported below . Please submit your revised manuscript by Sep 25 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. 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, David Caramelli, Ph.D Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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 Reviewer #2: (No Response) ******** 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 Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: 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 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 #1: Yes 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 #1: This new version of the manuscript is well-researched and presented in a better form. In my opinion, the authors have made good amendments. The "La Sicilia" reference be may grey literature but I am very skeptical about going to the media with certain claims and then issuing something different in a scientific paper, but thanks for clarifying that. I would only recommend adding a couple of general references when you discuss the pathogen-population interaction: 1) Bos KI, Kühnert D, Herbig A, et al. Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annu Rev Microbiol. 2019;73:639-666. 2) Rühli FJ, Galassi FM, Haeusler M. Palaeopathology: Current challenges and medical impact. Clin Anat. 2016;29(7):816-822. Reviewer #2: Edits made in an orderly and clear way. I think the authors have answered the main critical points of the previous version of this manuscript. ****** 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 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.] 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.0239526.r003
Revision 2
18 Aug 2020 Author Response Dear Editor, Please find enclosed the second revised version of the manuscript PONE-D-20-07460 entitled: “Five millennia of Bartonella quintana bacteremia” along with the answers of the authors to the reviewers ‘ comments. Reviewers' comments: Reviewer #1: This new version of the manuscript is well-researched and presented in a better form. In my opinion, the authors have made good amendments. The "La Sicilia" reference be may grey literature but I am very skeptical about going to the media with certain claims and then issuing something different in a scientific paper, but thanks for clarifying that. Authors’answer: The authors acknowledge this positive remark. I would only recommend adding a couple of general references when you discuss the pathogen-population interaction: 1) Bos KI, Kühnert D, Herbig A, et al. Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annu Rev Microbiol. 2019;73:639-666. 2) Rühli FJ, Galassi FM, Haeusler M. Palaeopathology: Current challenges and medical impact. Clin Anat. 2016;29(7):816-822. Authors’answer: The reviewer is perfectly suggesting to broaden the Discussion section, these two references are now cited in the Discussion section (Lines 213-215), and listed as new references 44 and 45, accordingly. Reviewer #2: Edits made in an orderly and clear way. I think the authors have answered the main critical points of the previous version of this manuscript. Authors’answer: The authors acknowledge this positive remark. As the authors answered the Reviewer n°1 remark and corrected the manuscript accordingly, the authors hope that this second revised version will be accepted for publication, Sincerely Gérard ABOUDHARAM, Corresponding author. Attachments Attachment Submitted filename: Rebuttal Letter.docx https://doi.org/10.1371/journal.pone.0239526.r004
9 Sep 2020 Decision Letter - David Caramelli, Editor Five millennia of Bartonella quintana bacteremia. PONE-D-20-07460R2 Dear Dr. Aboudharam, 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, David Caramelli, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0239526.r005
Formally Accepted
7 Oct 2020 Acceptance Letter - David Caramelli, Editor PONE-D-20-07460R2 Five millennia of Bartonella quintana bacteraemia. Dear Dr. Aboudharam: 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 Professor David Caramelli Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0239526.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 .