Optimizing hierarchical tree dissection parameters using historic epidemiologic data as ‘ground truth’

David Jacobson; Joel Barratt

doi:10.1371/journal.pone.0282154

Peer Review History

Original SubmissionSeptember 15, 2022
19 Jan 2023 Decision Letter - Nazanin Tajik, Editor PONE-D-22-25671Optimizing hierarchical tree dissection parameters using historic epidemiologic data as ‘ground truth’PLOS ONE Dear Dr. Jacobson, 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 Mar 05 2023 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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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf. 2. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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: Yes ****** 3. 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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: In this paper, the authors main research question is to optimize the hierarchical tree dissection parameter “stringency parameter” using historic epidemiologic data in order to improve the partitioning accuracy which represents the degree to which the tree partitions in this case genetic groupings of pathogens are similar to known epidemiologic groupings. The authors hierarchically clustered 1,873 genotypes of the foodborne pathogen Cyclospora cayetanensis and dissected the tree using multiple values of the stringency parameter from 94% to 99.5% with increments of 0.25% in order to determine the optimal s value that maximizes the accuracy. The study shows that out of 23 different stringency values, clustering the C. cayetanensis isolates with known epidemiologic linkages using stringency parameters of 96.5% and 96.75% yield higher accuracy than values selected empirically. The paper is well-written, and the results are helpful for interested readers of this journal. I believe that the article deserves publication. However, in my opinion, the following minor revision is needed. Comments on the manuscript are as follows: - Why did the author omit the Simpson index results and did not add to a table of results like Table 2 for example? - The authors reported just the accuracy of the trees, why not add sensitivity specificity and precision as performance metrics as well to their results? - The quality of the figure is very high, however in my opinion, the results can be better presented if each tree A, B and C are presented in separate figures. Reviewer #2: 1. In table 2, various performance metrics such as sensitivity, specificity, PPV, and NPV can be calculated and compared. 2. Since choosing an appropriate distance statistic is fundamental, please explain why using Barratt’s heuristic definition of genetic distance is the best option. 3. It seems that references 16 and 22 are the same. Please omit one of them. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). 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Revision 1
23 Jan 2023 Author Response We appreciate the comments from the reviewers and we believe that we have addressed all of the comments listed below. Of interest, both reviewers suggested including additional performance metrics (e.g., specificity, precision, PPV) and this was a point of discussion between the authors before finalizing our initial submission. In our original submission, we ultimately decided to only include accuracy for the sake of brevity in the tables/text; however, it is clear that additional performance metrics would be useful, and we have now included sensitivity, specificity, PPV (i.e., precision), and NPV in our tables and results text in the revised manuscript. A further note is that our group has published an update regarding species naming for human-infecting Cyclospora parasites while this present manuscript was in review. We have updated our Cyclospora species naming convention in the revised manuscript to state Cyclospora spp. or Cyclospora sp., rather than Cyclospora cayetanensis. Please see our response to specific comments below. Reviewer #1: Comments on the manuscript are as follows: 1. - Why did the author omit the Simpson index results and did not add to a table of results like Table 2 for example? a. Simpson index results for all stringency values have been added to Table 2. 2. - The authors reported just the accuracy of the trees, why not add sensitivity specificity and precision as performance metrics as well to their results? a. Sensitivity, specificity, PPV, and NPV values have been added to Table 2 and the text results. Methods have been updated to mention calculation of these performance metrics. 3. - The quality of the figure is very high, however in my opinion, the results can be better presented if each tree A, B and C are presented in separate figures. a. This is a good point and we agree that splitting the figure into separate figures makes for easier interpretation. As such, Figure 1 A-C has been split into Fig 1, Fig 2, and Fig 3, respectively. Manuscript text and figure legends have been updated appropriately. Reviewer #2: 1. In table 2, various performance metrics such as sensitivity, specificity, PPV, and NPV can be calculated and compared. a. Sensitivity, specificity, PPV, and NPV values have been added to Table 2 and the text results. Methods have been updated to mention calculation of these performance metrics. 2. Since choosing an appropriate distance statistic is fundamental, please explain why using Barratt’s heuristic definition of genetic distance is the best option. a. We have added text in the introduction section describing why Barratt’s heuristic was chosen to calculate genetic distances. 3. It seems that references 16 and 22 are the same. Please omit one of them. a. Thank you for the attention to detail. This issue has been resolved and the initial citation #22 has been removed Attachments Attachment Submitted filename: StringencyOptimization_ResponsetoReviewers.docx https://doi.org/10.1371/journal.pone.0282154.r002
8 Feb 2023 Decision Letter - Nazanin Tajik, Editor Optimizing hierarchical tree dissection parameters using historic epidemiologic data as ‘ground truth’ PONE-D-22-25671R1 Dear Dr. Jacobson, 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, Nazanin Tajik Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0282154.r003
Formally Accepted
14 Feb 2023 Acceptance Letter - Nazanin Tajik, Editor PONE-D-22-25671R1 Optimizing hierarchical tree dissection parameters using historic epidemiologic data as ‘ground truth’ Dear Dr. Jacobson: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Nazanin Tajik Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0282154.r004

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