Developing the Pneumonia-Optimized Ratio for Community-acquired pneumonia: An easy, inexpensive and accurate prognostic biomarker

Vinícius Ferraz Cury; Lucas Quadros Antoniazzi; Paulo Henrique Kranz de Oliveira; Wyllians Vendramini Borelli; Sainan Voss da Cunha; Guilherme Cristianetti Frison; Enrico Emerim Moretto; Renato Seligman

doi:10.1371/journal.pone.0248897

Peer Review History

Original SubmissionJanuary 22, 2021
15 Feb 2021 Decision Letter - Aleksandar R. Zivkovic, Editor PONE-D-21-02311 Developing the Pneumonia-Optimized Ratio for Community-acquired pneumonia: an easy, inexpensive and accurate prognostic biomarker PLOS ONE Dear Dr. Seligman, 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 29 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. 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, Aleksandar R. Zivkovic 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 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. Thank you for providing the date(s) when patient medical information was initially recorded. Please also include the date(s) on which your research team accessed the databases/records to obtain the retrospective data used in your study. 3. We note that you have included a TRIPOD checklist, but have not included the page numbers where these items can be found. Please complete the checklist and upload it as a supplementary file. 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 [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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Reviewer #1: In the manuscript the authors present the results of a retrospective observational study. Receiver operating characteristic curve analysis was performed to show the utility of the biomarkers NLCR, MLR and PLR in predicting mortality in patients with CAP. The authors evaluated the correlation of these biomarkers level at admission with mortality and revealed whether the predictive power for mortality rates in patients with CAP could be improved by combining NLCR with CURB-65 scores. Based on NLCR multiplied by the CURB-65 score the authors created a new Pneumonia-Optimized Ratio (POR) score. POR based on a simple, cheap, and rapidly available biomarker NLCR does not require additional payment upon admission. This new POR score may be useful in identifying patients at high risk of mortality who require aggressive treatment. General Comments: 1) How accurate was CURB-65 measured with AUC in terms of predicting mortality? What was the sensitivity and specificity of CURB-65 score for this cohort? 2) Authors include information about CURB-65 score for 97.8% patients: “CURB-65 score were low (score 0-1) for 50%, intermediate (score 2) for 28.9% and high (score 3-5) for 18.9%”. But it stays unclear what CURB-65 score had non-survivors patients. And more to the point it should be clear connection between this data and CURB-65 “range” in Table1 “1.0-2.0 For Survivors” and “2.0 - 3.0 for Non-survivors” 4) On the basis of survival over what period were the patients divided into 2 groups (Survival and Non-survival)? 5) It should be discussed how significant the difference is between AUC 0.706 and 0.753. How much better is the combined POR biomarker than the NLCR and CURB-65 alone? 6) The high percentage of patients with cancer (32.5% Survivors and 47.7% Non-survivors) should be discussed. Did the patients receive therapy, could this affect the results of the blood tests? Perhaps in table 1 it is worth indicating what types of cancers the patients had. 7) Why were mortality rates calculated for POR for 62 patients, while for biomarkers NLCR, PLR and MLR for 65 patients (see tables on Fig1 and Fig2, column “Number”)? 8) Authors should carefully check all the numerical values given in the work, as well as the correspondence of those indicated in the text and tables: a. The Authors say that “The median age of the cohort was 66 years (IQR, 18-103), 53.9% were female, and the median days of hospitalization was 6 (0-140)” While in table 1 age range is 52.0-76.0 for Survivors and и 63.0-88.0 for Non-survivors. There are 18 and 103? b. Also in table 1 the number of male “M” patients is 348 for Survivors and 42 for Non-survivors, which is inconsistent with 53.9% female patients in text. c. Also the range for days of hospitalization in text (0-140) does not correspond to data in Table1 (ranges 2.0-10.0 and и 3.0-17.0). d. Similar mismatch between the specified ranges in text and Table 1, for NLCR in Table1 (3.3-11.5 for Survivors), (7.1-22 for Non-survivors) and range (0.06-137.6) in text for the whole cohort. Range mismatch can also be seen for PLR and MLR. e. In Abstract authors say that “Our sample consisted of 646 individuals” But next: “Patients scored 0-1 (323, 50%), 2 (187, 28.9%), or 3 or above (122, 18.9%) in the CURB-65, and 65 (10%) presented the primary outcome of death.” Totally it’s 632 patients. f. All percentages in the "Number" column should be carefully checked (see tables in Fig. 1 and Fig. 2). 9) The abstract should contain "Conclusion", not "Discussion" 10) Also, the article would be more complete by adding the section "Conclusion" Minor Corrections: 1) Throughout the text: pay attention to the spaces before and after the inserted citations 2) Perhaps for a better perception, it is worth presenting the X-axis in the generally accepted form of '1-Specificity' in Figures 1 and 2. 3) In Figure 1 “AUC: 0.753” the two-dot ":" should be removed so that Figure 1 and Figure 2 are signed uniformly 4) It would be better to make an explanation of "CKD" in table 1, and "Ref." in Figure 1 and Figure 2 5) In Table 1, it is better not to indicate tenths of the value for categories such as age and CURB-65, possibly also for hospitalization days. Reviewer #2: There was a similar article published in Clin Lab. 2019 May 1;65(5). doi: 10.7754/Clin.Lab.2018.181042. "Neutrophil-to-Lymphocyte Ratio in Adult Community-Acquired Pneumonia Patients Correlates with Unfavorable Clinical Outcome" Ge YL et al. revealed NLR combined CURB-65 has better sensitivity and specificity (89.40% versus 91.30%) for unfavorable outcomes of CAP (ICU admission and 30-day mortality) ****** 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.] 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.0248897.r001
Revision 1
5 Mar 2021 Author Response REVIEWER 1 Comment 1) "How accurate was CURB-65 measured with AUC in terms of predicting mortality? What was the sensitivity and specificity of CURB-65 score for this cohort?" Answer. We would like to thank the reviewer for a careful reading and detailed contributions for our study. We've measured CURB-65 accuracy, but we did not include in the manuscript because it's been widely addressed by other authors. However, we included our analysis in the supplementary material (Supplementary Figure 1). CURB-65 showed sensitivity and specificity for the outcome (death) of 0.76 and 0.54 respectively, and an AUC of 0.712. Comment 2) "Authors include information about CURB-65 score for 97.8% patients: “CURB-65 score were low (score 0-1) for 50%, intermediate (score 2) for 28.9% and high (score 3-5) for 18.9%”. But it stays unclear what CURB-65 score had non-survivors patients. And more to the point it should be clear connection between this data and CURB-65 “range” in Table1 “1.0-2.0 For Survivors” and “2.0 - 3.0 for Non-survivors”" Answer. Thanks for the opportunity in clarifying this information. We've described the 95% range of each variable in Table 1. However, median CURB-65 scores for both Survivors and Non-Survivors are still the same presented in Table 1. We've previously calculated the CURB-65 scores for a total of 646 individuals of the sample. Actually, we've now corrected the percentage for the actual number of individuals with CURB (14 missing CURB-65, 2.16%). We've corrected this information in the Results section, transcribed below (P. 6): "The percentage of individuals with CURB-65 scores was as follows: 0-1: 51.1%, 2: 29.58%, 3 or more: 19.3% (14 missing data, 2.16%)." We've also corrected Table 1 using the correct range. Comment 4) "On the basis of survival over what period were the patients divided into 2 groups (Survival and Non-survival)?" Answer. The outcome was collected from patients admitted from 2019 to 2020. At the time of the analysis (October 2020), all patients had one of the following outcomes: Death (within 24 hours or not) or discharged (home or to a secondary care center). Thus, survival analysis included the whole hospitalization of all subjects. Comment 5) It should be discussed how significant the difference is between AUC 0.706 and 0.753. How much better is the combined POR biomarker than the NLCR and CURB-65 alone? Answer. Thank you for the opportunity to discuss this further. Indeed, an increased test accuracy allows a better identification of individuals with increased risk of death. Objectively, using the optimal cutpoint for both NLCR, CURB-65 and POR, we'd be able to identify, respectively, 59/100, 76/100 and 72/100. However, the rate of false positives is respectively 41.9%, 42%, and 28.47%. The difference between AUC may be modest, but it plays a massive impact in a public health context, such as the one described in this study. We've discussed this result further in the Discussion section, 4th paragraph: Regarding the public health system in low and middle-income countries, health depenses are decisive for equality and distribution of care. CAP is still a major public health issue in these countries, especially because of the costs of hospital admissions and severe cases[25]. The usage of simple prognostic biomarkers are stimulated due to their increased ability to predict death in such contexts[26]. The fourth quartile of the NLCR showed approximately 4 more days of hospitalization than the first quartile. This finding raises awareness of the increased financial burden of patients with higher NLCR, potentially investing higher resources in these individuals. Comment 6) The high percentage of patients with cancer (32.5% Survivors and 47.7% Non-survivors) should be discussed. Did the patients receive therapy, could this affect the results of the blood tests? Perhaps in table 1 it is worth indicating what types of cancers the patients had. Answer. In the inclusion criteria, we defined to include only non-end stage cancer. We corrected in table 1. Comment 7) Why were mortality rates calculated for POR for 62 patients, while for biomarkers NLCR, PLR and MLR for 65 patients (see tables on Fig1 and Fig2, column “Number”)? Answer. The difference presented by different biomarkers is due to the missing CURB-65 data of 3 patients in this sample, which limited the application of POR accuracy analysis to 62 patients. Comment 8) Authors should carefully check all the numerical values given in the work, as well as the correspondence of those indicated in the text and tables: a. The Authors say that “The median age of the cohort was 66 years (IQR, 18-103), 53.9% were female, and the median days of hospitalization was 6 (0-140)” While in table 1 age range is 52.0-76.0 for Survivors and и 63.0-88.0 for Non-survivors. There are 18 and 103? Answer. We want to thank the reviewer for this careful reading of the manuscript. Please see Answer to Comment 2 above. We've corrected the range in Table 1. b. Also in table 1 the number of male “M” patients is 348 for Survivors and 42 for Non-survivors, which is inconsistent with 53.9% female patients in text. Answer. Again, we apologize for the inconsistency between Table 1 and the body text. Table 1 refers to Female individuals (306+42 = 348. 348/646 = 53.9% in text). We've corrected Table 1 accordingly. c. Also the range for days of hospitalization in text (0-140) does not correspond to data in Table1 (ranges 2.0-10.0 and и 3.0-17.0). Answer. We've corrected this information in Table 1. d. Similar mismatch between the specified ranges in text and Table 1, for NLCR in Table1 (3.3-11.5 for Survivors), (7.1-22 for Non-survivors) and range (0.06-137.6) in text for the whole cohort. Range mismatch can also be seen for PLR and MLR. Answer. We've corrected this information in Table 1. e. In Abstract authors say that “Our sample consisted of 646 individuals” But next: “Patients scored 0-1 (323, 50%), 2 (187, 28.9%), or 3 or above (122, 18.9%) in the CURB-65, and 65 (10%) presented the primary outcome of death.” Totally it’s 632 patients. Answer. Please see Answer Comment 2. We've corrected this information in the Results section. f. All percentages in the "Number" column should be carefully checked (see tables in Fig. 1 and Fig. 2). Answer. We've carefully checked all values described in Figure 1, Figure 2 and Table 1 as well. Small changes in the "Number" column regarding percentages (maximum change = 0.2%). We thank the reviewer for the opportunity to clarify and correct these values. Comment 9) The abstract should contain "Conclusion", not "Discussion". Answer. We've corrected this point in the abstract. Comment 10) Also, the article would be more complete by adding the section "Conclusion" Answer. We've corrected this point in the manuscript. Comment "Minor Corrections": 1) Throughout the text: pay attention to the spaces before and after the inserted citations 2) Perhaps for a better perception, it is worth presenting the X-axis in the generally accepted form of '1-Specificity' in Figures 1 and 2. 3) In Figure 1 “AUC: 0.753” the two-dot ":" should be removed so that Figure 1 and Figure 2 are signed uniformly 4) It would be better to make an explanation of "CKD" in table 1, and "Ref." in Figure 1 and Figure 2 5) In Table 1, it is better not to indicate tenths of the value for categories such as age and CURB-65, possibly also for hospitalization days. Answer. We've corrected these points in the manuscript. REVIEWER 2 Comment 1) "There was a similar article published in Clin Lab. 2019 May 1;65(5). doi: 10.7754/Clin.Lab.2018.181042. "Neutrophil-to-Lymphocyte Ratio in Adult Community-Acquired Pneumonia Patients Correlates with Unfavorable Clinical Outcome" Ge YL et al. revealed NLR combined CURB-65 has better sensitivity and specificity (89.40% versus 91.30%) for unfavorable outcomes of CAP (ICU admission and 30-day mortality)" Answer. We would like to thank the reviewer for a detailed reading and analysis of the manuscript we submitted. Indeed, previous studies have mentioned biomarkers as predictors of mortality in Community-Acquired Pneumonia. Specifically the study conducted by Ge et al mentioned by the reviewer, our study distinguishes because of the population studied. We demonstrated that an NLR combined with CURB-65 is a useful predictor biomarker for mild cases and for patients with CAP hospitalized in the ICU. We included a citation of this article in introduction, paragraph 2. Attachments Attachment Submitted filename: Response Letter.docx https://doi.org/10.1371/journal.pone.0248897.r002
8 Mar 2021 Decision Letter - Aleksandar R. Zivkovic, Editor Developing the Pneumonia-Optimized Ratio for Community-acquired pneumonia: an easy, inexpensive and accurate prognostic biomarker PONE-D-21-02311R1 Dear Dr. Seligman, 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, Aleksandar R. Zivkovic Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0248897.r003
Formally Accepted
11 Mar 2021 Acceptance Letter - Aleksandar R. Zivkovic, Editor PONE-D-21-02311R1 Developing the Pneumonia-Optimized Ratio for Community-acquired pneumonia: an easy, inexpensive and accurate prognostic biomarker Dear Dr. Seligman: 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. Aleksandar R. Zivkovic Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0248897.r004

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 .