A simplified pneumonia severity index (PSI) for clinical outcome prediction in COVID-19

Shu-Ching Chang; Gary L. Grunkemeier; Jason D. Goldman; Mansen Wang; Paul A. McKelvey; Jennifer Hadlock; Qi Wei; George A. Diaz

doi:10.1371/journal.pone.0303899

Peer Review History

Original SubmissionJanuary 29, 2024
14 Mar 2024 Decision Letter - Kuo-Cherh Huang, Editor PONE-D-24-00824A Simplified Pneumonia Severity Index (PSI) for Clinical Outcome Prediction in COVID-19PLOS ONE Dear Dr. Chang, 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 Apr 28 2024 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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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: The study titled presents a thorough investigation into the effectiveness of a simplified version of the Pneumonia Severity Index (PSI) in predicting 30-day mortality among COVID-19 patients. The research addresses the challenge of manual chart review posed by certain variables in the original PSI, proposing a streamlined version termed PSI-17. Through a retrospective cohort study involving 1,138 hospitalized COVID-19 patients, the study demonstrates that PSI-17 exhibits comparable predictive performance to PSI-20, as measured by various metrics including area under the curve (AUC), Integrated Calibration Index (ICI), and Brier Score. Notably, PSI-17 eliminates the need for manual chart review, enabling automated risk calculation within electronic medical records (EMRs). While the study's findings offer promising implications for clinical practice, such as facilitating timely risk assessment and resource allocation, potential limitations such as limited generalizability and variable selection nuances are acknowledged. The authors advocate for further validation and exploration to consolidate the utility of PSI-17 across diverse patient populations and healthcare settings. Overall, the study contributes valuable insights to the ongoing efforts in optimizing risk prediction models for COVID-19 management, emphasizing the importance of practical adaptation and implementation of existing tools in real-world clinical contexts. Additional literature can help with the study and pneumonia and covid • File TM Jr, Ramirez JA. Community-Acquired Pneumonia. N Engl J Med. 2023 Aug 17;389(7):632-641. doi: 10.1056/NEJMcp2303286. PMID: 37585629. • Huang AA, Huang SY. Hospitalized COVID-19 patients with diabetes have an increased risk for pneumonia, intensive care unit requirement, intubation, and death: A cross-sectional cohort study in Mexico in 2020. Health Sci Rep. 2023 Apr 18;6(4):e1222. doi: 10.1002/hsr2.1222. PMID: 37081996; PMCID: PMC10112272. • Fine MJ, Auble TE, Yealy DM, Hanusa BH, Weissfeld LA, Singer DE, Coley CM, Marrie TJ, Kapoor WN. A prediction rule to identify low-risk patients with community-acquired pneumonia. N Engl J Med. 1997 Jan 23;336(4):243-50. doi: 10.1056/NEJM199701233360402. PMID: 8995086. The conclusions drawn in this study elegantly stem from the meticulously designed methods, presenting a logical approach for studying pneumonia severity in the context of COVID-19. By retrospectively analyzing a sizable cohort of hospitalized COVID-19 patients, the researchers effectively compared the performance of the simplified Pneumonia Severity Index (PSI-17) with the original PSI-20. Through rigorous statistical analyses, including correlation assessments and logistic regressions for 30-day mortality prediction, the study robustly evaluated the predictive abilities of both indices. The findings, indicating comparable performance between PSI-17 and PSI-20 across multiple metrics, underscore the feasibility and reliability of the simplified index. Moreover, the pragmatic adaptation of PSI-17, eliminating the need for manual chart review, underscores the study's commitment to enhancing clinical utility and efficiency. Thus, the study's conclusions not only reflect the logical progression of its methods but also provide actionable insights into optimizing pneumonia severity assessment in COVID-19 patients. Reviewer #2: Manuscript ID: PONE-D-24-00824 A Simplified Pneumonia Severity Index (PSI) for Clinical Outcome Prediction in COVID-19 Summary: This study shows that a simpler version of the PSI score has equivalent forecasting ability for COVID-19 than the original version. Major findings: The PSI score has 20 variables of which 17 can be obtained from EMR and the last 3 must be evaluated manually from the patient's charts. A comparison of a 17 variable PSI score with the original 20 variable version showed little loss of prediction ability of COVID mortality. Strengths: This is a large database of 1138 patients from the beginning of the COVID-19 pandemic. Major comments / Weaknesses: 1. This is a special application of the PSI 17-score to a specific disease (COVID-19) in a specific period. The mortality found in the onset of the pandemic is not the same as the mortality found now. Could the authors comment on current the COVID-19 situation. 2. Could this simpler PSI version be extrapolated to community acquired pneumonia or is this a COVID-19 special case related to pleural effusion, altered mental status and skilled nursing facility? Minor comments: 1. How long did it take the researchers to assemble the 3-variable data (pleural efussion, altered mental status and skilled nursing facility) from the 1138 patients? 2. This study is of special importance to other retrospective studies of COVID-19 but not in the individual assessment of a COVID-19 patient where these three variables are readily obtainable. This might warrant a comment in the discussion. 3. An article with 1363 patients tested 11 different scores for mortality assessment (10.1016/j.cmi.2021.03.002). PSI was one of the better performing scores for 30-day COVID mortality (in the onset of the pandemic) along with CURB-65, and covid specific scores: 4C and COVID GRAM. ****** 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: Yes: Julio Marchini ******** [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.0303899.r001
Revision 1
28 Apr 2024 Author Response Dear editors and reviewers, We appreciate valuable comments from the reviewers. Your insightful comments have been instrumental in enhancing the quality of our manuscript. We are hopeful that you will find the manuscript acceptable for publication in its new and improved form. Reviewer #1: The study titled presents a thorough investigation into the effectiveness of a simplified version of the Pneumonia Severity Index (PSI) in predicting 30-day mortality among COVID-19 patients. The research addresses the challenge of manual chart review posed by certain variables in the original PSI, proposing a streamlined version termed PSI-17. Through a retrospective cohort study involving 1,138 hospitalized COVID-19 patients, the study demonstrates that PSI-17 exhibits comparable predictive performance to PSI-20, as measured by various metrics including area under the curve (AUC), Integrated Calibration Index (ICI), and Brier Score. Notably, PSI-17 eliminates the need for manual chart review, enabling automated risk calculation within electronic medical records (EMRs). While the study's findings offer promising implications for clinical practice, such as facilitating timely risk assessment and resource allocation, potential limitations such as limited generalizability and variable selection nuances are acknowledged. The authors advocate for further validation and exploration to consolidate the utility of PSI-17 across diverse patient populations and healthcare settings. Overall, the study contributes valuable insights to the ongoing efforts in optimizing risk prediction models for COVID-19 management, emphasizing the importance of practical adaptation and implementation of existing tools in real-world clinical contexts. Additional literature can help with the study and pneumonia and covid • File TM Jr, Ramirez JA. Community-Acquired Pneumonia. N Engl J Med. 2023 Aug 17;389(7):632-641. doi: 10.1056/NEJMcp2303286. PMID: 37585629. • Huang AA, Huang SY. Hospitalized COVID-19 patients with diabetes have an increased risk for pneumonia, intensive care unit requirement, intubation, and death: A cross-sectional cohort study in Mexico in 2020. Health Sci Rep. 2023 Apr 18;6(4):e1222. doi: 10.1002/hsr2.1222. PMID: 37081996; PMCID: PMC10112272. • Fine MJ, Auble TE, Yealy DM, Hanusa BH, Weissfeld LA, Singer DE, Coley CM, Marrie TJ, Kapoor WN. A prediction rule to identify low-risk patients with community-acquired pneumonia. N Engl J Med. 1997 Jan 23;336(4):243-50. doi: 10.1056/NEJM199701233360402. PMID: 8995086. The conclusions drawn in this study elegantly stem from the meticulously designed methods, presenting a logical approach for studying pneumonia severity in the context of COVID-19. By retrospectively analyzing a sizable cohort of hospitalized COVID-19 patients, the researchers effectively compared the performance of the simplified Pneumonia Severity Index (PSI-17) with the original PSI-20. Through rigorous statistical analyses, including correlation assessments and logistic regressions for 30-day mortality prediction, the study robustly evaluated the predictive abilities of both indices. The findings, indicating comparable performance between PSI-17 and PSI-20 across multiple metrics, underscore the feasibility and reliability of the simplified index. Moreover, the pragmatic adaptation of PSI-17, eliminating the need for manual chart review, underscores the study's commitment to enhancing clinical utility and efficiency. Thus, the study's conclusions not only reflect the logical progression of its methods but also provide actionable insights into optimizing pneumonia severity assessment in COVID-19 patients. Response: The authors thank the reviewer for the positive and insightful comments. We have updated the discussion with these references, especially to note that the PSI is not comprehensive on known risk factors, as the reviewer points out with the suggested references. For instance: “The PSI is not comprehensive and other model features could be added, such as diabetes, which is a known risk factor for poor outcomes in COVID-19 [ref] and is not one of the listed co-morbidities in PSI (Table S1).” We have also included the excellent review of community acquired pneumonia in response to point 2 of reviewer #2 (see below). The original Fine et al study was already referenced in the manuscript. Reviewer #2: Manuscript ID: PONE-D-24-00824 A Simplified Pneumonia Severity Index (PSI) for Clinical Outcome Prediction in COVID-19 Summary: This study shows that a simpler version of the PSI score has equivalent forecasting ability for COVID-19 than the original version. Major findings: The PSI score has 20 variables of which 17 can be obtained from EMR and the last 3 must be evaluated manually from the patient's charts. A comparison of a 17 variable PSI score with the original 20 variable version showed little loss of prediction ability of COVID mortality. Strengths: This is a large database of 1138 patients from the beginning of the COVID-19 pandemic. Response: The authors thank the reviewer for the positive review and concise summary. Major comments / Weaknesses: 1. This is a special application of the PSI 17-score to a specific disease (COVID-19) in a specific period. The mortality found in the onset of the pandemic is not the same as the mortality found now. Could the authors comment on current the COVID-19 situation. Response: We agree that the mortality found throughout the pandemic waves differs. While this study assesses the PSI-17 as a mortality prediction tool in the early pandemic era, we see this as a proof of concept for the comparability of PSI-20 and PSI-17. To conclusively determine if PSI-17 predicts mortality during other variant eras, the PSI-17 would need to be studied in other variant eras to determine predictive ability in these other eras. This analysis is beyond the scope of this article, but we plan to use PSI-17 to study subsequent variant eras. We have updated the Discussion for improved clarity on this point: “Similarly, as the mortality has decreased over time through evolving SARS-CoV-2 variants [refs], the application of a mortality prediction tool would need to be validated in different variant eras.” 2. Could this simpler PSI version be extrapolated to community acquired pneumonia or is this a COVID-19 special case related to pleural effusion, altered mental status and skilled nursing facility? Response: The authors thank the reviewer for the insightful comments and thought-provoking questions. While we hesitate to speculate about the ability of PSI-17 to accurately predict mortality in community acquired pneumonia (CAP), we do think the simplified PSI-17 tool would be easier to implement in clinical care or research on CAP. Further study is needed to validate PSI-17 in CAP. We have added to the Discussion: “To determine whether PSI-17 is predictive of mortality in community acquired pneumonia [ref], validation is an appropriate cohort would need to be performed.” Minor comments: 1. How long did it take the researchers to assemble the 3-variable data (pleural efussion, altered mental status and skilled nursing facility) from the 1138 patients? Response: The authors thank the reviewer for the insights and great questions. Data extraction for the 3 variables from PSI-20 which required manual extraction into a REDCap database was an intensive process, in part because of the subjective nature of these variables. Supervision for 10 reviewers (senior research coordinators and medical students) was performed by 3 senior investigators who conducted training, answered queries from reviewers, resolved discrepancies and reviewed in duplicate 20% of the cases to validate individual reviewers. In total, we estimate approximately 400+ person-hours were spent in manually extracting these variables. 2. This study is of special importance to other retrospective studies of COVID-19 but not in the individual assessment of a COVID-19 patient where these three variables are readily obtainable. This might warrant a comment in the discussion. Response: The authors thank the reviewer for the constructive suggestions and insights. We agree that this study is of special importance to other retrospective studies of COVID-19 but may not be relevant in the individual assessment of a COVID-19 patient where these three variables are readily obtainable. We included below comments in the Discussion. “The simplification of PSI-17 to remove fields not easily accessible by automated data extraction can serve for integration of scores into clinical interfaces of electronic health records to be accessed at the point of care, or for controlling of confounders in retrospective studies of COVID-19. However, use of PSI-17 may not be relevant in the individual assessment of a COVID-19 patient where these three variables are readily obtainable.” 3. An article with 1363 patients tested 11 different scores for mortality assessment (10.1016/j.cmi.2021.03.002). PSI was one of the better performing scores for 30-day COVID mortality (in the onset of the pandemic) along with CURB-65, and covid specific scores: 4C and COVID GRAM. Response: The authors thank the reviewer for the helpful comments and the reference. We have added a comment with reference to the Discussion section: “Pneumonia predictive scores have been studied in COVID-19 and PSI was shown as one of the better performing scores for 30-day COVID mortality (in the onset of the pandemic) along with CURB-65, and covid specific scores: 4C and COVID GRAM among 11 different scores for mortality assessment [ref].” Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0303899.r002
3 May 2024 Decision Letter - Kuo-Cherh Huang, Editor A Simplified Pneumonia Severity Index (PSI) for Clinical Outcome Prediction in COVID-19 PONE-D-24-00824R1 Dear Dr. Chang, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. 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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: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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: Thank you for your corrections. They adequately answered line by line each of the reviews and comments provided in the previous iteration. Reviewer #2: Manuscript ID: PONE-D-24-00824 A Simplified Pneumonia Severity Index (PSI) for Clinical Outcome Prediction in COVID-19 Summary: This study shows that a simpler version of the PSI score has equivalent forecasting ability for COVID-19 than the original version. Major findings: The PSI score has 20 variables of which 17 can be obtained from EMR and the last 3 must be evaluated manually from the patient's charts. A comparison of a 17 variable PSI score with the original 20 variable version showed little loss of prediction ability of COVID mortality. Comments: All my questions have been addressed by the authors. I have no further comments. ****** 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 ******** https://doi.org/10.1371/journal.pone.0303899.r003
Formally Accepted
10 May 2024 Acceptance Letter - Kuo-Cherh Huang, Editor PONE-D-24-00824R1 PLOS ONE Dear Dr. Chang, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Kuo-Cherh Huang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0303899.r004

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