Factors associated with admission to the intensive care unit and mortality in patients with COVID-19, Colombia

Jorge Enrique Machado-Alba; Luis Fernando Valladales-Restrepo; Manuel Enrique Machado-Duque; Andrés Gaviria-Mendoza; Nicolás Sánchez-Ramírez; Andrés Felipe Usma-Valencia; Esteban Rodríguez-Martínez; Eliana Rengifo-Franco; Víctor Hugo Forero-Supelano; Diego Mauricio Gómez-Ramirez; Alejandra Sabogal-Ortiz

doi:10.1371/journal.pone.0260169

Peer Review History

Original SubmissionJune 2, 2021
13 Jul 2021 Decision Letter - Tai-Heng Chen, Editor PONE-D-21-18267 Factors associated with admission to the intensive care unit and mortality in patients with COVID-19, Colombia PLOS ONE Dear Dr. Machado-Alba, 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 Aug 27 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. 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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: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: No ****** 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: 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: 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: Authors have submitted a manuscript of significant importance. It is essential to present COVID-19 related data that originate outside developed countries since there is obvious and dramatic disparity in availability and quality if patient care between developed and developing countries. I recommend acceptance after minor but careful revision. Specific comments are listed below. 1. Reconsider keywords. 2. In Introduction: The first paragraph is redundant. Overall , Introduction should be shorter and more to the point. 3. A phrase „behavior of the infection“ should be reconsidered. 4. In Methods: A sentence „Subjects of any age, sex and city of residence were selected between March 6 and August 31, 2020.” should be rephrased to clearly state if all patients admitted to hospital during this time frame were screened for inclusion. 5. In Methods: Which CXR or CT scans were used? The ones on admission to hospital or the ones with the worst scores. COVID-19 is fast evolving and repeated CXRs and CT scans are a necessity. 6. Line 112: symptoms and signs should be listed in methods. In fact, list of all variables shown in Table 1 and 2 should be listed in methods. Those variables that are not shown in Results and used for statistical analysis should be omitted. 7. Line 118: „in general“ should be substituted for „from the hospital“. 8. Line 130/131: Were there any patients with tracheotomy? 9. Line 160/161: Sentence „among the females.....were pregnant“ should definitely undergo respectful rephrasing. 10. Line 199: „ days of intubation“ referes to duration of intubation or days between hospital admission and intubation? 11. Tables 1 to 4 show differences between survivors and non survivors. Somehow, we have „jumped“ from there to prediction of ICU admission. Steps before prediction modeling should be shown as well, process of selection of variables included in the prediction model should be clear. On the same note, it is not clear how selection of variables included in the mortality prediction was performed. Reviewer #2: I would like to thank the editors of Plos One for giving me the opportunity to review the manuscript “factors associated with admission to the intensive care unit and mortality in patients with COVID-19 in Colombia”. In this observational cohort study, the authors described the characteristics of 780 patients admitted to 4 clinics for COVID-19 in Colombia between march 6 and august 31, 2020 and tried to identify factor associated with death or ICU admission. The authors confirmed previous risk factors for poor outcomes described in much larger cohorts, including from south America. They also identified that, at the time of the study, patients from Cali had poorer outcomes. This report appears now as completely anachronic since both viruses and treatments have profoundly changed. The study provides no new information that can be relevant for other caregivers. Another major limitation of this study is that authors provided comparison between survivors and deceased patients (they report in the methods that they followed-up patient until death…) whereas the main result (as indicated in the title) was the factors associated with either ICU admission or death. In multivariate analysis, the found that coming from Cali, COPD and severe pneumoniae were associated with ICU admission or death. I really don’t understand how this finding may “greatly contribute to improving the prognosis of these patients” as concluded by the authors. ****** 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: Yes:** Suzana Bojic 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.0260169.r001
Revision 1
28 Jul 2021 Author Response Pereira, July 23 of 2021 Response to reviewers Journal: PLOS ONE Manuscript ID: PONE-D-21-18267 Title: Factors associated with admission to the intensive care unit and mortality in patients with COVID-19, Colombia Thank you for the review. Here, we answer the reviewers’ comments point by point. Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes Reviewer #2: No 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: No 3. Have the authors made all data underlying the findings in their manuscript fully available? Reviewer #1: Yes Reviewer #2: No 4. Is the manuscript presented in an intelligible fashion and written in standard English? Reviewer #1: Yes Reviewer #2: Yes 5. Review Comments to the Author Reviewer #1: Authors have submitted a manuscript of significant importance. It is essential to present COVID-19 related data that originate outside developed countries since there is obvious and dramatic disparity in availability and quality if patient care between developed and developing countries. I recommend acceptance after minor but careful revision. Specific comments are listed below. Response/ Thank you 1. Reconsider keywords. Response/ we have adjusted the keywords 2. In Introduction: The first paragraph is redundant. Overall, Introduction should be shorter and more to the point. Response/ the introduction has been shortened and some phrases have been simplified. 3. A phrase „behavior of the infection“ should be reconsidered. Response/ The phrase was simplified. 4. In Methods: A sentence „Subjects of any age, sex and city of residence were selected between March 6 and August 31, 2020.” should be rephrased to clearly state if all patients admitted to hospital during this time frame were screened for inclusion. Response/ The phrase has been adjusted. 5. In Methods: Which CXR or CT scans were used? The ones on admission to hospital or the ones with the worst scores. COVID-19 is fast evolving and repeated CXRs and CT scans are a necessity. Response/ We report these images on admission. We have now clarified this in the methods section. 6. Line 112: symptoms and signs should be listed in methods. In fact, list of all variables shown in Table 1 and 2 should be listed in methods. Those variables that are not shown in Results and used for statistical analysis should be omitted. Response/ The variables shown in tables / results are now also consistent with those in the methods section. 7. Line 118: „in general“ should be substituted for „from the hospital“. Response / Corrected 8. Line 130/131: Were there any patients with tracheotomy? Response/ This information is not available, we did not searched this variable. 9. Line 160/161: Sentence „among the females.....were pregnant“ should definitely undergo respectful rephrasing. Response/ we rephrased the sentence. 10. Line 199: „ days of intubation“ referes to duration of intubation or days between hospital admission and intubation? Response/ This refers to “duration”. The phrase has been adjusted accordingly. 11. Tables 1 to 4 show differences between survivors and non survivors. Somehow, we have „jumped“ from there to prediction of ICU admission. Steps before prediction modeling should be shown as well, process of selection of variables included in the prediction model should be clear. On the same note, it is not clear how selection of variables included in the mortality prediction was performed. Response/ We included survival status in the tables in order to show the distribution of the variables among survivors and deceased. The step-by-step process for variable selection is not shown explicitly, but we have now changed the sentence in methods in this regard. We now explain that “Covariates included age, sex and those variables that were significantly associated the dependent variables in the bivariate analysis”. We have also indicated that this is an exploratory analysis, not a predictive one. Reviewer #2: I would like to thank the editors of Plos One for giving me the opportunity to review the manuscript “factors associated with admission to the intensive care unit and mortality in patients with COVID-19 in Colombia”. In this observational cohort study, the authors described the characteristics of 780 patients admitted to 4 clinics for COVID-19 in Colombia between march 6 and august 31, 2020 and tried to identify factor associated with death or ICU admission. The authors confirmed previous risk factors for poor outcomes described in much larger cohorts, including from south America. They also identified that, at the time of the study, patients from Cali had poorer outcomes. This report appears now as completely anachronic since both viruses and treatments have profoundly changed. The study provides no new information that can be relevant for other caregivers. Response/ Thank you, but we believe this data are still of importance, especially in the colombian context. Another major limitation of this study is that authors provided comparison between survivors and deceased patients (they report in the methods that they followed-up patient until death…) whereas the main result (as indicated in the title) was the factors associated with either ICU admission or death. Response/ We indeed reported both outcomes (i.e: table 5 and 6 show multivariate analysis considering each of these outcomes). We did not use a composite outcome of ICU admission + death. In multivariate analysis, the found that coming from Cali, COPD and severe pneumoniae were associated with ICU admission or death. I really don’t understand how this finding may “greatly contribute to improving the prognosis of these patients” as concluded by the authors. Response/ The phrase has been adjusted. Thank you, we will be aware of new observations. The authors Attachments Attachment Submitted filename: Reviewer Answers Viral infections Antibiotics (2).docx https://doi.org/10.1371/journal.pone.0260169.r002
4 Nov 2021 Decision Letter - Wenbin Tan, Editor Factors associated with admission to the intensive care unit and mortality in patients with COVID-19, Colombia PONE-D-21-18267R1 Dear Dr. Machado-Alba, 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, Wenbin Tan Academic Editor PLOS ONE Reviewers' comments: Reviewer's Responses to Questions Reviewer #3: All comments have been addressed ********** https://doi.org/10.1371/journal.pone.0260169.r003
Formally Accepted
9 Nov 2021 Acceptance Letter - Wenbin Tan, Editor PONE-D-21-18267R1 Factors associated with admission to the intensive care unit and mortality in patients with COVID-19, Colombia Dear Dr. Machado-Alba: 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. Wenbin Tan Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0260169.r004

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