Derivation, Validation, and Potential Treatment Implications of Novel Clinical Phenotypes for Sepsis

Sepsis is a heterogeneous syndrome. Identification of distinct clinical phenotypes may allow more precise therapy and improve care. To derive sepsis phenotypes from clinical data, determine their reproducibility and correlation with host-response biomarkers and clinical outcomes, and assess the pote...

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Published in:JAMA : the journal of the American Medical Association Vol. 321; no. 20; p. 2003
Main Authors: Seymour, Christopher W, Kennedy, Jason N, Wang, Shu, Chang, Chung-Chou H, Elliott, Corrine F, Xu, Zhongying, Berry, Scott, Clermont, Gilles, Cooper, Gregory, Gomez, Hernando, Huang, David T, Kellum, John A, Mi, Qi, Opal, Steven M, Talisa, Victor, van der Poll, Tom, Visweswaran, Shyam, Vodovotz, Yoram, Weiss, Jeremy C, Yealy, Donald M, Yende, Sachin, Angus, Derek C
Format: Journal Article
Language:English
Published: United States 28.05.2019
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ISSN:1538-3598, 1538-3598
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Abstract Sepsis is a heterogeneous syndrome. Identification of distinct clinical phenotypes may allow more precise therapy and improve care. To derive sepsis phenotypes from clinical data, determine their reproducibility and correlation with host-response biomarkers and clinical outcomes, and assess the potential causal relationship with results from randomized clinical trials (RCTs). Retrospective analysis of data sets using statistical, machine learning, and simulation tools. Phenotypes were derived among 20 189 total patients (16 552 unique patients) who met Sepsis-3 criteria within 6 hours of hospital presentation at 12 Pennsylvania hospitals (2010-2012) using consensus k means clustering applied to 29 variables. Reproducibility and correlation with biological parameters and clinical outcomes were assessed in a second database (2013-2014; n = 43 086 total patients and n = 31 160 unique patients), in a prospective cohort study of sepsis due to pneumonia (n = 583), and in 3 sepsis RCTs (n = 4737). All clinical and laboratory variables in the electronic health record. Derived phenotype (α, β, γ, and δ) frequency, host-response biomarkers, 28-day and 365-day mortality, and RCT simulation outputs. The derivation cohort included 20 189 patients with sepsis (mean age, 64 [SD, 17] years; 10 022 [50%] male; mean maximum 24-hour Sequential Organ Failure Assessment [SOFA] score, 3.9 [SD, 2.4]). The validation cohort included 43 086 patients (mean age, 67 [SD, 17] years; 21 993 [51%] male; mean maximum 24-hour SOFA score, 3.6 [SD, 2.0]). Of the 4 derived phenotypes, the α phenotype was the most common (n = 6625; 33%) and included patients with the lowest administration of a vasopressor; in the β phenotype (n = 5512; 27%), patients were older and had more chronic illness and renal dysfunction; in the γ phenotype (n = 5385; 27%), patients had more inflammation and pulmonary dysfunction; and in the δ phenotype (n = 2667; 13%), patients had more liver dysfunction and septic shock. Phenotype distributions were similar in the validation cohort. There were consistent differences in biomarker patterns by phenotype. In the derivation cohort, cumulative 28-day mortality was 287 deaths of 5691 unique patients (5%) for the α phenotype; 561 of 4420 (13%) for the β phenotype; 1031 of 4318 (24%) for the γ phenotype; and 897 of 2223 (40%) for the δ phenotype. Across all cohorts and trials, 28-day and 365-day mortality were highest among the δ phenotype vs the other 3 phenotypes (P < .001). In simulation models, the proportion of RCTs reporting benefit, harm, or no effect changed considerably (eg, varying the phenotype frequencies within an RCT of early goal-directed therapy changed the results from >33% chance of benefit to >60% chance of harm). In this retrospective analysis of data sets from patients with sepsis, 4 clinical phenotypes were identified that correlated with host-response patterns and clinical outcomes, and simulations suggested these phenotypes may help in understanding heterogeneity of treatment effects. Further research is needed to determine the utility of these phenotypes in clinical care and for informing trial design and interpretation.
AbstractList Sepsis is a heterogeneous syndrome. Identification of distinct clinical phenotypes may allow more precise therapy and improve care.ImportanceSepsis is a heterogeneous syndrome. Identification of distinct clinical phenotypes may allow more precise therapy and improve care.To derive sepsis phenotypes from clinical data, determine their reproducibility and correlation with host-response biomarkers and clinical outcomes, and assess the potential causal relationship with results from randomized clinical trials (RCTs).ObjectiveTo derive sepsis phenotypes from clinical data, determine their reproducibility and correlation with host-response biomarkers and clinical outcomes, and assess the potential causal relationship with results from randomized clinical trials (RCTs).Retrospective analysis of data sets using statistical, machine learning, and simulation tools. Phenotypes were derived among 20 189 total patients (16 552 unique patients) who met Sepsis-3 criteria within 6 hours of hospital presentation at 12 Pennsylvania hospitals (2010-2012) using consensus k means clustering applied to 29 variables. Reproducibility and correlation with biological parameters and clinical outcomes were assessed in a second database (2013-2014; n = 43 086 total patients and n = 31 160 unique patients), in a prospective cohort study of sepsis due to pneumonia (n = 583), and in 3 sepsis RCTs (n = 4737).Design, Settings, and ParticipantsRetrospective analysis of data sets using statistical, machine learning, and simulation tools. Phenotypes were derived among 20 189 total patients (16 552 unique patients) who met Sepsis-3 criteria within 6 hours of hospital presentation at 12 Pennsylvania hospitals (2010-2012) using consensus k means clustering applied to 29 variables. Reproducibility and correlation with biological parameters and clinical outcomes were assessed in a second database (2013-2014; n = 43 086 total patients and n = 31 160 unique patients), in a prospective cohort study of sepsis due to pneumonia (n = 583), and in 3 sepsis RCTs (n = 4737).All clinical and laboratory variables in the electronic health record.ExposuresAll clinical and laboratory variables in the electronic health record.Derived phenotype (α, β, γ, and δ) frequency, host-response biomarkers, 28-day and 365-day mortality, and RCT simulation outputs.Main Outcomes and MeasuresDerived phenotype (α, β, γ, and δ) frequency, host-response biomarkers, 28-day and 365-day mortality, and RCT simulation outputs.The derivation cohort included 20 189 patients with sepsis (mean age, 64 [SD, 17] years; 10 022 [50%] male; mean maximum 24-hour Sequential Organ Failure Assessment [SOFA] score, 3.9 [SD, 2.4]). The validation cohort included 43 086 patients (mean age, 67 [SD, 17] years; 21 993 [51%] male; mean maximum 24-hour SOFA score, 3.6 [SD, 2.0]). Of the 4 derived phenotypes, the α phenotype was the most common (n = 6625; 33%) and included patients with the lowest administration of a vasopressor; in the β phenotype (n = 5512; 27%), patients were older and had more chronic illness and renal dysfunction; in the γ phenotype (n = 5385; 27%), patients had more inflammation and pulmonary dysfunction; and in the δ phenotype (n = 2667; 13%), patients had more liver dysfunction and septic shock. Phenotype distributions were similar in the validation cohort. There were consistent differences in biomarker patterns by phenotype. In the derivation cohort, cumulative 28-day mortality was 287 deaths of 5691 unique patients (5%) for the α phenotype; 561 of 4420 (13%) for the β phenotype; 1031 of 4318 (24%) for the γ phenotype; and 897 of 2223 (40%) for the δ phenotype. Across all cohorts and trials, 28-day and 365-day mortality were highest among the δ phenotype vs the other 3 phenotypes (P < .001). In simulation models, the proportion of RCTs reporting benefit, harm, or no effect changed considerably (eg, varying the phenotype frequencies within an RCT of early goal-directed therapy changed the results from >33% chance of benefit to >60% chance of harm).ResultsThe derivation cohort included 20 189 patients with sepsis (mean age, 64 [SD, 17] years; 10 022 [50%] male; mean maximum 24-hour Sequential Organ Failure Assessment [SOFA] score, 3.9 [SD, 2.4]). The validation cohort included 43 086 patients (mean age, 67 [SD, 17] years; 21 993 [51%] male; mean maximum 24-hour SOFA score, 3.6 [SD, 2.0]). Of the 4 derived phenotypes, the α phenotype was the most common (n = 6625; 33%) and included patients with the lowest administration of a vasopressor; in the β phenotype (n = 5512; 27%), patients were older and had more chronic illness and renal dysfunction; in the γ phenotype (n = 5385; 27%), patients had more inflammation and pulmonary dysfunction; and in the δ phenotype (n = 2667; 13%), patients had more liver dysfunction and septic shock. Phenotype distributions were similar in the validation cohort. There were consistent differences in biomarker patterns by phenotype. In the derivation cohort, cumulative 28-day mortality was 287 deaths of 5691 unique patients (5%) for the α phenotype; 561 of 4420 (13%) for the β phenotype; 1031 of 4318 (24%) for the γ phenotype; and 897 of 2223 (40%) for the δ phenotype. Across all cohorts and trials, 28-day and 365-day mortality were highest among the δ phenotype vs the other 3 phenotypes (P < .001). In simulation models, the proportion of RCTs reporting benefit, harm, or no effect changed considerably (eg, varying the phenotype frequencies within an RCT of early goal-directed therapy changed the results from >33% chance of benefit to >60% chance of harm).In this retrospective analysis of data sets from patients with sepsis, 4 clinical phenotypes were identified that correlated with host-response patterns and clinical outcomes, and simulations suggested these phenotypes may help in understanding heterogeneity of treatment effects. Further research is needed to determine the utility of these phenotypes in clinical care and for informing trial design and interpretation.Conclusions and RelevanceIn this retrospective analysis of data sets from patients with sepsis, 4 clinical phenotypes were identified that correlated with host-response patterns and clinical outcomes, and simulations suggested these phenotypes may help in understanding heterogeneity of treatment effects. Further research is needed to determine the utility of these phenotypes in clinical care and for informing trial design and interpretation.
Sepsis is a heterogeneous syndrome. Identification of distinct clinical phenotypes may allow more precise therapy and improve care. To derive sepsis phenotypes from clinical data, determine their reproducibility and correlation with host-response biomarkers and clinical outcomes, and assess the potential causal relationship with results from randomized clinical trials (RCTs). Retrospective analysis of data sets using statistical, machine learning, and simulation tools. Phenotypes were derived among 20 189 total patients (16 552 unique patients) who met Sepsis-3 criteria within 6 hours of hospital presentation at 12 Pennsylvania hospitals (2010-2012) using consensus k means clustering applied to 29 variables. Reproducibility and correlation with biological parameters and clinical outcomes were assessed in a second database (2013-2014; n = 43 086 total patients and n = 31 160 unique patients), in a prospective cohort study of sepsis due to pneumonia (n = 583), and in 3 sepsis RCTs (n = 4737). All clinical and laboratory variables in the electronic health record. Derived phenotype (α, β, γ, and δ) frequency, host-response biomarkers, 28-day and 365-day mortality, and RCT simulation outputs. The derivation cohort included 20 189 patients with sepsis (mean age, 64 [SD, 17] years; 10 022 [50%] male; mean maximum 24-hour Sequential Organ Failure Assessment [SOFA] score, 3.9 [SD, 2.4]). The validation cohort included 43 086 patients (mean age, 67 [SD, 17] years; 21 993 [51%] male; mean maximum 24-hour SOFA score, 3.6 [SD, 2.0]). Of the 4 derived phenotypes, the α phenotype was the most common (n = 6625; 33%) and included patients with the lowest administration of a vasopressor; in the β phenotype (n = 5512; 27%), patients were older and had more chronic illness and renal dysfunction; in the γ phenotype (n = 5385; 27%), patients had more inflammation and pulmonary dysfunction; and in the δ phenotype (n = 2667; 13%), patients had more liver dysfunction and septic shock. Phenotype distributions were similar in the validation cohort. There were consistent differences in biomarker patterns by phenotype. In the derivation cohort, cumulative 28-day mortality was 287 deaths of 5691 unique patients (5%) for the α phenotype; 561 of 4420 (13%) for the β phenotype; 1031 of 4318 (24%) for the γ phenotype; and 897 of 2223 (40%) for the δ phenotype. Across all cohorts and trials, 28-day and 365-day mortality were highest among the δ phenotype vs the other 3 phenotypes (P < .001). In simulation models, the proportion of RCTs reporting benefit, harm, or no effect changed considerably (eg, varying the phenotype frequencies within an RCT of early goal-directed therapy changed the results from >33% chance of benefit to >60% chance of harm). In this retrospective analysis of data sets from patients with sepsis, 4 clinical phenotypes were identified that correlated with host-response patterns and clinical outcomes, and simulations suggested these phenotypes may help in understanding heterogeneity of treatment effects. Further research is needed to determine the utility of these phenotypes in clinical care and for informing trial design and interpretation.
Author Seymour, Christopher W
Chang, Chung-Chou H
Vodovotz, Yoram
Cooper, Gregory
Gomez, Hernando
Elliott, Corrine F
Berry, Scott
Wang, Shu
Kellum, John A
Mi, Qi
Huang, David T
Clermont, Gilles
Opal, Steven M
Weiss, Jeremy C
Visweswaran, Shyam
Yende, Sachin
Angus, Derek C
Kennedy, Jason N
van der Poll, Tom
Talisa, Victor
Yealy, Donald M
Xu, Zhongying
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  givenname: Christopher W
  surname: Seymour
  fullname: Seymour, Christopher W
  organization: Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
– sequence: 2
  givenname: Jason N
  surname: Kennedy
  fullname: Kennedy, Jason N
  organization: Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
– sequence: 3
  givenname: Shu
  surname: Wang
  fullname: Wang, Shu
  organization: Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
– sequence: 4
  givenname: Chung-Chou H
  surname: Chang
  fullname: Chang, Chung-Chou H
  organization: Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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  givenname: Corrine F
  surname: Elliott
  fullname: Elliott, Corrine F
  organization: Berry Consultants, Austin, Texas
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  surname: Xu
  fullname: Xu, Zhongying
  organization: Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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  givenname: Scott
  surname: Berry
  fullname: Berry, Scott
  organization: Berry Consultants, Austin, Texas
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  organization: Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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  givenname: Gregory
  surname: Cooper
  fullname: Cooper, Gregory
  organization: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
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  givenname: Hernando
  surname: Gomez
  fullname: Gomez, Hernando
  organization: Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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  givenname: David T
  surname: Huang
  fullname: Huang, David T
  organization: Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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  givenname: John A
  surname: Kellum
  fullname: Kellum, John A
  organization: Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
– sequence: 13
  givenname: Qi
  surname: Mi
  fullname: Mi, Qi
  organization: Department of Sports Medicine and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania
– sequence: 14
  givenname: Steven M
  surname: Opal
  fullname: Opal, Steven M
  organization: Department of Medicine, Infectious Disease Division, Rhode Island Hospital, Providence
– sequence: 15
  givenname: Victor
  surname: Talisa
  fullname: Talisa, Victor
  organization: Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
– sequence: 16
  givenname: Tom
  surname: van der Poll
  fullname: van der Poll, Tom
  organization: Center of Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
– sequence: 17
  givenname: Shyam
  surname: Visweswaran
  fullname: Visweswaran, Shyam
  organization: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
– sequence: 18
  givenname: Yoram
  surname: Vodovotz
  fullname: Vodovotz, Yoram
  organization: Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
– sequence: 19
  givenname: Jeremy C
  surname: Weiss
  fullname: Weiss, Jeremy C
  organization: Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania
– sequence: 20
  givenname: Donald M
  surname: Yealy
  fullname: Yealy, Donald M
  organization: Department of Emergency Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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  givenname: Sachin
  surname: Yende
  fullname: Yende, Sachin
  organization: Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
– sequence: 22
  givenname: Derek C
  surname: Angus
  fullname: Angus, Derek C
  organization: Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
BackLink https://www.ncbi.nlm.nih.gov/pubmed/31104070$$D View this record in MEDLINE/PubMed
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References 31104067 - JAMA. 2019 May 28;321(20):1981-1982
31593266 - JAMA. 2019 Oct 8;322(14):1416-1417
31656636 - J Thorac Dis. 2019 Sep;11(9):3672-3675
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Snippet Sepsis is a heterogeneous syndrome. Identification of distinct clinical phenotypes may allow more precise therapy and improve care. To derive sepsis phenotypes...
Sepsis is a heterogeneous syndrome. Identification of distinct clinical phenotypes may allow more precise therapy and improve care.ImportanceSepsis is a...
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Cluster Analysis
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Hospital Mortality
Humans
Machine Learning
Organ Dysfunction Scores
Phenotype
Reproducibility of Results
Retrospective Studies
Sepsis - classification
Sepsis - mortality
Sepsis - therapy
Title Derivation, Validation, and Potential Treatment Implications of Novel Clinical Phenotypes for Sepsis
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