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Logical problems with relationships between some “sepsis” concepts in OMOP vocabularies

According to “The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3)” (Consensus Definitions for Sepsis and Septic Shock) sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. The identification of an organism in culture in a patient who corresponds to the definition of sepsis is highly supportive of the diagnosis of sepsis but is not necessary because a culprit organism is frequently not identified in up to 50% of patients who present with sepsis syndrome. Negative blood culture doesn’t mean that patient doesn’t have sepsis as positive blood culture may occur without developing sepsis syndrome.

We suppose that it’s not entirely true to map “Septicemia” (Athena) to “Sepsis” (Athena) because they mean different conditions. We propose to remap “Toxaemia” (“Blood poisoning”) (Athena), “Septicemia” and similar concepts with microorganisms (bacteria, fungi, viruses etc.) in blood to “Infection of bloodstream” (Athena).

We propose to discuss this issue and evaluate how possible changes may affect existing projects.


You seem to be equating septicemia with bacteremia. The latter is what a positive bacterial blood culture implies. Septicemia is an obsolete ill-defined term, which essentially means “septic infection in the blood”. The “mapping” you are talking about is provided by SNOMED, not us, who decided that septicemia is obsolete and should be supplanted by sepsis. Toxemia and blood poisoning are lay terms that have even less standing.

You may want bring up this discussion in the phenotype working group, in order to add a proper sepsis definition to the phenotype library.

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@Mikita_Salavei you are welcome to discuss your idea in the phentoype working group. We ask that the first step to be arriving (attempting to) at an unambiguous shared understanding of the clinical idea. This mean authoring a verbose clinical description. This allows all collaborators to talk constructively and contribute to the work.

There is a proposal for an upcoming initiative by the phenotype working group. Sepsis/bacteremia may fit in there as a priority clinical idea. We will discuss at the next workgroup meeting.

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@Gowtham_Rao Please add me to the phenotype working group. I’ll prepare detailed description of this clinical problem before meeting.