MII Core Data Set Module “Microbiology” Implemented at the Data Integration Center Halle (Saale)

Standardized microbiological routine data available for cross-site research

The Data Integration Center at University Medicine Halle has implemented the “Microbiology” module of the core data set of the Medical Informatics Initiative (MII). With this step, the site reaches another milestone and expands its interoperable data infrastructure to include structured microbiological findings.

The core data set of the Medical Informatics Initiative defines which clinical routine data must be made available in a standardized format at all participating sites. Its goal is to structure data uniformly across sites in order to facilitate the exchange of health data for research. The MII core data set is divided into basic modules and extension modules. While the base modules “Diagnosis,” “Laboratory Result,” “Procedure,” “Medication,” “Consent,” “Person,” and “Case” are defined across clinical domains, the extension modules represent data from specific application areas and medical specialties.

MII Core Data Set Extension Module “Microbiology” Structures Microbiological Findings

At University Medicine Halle, the “Microbiology” module is the fourth extension module to be implemented in addition to the basic modules. The module enables the standardized capture and structuring of microbiological diagnostics.
These include:

• Culture-based diagnostics (cultivation of pathogens from sample material)
• Microscopic examinations
• Molecular diagnostics (e.g., PCR methods for the direct detection of pathogen genetic material)
• Serological and immunological analyses (detection of antibodies or antigens in blood)
• Sample information and characteristics of identified microorganisms

“At the Data Integration Center Halle, culture diagnostics as well as immunological or serological and molecular diagnostic tests are represented,” explains Dr. Anne-Kathrin Hartig, who is largely responsible for the implementation and operation of the microbiology module in Halle.

Dr. Daniel Tiller, head of the Data Integration Center, adds: “Currently, microbiological data from March 2023 onwards are available for research projects in an interoperable format.”

Data Integration Center Halle Enabled Microbiological Data for the SMITH Use Case HELP

Already during the development and networking phase of the MII (2018–2022), the Data Integration Center Halle worked closely with the Department of Clinical Infectiology, led by Dr. Stefan Moritz, on making microbiological data available for research.

Among other activities, the site participated in the infectious disease Use Case HELP within the SMITH Consortium, where a manual for the responsible use of antibiotics in cases of Staphylococcus bloodstream infections was developed.

In addition, the Data Integration Center Halle was the first Data Integration Center to provide infection-related data to the Dashboard of the Network of University Medicine (NUM) for supra-regional monitoring.

Use Case Examines the Quality of Epidemiological Sepsis Data in the MII

A current application example is the data use project EpiQualiSep, conducted via the German Portal for Medical Research Data Portal (FDPG). The aim is to identify sepsis cases in routine clinical data more reliably.

Sepsis is a life-threatening organ dysfunction caused by a dysregulated immune response to an infection. Despite its high mortality rate, sepsis is often insufficiently documented in clinical records. As a result, it remains unclear how many patients in Germany are actually affected.

To generate more reliable insights, the EpiQualiSep project analyzes data from electronic hospital records. Sepsis cases are identified indirectly using indicators such as blood culture sampling, administration of antibiotics, or specific laboratory values. The “Microbiology” module provides a key data basis for this work. Without structured and standardized microbiological findings, the validity of such analyses based on secondary routine data would be severely limited.

Core Data Set Module “Microbiology” Advances Data-Driven Research

Overall, the “Microbiology” module creates the technical foundation for scalable, data-driven research projects. It enables the standardized, reproducible, and efficient use of clinical and microbiological data, thereby opening new opportunities for clinical research and microbiological analysis.