Healthcare-associated infections (HAIs) may have grave consequences for patients. In the case of sepsis, the 30-day mortality rate is about 25%. HAIs cost EU member states an estimated 7 billion Euros annually. Clinical decision support tools may be useful for infection monitoring, early warning, and alerts. MONI, a tool for monitoring nosocomial infections, is used at University Hospital Vienna, but needs to be clinically and technically revised and updated. A new, completely configurable pipeline-based system for defining and processing HAI definitions was developed and validated. A network of data access points, clinical rules, and explanatory output is arranged as an inference network, a clinical pipeline as it is called, and processed in a stepwise manner. Arden-Syntax-based medical logic modules were used to implement the respective rules. The system was validated by creating a pipeline for the ECDC PN5 pneumonia rule. It was tested on a set of patient data from intensive care medicine. The results were compared with previously obtained MONI output as a suitable reference, yielding a sensitivity of 93.8% and a specificity of 99.8%. Clinical pipelines show promise as an open and configurable approach to graphically-based, human-readable, machine-executable HAI definitions.