Antibiotics resistance poses a significant problem in today’s hospital care. Although large amounts of resistance data are gathered locally, they cannot be compared globally due to format and access diversity. We present an ontology-based integration approach serving an EU project in making antibiotics resistance data semantically and geographically interoperable. We particularly focus on EU-wide clinical data integration for real-time antibiotic resistance surveillance. The data semantics is formalized by multiple layers of terminology-bound description logic ontologies. Local database-to-RDF (D2R) converters, normalizers and data wrapper ontologies render hospital data accessible to SPARQL queries, which populate a mediator layer. This semiformal data is then integrated and rendered comparable via formal OWL domain ontologies and rule-driven reasoning applications. The presented integration layer enables clinical data miners to query over multiple hospitals which behave like one homogeneous ‘virtual clinical information system’. We show how cross-site querying can be achieved across borders, languages and different data models. Aside the drawbacks, we elaborate on the unique advantages over comparable previous efforts, i.e. tackling real-time data access and scalability.