Highlights:
- Whole-genome sequencing (WGS) can be applied to trace environmental origins of L pneumophila infections.
- This study explored the evolutionary and epidemiological relationships in a 36-year Scottish L pneumophila reference isolate collection.
- The data revealed the existence of previously undetected endemic clones of L pneumophila that existed for many years in hospital, community, and travel-associated environments.
- In light of these findings, the authors suggest that cluster and outbreak definitions should be reconsidered, and propose WGS-based surveillance as a critical public health tool for real-time identification and mitigation of clinically important endemic clones.