Some candidate examples include
- Artemisinin resistance in malaria: see http://www.nejm.org/doi/full/10.1056/NEJMoa0808859
- Flu evolution and pandemics - many examples from swine flu, etc.
- MRSA evolution - many papers. See for example Evolution of MRSA During Hospital Transmission and Intercontinental Spread. Science, 327 (5964), 469-474
- PCB resistance in fish
- See this recent Economist article.
- Also see Hudson River Fish Evolves to Live With PCBs - NYTimes.com