1) Avian flu. Is it a big deal? Yes. Are we prepared? Not yet. Has it been hyped? Definitely. I have posted several times on this topic through the course of the year.       Unanswered questions include: When will it arrive? Will the genetic shift necessary for efficient human to human transmission also weaken its virulence? (Let’s hope so. That’s what happened with two of the three pandemics this century).
2) Community associated methicillin resistant Staphylococcus aureus. It’s different from the old MRSA. The resistance pattern and the genome are distinct. Although we’ve had a friendly debate here on the blogosphere about the clinical significance (or lack thereof) of certain unique virulence factors, the clinical profile is different, with more skin and soft tissue infections, occasional necrotizing fasciitis, a possible increased threat of necrotizing pneumonia, and increased transmissibility. On the other hand the risk of intravascular and bone and joint infections may be less. Here are my previous posts on the topic.    
3) New profiles of Clostridium difficile infection. I blogged previously about the outbreak of a new strain of C. diff in Quebec. An alarmingly higher mortality compared to usual infections was noted, attributable to a mutation in a regulator gene which controls toxin production, resulting in production of 15-20 times more toxin than usual. The reports from Canadian Medical Association Journal which I cited suggested that shared bathrooms in outmoded hospital facilities was the most important risk factor. Subsequently, two reports   and an accompanying editorial in NEJM described outbreaks in the U.S. as well as the Quebec outbreak. It appears that the U.S. outbreak is similar to the Quebec outbreak, in that both are due to a strain that contains the toxin regulator gene deletion and has the ability to produce a previously uncommon binary toxin. The virulence potential of the regulator gene mutation is well known, while the significance of the binary toxin is less clear. The NEJM editorial by J. Bartlett summarizes the problem nicely, and points to two curious features of the severe cases, those being leukemoid reactions and hypoalbuminemia.