Are your numbers for one year, or the sums over more than one year? If your numbers are just for one year, then your hypothesis would just be for that year, and I do not think you would have to do any further statistics. Just say, "For 2008, MRSA killed more people, but was reported on less often." If you have more than one year of data, or can break it down by month, you might find interesting trends (maybe news reports come out a short time after an increase in deaths, and C.Diff reports are catching up to an increase in deaths while MRSA reports are still high despite a recent decline in deaths). You might do a 2-way ANOVA with time and deaths as the independent variables.
On more of a methodology note, I would recommend looking at hospitalizations, health care costs, and days of lost productivity in addition to just deaths, if you can get that data. Perhaps you could do a regression on what variables most determine frequency of reporting in newspapers. I am sure that other factors, such as age of patients, are important. At least in the US, MRSA causes big scares in schools, and people worry a lot about children (who typically have low mortality rates), so it is newsworthy, but C. Diff is far more common among the elderly, and since we expect the elderly to suffer more illness and have higher mortality rates, it is less newsworthy.