Great question! There are a number of reasons why we might want to look at mutations. For tracking how a disease is spreading, I look for an accumulation of mutations as the disease spread from person to person. For example, if we had:
we’d say that Patient2 most likely got it from Patient1 (G mutated to A), and Patient3 got it from Patient2 (G to A like Patient2, and then an additional C to T). However, Patient4 is completely different, so probably not in the transmission chain at all, and was infected by a completely different source. If we understand how a disease spreads better, then we can think of better ways to treat it – for example, targeting treatments for people most at risk of the disease.
It might be the case that the disease isn’t spreading between patients at all – a recent study using a similar method to that above showed that 75% of C. difficile cases in a hospital were not related (the equivalent of Patient4). This means we need to think about where else patients could be getting it from.