there is alteration in number and may be structural changes in surface of bacterial receptors/molecules when they acquire the resistance .To observe this change which microscopy will be more beneficial-SEM or TEM
It depends on the size of feature you want to see. But SEM might be a better option since it operates on lower energy and hence will cause lower damage. Another advantage of using SEM will be easy visualization of surface topography which is not visible in TEM.
I`d say that these methods are not alternative, but complementary. Depending on task you may choose any. For bio-applications it is better to deal with Low-vacuum (variable pressure) SEM or E-TEM (environmental).