Yes, in some sense
Do not repeat that thypical mistake of genetically modified creatures adapting for each and everyone planet.
Use google glasses or equivalent and appropriate, technology based sensors and convert their signals to visual information.
Optical means for shure do not help you see vuruses, and apparently you have no idea how messy skin would look like under a microscope, and that many bacterias are part of our symbiosis.
But what you are looking for, partially, called AFM which is basically a micro wisker scanning a surface.
So it can be not like you solve the problem of how much optical component you can squish in someones head, but by some technology you have array of such wiskers on a tip of ones finger and you move it across some surface and get the information, already filtered for features you are looking for.
It may be part of efforts of controlling spreading and elemination antibiotic resistant bacterias, and other microbiological stuff, but it does not describe it in full - how it should be done and alone it is definitely not an ultimate answer for the situation. Capacities of our bodies aren't that bad and it can be used as a detector, or part of the detector - I mean body contains tools which can be used on cellular level and it just needs better and digital/chemical interface.
As potencial technology - nanomachines son - really that could be useful, a lot of things can be done with our ability to work more freely in confines of few microns. Including that we could eliminate all harmfull microbiological materials, in a way which they can't adapt for, and/or create additioanl barriers for them, and bug fix the responses of immune system etc.
So what you are looking for is nanotech.