Functional, controllable nanomachinery which is capable of the level of fidelity required to combat bacterial infections within the body is highly unlikely in the sort of time-frame we're discussing here. We're still decades away, billions will be dead prematurely by the time nanomachines are capable of helping with this issue.
But, it's not quite as doom and gloom as the original article supposes, because they're taking this trend of resistant bacterium in isolation. Advances in regenerative medicine will eliminate many of the issues surrounding organ transplantation, synthetic biology will allow us to customise our immune systems, and more effective vaccination will stem at least a portion of the flood.
Of course, we swing back into the "holy shit, PANIC!" zone again when you consider all the other bullshit going on right now. Science is under assault in schools by wingnuts, and cynical media manipulation by certain corporate interests has resulted in trust in science among the public being at an all-time low. Parents who would rather find comfort in lies than deal with truth are refusing to vaccinate their children. Drug companies, as mentioned, are investing very little money in necessary advances, because they are currently unprofitable, forgetting that A: in the future, they will be very profitable, and B: without them they may no longer have any customers, what with humanity being a dead species. Governments are investing less and less money in scientific research and education, instead choosing to pump funds into "quick fix" policies to up their poll ratings, or feed their nation's military industrial and financial sectors.
Frankly, unless we have some kind of paradigm-shift in our thinking, we're fucked.