A severe mutation of Necrotising Fasciitis could do it. (See: https://www.webmd.com/skin-problems-and-treatments/tc/necrotizing-fasciitis-flesh-eating-bacteria-topic-overview).
Currently, it’s a flesh-eating bacterial disease, with a pretty high mortality rate. It spreads through physical contact, but generally only to those with low immune systems, cuts/abrasions, or infections like chickenpox. However, the initial infection can happen to people even with good health.
If it manages to mutate to an airborne disease, then it becomes a lot harder to treat. At the moment, the main treatment is simply to amputate the infected region - if you breathe it in, then it gets a lot harder to amputate.
If the disease spreads rapidly, people might not get any warning that they’re ill (generally about 24-36 hours after an initial injury do signs of Necrotising Fasciitis tend to appear), and by then everyone is infected, apart from Bob (and maybe a few other people in extremely isolated settings - is that a problem?) The disease doesn’t make it to Bob’s island, because no human carrier goes there.
24 hours might be enough time for people to start shutting things down safely (nuclear power stations, for instance), and creating instructions for any hypothetical surviving layperson to finish anything off.
As the disease is flesh-eating, it could hypothetically spread rapidly through the entire body, causing total organ failure and death - and the bacteria would continue to eat through the tissue until nothing survived. Assuming the bacteria could only survive in humans, it would die out after all humans had decomposed, so Bob wouldn’t be at risk of it if he returned to land a few weeks later - and no human evidence would survive.