I'm sorry to hear that. It's quite rare but it does happen. I don't generally recommend antibiotics without a clear indication - an annual round of doxycycline isn't likely to be helpful unless he's actively infected. It's not likely to help, and it may drive antibiotic resistance in the environment.
Lots of dogs will get exposed to Borrelia burgdoeferi (which causes Lyme disease), clear it like they would a cold, and then never have any more long-term problems. A small percentage will develop a life-threatening kidney problem. There doesn't seem to be a recurrent form in dogs - a few case-study genetic analyses of the bacteria have shown that if they get Lyme multiple times, it's because they were bitten by a tick again.
The good news in all this is that the Zoetis crLyme recombinant vaccine is incredibly effective, and incredibly safe. Other Lyme vaccines are also safe and effective, but for my money, crLyme is the industry standard. Even for dogs that have had Lyme Disease, it's still worthwhile to vaccinate them to prevent re-exposure. Preventatives when you can. Tick checks all the time. Prayers and rain dances for good measure.
It's a numbers game in this area - it's not uncommon for a dog to be exposed to 10,000 ticks in a year if they're spending any time outdoors, so even the best preventative's 99% efficacy means a few ticks will get through.
Nasty little creatures, man. Nasty.
