A common misconception by those not affected by an autoimmune condition is that we have suppressed immune systems. In fact, it is just the opposite, our immune systems are hyper-responsive. After finally being diagnosed, I realized that I hadn't truly been "sick" (caught a cold, etc) in nearly two years. The times that I thought I was sick were flares. For me a flare causes the following symptoms: low grade fever (up to 99.5, I typically run 97.4 or so), vague right sided ear pain, flu-like (joint pain, exhaustion, etc).
The goal with treatment of an autoimmune condition is to suppress the immune system back down to normal levels. Tamp it down, so it no longer views our body as a threat, but not to the point that it does not fight disease. It is a delicate balance.
My husband has occupational/environmental AND exercise induced asthma. To get him managed he has been on allergy shots for nearly two years and is almost to maintenance phase, he also takes a long acting inhaled corticosteroid and bronchodilator. When we get sick, we often inhale the contagion (it can also be ingested or be transmitted by contact in mucous membranes) . . . a common side effect for asthmatics on these types of treatments is rapid onset of an upper respiratory infection that can quickly turn into pneumonia and/or bronchitis.
Why do I bring up asthma in an autoimmune blog? I bring it up because, corticosteroids are immunosuppresants . . .
One of our personal requirements for going on vacation is I need to be medically managed. This reduces the chances of becoming sick while traveling. We will probably avoid air travel because of the recirculation of contained air . . . not good for either of us. This situation is hard enough for a healthy individual, let alone a person on immunosuppresants.
The article link I found via medlineplus.gov cites that methotrexate monotherapy does not interfere with the influenza vaccine, but has shown inhibition of response to the pneumonia vaccine. It also does not cite methotrexate as an anti-metabolite (which it is, according to drugs.com and my handy-dandy pamphlet from the pharmacy) . . . Click on "article link" for full text.
Anyway, the short of it is, consult you rheumatologist prior to any travel, but especially with travel requiring anti-malarials, vaccines, etc. If anything, your rheumatologist may possibly want you on a medrol dose-pak during travel to help ease symptoms . . .
Good luck and happy traveling!