While autoimmune and inflammatory disease may be more prevalent in the industrial world, compared to the Third world, the Third world's infant mortality rate is, as the article states, 3 times higher.
Perhaps those people who would have died in the Third world are those very people who would get the autoimmune diseases we have in the West.
So one might say the parasites, viruses and germs may strengthen us, but one could ALSO say that those same germs just kill off those with faulty immune systems. We manage to keep them alive in the industrial world, so that as they grow their autoimmune and inflammatory disease can manifest themselves.
thereby weakening the genetic stock in our own culture. Consider if we actually have a collapse and things like getting these vaccines becomes an item only for the rich or the regime du jour...a lot of kids will die. Most likely more than in a Third World country because we've had no natural selection going on for decades.