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The disease strain has shown up in Africa, the Middle East and Asia, and has hiked food prices in the Arab world, Mexico, Haiti and beyond.
"Stem rust, when it goes epidemic, destroys a crop," said Ronnie Coffman, a leading expert on wheat disease and chair of the department of plant breeding and genetics at Cornell University.
"There is nothing left but black stems, zero grain. It is just an absolute devastation," Coffman told the AFP news agency.
The last major epidemic of the fungal disease broke out in 1953 but was quelled with the introduction of a resistant strain of plants in the 1970s, an initiative spearheaded by the late Norman Borlaug.
A new wave of the stem rust fungus, Ug99, turned up in Uganda in 1998, overcoming crops that were once resistant and wielding the potential to kill as much as 90 percent of the world's wheat.
Winds can transport spores as many as 100 miles per day, raising concerns among scientists about where the epidemic could turn up next.
"From Yemen, the wind currents are such that it could be carried to almost any part of the world -- winds blow into south Asia, they blow into central Asia, they blow into Europe even," Coffman told AFP.
Winds could send the plague to the southern cone of Latin America or to Australia from South Africa.
Wheat makes up a fifth of the world's food and is second only to rice in the diets of people in developing countries.
According to Peter Njau, an expert at the Kenya Agriculture Research Institute, Kenya is one country already grappling with a crisis in wheat production, as small farmers face a loss of as much as 70 percent of their yield.
Njau said in an interview with AFP that large-scale farmers who can afford chemicals to kill the fungus still face rising costs of production, as much as 40 percent higher than in normal years.
He said the price of a bag of wheat has risen by about a third. This spikes fuel costs, and when combined with a recent reduction on import tax for wheat, it will put a squeeze on local farmers unseen in many years.
"The farmers, when they harvest their crop, they will end up being paid less for their product and that might be a bone of contention between the farmers and the government," Njau said in a statement.
Kenya is working with experts at Cornell University and in Mexico to deliver new strains that may be able to resist the latest wave of stem rust.
Experts around the world are heading to Minnesota next week to share their latest research as part of an annual meeting beginning June 13 by the Borlaug Global Rust Initiative project that was launched in 2005.
New approaches including combining multiple resistant genes into a single plant so that it will withstand any mutations that might allow stem rust to take over again.
According to Ravi Singh of the International Maize and Wheat Improvement Center (CIMMYT) in Mexico, "significant progress" has been made, with some new varieties even boosting yields by up to 15 percent.
Singh said world governments must now take steps to replace their wheat crops.
"Scientists can only do so much," Singh said in a statement. "We need to see national governments making the investments in seed systems development."
It doesn't take long for mother nature to find a chink in the armour of any species which is too genetically similar. Its happened before, effecting mostly Ireland in the 1940's.