"The strain is tricky," said Smith. "And it's asymptomatic, meaning people might not know they have it because they are not showing symptoms for it. And we don't have the diagnostics to know what type of mutations are happening."
To help develop more antibiotics for resistant strains of all bacteria, Congress passed the Gain Act in 2012. The law provides an additional five years of market exclusivity to pharmaceutical companies for new drugs while giving the drugs priority with the Food and Drug Administration for quicker review and approval.
Much of the current research in antibiotics is being done by small biotech companies. A new drug, solithromycin, is being tested for gonorrhea by Cempra. The drug is in phase two of development, with several more phases needed before it's presented to the FDA for approval.
According to the CDC, at least 2 million people in the U.S. become infected with bacteria that are resistant to antibiotics, and at least 23,000 people die each year as a direct result of those infections. Many more people die from other conditions that were complicated by an antibiotic-resistant infection.
The concerns are that overuse of antibiotics in humans and animals is making bacteria drug-resistant. The CDC found that up to half of the antibiotics prescribed to people are unnecessary. Researchers also believe antibiotics to treat farm animals are often overused.
Besides gonorrhea, two other strains of drug-resistant bacteria are listed as "urgent threats." Clostridium difficile causes life-threatening diarrhea, and carbapenem-resistant Enterobacteriaceae, or CRE, is also life threatening and mostly found in hospital patients.
(Read more: Rare disease at hospital raises concerns about VA health care)
For treatment of gonorrhea, the CDC now recommends only ceftriaxone plus either azithromycin or doxycycline as a first-line treatment. The full emergence of a ceftriaxone-resistant strain would greatly limit treatment options and could cripple gonorrhea control efforts, says the CDC.
And for those worried about contracting the drug-resistant strain of gonorrhea, the NCSD's Smith had some simple advice.
"Use a condom if you're not in a monogamous relationship, and get yourself tested on a regular basis. But nothing is 100 percent guaranteed for protection," he said.
—By CNBC's Mark Koba. Follow him on Twitter