Continued surveillance and isolate collection will enable tracking of whether these gonococcal sequences become more frequent in urethritis-associated N. meningitidis. Of note, a single isolate from the U.S. NmNG urethritis clade contained an mtrR promoter and coding sequence that had been associated with decreased susceptibility to azithromycin in N. gonorrhoeae. Here, MTRR is linked to urethritis.