Genomic Characterization of Emerging Bacterial Uropathogen Neisseria meningitidis, Which Was Misidentified as Neisseria gonorrhoeae by Nucleic Acid Amplification Testing

and are pathogenic bacteria that can cause human infections. While infections are associated with bacterial meningitis and bacteremia, a strain of , isolated from the urogenital system, has recently been associated with urethritis. As this strain is becoming prominent as an emerging pathogen, it is essential to assess identification tools for and urogenital isolates. Consecutive isolates recovered from urogenital cultures of symptomatic patients with presumptive diagnoses of gonorrhea and a random selection of isolates recovered from the same population within the same time frame were characterized with routine identification systems, antimicrobial susceptibility testing, and whole-genome sequencing. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), multilocus sequence typing, 16S rRNA gene sequence, and average nucleotide identity methods accurately identified 95% (18/19) of and isolates. With the Aptima Combo 2 CT/NG test, 30% (3/10) of isolates were misidentified as , but no misidentifications were found with the Xpert CT/NG nucleic acid amplification test (NAAT). Phylogenetic core genome and single nucleotide polymorphism (SNP)-based grouping analyses showed that urogenital isolates were highly related and phylogenetically distinct from and respiratory isolates but similar to urogenital isolates from patients with urethritis in the United States. Urogenital isolates were predominantly azithromycin resistant, while isolates were azithromycin susceptible. These data indicate that urogenital isolates of can cause false-positive detections with diagnostic assays. Misidentification of urogenital isolates may confound public health-related activities for gonorrhea, and future studies are needed to understand the impact on clinical outcome of urogenital infection.