Genomic characterization of emerging bacterial uropathogen Neisseria meningitidis misidentified as Neisseria gonorrhoeae by nucleic acid amplification testing.

Neisseria meningitidis (Nm) and Neisseria gonorrhoeae (Ng) are pathogenic bacteria that can cause human infections. While Nm infections are associated with bacterial meningitis and bacteremia, a strain of Nm, 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 Nm and Ng urogenital isolates. Consecutive Nm isolates recovered from urogenital cultures of symptomatic patients with presumptive diagnoses of gonorrhea and a random selection of Ng isolates recovered from the same population within the same time frame were characterized with routine identification systems, antimicrobial susceptibility testing, and whole genome sequencing. MALDI-ToF MS, multilocus sequence typing, 16S rRNA gene sequence, and average nucleotide identity methods accurately identified 95% (18/19) of Nm and Ng isolates. 30% (3/10) of Nm isolates were misidentified as Ng with Aptima Combo 2 CT/NG but no misidentifications were found with the Xpert CT/NG NAAT. Phylogenetic core genome and SNP-based grouping analyses showed that urogenital Nm isolates were highly related, and phylogenetically distinct from Ng and respiratory Nm isolates but similar to urogenital Nm isolates from patients with urethritis in the US. Urogenital Nm isolates were predominantly azithromycin resistant while Ng isolates were azithromycin susceptible. These data indicate that urogenital isolates of Nm can cause false-positive detections with Ng diagnostic assays. Misidentification of urogenital Nm isolates may confound public health-related activities for gonorrhea and future studies are needed to understand the impact on clinical outcome of Nm urogenital infection.