Evaluation of urethrotropic clade meningococcal infection by urine metagenomic shotgun sequencing.

Background Urethral infections caused by an emerging nongroupable (NG) urethrotropic clade of Neisseria meningitidis (Nm) were first reported in the United States in 2015 (the "U.S. NmNG urethritis clade"). Here we evaluate for the presence of other urethral pathogens in men with U.S. NmNG urethritis clade infection. Methods: We evaluated 129 urine specimens collected from men at a sexual health clinic, including 33 from patients with culture-confirmed or suspected urethral Nm infection and 96 specimens in which nucleic acid amplification test detected Neisseria gonorrhoeae (Ng), Chlamydia trachomatis (Ct), both pathogens, or neither pathogen. Nm was detected first by real-time PCR, followed by metagenomic shotgun sequencing of 91 specimens to identify coinfections. Nm genomes were sequenced following selective whole genome amplification when possible. Results: Metagenomic sequencing detected Nm in 16 of 17 specimens from culture-confirmed Nm cases, with no coinfection by other conventional urethral pathogens. Metagenomic sequencing also detected Nm in three Ct positive specimens, one specimen positive for both Ng and Ct, and nine specimens with negative Ng and Ct results, eight of which had suspected Neisseria infections. Nm from culture-confirmed Nm cases belonged to the U.S. NmNG urethritis clade, while Nm identified in other specimens belonged to multiple clonal complexes. Additional urethral pathogens were predominant in non-Nm specimens, including Ng, Ct, Mycoplasma genitalium, Ureaplasma urealyticum, and herpes simplex virus type-2. Conclusions: Coinfection with other conventional urethral pathogens is rare in men with culture-confirmed U.S. NmNG urethritis clade infection and points to the strong association of this clade with disease.