Genomic Typing of Meningococcal Carriage Isolates in an Urban Sexual Health Clinic.

Asymptomatic pharyngeal Neisseria meningitidis (Nm) carriage is seen in >30% of sexually transmitted infection (STI) clinic attendees. With increasing reports of Nm urethritis and STI-related invasive disease outbreaks, longitudinal assessment and genomic characterization of Nm among patients at an urban STI clinic population in Columbus, Ohio, was undertaken. This study determined the genomic basis of oropharyngeal, urogenital and rectal Nm isolates carried by patients presenting for care. Cultures using media selective for Neisseria spp., Nm-specific PCR screening of colonies with oxidase-positive Gram-negative diplococci, PCR-based genogrouping and whole-genome sequencing of confirmed Nm were performed. Overall, genomic data of 453 oropharyngeal, 10 urethral, 5 rectal and 1 cervical Nm isolate were obtained between January 2018 and December 2019. Among oropharyngeal Nm isolates, genogrouping identified 37.7% as cnl (capsule null locus), 28% B, 13.5% E, 10.8% Z, 2.6% C and 2.6% Y. However, the cps locus was inactivated in ≥80% of isolates with specified genogroups. The major clonal complexes (ccs) were cc53, cc32, cc41/44, cc1157, cc198 and cc4821. Two oropharyngeal, one rectal and three urethral isolates belonged to the ST-11 Nm urethritis clade (NmUC). Group Y ST-1466 Nm, recently linked to global urogenital and systemic infections, was also identified in the oropharynx.