Genomic characterization of Neisseria meningitidis carriage isolates from an urban STI clinic revealed diverse clonal complexes including the ST-11 NmUC urethritis clade and Group Y ST-1466, with capsule locus inactivation in ≥80% of isolates with specified genogroups.
Key Findings
Methods
Asymptomatic pharyngeal Neisseria meningitidis carriage was identified in >30% of STI clinic attendees at an urban sexual health clinic.
Study was conducted at an urban STI clinic in Columbus, Ohio
Longitudinal assessment was performed between January 2018 and December 2019
Cultures using media selective for Neisseria spp. and Nm-specific PCR screening were used to confirm isolates
Overall genomic data were obtained from 453 oropharyngeal, 10 urethral, 5 rectal, and 1 cervical Nm isolate
Results
Genogrouping of oropharyngeal Nm isolates revealed cnl (capsule null locus) as the most common genogroup, followed by B, E, Z, C, and Y.
Among oropharyngeal Nm isolates: 37.7% were cnl, 28% B, 13.5% E, 10.8% Z, 2.6% C, and 2.6% Y
PCR-based genogrouping was used to classify isolates
A total of 453 oropharyngeal isolates were genomically characterized
Whole-genome sequencing was performed on confirmed Nm isolates
Results
The capsule polysaccharide synthesis (cps) locus was inactivated in ≥80% of isolates with specified genogroups.
Capsule locus inactivation was found in isolates across multiple genogroups including B, E, Z, C, and Y
This finding applied to isolates that had been assigned a specific genogroup designation (i.e., not cnl)
Whole-genome sequencing provided the genomic basis for identifying cps locus inactivation
Capsule inactivation is a notable feature potentially relevant to mucosal colonization and immune evasion
Results
The major clonal complexes identified among Nm isolates were cc53, cc32, cc41/44, cc1157, cc198, and cc4821.
Clonal complex designation was determined by whole-genome sequencing
These clonal complexes were identified across oropharyngeal, urethral, rectal, and cervical isolates
cc4821 is a clonal complex previously associated with invasive meningococcal disease globally
cc32 and cc41/44 are recognized hypervirulent lineages associated with invasive disease
Results
Six isolates belonging to the ST-11 Neisseria meningitidis urethritis clade (NmUC) were identified across multiple anatomical sites.
Two oropharyngeal, one rectal, and three urethral isolates belonged to the ST-11 NmUC
ST-11 NmUC has been associated with increasing reports of Nm urethritis
Urethral isolates were among the 10 total urethral Nm isolates in the study
Rectal ST-11 NmUC isolate was among 5 total rectal Nm isolates genomically characterized
Results
Group Y ST-1466 Neisseria meningitidis, recently linked to global urogenital and systemic infections, was identified in oropharyngeal isolates.
Group Y ST-1466 was detected in the oropharynx of STI clinic attendees
This strain has been described as recently linked to global urogenital and systemic infections
Its identification in the oropharynx suggests potential for transmission via the oral-genital route
Detection occurred within the January 2018 to December 2019 study period
Results
Neisseria meningitidis was recovered from urogenital and rectal sites in addition to the oropharynx among STI clinic patients.
10 urethral, 5 rectal, and 1 cervical Nm isolates were genomically characterized
Recovery from multiple anatomical sites supports the role of sexual transmission in Nm spread
This finding is consistent with increasing reports of Nm urethritis and STI-related invasive disease outbreaks noted in the introduction
Cultures using Neisseria spp.-selective media were applied across anatomical sites
What This Means
This research suggests that Neisseria meningitidis (Nm), the bacterium that causes meningitis, is commonly carried without symptoms in the throats of more than 30% of people attending a sexual health clinic in Columbus, Ohio. The researchers collected bacterial samples from the throats, urethras, rectums, and cervixes of clinic patients between 2018 and 2019, then used advanced genetic sequencing to characterize over 460 Nm isolates. They found a wide variety of bacterial strains, and importantly identified strains associated with a rise in sexually transmitted meningococcal infections, including the ST-11 urethritis clade found in urethral and rectal samples, and a Group Y strain (ST-1466) in throat samples that has been linked to urogenital and systemic infections worldwide.
One notable finding is that in the vast majority (≥80%) of the bacterial isolates that were initially typed as belonging to a specific group, the gene region responsible for producing the capsule—a protective outer layer that helps the bacterium evade the immune system and is the target of meningococcal vaccines—was non-functional. This means current vaccines, which work by targeting the capsule, may not protect against many of the strains being carried and potentially transmitted in this population. The oropharynx (throat) appears to be a key reservoir from which strains can spread to genital and rectal sites through sexual contact.
This research suggests that STI clinics may be important settings for monitoring the spread of meningococcal bacteria, particularly as new sexually transmitted forms of meningococcal disease emerge. The identification of diverse and potentially vaccine-resistant strains circulating in this population highlights the need for continued genomic surveillance and raises questions about whether existing prevention strategies are adequate for this type of transmission.
Tzeng Y, Sannigrahi S, Turner A, Carter A, Snyder B, Bazan J, et al.. (2026). Genomic Typing of Meningococcal Carriage Isolates in an Urban Sexual Health Clinic.. Pathogens (Basel, Switzerland). https://doi.org/10.3390/pathogens15050516