Clinical Report: Whole-Genome Sequencing of Neisseria meningitidis in Chad
Overview
This study used direct whole-genome sequencing to identify and characterize Neisseria meningitidis strains associated with invasive meningococcal disease in Chad. CC10217, including ST-10217 and the newly assigned ST-18990, caused a large serogroup C outbreak in 2025.
Background
Invasive meningococcal disease is a major public health concern in the meningitis belt of sub-Saharan Africa. Before MenAfriVac was introduced in 2010, large regional epidemics were primarily caused by serogroup A. Following the elimination of serogroup A invasive meningococcal disease, strains belonging to other serogroups, including C, W, and X, emerged and spread across the meningitis belt. ST-10217 previously caused outbreaks and epidemics in Nigeria and Niger.
Data Highlights
Cerebrospinal fluid specimens analyzed: 90
Specimens collected in 2024: 25
Specimens collected in 2025: 65
2025 specimens positive for N meningitidis: 18
Meningococcal-positive specimens sequenced: 16
ST-10217 genomes: 10
New ST-18990 genome: 1
ST-11 genomes: 4
ST-5789 genome: 1
Key Findings
CC10217 was responsible for the large serogroup C invasive meningococcal disease outbreak in Chad in 2025.
Direct sequencing identified 10 ST-10217 genomes and 1 newly assigned ST-18990 genome within CC10217.
Four genogroup W ST-11 genomes and 1 non-groupable ST-5789 genome were also identified.
ST-10217 and ST-18990 carried gyrA mutations associated with reduced ciprofloxacin susceptibility.
The ST-18990 genome additionally carried a parC mutation associated with reduced ciprofloxacin susceptibility.
The findings demonstrated a significant change in the epidemiology of meningococcal disease in Chad.
Clinical Implications
Direct whole-genome sequencing can strengthen meningococcal surveillance in settings where limited culture capacity restricts the availability of bacterial isolates. The emergence of CC10217 with mutations associated with reduced ciprofloxacin susceptibility requires close epidemiological monitoring. The study did not evaluate treatment or establish clinical management recommendations.
Conclusion
CC10217, which has caused epidemics in Nigeria and Niger since 2015, reached Chad and caused a large serogroup C invasive meningococcal disease outbreak in 2025. Enhanced surveillance, timely sharing of representative strains or patient specimens, and genomic characterization are needed to monitor epidemiological trends and inform disease-control strategies.
Related Resources & Content
Direct Whole-Genome Sequencing of Clinical Specimens Highlights the Emergence of Neisseria meningitidis ST-10217 in Chad — Børud B, Witsø A, Ngam-Asra N, et al. International Journal of Infectious Diseases. 2026;170:108916. doi:10.1016/j.ijid.2026.108916.
Standard Operating Procedures for Surveillance of Meningitis Preparedness and Response to Epidemics in Africa — World Health Organization Regional Office for Africa. 2018.
Enhancing Meningococcal Genomic Surveillance in the Meningitis Belt Using High-Resolution Culture-Free Whole-Genome Sequencing — Itsko M, Topaz N, Ousmane-Traore S, et al. Journal of Infectious Diseases. 2022;226:729–737.
Meningococcus Serogroup C Clonal Complex ST-10217 Outbreak in Zamfara State, Northern Nigeria — Kwambana-Adams BA, Amaza RC, Okoi C, et al. Scientific Reports. 2018;8:14194.
Deep sequencing found no significant association between minor-variant burden and disease severity, although several newborns had unusually high within-host viral diversity.
