Direct whole-genome sequencing of clinical specimens highlights the emergence of Neisseria meningitidis ST-10217 in Chad

OBJECTIVES: To identify and characterize the pathogens responsible for the outbreak of invasive meningococcal disease in Chad during 2024-2025. METHODS: Surveillance included demographic data and cerebrospinal fluid samples from meningitis patients. Samples were tested using RT-PCR to detect Neisseria meningitidis, Streptococcus pneumoniae, or Haemophilus influenzae. Samples positive for N. meningitidis were further analyzed by direct sequencing, with phylogenetic analysis incorporating published genomes of the same sequence types. RESULTS: In 2024, 12/25 samples were RT-PCR positive for S. pneumoniae. In 2025, among 65 samples, 2 were positive for H. influenzae, 12 for S. pneumoniae, and 18 for N. meningitidis; the rest were negative. Four sequence types of N. meningitidis were identified: non-groupable ST-5789 (n = 1); ST-11 (n = 4), associated with genogroup W; and ST-10217 (n = 10) and the new ST-18990 (n = 1) of the clonal complex CC10217, both genogroup C. The ST-10217 genomes had mutations in gyrA, while the ST-18990 genome possessed additionally a parC mutation, both associated with reduced ciprofloxacin susceptibility. CONCLUSIONS: CC10217, responsible for epidemics in Nigeria and Niger since 2015, caused a significant outbreak of serogroup C invasive meningococcal disease in Chad in 2025. The emergence of CC10217 with mutations linked to reduced ciprofloxacin susceptibility is concerning and demands close epidemiological monitoring.