Bacteriological and Molecular Diagnosis, a Significant Contribution to Cholera Surveillance in Niger, 2018–2024

Cholera remains a major public health problem in Niger, characterized by recurrent epidemics, particularly in the border regions of the Lake Chad Basin. Conventional epidemiological surveillance, while essential, has limitations in understanding transmission dynamics and effectively guiding the response. This study aimed to evaluate the contribution of the bacteriological and molecular characterization of Vibrio cholerae strains to strengthen surveillance in Niger. Isolates collected between 2018 and 2024 from suspected cases in the main affected regions were analysed. Methods included biochemical identification, serotyping, disc diffusion susceptibility testing, and molecular characterization by PCR for virulence genes (ctxA, tcpA) and whole genome sequencing (WGS) for phylogenomic analysis. A total of 258 isolates have been confirmed, all of which belonged to serogroup O1, El Tor biotype, Ogawa serotype. All strains carried the ctxA and tcpA genes. Antibiotic resistance patterns revealed high resistance to tetracycline (85%) and cotrimoxazole (92%), but maintained susceptibility to ciprofloxacin and azithromycin. Phylogenomic analysis on strains from 2018-2024 showed that the Nigerien strains form a distinct clonal group but are closely related to the strains circulating in neighbouring Nigeria, suggesting repeated cross-border introductions as the main driver of outbreaks. These results demonstrate that the integration of molecular surveillance is crucial to identify transmission routes, adapt treatment protocols and guide cross-border prevention strategies. Strengthening laboratory capacity is essential for an effective and targeted cholera response in Niger.