Recent and convergent reversion to serotype Ogawa in the AFR12 sublineage of Vibrio cholerae O1 El Tor in Cameroon.

Since 1971, Cameroon has experienced several outbreaks of cholera due to strains of the seventh pandemic Vibrio cholerae O1 El Tor (7PET) lineage originating from South Asia. Over the last 6 years, more than 26,000 cholera cases have been reported. The aim of this study was to perform a genomic characterization of the V. cholerae O1 isolates collected during recent cholera outbreaks in Cameroon. We investigated the virulence, antimicrobial resistance (AMR) signatures and phylogenetic relationships of 164 clinical V. cholerae isolates representative of the successive outbreaks collected between 2018 and 2023. A phylogenomic analysis of more than 1,700 7PET genomes - including 45 from isolates collected in Cameroon between 1971 and 2011 - was performed to place the recent 7PET strains in a broader phylogenetic context. We found that all the recent Cameroonian isolates studied belonged to genomic wave 3 of the 7PET lineage. They clustered together within the AFR12 sublineage (which was identified for the first time in Cameroon in 2009) and with contemporary isolates from other countries in the same region. Serotyping and genome analysis revealed a reversion from serotype Inaba (all isolates between 2018 and 2019) to Ogawa (all isolates between 2021 and 2023) in two different strains originating from different regions of Cameroon. Finally, the AFR12 isolates studied here were less resistant to antimicrobial drugs than the AFR12 isolates identified in Cameroon between 2009 and 2011 due to a 10 kb deletion in the integrative conjugative element conferring multidrug resistance, ICEVchInd5, resulting in the loss of four AMR genes (strA, strB, floR and sul2). Our findings confirm the complementarity between traditional microbiological methods and microbial genomics for monitoring circulating 7PET strains and tracking their evolution and the development of AMR.