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Background   V. cholerae  is the etiological agent of cholera, a major public health concern in most developing countries. Virulence of  V. cholerae  relies on the powerful cholera toxin, encoded by the CTX prophage. The emergence of new pathogenic variants in the recent years has been mostly associated with new CTX prophage rearrangements.    Results  In this retrospective study, we show that the epidemic  V. cholerae  O1 El Tor strain responsible for the 2006 outbreak in Angola is clonally and genetically different from El Tor strains circulating in the 1990s in the same area. Strains from 2006 carry ICE Vch Ang3 of the SXT/R391 family. This ICE is associated with a narrower multidrug resistance profile compared to the one conferred by plasmid p3iANG to strains of the 1990s. The CTX prophage carried by 2006 El Tor strains is characterized by  rstR ET   and  ctxB Cla   alleles organized in a RS1-RS2-Core array on chromosome I. Interestingly, the newly emerging atypical strain belongs to a clade previously known to comprise only clinical isolates from the Indian subcontinent that also contain the same ICE of the SXT/R391 family.    Conclusions  Our findings remark the appearance of a novel  V. cholerae  epidemic variant in Africa with a new CTXΦ arrangement previously described only in the Indian Subcontinent.

New V. cholerae atypical El Tor variant emerged during the 2006 epidemic outbreak in Angola