Cholera is thought by many to be a disease of the Victorian era. However, Yemen has recently experienced one of the largest ever cholera epidemics. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported. We investigated the phylogenetic relationships between strains, disease pathogenesis and the determinants of antimicrobial resistance, by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighboring regions. The 116 genomic sequences obtained were placed within the phylogenetic context of a global collection of 1,087 7PET isolates. We showed that the isolates from Yemen collected during the two epidemiological waves of the epidemic — which had very different clinical attack rates— were V. cholerae serotype Ogawa isolates from a single sublineage. Using genomic approaches, we linked the epidemic in Yemen to global radiations of pandemic V. cholerae and showed that this sublineage originated from South Asia and had recently caused outbreaks in East Africa (most recent introduction into Africa, T13) before appearing in Yemen.Furthermore, we showed that the isolates from Yemen are unexpectedly susceptible to several antibiotics widely used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype. This study thus illustrated the key role of genomic microbial surveillance and cross-border collaborations in understanding the global spread of cholera.
The study was published in the Journal Nature in January 2019.
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