Supporting data for "Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae"

In order to control and eradicate epidemic cholera, we need to understand how epidemics
begin, how they spread, and how they decline and eventually end. This requires extensive
sampling of epidemic disease over time, alongside the background of endemic disease that
may exist concurrently with the epidemic. The unique circumstances surrounding the
Argentinian cholera epidemic of 1992–1998 presented an opportunity to do this. Here, we use
490 Argentinian V. cholerae genome sequences to characterise the variation within, and
between, epidemic and endemic V. cholerae. We show that, during the 1992–1998 cholera
epidemic, the invariant epidemic clone co-existed alongside highly diverse members of the
Vibrio cholerae species in Argentina, and we contrast the clonality of epidemic V. cholerae with
the background diversity of local endemic bacteria. Our findings refine and add nuance to our
genomic definitions of epidemic and endemic cholera, and are of direct relevance to controlling current and future cholera epidemics.