Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae

Abstract

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.

Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection

“…cholerae from Argentina and the Americas harbour the most similar VCR alleles to that amplified from aDNA dating from the fifth pandemic. ( a ) A phylogenetic tree [1] containing 380 diverse V. cholerae sequences, as well as an outgroup of three Vibrio species, on which the tree is rooted.…”

“…No whole-genome sequencing data were generated in this study. Accession numbers for the publicly available sequences collated and/or generated in a previous study [1] and used in this analysis are listed in Table S2 (available in the online version of this article) (https://doi.org/10.6084/m9.figshare.14384225.v1).…”

“…Other metadata, including genome accession numbers and the serogroup for each isolate (simplified to O1 or non-O1/O139), were taken from the supplementary data of Dorman et al . [1] and are provided in Table S2 (https://doi.org/10.6084/m9.figshare.14384225.v1).…”

“…Raw blast n output files, annotated genome assemblies originally collated and used in [1], the VCR query sequence transcribed from Ramirez and colleagues' article [2], and the tree in are provided in a Figshare repository linked to this study: https://dx.doi.org/10.6084/m9.figshare.13636577.…”

“…The phylogenetic tree presented in , and the gene presence/absence matrix used to classify isolates as toxigenic, are available from the Figshare repository linked to Dorman et al . [1]: https://doi.org/10.6084/m9.figshare.11310131.…”