Fig. 1. Geographic and temporal origin of Vibrio cholerae stored at INEI.

Cholera cases were reported to WHO and PAHO throughout the epidemic period. a V. cholerae O1 and non-O1 were received by INEI from the North of Argentina. b The diameter of each circle scales with the number of isolates recorded to have originated from the indicated region. Circles are coloured by the year of receipt. Locations were inferred from the city (where recorded) or from the province which sent the isolate to INEI. These isolates were received between 1992 and 2002. c The V. cholerae O1 received were principally clinical isolates, whereas non-O1 V. cholerae were both clinical and environmental isolates. In our study, we sought to capture the genetic changes that occurred in V. cholerae O1 at the beginning and the end of the cholera epidemic (d), and included contemporaneous non-O1 isolates. Geographic data were unavailable for six O1 and 14 non-O1 V. cholerae (b); dates of isolation were not recorded for five V. cholerae (c). Four sequenced isolates had no date of isolation (d). It should be noted that the peaks in V. cholerae receipt in 1997–1998 predate Hurricane Mitch (October 1998), a natural disaster which led to the increase of cholera incidence in Central America⁹⁴. Seven isolates from 2003 onwards that were sequenced as part of this study post-date the epidemic, and were not included in the metadata used to produce (c). Y-axes in (c) and (d): number of isolates received/sequenced. Publicly-available data were taken from^17–21, https://www.who.int/cholera/statistics/en/, and http://ais.paho.org/phip/viz/ed_colera_casesamericas.asp, to produce (a).