The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa

Yemen is currently experiencing the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. We investigated the phylogenetic relationships, pathogenesis, and antimicrobial resistance determinants by sequencing the genomes of Vibrio cholerae isolates from the Yemen epidemic and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1087 seventh pandemic V. cholerae serogroup O1 and O139 biotype El Tor isolates [2–4]. We show that the Yemeni isolates collected during the two epidemiological waves of the epidemic [1], —the first between September 28th 2016 and April 23rd 2017 (25,839 suspected cases) and the second beginning on April 24th, 2017 (more than one million suspected cases), — are seventh pandemic V. cholerae O1 El Tor (7PET) serotype Ogawa isolates from a single sublineage. Using genomic approaches, we link the Yemen epidemic to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. We also show that the Yemeni isolates are susceptible to several antibiotics commonly used to treat cholera, and to polymyxins, resistance to which is used as a marker of the El Tor biotype.

SummaryBackgroundIn war-torn Yemen, reports of confirmed cholera started in late September, 2016. The disease continues to plague Yemen today in what has become the largest documented cholera epidemic of modern times. We aimed to describe the key epidemiological features of this epidemic, including the drivers of cholera transmission during the outbreak.MethodsThe Yemen Health Authorities set up a national cholera surveillance system to collect information on suspected cholera cases presenting at health facilities. Individual variables included symptom onset date, age, severity of dehydration, and rapid diagnostic test result. Suspected cholera cases were confirmed by culture, and a subset of samples had additional phenotypic and genotypic analysis. We first conducted descriptive analyses at national and governorate levels. We divided the epidemic into three time periods: the first wave (Sept 28, 2016, to April 23, 2017), the increasing phase of the second wave (April 24, 2017, to July 2, 2017), and the decreasing phase of the second wave (July 3, 2017, to March 12, 2018). We reconstructed the changes in cholera transmission over time by estimating the instantaneous reproduction number, Rt. Finally, we estimated the association between rainfall and the daily cholera incidence during the increasing phase of the second epidemic wave by fitting a spatiotemporal regression model.FindingsFrom Sept 28, 2016, to March 12, 2018, 1 103 683 suspected cholera cases (attack rate 3·69%) and 2385 deaths (case fatality risk 0·22%) were reported countrywide. The epidemic consisted of two distinct waves with a surge in transmission in May, 2017, corresponding to a median Rt of more than 2 in 13 of 23 governorates. Microbiological analyses suggested that the same Vibrio cholerae O1 Ogawa strain circulated in both waves. We found a positive, non-linear, association between weekly rainfall and suspected cholera incidence in the following 10 days; the relative risk of cholera after a weekly rainfall of 25 mm was 1·42 (95% CI 1·31–1·55) compared with a week without rain.InterpretationOur analysis suggests that the small first cholera epidemic wave seeded cholera across Yemen during the dry season. When the rains returned in April, 2017, they triggered widespread cholera transmission that led to the large second wave. These results suggest that cholera could resurge during the ongoing 2018 rainy season if transmission remains active. Therefore, health authorities and partners should immediately enhance current control efforts to mitigate the risk of a new cholera epidemic wave in Yemen.FundingHealth Authorities of Yemen, WHO, and Médecins Sans Frontières.

Médecins Sans Frontières.

To the Editor: Killed oral cholera vaccines (OCVs) are part of the standard response package to a cholera outbreak, although the two-dose regimen of vaccines that has been prequalified by the World Health Organization (WHO) poses challenges to timely and efficient reactive vaccination campaigns. 1 Recent data suggest that the first dose alone provides short-term protection, similar to that of two doses, which may largely dictate the effect of OCVs during epidemics. [2][3][4] A cholera outbreak was detected in Lusaka, Zambia, in February 2016, after a period of 4 years without a reported case of cholera. An emergency reactive vaccination campaign was implemented in April 2016, targeting more than 500,000 persons who were at high risk for cholera in Lusaka (population, >2 million persons). The Ministry of Health, with support from Médecins sans Frontières and the WHO, decided to implement a single-dose campaign to quell the epidemic rapidly, in view of the insufficient number of vaccine doses that were available in the global stockpile to complete a two-dose campaign. In December 2016, when more doses became available, a second round of vaccination was organized and the second vaccine dose was offered to persons at risk.We conducted a matched case-control study to quantify the short-term effectiveness of a single-dose OCV regimen (Shanchol) between April 25, 2016, and June 15, 2016. The study was approved by two institutional review boards, and written informed consent was obtained from all the participants (see the Supplementary Appendix, available with the full text of this letter at NEJM.org). Cases of cholera were confirmed by means of culture, polymerase-chain-reaction as-