• Cholera Epidemic in South Sudan and Uganda and Need for International Collaboration in Cholera Control

      Abubakar, A; Bwire, G; Azman, AS; Bouhenia, M; Deng, LL; Wamala, JF; Rumunu, J; Kagirita, A; Rauzier, J; Grout, L; et al. (Center for Disease Control, 2018-05-01)
    • Cholera Rapid Test with Enrichment Step Has Diagnostic Performance Equivalent to Culture

      Ontweka, LN; Deng, LO; Rauzier, J; Debes, AK; Tadesse, F; Parker, LA; Wamala, JF; Bior, BK; Lasuba, M; But, AB; et al. (Public Library of Science, 2016-12-19)
      Cholera rapid diagnostic tests (RDT) could play a central role in outbreak detection and surveillance in low-resource settings, but their modest performance has hindered their broad adoption. The addition of an enrichment step may improve test specificity. We describe the results of a prospective diagnostic evaluation of the Crystal VC RDT (Span Diagnostics, India) with enrichment step and of culture, each compared to polymerase chain reaction (PCR), during a cholera outbreak in South Sudan. RDTs were performed on alkaline peptone water inoculated with stool and incubated for 4-6 hours at ambient temperature. Cholera culture was performed from wet filter paper inoculated with stool. Molecular detection of Vibrio cholerae O1 by PCR was done from dry Whatman 903 filter papers inoculated with stool, and from wet filter paper supernatant. In August and September 2015, 101 consecutive suspected cholera cases were enrolled, of which 36 were confirmed by PCR. The enriched RDT had 86.1% (95% CI: 70.5-95.3) sensitivity and 100% (95% CI: 94.4-100) specificity compared to PCR as the reference standard. The sensitivity of culture versus PCR was 83.3% (95% CI: 67.2-93.6) for culture performed on site and 72.2% (95% CI: 54.8-85.8) at the international reference laboratory, where samples were tested after an average delay of two months after sample collection, and specificity was 98.5% (95% CI: 91.7-100) and 100% (95% CI: 94.5-100), respectively. The RDT with enrichment showed performance comparable to that of culture and could be a sustainable alternative to culture confirmation where laboratory capacity is limited.
    • Evaluation of the SD Bioline Cholera Rapid Diagnostic Test During the 2016 Cholera Outbreak in Lusaka, Zambia

      Mwaba, J; Ferreras, E; Chizema-Kawesa, E; Mwimbe, D; Tafirenyika, F; Rauzier, J; Blake, A; Rakesh, A; Poncin, M; Stoitsova, S; et al. (2018-05-31)
      To assess the performance of the SD Bioline Cholera Ag O1/O139 rapid diagnostic test (RDT) compared to a reference standard combining culture and PCR for the diagnosis of cholera cases during an outbreak.
    • Genomic History of the seventh Pandemic of Cholera in Africa

      Weill, FX; Domman, D; Njamkepo, E; Tarr, C; Rauzier, J; Fawal, N; Keddy, KH; Salje, H; Moore, S; Mukhopadhyay, AK; et al. (American Association for the Advancement of Science, 2017-11-10)
      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.
    • Genomic Insights into the 2016-2017 Cholera Epidemic in Yemen

      Weill, FX; Domman, D; Njamkepo, E; Almesbahi, AA; Naji, M; Nasher, SS; Rakesh, A; Assiri, AM; Sharma, NC; Kariuki, S; et al. (Nature Publishing Group, 2019-01-02)
      Yemen is currently experiencing, to our knowledge, 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. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen 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. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.