An unusual two-strain cholera outbreak in Lebanon, 2022-2023: a genomic epidemiology study

Antoine Abou Fayad, Rayane Rafei, Elisabeth Njamkepo, Jana Ezzeddine, Hadi Hussein, Solara Sinno, Jose-Rita Gerges, Sara Barada, Ahmad Sleiman, Moubadda Assi, Maryo Baakliny, Lama Hamedeh, Rami Mahfouz, Fouad Dabboussi, Rita Feghali, Zeina Mohsen, Alisar Rady, Nada Ghosn, Firas Abiad, Abdinasir Abubakar, Amal Barakat, Nadia Wauquier, Marie-Laure Quilici, Monzer Hamze (), François-Xavier Weill () and Ghassan M. Matar ()
Additional contact information
Antoine Abou Fayad: American University of Beirut
Rayane Rafei: Lebanese University
Elisabeth Njamkepo: Centre National de Référence des vibrions et du choléra
Jana Ezzeddine: American University of Beirut
Hadi Hussein: American University of Beirut
Solara Sinno: World Health Organization
Jose-Rita Gerges: American University of Beirut
Sara Barada: American University of Beirut
Ahmad Sleiman: American University of Beirut
Moubadda Assi: World Health Organization
Maryo Baakliny: Ministry of Public Health
Lama Hamedeh: American University of Beirut
Rami Mahfouz: American University of Beirut
Fouad Dabboussi: Lebanese University
Rita Feghali: Rafik Hariri University Hospital
Zeina Mohsen: Rafik Hariri University Hospital
Alisar Rady: World Health Organization
Nada Ghosn: Ministry of Public Health
Firas Abiad: Ministry of Public Health
Abdinasir Abubakar: World Health Organization
Amal Barakat: Eastern Mediterranean Regional Office Cairo
Nadia Wauquier: World Health Organisation
Marie-Laure Quilici: Centre National de Référence des vibrions et du choléra
Monzer Hamze: Lebanese University
François-Xavier Weill: Centre National de Référence des vibrions et du choléra
Ghassan M. Matar: American University of Beirut

Nature Communications, 2024, vol. 15, issue 1, 1-10

Abstract: Abstract Cholera is a life-threatening gastrointestinal infection caused by a toxigenic bacterium, Vibrio cholerae. After a lull of almost 30 years, a first case of cholera was detected in Lebanon in October 2022. The outbreak lasted three months, with 8007 suspected cases (671 laboratory-confirmed) and 23 deaths. In this study, we use phenotypic methods and microbial genomics to study 34 clinical and environmental Vibrio cholerae isolates collected throughout this outbreak. All isolates are identified as V. cholerae O1, serotype Ogawa strains from wave 3 of the seventh pandemic El Tor (7PET) lineage. Phylogenomic analysis unexpectedly reveals the presence of two different strains of the seventh pandemic El Tor (7PET) lineage. The dominant strain has a narrow antibiotic resistance profile and is phylogenetically related to South Asian V. cholerae isolates and derived African isolates from the AFR15 sublineage. The second strain is geographically restricted and extensively drug-resistant. It belongs to the AFR13 sublineage and clusters with V. cholerae isolates collected in Yemen. In conclusion, the 2022-2023 Lebanese cholera outbreak is caused by the simultaneous introduction of two different 7PET strains. Genomic surveillance with cross-border collaboration is therefore crucial for the identification of new introductions and routes of circulation of cholera, improving our understanding of cholera epidemiology.

Date: 2024
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DOI: 10.1038/s41467-024-51428-0

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