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bioRxiv · 10.64898/2026.09.18.752729

Continued genomic surveillance of Vibrio cholerae O1 isolates from cholera cases in Europe, 2023-2024

Njamkepo, E.·Dupke, S.·Tauhid, T.·Stephan, R.·van der Putten, B.·Nyholm, O.·Herrera-Leon, S.·Drew, R. J.·Cormican, M.·Greig, D. R.·Tsafarova, B.·Sacheli, R.·Clarke, C.·Ivanov, I. N.·Jenkins, C.·Lanzl, M.·Froding, I.·Scholz, H.·Rouard, C.·Weill, F.-X.
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Abstract

Background: Following the global resurgence of cholera in 2022, 51 cholera cases were reported by European countries. We previously characterised 49 Vibrio cholerae O1 isolates from these cases using whole genome sequencing. In 2023 and 2024, 59 additional cholera cases were reported by 11 European countries. Aim: We aimed to confirm that V. cholerae O1 isolates associated with cholera cases reported in Europe in 2023-2024 belonged to the epidemic seventh pandemic El Tor (7PET) lineage rather than to non-epidemic V. cholerae O1 lineages, and to characterise their virulence, antimicrobial resistance (AMR) determinants and phylogenetic relationships. Methods: Fifty V. cholerae O1 isolates were available for whole genome sequencing, of which 49 yielded genomes of sufficient quality for analysis. Genomes were analysed together with more than 1,500 publicly available 7PET genomes to place the European isolates into a global phylogenetic context. Results: All 49 genomes belonged to the 7PET lineage and Wave 3. Four sub-lineages were identified: BD1.2 (2/49), AFR12 (6/49), AFR13 (8/49) and Pre-AFR15 (33/49). The predominance of Pre-AFR15 confirms its continued contribution to the ongoing global cholera resurgence. In contrast to our 2022 survey, eight highly drug-resistant AFR13 isolates were detected, documenting the international spread of this highly drug-resistant clone resistant to multiple first-line antimicrobial agents. Conclusion: Whole genome sequencing should be routinely used by reference laboratories to distinguish epidemic 7PET from non-epidemic V. cholerae O1 lineages and to monitor the emergence and international spread of AMR clones. Continued collaborative genomic surveillance of travel-associated cholera cases can provide early insights into the emergence, international spread and antimicrobial resistance of 7PET sub-lineages.

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Njamkepo, E., Dupke, S., Tauhid, T., Stephan, R., van der Putten, B., Nyholm, O., Herrera-Leon, S., Drew, R. J., Cormican, M., Greig, D. R., Tsafarova, B., Sacheli, R., Clarke, C., Ivanov, I. N., Jenkins, C., Lanzl, M., Froding, I., Scholz, H., Rouard, C., Weill, F.-X.. 2026-09-24. Continued genomic surveillance of Vibrio cholerae O1 isolates from cholera cases in Europe, 2023-2024. https://doi.org/10.64898/2026.09.18.752729

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