Continued genomic surveillance of Vibrio cholerae O1 isolates from cholera cases in Europe, 2023-2024
- 1Institut Pasteur
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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BibTeX
@misc{njamkepo2026continued,
title = {{Continued genomic surveillance of Vibrio cholerae O1 isolates from cholera cases in Europe, 2023-2024}},
author = {E. Njamkepo and S. Dupke and T. Tauhid and R. Stephan and B. van der Putten and O. Nyholm and S. Herrera-Leon and R. J. Drew and M. Cormican and D. R. Greig and B. Tsafarova and R. Sacheli and C. Clarke and I. N. Ivanov and C. Jenkins and M. Lanzl and I. Froding and H. Scholz and C. Rouard and F.-X. Weill},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.18.752729},
url = {https://www.biorxiv.org/content/10.64898/2026.09.18.752729v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Continued genomic surveillance of Vibrio cholerae O1 isolates from cholera cases in Europe, 2023-2024
AU - E. Njamkepo
AU - S. Dupke
AU - T. Tauhid
AU - R. Stephan
AU - B. van der Putten
AU - O. Nyholm
AU - S. Herrera-Leon
AU - R. J. Drew
AU - M. Cormican
AU - D. R. Greig
AU - B. Tsafarova
AU - R. Sacheli
AU - C. Clarke
AU - I. N. Ivanov
AU - C. Jenkins
AU - M. Lanzl
AU - I. Froding
AU - H. Scholz
AU - C. Rouard
AU - F.-X. Weill
PY - 2026
DA - 2026/09/18
PB - bioRxiv
DO - 10.64898/2026.09.18.752729
UR - https://www.biorxiv.org/content/10.64898/2026.09.18.752729v1
AB - 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.
ER -