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

In 2022, a global resurgence of cholera was observed, resulting in 51 reported cases in Europe. Subsequent analysis of 49 Vibrio cholerae O1 isolates from these cases revealed their association with the seventh pandemic El Tor (7PET) lineage. As of 2023 and 2024, a further 59 cholera cases were reported by 11 European countries.

The study aimed to confirm that the V. cholerae O1 isolates linked to these European cases belonged to the epidemic 7PET lineage and to evaluate their virulence, antimicrobial resistance (AMR) determinants, and phylogenetic relationships.

Of the 49 V. cholerae O1 isolates available for whole genome sequencing, 49 yielded genomes of sufficient quality for analysis. These genomes were then compared with over 1,500 publicly available 7PET genomes to establish their position within a global phylogenetic context. The results demonstrated that all 49 genomes belonged to the 7PET lineage, specifically Wave 3.

Four sub-lineages were identified within this group: BD1.2 (2/49), AFR12 (6/49), AFR13 (8/49), and Pre-AFR15 (33/49). Notably, the Pre-AFR15 sub-lineage emerged as the most prevalent, suggesting its continued role in the ongoing global cholera resurgence.

In contrast to the 2022 findings, the 2023-2024 study also detected eight highly drug-resistant AFR13 isolates. This detection highlighted the international dissemination of this highly drug-resistant clone, which exhibits resistance to multiple first-line antimicrobial agents. The study concluded that routine use of whole genome sequencing by reference laboratories is crucial for differentiating epidemic 7PET from non-epidemic V. cholerae O1 lineages.

Additionally, it emphasized the importance of continued collaborative genomic surveillance of travel-associated cholera cases to provide early insights into the emergence, worldwide spread, and antimicrobial resistance of 7PET sub-lineages.