Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Vibrions et du choléra, Paris, France.
Gastrointestinal Bacteria Reference Unit (GBRU), UK Health Security Agency, London, United Kingdom.
Euro Surveill. 2024 Sep;29(36). doi: 10.2807/1560-7917.ES.2024.29.36.2400069.
BackgroundThe number of cholera cases reported to the World Health Organization (WHO) in 2022 was more than double that of 2021. Nine countries of the WHO European Region reported 51 cases of cholera in 2022 vs five reported cases in 2021.AimWe aimed to confirm that the O1 isolates reported by WHO European Region countries in 2022 belonged to the seventh pandemic El Tor lineage (7PET). We also studied their virulence, antimicrobial resistance (AMR) determinants and phylogenetic relationships.MethodsWe used microbial genomics to study the 49 O1 isolates recovered from the 51 European cases. We also used > 1,450 publicly available 7PET genomes to provide a global phylogenetic context for these 49 isolates.ResultsAll 46 good-quality genomes obtained belonged to the 7PET lineage. All but two isolates belonged to genomic Wave 3 and were grouped within three sub-lineages, one of which, Pre-AFR15, predominated (34/44). This sub-lineage, corresponding to isolates from several countries in Southern Asia, the Middle East and Eastern or Southern Africa, was probably a major contributor to the global upsurge of cholera cases in 2022. No unusual AMR profiles were inferred from analysis of the AMR gene content of the 46 genomes.ConclusionReference laboratories in high-income countries should use whole genome sequencing to assign O1 isolates formally to the 7PET or non-epidemic lineages. Periodic collaborative genomic studies based on isolates from travellers can provide useful information on the circulating strains and their evolution, particularly as concerns AMR.
2022 年向世界卫生组织（世卫组织）报告的霍乱病例数是 2021 年的两倍多。世卫组织欧洲区域的九个国家报告 2022 年有 51 例霍乱病例，而 2021 年报告的病例为 5 例。
我们旨在确认世卫组织欧洲区域国家报告的 2022 年 O1 分离株属于第七次大流行埃尔托谱系（7PET）。我们还研究了它们的毒力、抗菌药物耐药性（AMR）决定因素和系统发育关系。
我们使用微生物基因组学研究了从 51 例欧洲病例中恢复的 49 株 O1 分离株。我们还使用了超过 1450 个公开的 7PET 基因组，为这 49 个分离株提供了全球系统发育背景。
获得的 46 个高质量基因组均属于 7PET 谱系。除了两个分离株外，所有分离株均属于基因组波 3，分为三个亚谱系，其中一个主要是 Pre-AFR15（34/44）。这个亚谱系与南亚、中东和东非或南非的几个国家的分离株相对应，可能是 2022 年霍乱病例全球激增的主要原因。从 46 个基因组的 AMR 基因含量分析中推断，没有不寻常的 AMR 谱。
高收入国家的参考实验室应使用全基因组测序将 O1 分离株正式分配到 7PET 或非流行谱系。基于旅行者分离株的定期合作基因组研究可以提供有关循环菌株及其进化的有用信息，特别是在 AMR 方面。
