The emergence of antimicrobial resistance (AMR) to first- and second-line treatment regimens of enteric fever is a global public-health problem, and routine genomic surveillance to inform clinical and public-health management guidance is essential. Here, we present the prospective analysis of genomic data to monitor trends in incidence, AMR and travel, and assess hierarchical clustering (HierCC) methodology of 1742 isolates of typhoidal salmonellae. Trend analysis of Salmonella Typhi and S. Paratyphi A cases per year increased 48 and 17.3%, respectively, between 2016 and 2019 in England, mainly associated with travel to South Asia. S. Paratyphi B cases have remained stable and are mainly associated with travel to the Middle East and South America. There has been an increase in the number of S. Typhi exhibiting a multidrug-resistant (MDR) profile and the emergence of extensively drug resistant (XDR) profiles. HierCC was a robust method to categorize clonal groups into clades and clusters associated with travel and AMR profiles. The majority of cases that had XDR S. Typhi reported recent travel to Pakistan (94 %) and belonged to a subpopulation of the 4.3.1 (H58) clone (HC5_1452). The phenotypic and genotypic AMR results showed high concordance for S. Typhi and S. Paratyphi A, B and C, with 99.99 % concordance and only three (0.01 %) discordant results out of a possible 23 178 isolate/antibiotic combinations. Genomic surveillance of enteric fever has shown the recent emergence and increase of MDR and XDR S. Typhi strains, resulting in a review of clinical guidelines to improve management of imported infections.

中文翻译：

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2016-2019 年英格兰伤寒沙门氏菌和副伤寒杆菌 A、B 和 C 的系统基因组学和抗菌素耐药性

肠热病一线和二线治疗方案出现抗菌素耐药性 (AMR) 是一个全球公共卫生问题，常规基因组监测为临床和公共卫生管理指导提供信息至关重要。在这里，我们对基因组数据进行前瞻性分析，以监测发病率、AMR 和旅行的趋势，并评估 1742 株伤寒沙门氏菌的层次聚类 (HierCC) 方法。伤寒沙门氏菌和沙门氏菌趋势分析。2016 年至 2019 年间，英格兰的甲型副伤寒病例每年分别增加 48% 和 17.3%，主要与前往南亚的旅行有关。小号 . 副伤寒乙型病例保持稳定，主要与前往中东和南美的旅行有关。S的数量有所增加。伤寒表现出多重耐药 (MDR) 特征和广泛耐药 (XDR) 特征的出现。HierCC 是将克隆群分类为与旅行和 AMR 概况相关的进化枝和集群的稳健方法。大多数有 XDR S的病例。伤寒报告了最近到巴基斯坦的旅行 (94%)，属于 4.3.1 (H58) 克隆 (HC5_1452) 的一个亚群。表型和基因型 AMR 结果显示S的高度一致性。伤寒和S. 在可能的 23 178 种分离物/抗生素组合中，副伤寒 A、B 和 C 的一致性为 99.99%，只有三个 (0.01%) 不一致。肠热的基因组监测显示最近出现和增加了 MDR 和 XDR S。伤寒菌株，导致对临床指南进行审查，以改善对输入性感染的管理。