Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA.
Microb Genom. 2023 Aug;9(8). doi: 10.1099/mgen.0.001073.
Application of whole-genome sequencing (WGS) to characterize foodborne pathogens has advanced our understanding of circulating genotypes and evolutionary relationships. Herein, we used WGS to investigate the genomic epidemiology of , a leading cause of foodborne disease. Among the 214 strains recovered from patients with gastroenteritis in Michigan, USA, 85 multilocus sequence types (STs) were represented and 135 (63.1 %) were phenotypically resistant to at least one antibiotic. Horizontally acquired antibiotic resistance genes were detected in 128 (59.8 %) strains and the genotypic resistance profiles were mostly consistent with the phenotypes. Core-gene phylogenetic reconstruction identified three sequence clusters that varied in frequency, while a neighbour-net tree detected significant recombination among the genotypes (pairwise homoplasy index <0.01). Epidemiological analyses revealed that travel was a significant contributor to pangenomic and ST diversity of , while some lineages were unique to rural counties and more commonly possessed clinically important resistance determinants. Variation was also observed in the frequency of lineages over the 4 year period with chicken and cattle specialists predominating. Altogether, these findings highlight the importance of geographically specific factors, recombination and horizontal gene transfer in shaping the population structure of . They also illustrate the usefulness of WGS data for predicting antibiotic susceptibilities and surveillance, which are important for guiding treatment and prevention strategies.
全基因组测序（WGS）在描述食源性病原体中的应用，加深了我们对循环基因型和进化关系的理解。在此，我们使用 WGS 来研究食源性疾病主要致病菌——的基因组流行病学。在美国密歇根州的肠胃炎患者中分离到的 214 株 中，有 85 个多位点序列型（ST），其中 135 株（63.1%）对至少一种抗生素表现出表型耐药。在 128 株（59.8%）中检测到水平获得的抗生素耐药基因，基因型耐药谱与表型大多一致。核心基因系统发育重建确定了三个序列簇，其频率不同，而邻接法树检测到基因型之间存在明显的重组（成对同系物指数 <0.01）。流行病学分析表明，旅行是导致 泛基因组和 ST 多样性的重要因素，而一些谱系是农村县特有的，且更常携带具有临床重要性的耐药决定因素。在 4 年的时间里，不同谱系的频率也存在变化，鸡和牛专业菌居多。总的来说，这些发现强调了地理位置特定因素、重组和水平基因转移在塑造 种群结构中的重要性。它们还说明了 WGS 数据在预测抗生素敏感性和监测方面的有用性，这对于指导治疗和预防策略非常重要。
