Data Sheet 1_Genomic insights into within-farm persistence and global phylogenetic relatedness of Shiga toxin-producing Escherichia coli O26 in a dairy cattle farm in the UK.pdf

BackgroundShiga toxin-producing Escherichia coli (STEC) O26 is increasingly implicated in human hemolytic uremic syndrome globally. As cattle are an important reservoir, we conducted a year-long pilot study on a dairy farm in England (~200 cattle) to investigate the occurrence, persistence, and genomics of STEC O26.
MethodsAcross four visits, 250 samples were collected (fecal pats n = 143, boot swabs n = 58, environmental n = 49). All E. coli O26 isolates were confirmed by real-time PCR and characterized using short-read whole-genome sequencing (WGS) for serotype, sequence type (ST), clonal complex (CC), phylogeny, stx subtyping, locus of enterocyte effacement pathogenicity island, and virulence genes. A Bayesian logistic regression model evaluated associations between STEC presence and predictors.
ResultsA total of 23 E. coli O26 isolates were recovered from 250 samples, with 14 STEC O26 carrying stx1, stx2, and eae, and nine non-STEC O26 were identified. Successful sequencing of a subset of 20 E. coli O26 confirmed all as O26:H11, of which, 12 STEC belonged to ST21 harboring stx1a and stx2a, and eight were non-STEC ST29, both being within CC29. Two non-O26 STEC were also recovered (STEC O130:H53 and STEC O145:H12). SNP analysis demonstrated STEC O26 clones were persisting within the herd; while non-STEC ST29 clones only emerged in visits 3 and 4. Although clustering with human STEC O26 isolates, the study isolates did not show any epidemiological or genetic link to human isolates, as they differed by at least 51 SNPs. We observed clear temporal and environmental variation in STEC O26 detection and Bayesian logistic regression modeling showed significantly reduced odds of STEC detection outdoors.
ConclusionsSTEC O26:H11 ST21 was consistently detected on a dairy farm in England over a year. Despite low detection rates, the persistence of STEC O26 in cattle and their environment poses a public health risk due to its low infectious dose. These findings provide insight into STEC occurrence and genomic diversity within a cattle farm, its zoonotic risks, and suggest that multiple factors including temporal and housing condition may influence detection.

背景：产志贺毒素大肠杆菌（Shiga toxin-producing Escherichia coli, STEC）O26在全球范围内与人类溶血性尿毒症综合征的关联日益密切。由于牛是重要的宿主库，我们在英格兰的一座奶牛场（约200头奶牛）开展了一项为期一年的初步研究，以调查STEC O26的检出情况、持续性及基因组特征。
方法：研究共开展4次采样，累计收集250份样本（粪便样本143份、靴拭样本58份、环境样本49份）。所有大肠杆菌O26分离株均经实时PCR确认，并通过短读长全基因组测序（short-read whole-genome sequencing, WGS）进行分型鉴定，涵盖血清型、序列型（sequence type, ST）、克隆复合体（clonal complex, CC）、系统发育、志贺毒素亚型、肠细胞脱落位点致病岛及毒力基因等维度。采用贝叶斯逻辑回归模型评估STEC检出情况与各预测因子间的关联。
结果：本研究从250份样本中共分离得到23株大肠杆菌O26，其中14株为携带stx1、stx2及eae基因的STEC O26，剩余9株为非STEC O26。对其中20株大肠杆菌O26进行成功测序后确认，所有菌株均为O26:H11血清型，其中12株STEC属于ST21型，携带stx1a和stx2a基因，另外8株非STEC属于ST29型，二者均归属于CC29克隆复合体。此外还分离得到2株非O26型STEC（STEC O130:H53与STEC O145:H12）。单核苷酸多态性（single nucleotide polymorphism, SNP）分析显示，STEC O26克隆株在牛群中持续存在；而非STEC ST29克隆株仅在第3、4次采样中被检出。尽管本研究分离株与人类STEC O26分离株聚类在一起，但二者至少存在51个单核苷酸多态性位点的差异，未显示出流行病学或遗传学关联。研究观察到STEC O26的检出率存在显著的时间与环境差异，贝叶斯逻辑回归模型显示，户外环境中STEC的检出几率显著降低。
结论：本研究证实，STEC O26:H11 ST21型菌株在英格兰的一座奶牛场中持续存在达一年之久。尽管检出率较低，但牛群及其环境中STEC O26的持续性仍构成公共卫生风险，因其感染剂量极低。本研究结果揭示了奶牛场中STEC的发生情况与基因组多样性，及其人畜共患病风险，并提示包括时间因素与饲养条件在内的多种因素可能影响STEC的检出率。