Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli ; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.

中文翻译：

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评估加拿大封闭牛群内持久性产毒素大肠埃希菌血清型的基因组相关性和进化速率。

产毒素大肠埃希菌 （VTEC）是与零星疾病和肠道疾病暴发相关的食物和水传播病原体。尽管已知牛是VTEC的宿主，但对牛VTEC的基因组变异以及人类暴发菌株报道的基因组变异是否与单个动物或群体/畜群感染源一致的了解甚少。VTEC患病率的先前研究确定了封闭的牛群中三个连续的小母牛群持续携带的血清型。本研究旨在：（i）确定牛分离株的基因组相关性是否与报道的与单一来源暴发相关的人类菌株的基因组相似性；（ii）估算牛群内主要血清型随时间推移的基因组变化率，（iii）确定与牛的持久性相关的血清型的基因组特征。完成了基于等位基因和单核苷酸变异的Illumina MiSeq基因组测序和基因分型，同时使用贝叶斯进化分析采样树测量了基因组随时间的变化。辅助基因组，包括非蛋白质编码基因间区域（IGRs），毒力因子，抗微生物基因和代表性持久性和散发性牛品系的质粒基因含量，均通过费舍尔精确检验进行了多重比较校正。O6：H34血清型的牛群菌株 而基因组随时间的变化则使用贝叶斯进化分析采样树进行了测量。辅助基因组，包括非蛋白质编码基因间区域（IGRs），毒力因子，抗微生物基因和代表性持久性和散发性牛品系的质粒基因含量，均通过费舍尔精确检验进行了多重比较校正。血清型O6：H34的牛群菌株（而基因组随时间的变化则使用贝叶斯进化分析采样树进行了测量。辅助基因组，包括非蛋白质编码基因间区域（IGRs），毒力因子，抗微生物基因和代表性持久性和散发性牛品系的质粒基因含量，均通过费舍尔精确检验进行了多重比较校正。O6：H34血清型的牛群菌株n = 22），O22：H8（n = 30），O108：H8（n = 39），O139：H19（n = 44）和O157：H7（n = 106）可以与流行病学无关的相同菌株区分开在相邻节点之间使用10个或更少等位基因差异的相似性阈值进行血清分型。日期随机化分析支持每种血清型中的时间队列聚类。每年每个站点的替换与以前报告的大肠杆菌值一致; 但是，这些值的分支支持较低。观察到血清型为O22：H8的噬菌体编码志贺毒素2基因的获取。泛基因组分析确定了在持续血清型中更普遍的辅助区域（P ≤0.05）。这些结果表明，来自特定牛群的VTEC血清型是高度克隆的，具有与人类单源暴发相关菌株相似的相关水平，但是随着时间的推移，基因组的变化会逐渐发生。另外，辅助基因组中的元素可以为牛群中VTEC的持久性提供选择性优势。