United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA.
Mol Biol Evol. 2012 Aug;29(8):2047-62. doi: 10.1093/molbev/mss072. Epub 2012 Feb 21.
Cattle are a major reservoir for Shiga toxin-producing Escherichia coli O157 (STEC O157) and harbor multiple genetic subtypes that do not all associate with human disease. STEC O157 evolved from an E. coli O55:H7 progenitor; however, a lack of genome sequence has hindered investigations on the divergence of human- and/or cattle-associated subtypes. Our goals were to 1) identify nucleotide polymorphisms for STEC O157 genetic subtype detection, 2) determine the phylogeny of STEC O157 genetic subtypes using polymorphism-derived genotypes and a phage insertion typing system, and 3) compare polymorphism-derived genotypes identified in this study with pulsed field gel electrophoresis (PFGE), the current gold standard for evaluating STEC O157 diversity. Using 762 nucleotide polymorphisms that were originally identified through whole-genome sequencing of 189 STEC O157 human- and cattle-isolated strains, we genotyped a collection of 426 STEC O157 strains. Concatenated polymorphism alleles defined 175 genotypes that were tagged by a minimal set of 138 polymorphisms. Eight major lineages of STEC O157 were identified, of which cattle are a reservoir for seven. Two lineages regularly harbored by cattle accounted for the majority of human disease in this study, whereas another was rarely represented in humans and may have evolved toward reduced human virulence. Notably, cattle are not a known reservoir for E. coli O55:H7 or STEC O157:H(-) (the first lineage to diverge within the STEC O157 serogroup), which both cause human disease. This result calls into question how cattle may have originally acquired STEC O157. The polymorphism-derived genotypes identified in this study did not surpass PFGE diversity assessed by BlnI and XbaI digestions in a subset of 93 strains. However, our results show that they are highly effective in assessing the evolutionary relatedness of epidemiologically unrelated STEC O157 genetic subtypes, including those associated with the cattle reservoir and human disease.
牛是产志贺毒素大肠杆菌 O157（STEC O157）的主要宿主，携带多种与人类疾病无关的遗传亚型。STEC O157 源自大肠杆菌 O55:H7 前体；然而，由于缺乏基因组序列，阻碍了对人类和/或牛相关亚型分化的研究。我们的目标是：1）鉴定 STEC O157 遗传亚型检测的核苷酸多态性；2）使用多态性衍生的基因型和噬菌体插入分型系统确定 STEC O157 遗传亚型的系统发育；3）将本研究中鉴定的多态性衍生基因型与脉冲场凝胶电泳（PFGE）进行比较，PFGE 是评估 STEC O157 多样性的当前金标准。我们使用最初通过对 189 株 STEC O157 人源和牛源分离株进行全基因组测序确定的 762 个核苷酸多态性，对 426 株 STEC O157 菌株进行了基因分型。连锁多态性等位基因定义了 175 种基因型，这些基因型由最小的 138 个多态性标记。鉴定出 STEC O157 的 8 个主要谱系，其中牛是 7 个谱系的宿主。本研究中，两种经常存在于牛中的谱系导致了大多数人类疾病，而另一种谱系在人类中很少出现，可能已经向降低人类毒力的方向进化。值得注意的是，牛不是大肠杆菌 O55:H7 或 STEC O157:H（-）（STEC O157 血清群内第一个分化的谱系）的已知宿主，这两种细菌都会导致人类疾病。这一结果引发了对牛最初如何获得 STEC O157 的疑问。本研究中鉴定的多态性衍生基因型并未超过 BlnI 和 XbaI 消化评估的 PFGE 多样性，在 93 株菌株的子集中。然而，我们的结果表明，它们在评估流行病学上无关的 STEC O157 遗传亚型的进化相关性方面非常有效，包括与牛宿主和人类疾病相关的遗传亚型。
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