Genomic Diversity of Escherichia Isolates from Diverse Habitats

Our understanding of the Escherichia genus is heavily biased toward pathogenic or commensal isolates from human or animal hosts. Recent studies have recovered Escherichia isolates that persist, and even grow, outside these hosts. Although the environmental isolates are typically phylogenetically distinct, they are highly related to and phenotypically indistinguishable from their human counterparts, including for the coliform test. To gain insights into the genomic diversity of Escherichia isolates from diverse habitats, including freshwater, soil, animal, and human sources, we carried out comparative DNA-DNA hybridizations using a multi-genome E. coli DNA microarray. The microarray was validated based on hybridizations with selected strains whose genome sequences were available and used to assess the frequency of microarray false positive and negative signals. Our results showed that human fecal isolates share two sets of genes (n>90) that are rarely found among environmental isolates, including genes presumably important for evading host immune mechanisms (e.g., a multi-drug transporter for acids and antimicrobials) and adhering to epithelial cells (e.g., hemolysin E and fimbrial-like adhesin protein). These results imply that environmental isolates are characterized by decreased ability to colonize host cells relative to human isolates. Our study also provides gene markers that can distinguish human isolates from those of warm-blooded animal and environmental origins, and thus can be used to more reliably assess fecal contamination in natural ecosystems.目前学界对埃希氏菌属（Escherichia genus）的认知，高度偏向于人类或动物宿主来源的致病型与共生型分离株。近期已有研究从上述宿主以外的环境中分离得到埃希氏菌，这类菌株不仅能存活，甚至可在环境中增殖。尽管这类环境来源的分离株通常在系统发育上存在差异，但它们与人类来源的对应菌株亲缘关系极近，且表型特征无法区分——包括大肠菌群检测结果也一致。为解析淡水、土壤、动物及人类等不同生境来源的埃希氏菌分离株的基因组多样性，本研究采用多基因组大肠杆菌DNA微阵列（DNA microarray）开展了比较DNA-DNA杂交（DNA-DNA hybridization）实验。本研究通过对已完成全基因组测序的选定菌株进行杂交实验，对该微阵列进行了有效性验证，并以此评估了微阵列假阳性与假阴性信号的出现频率。本研究结果显示，人类粪便来源的埃希氏菌分离株携带两组共90余个专属基因，这类基因在环境分离株中极为罕见；其中包括推测在逃避宿主免疫机制（如针对酸类与抗菌物质的多药转运体）以及黏附上皮细胞（如溶血素E（hemolysin E）与菌毛样黏附蛋白（fimbrial-like adhesin protein））过程中发挥关键作用的基因。上述结果表明，相较于人类来源的埃希氏菌分离株，环境分离株的宿主细胞定殖能力显著降低。本研究还筛选得到可区分人类来源、温血动物来源与环境来源埃希氏菌分离株的基因标记物，因此可用于更可靠地评估自然生态系统中的粪便污染情况。