Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, CP 6010, 13083-875 Campinas, SP, Brasil.
BMC Microbiol. 2010 Jun 1;10:161. doi: 10.1186/1471-2180-10-161.
Escherichia coli strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A0, A1, B1, B22, B23, D1 and D2), according to the combination of the three genetic markers chuA, yjaA and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these E. coli phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.
The results indicated that the distribution of phylogenetic groups, subgroups and genetic markers is non-random in the hosts analyzed. Strains from group B1 were present in all hosts analyzed but were more prevalent in cow, goat and sheep samples. Subgroup B23 was only found in human samples. The diversity and the similarity indexes have indicated a similarity between the E. coli population structure of human and pig samples and among cow, goat and sheep samples. Correspondence analysis using contingence tables of subgroups, groups and genetic markers frequencies allowed the visualization of the differences among animal samples and the identification of the animal source of an external validation set. The classifier tools Binary logistic regression and Partial least square--discriminant analysis, using the genetic markers profile of the strains, differentiated the herbivorous from the omnivorous strains, with an average error rate of 17%.
This is the first work, as far as we are aware, that identifies the major source of fecal contamination of a pool of strains instead of a unique strain. We concluded that the analysis of the E. coli population structure can be useful as a supplementary bacterial source tracking tool.
大肠杆菌菌株通常存在于温血动物的肠道微生物群中。这些菌株可以根据 chuA、yjaA 和 DNA 片段 TspE4.C2 这三个遗传标记的组合，分为 A、B1、B2 和 D 这四个主要的系统发育群，然后再进一步细分为七个亚群（A0、A1、B1、B22、B23、D1 和 D2）。许多研究表明，这些系统发育群在毒力因子、生态位和生活史方面存在差异。因此，本研究旨在分析 94 株人源、13 株鸡源、50 株牛源、16 株羊源、39 株猪源和 29 株羊源大肠杆菌的这些系统发育群的分布情况，并验证该分析方法用于调查粪便污染来源的潜力。
结果表明，在所分析的宿主中，系统发育群、亚群和遗传标记的分布并非随机的。B1 群的菌株存在于所有分析的宿主中，但在牛、山羊和绵羊样本中更为普遍。B23 亚群仅在人源样本中发现。多样性和相似性指数表明，人源和猪源大肠杆菌种群结构之间以及牛、山羊和绵羊样本之间存在相似性。使用亚群、群和遗传标记频率的列联表进行对应分析，能够直观地显示动物样本之间的差异，并确定外部验证集的动物来源。使用菌株遗传标记特征的分类工具二项逻辑回归和偏最小二乘判别分析，能够区分食草动物和杂食动物，平均错误率为 17%。
据我们所知，这是首次确定了一组菌株而不是单一菌株粪便污染的主要来源。我们得出结论，分析大肠杆菌种群结构可以作为一种有用的细菌溯源补充工具。
