Jia Mo, Geornaras Ifigenia, Martin Jennifer N, Belk Keith E, Yang Hua
Center for Meat Safety and Quality, Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States.
Front Microbiol. 2021 Apr 1;12:647434. doi: 10.3389/fmicb.2021.647434. eCollection 2021.
A comparative whole genome analysis was performed on three newly sequenced O157:H7 strains with different profiles, previously isolated from feedlot cattle [C1-010 (, +), C1-057 (), and C1-067 (+, +)], as well as five foodborne outbreak strains and six -negative strains from NCBI. Phylogenomic analysis demonstrated that the -carrying C1-010 and -negative C1-057 strains were grouped with the six NCBI -negative O157:H7 strains in Cluster 1, whereas the -carrying C1-067 and five foodborne outbreak strains were clustered together in Cluster 2. Based on different clusters, we selected the three newly sequenced strains, one -carrying strain, and the six NCBI -negative strains and identify their prophages at the insertion sites. All -carrying prophages contained both the three Red recombination genes (, , ) and their repressor . On the other hand, the majority of the -negative prophages carried only the three Red recombination genes, but their repressor was absent. In the absence of the repressor , the consistent expression of the Red recombination genes in prophages might result in more frequent gene exchanges, potentially increasing the probability of the acquisition of genes. We further investigated each of the 10 selected O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two -carrying strains and one in the single -carrying and seven -negative strains were found to be associated with an upstream insertion sequence 629 within a conserved region among these strains. The presence of more unique metabolic pathway genes in -carrying O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the -carrying and -negative O157:H7 strains, the fact that they were grouped into the same phylogenomic cluster and had the same unique metabolic pathway genes suggested that they may also share closely related evolutionary pathways. As a consequence, gene exchange between them is more likely to occur. Results from this study could potentially serve as a basis to help develop strategies to reduce the prevalence of pathogenic O157:H7 in livestock and downstream food production environments.
对三个新测序的具有不同特征的O157:H7菌株进行了全基因组比较分析，这些菌株先前从饲养场牛中分离得到[C1 - 010(, +)、C1 - 057()和C1 - 067(+, +)]，以及来自NCBI的五个食源性暴发菌株和六个阴性菌株。系统基因组分析表明，携带的C1 - 010菌株和阴性的C1 - 057菌株与NCBI的六个阴性O157:H7菌株在簇1中归为一组，而携带的C1 - 067菌株和五个食源性暴发菌株在簇2中聚集在一起。基于不同的簇，我们选择了三个新测序的菌株、一个携带菌株和六个NCBI阴性菌株，并在插入位点鉴定它们的前噬菌体。所有携带的前噬菌体都包含三个Red重组基因(, , )及其阻遏物 。另一方面，大多数阴性前噬菌体仅携带三个Red重组基因，但缺少它们的阻遏物 。在没有阻遏物 的情况下，前噬菌体中Red重组基因的持续表达可能导致更频繁的基因交换，潜在地增加获得 基因的概率。我们进一步研究了10个选定的O157:H7菌株各自独特的代谢途径基因。在两个携带菌株中发现了七个独特的代谢途径基因，在单个携带菌株和七个阴性菌株中发现了一个独特的代谢途径基因，这些基因与这些菌株保守区域内的上游插入序列629相关。携带的O157:H7菌株中存在更多独特的代谢途径基因可能会增加它们在复杂环境（如饲养场牛）中的竞争力。对于携带和阴性的O157:H7菌株，它们被归为同一系统基因组簇且具有相同独特代谢途径基因这一事实表明，它们可能也共享密切相关的进化途径。因此，它们之间更有可能发生基因交换。本研究结果可能为制定减少致病性O157:H7在牲畜和下游食品生产环境中流行的策略提供依据。
