Food Safety and Enteric Pathogens Research Unit, USDA, ARS, National Animal Disease Center, 1920 Dayton Avenue, P.O. Box 70, Ames, IA, 50010, USA.
Oak Ridge Institute for Science and Education (ORISE), ARS Research Participation Program, MS 36, P.O. Box 117, Oak Ridge, TN, 37831, USA.
BMC Genomics. 2019 Mar 8;20(1):196. doi: 10.1186/s12864-019-5568-6.
Escherichia coli O157:H7 (O157) has been linked to numerous foodborne disease outbreaks. The ability to rapidly sequence and analyze genomes is important for understanding epidemiology, virulence, survival, and evolution of outbreak strains. In the current study, we performed comparative genomics to determine structural and functional features of the genome of a foodborne O157 isolate NADC 6564 and infer its evolutionary relationship to other O157 strains.
The chromosome of NADC 6564 contained 5466 kb compared to reference strains Sakai (5498 kb) and EDL933 (5547 kb) and shared 41 of its 43 Linear Conserved Blocks (LCB) with the reference strains. However, 18 of 41 LCB had inverse orientation in NADC 6564 compared to the reference strains. NADC 6564 shared 18 of 19 bacteriophages with reference strains except that the chromosomal positioning of some of the phages differed among these strains. The additional phage (P19) of NADC 6564 was located on a 39-kb insertion element (IE) encoding several hypothetical proteins, an integrase, transposases, transcriptional regulators, an adhesin, and a phosphoethanolamine transferase (PEA). The complete homologs of the 39-kb IE were found in E. coli PCN061 of porcine origin. The IE-encoded PEA showed low homology (32-33%) to four other PEA in NADC 6564 and PEA linked to mobilizable colistin resistance in E. coli but was highly homologous (95%) to a PEA of uropathogenic, avian pathogenic, and enteroaggregative E. coli. NADC 6564 showed slightly higher minimum inhibitory concentration of colistin compared to the reference strains. The 39-kb IE also contained dndBCDE and dptFGH operons encoding DNA S-modification and a restriction pathway, linked to oxidative stress tolerance and self-defense against foreign DNA, respectively. Evolutionary tree analysis grouped NADC 6564 with lineage I O157 strains.
These results indicated that differential phage counts and different chromosomal positioning of many bacteriophages and genomic islands might have resulted in recombination events causing altered chromosomal organization in NADC 6564. Evolutionary analysis grouped NADC 6564 with lineage I strains and suggested its earlier divergence from these strains. The ability to perform S-DNA modification might affect tolerance of NADC 6564 to various stressors.
产志贺毒素大肠杆菌 O157:H7（O157）与许多食源性疾病爆发有关。快速测序和分析基因组对于了解爆发菌株的流行病学、毒力、存活和进化非常重要。在本研究中，我们进行了比较基因组学分析，以确定食源性 O157 分离株 NADC 6564 的基因组结构和功能特征，并推断其与其他 O157 菌株的进化关系。
NADC 6564 的染色体与参考菌株 Sakai（5498kb）和 EDL933（5547kb）相比，含有 5466kb，与参考菌株共享 41 个线性保守块（LCB）中的 41 个。然而，与参考菌株相比，NADC 6564 的 41 个 LCB 中有 18 个具有反向取向。NADC 6564 与参考菌株共享 18 个噬菌体，除了这些菌株中一些噬菌体的染色体定位不同外。NADC 6564 的额外噬菌体（P19）位于一个 39kb 的插入元件（IE）上，该元件编码几个假定蛋白、一个整合酶、转座酶、转录调节剂、一个黏附素和一个磷酸乙醇胺转移酶（PEA）。在猪源大肠杆菌 PCN061 中发现了完整的 39kb IE 同源物。IE 编码的 PEA 与 NADC 6564 中的其他 4 个 PEA 以及与大肠杆菌中可移动多粘菌素抗性相关的 PEA 具有低同源性（32-33%），但与尿路致病性、禽致病性和肠聚集性大肠杆菌的 PEA 高度同源（95%）。与参考菌株相比，NADC 6564 对多粘菌素的最小抑菌浓度略高。39kb IE 还包含 dndBCDE 和 dptFGH 操纵子，分别编码 DNA S-修饰和限制途径，与氧化应激耐受和自身防御外来 DNA 有关。进化树分析将 NADC 6564 与 I 谱系 O157 菌株分组。
这些结果表明，噬菌体数量的差异以及许多噬菌体和基因组岛的不同染色体定位可能导致重组事件，导致 NADC 6564 染色体组织发生改变。进化分析将 NADC 6564 与 I 谱系菌株分组，并表明其较早地与这些菌株分离。进行 S-DNA 修饰的能力可能会影响 NADC 6564 对各种应激源的耐受能力。
