Department of Biophysics, University of Delhi South Campus, New Delhi, India.
Sci Data. 2023 Sep 1;10(1):573. doi: 10.1038/s41597-023-02444-0.
Escherichia coli are highly diverse bacteria with different pathogenic types, serotypes and phylogenetic types/phylotypes. In recent years, infections with E. coli have increased worldwide and so has the emergence of antibiotic resistant strains. In the present study we have assembled, annotated and analysed genome sequences of three strains of the phylogroup D of E. coli. These strains were isolated from the river Yamuna, a prominent anthropogenic urban river of northern India. These strains showed varied antibiotic susceptibilities, one was susceptible to all the antibiotics tested except ampicillin while of the other two, one was multi-β-lactam resistant and the other was multi-drug resistant (resistant to multiple β-lactams, fluoroquinolones and kanamycin). The short-sequence reads were assembled into contigs using the de-novo approach and further, scaffolding of contigs was performed by using the best reference genome for a particular isolate which resulted in a significant increase in the N value of each assembly. The bioinformatics assembly approach used in this study could be easily applied to study other bacterial genomes.
大肠杆菌是具有不同致病类型、血清型和系统发育型/系统发育型的高度多样化细菌。近年来，大肠杆菌感染在全球范围内有所增加，同时出现了抗生素耐药菌株。在本研究中，我们组装、注释和分析了三个肠杆菌科 D 群菌株的基因组序列。这些菌株是从印度北部的一条重要人为城市河流亚穆纳河(Yamuna River)中分离出来的。这些菌株表现出不同的抗生素敏感性，一种菌株除氨苄西林外对所有测试的抗生素均敏感，而另外两种菌株中，一种是多β-内酰胺耐药株，另一种是多药耐药株(对多种β-内酰胺类、氟喹诺酮类和卡那霉素耐药)。使用从头测序方法将短序列读组装成 contigs，然后使用最佳参考基因组对特定分离株进行 contigs 支架构建，从而显著提高了每个组装的 N 值。本研究中使用的生物信息学组装方法可轻松应用于研究其他细菌基因组。
