Genomic analyses of three waterborne Escherichia coli strains of phylogroup D

Infection with Escherichia coli E. coli has increased significantly worldwide and its treatment with antibiotics has shown a drastic increase in the emergence of antimicrobial resistance strains like Multi Beta lactams and Multi-Drug Resistant. In the present work, we provide genome sequences and annotations, gene ontology GO annotations, virulence factors, antimicrobial resistance genes, and mobile genetic elements MGEs data for E. coli strain IP9, KKA, and IPE isolated from water bodies prevailing in the Indian subcontinent and first to be reported under phylogroup D from India. The assembled genomes consist of E. coli strain IP9 drug-sensitive, draft genome 4,910,225 bp with no plasmids sequence. E. coli strain KKA multi Beta-lactam resistant) consists of draft genome 5,101,091 bp with no plasmids sequence. E. coli strain IPE Multi-drug resistant consists of draft chromosomal genome 5,225,435 bp and six complete circular plasmid genomes of 5,165 bp, 4,234 bp, 4,072 bp, 3,174 bp, 2,101 bp and 1,459 bp. Using gene annotation software 4,934, 4,772, and 4,545 protein-encoding genes were identified in IPE, KKA, and IP9 respectively, and further annotated with GO terms. Based upon SNP analysis of these genomes, we signify their genetic heterogeneity. Additionally, we designed an NGS bioinformatics analysis pipeline to assemble these genomes using both a de-novo and reference-based approach that has increased N50 value and termed it as de-novo guided reference-based genome assembly. The resulting approach could be found useful in the assembly of environmental isolates, and the approach can be applied easily to other bacterial genomes.