Whole Genome Sequencing of E. coli Isolates

From each specimen, at least three primarily identified E. coli isolates were sequenced. The E. coli strains were selected based on their different Microbact 24E and morphological profiles. DNA was extracted using the Wizard genomic extraction kit (Promega) per the manufacturer’s protocol, and then they were library prepared with the NEBNext Ultra II FS DNA library kit and whole genome sequenced on the Illumina platform at the Wellcome Sanger Institute. Raw read quality control was carried out using FastQC (Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom), and quality reports were aggregated using MultiQC.³⁴ (link) Reads were assembled using the SPAdes assembler, and assembly quality was determined using the Quality Assessment Tool for Genome Assemblies (QUAST)³⁵ (link) and CheckM.³⁶ (link) Reads were also assigned taxonomic identities using Kraken, and Bracken was used to determine species abundance of the taxonomic identities assigned by Kraken.³⁷ (link)^,³⁸ The virulence genes were identified using the ARIBA VirulenceFinder database.³⁹ (link) Isolate genomes were deposited in the European Nucleotide Archive (ENA) under project ID PRJEB8667 (https://www.ebi.ac.uk/ena/browser/view/PRJEB8667).

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Akinlabi O.C., Nwoko E.S., Dada R.A., Ekpo S., Omotuyi A., Nwimo C.C., Adepoju A., Popoola O., Dougan G., Thomson N.R, & Okeke I.N. (2023). Epidemiology and Risk Factors for Diarrheagenic Escherichia coli Carriage among Children in Northern Ibadan, Nigeria. The American Journal of Tropical Medicine and Hygiene, 109(6), 1223-1232.

Publication 2023

Wizard genomic extraction kit NEBNext Ultra II FS DNA library kit FastQC MultiQC

Corresponding Organization :

Other organizations : University of Ibadan, Ahmadu Bello University, Bowen University, Wellcome Sanger Institute, University of Cambridge

Top 5 similar protocols

Variable analysis

independent variables

Selection of E. coli isolates based on different Microbact 24E and morphological profiles

dependent variables

Whole genome sequencing of E. coli isolates

control variables

DNA extraction using Wizard genomic extraction kit (Promega) per the manufacturer's protocol
Library preparation with the NEBNext Ultra II FS DNA library kit
Quality control of raw reads using FastQC and MultiQC
Assembly of reads using the SPAdes assembler
Assessment of assembly quality using QUAST and CheckM
Taxonomic identification of reads using Kraken and Bracken
Identification of virulence genes using the ARIBA VirulenceFinder database

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