Whole-Genome Sequencing of E. coli Isolates from Meat Sources

A combination of cluster and simple random sampling were used to ensure that 14 isolates from the different meat sources and areas were chosen for WGS. A Genomic DNA (gDNA) of the E. coli isolates was extracted and purified using the QIAamp^R DNA Mini Kit (QIAGEN, Hilden, Germany). Following extraction, DNA quantification and the quality check was performed on a Qubit^® 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and Nanodrop 8000 (Thermo Scientific, Waltham, MA, USA), respectively [30 (link)]. The Nextera XT DNA Sample Preparation Kit was used to prepare the paired-end library and WGS was performed using the Illumina MiSeq machine (Illumina, San Diego, CA, USA). The obtained raw reads were de-novo assembled with the Shovill pipeline version 0.9.0 that uses SPAdes version 3.11.0. The assembled contigs were deposited in GenBank under project number PRJNA484345.