DNASeq of MDR E. coli from Cuba
For the short reads, Illumina sequencing technology was performed and sequencing library was prepared according to the Illumina standard library preparation protocol (Illumina, San Diego, CA).  Short reads were obtained using HiSeq2500, 2 x 150-bp paired-end sequencing technology, provided by Eurofins Genomics (Eurofins Genomics Europe Sequencing GmbH, Konstanz, Germany).In order to remove adaptor and low-quality reads (QV20), short reads were trimmed using Trimmomatic v0.36.