Long-read data and assemblies for E. coli genomes harbouring ESC-R genes in plasmids and chromosomes.

The emergence and persistence of extended-spectrum cephalosporin resistance (ESC-R) is a major public health problem worldwide. Previously we investigated the dynamic of the ESC-R over time in North America and Europe, and estimated the relative importance of plasmids expansion versus clonal spread (https://doi.org/10.1038/s41467-022-34970-7). To investigate the ESC-R plasmids in high resolution long-read data are necessary. This study aimed to generate long-read data for 172 ESC-R E. coli genomes, which are part of our larger collection, and their respective short-reads are publicly available (PRJEB38235, PRJEB42322, PRJNA596173, PRJEB50837 and PRJEB60750). These long-read data were used in combination with the short-reads to generate complete or nearly complete chromosome and plasmid assemblies; these assemblies are also available in this study. All 172 genomes were sequenced using the MinION sequencing device (Oxford Nanopore Technologies).