High-Quality Genome Sequence of an Escherichia coli O157 Strain Carrying an mcr-1 Resistance Gene Isolated from a Patient in the United States

Abstract

Enterobacteriaceae carrying plasmid-mediated colistin resistance have been found around the world. We report here the high-quality whole-genome sequence of an Escherichia coli O157:H48 isolate (2016C-3936C1) from Connecticut that carried the mcr-1 resistance gene on an IncX4-type plasmid.

PacBio Genome Sequences of Escherichia coli Serotype O157:H7, Diffusely Adherent E. coli, and Salmonella enterica Strains, All Carrying Plasmids with an mcr-1 Resistance Gene

“…Strains were grown on blood agar (Becton, Dickinson and Co., USA), and DNA was extracted using the Promega Wizard genomic DNA purification kit (Promega Corp., USA). PacBio and Illumina sequencing, assembly, finishing, and optical mapping were performed as previously described, except where noted ( 4 ). Following the manufacturers’ protocols, sequencing libraries were prepared with a Nextera XT library prep kit (Illumina, USA) or a NEBNext Ultra library prep kit (New England BioLabs, USA) and sequenced on the MiSeq platform ( 4 ).…”

“…PacBio and Illumina sequencing, assembly, finishing, and optical mapping were performed as previously described, except where noted ( 4 ). Following the manufacturers’ protocols, sequencing libraries were prepared with a Nextera XT library prep kit (Illumina, USA) or a NEBNext Ultra library prep kit (New England BioLabs, USA) and sequenced on the MiSeq platform ( 4 ). PacBio sequence reads were filtered and assembled de novo utilizing the PacBio Hierarchical Genome Assembly Process (HGAP) version 3 and polished using Quiver ( 5 ).…”

“…PacBio sequences were further corrected with Illumina sequencing reads using Pilon ( 6 ). WGMs were generated for 2017K-0021 according to the OpGen protocol, as previously described ( 4 ). The final assembly yielded single-chromosome sequences for all three isolates.…”

“…Two plasmids were identified in this isolate, an IncX4 plasmid (pMCR-1-CTSe) carrying the mcr-1 gene and an IncFII/FIB plasmid (p2017K-0021, replicon sequence type S1:A-:B22) carrying no known resistance genes. IncX4 plasmid pMCR-1-CTSe (GenBank accession number CP030795 ) was aligned to the previously described plasmid pMCR-1-CT ( CP018773 ), and they were determined to be identical ( 4 ).…”

Sequencing and Characterization of Five Extensively Drug-Resistant Salmonella enterica Serotype Typhi Isolates Implicated in Human Infections from Punjab, Pakistan

“…Five isolates (Table 1) identified as XDR Salmonella Typhi at the National Institute of Health in Pakistan were subcultured on blood agar, stored in 40% glycerol Trypticase soy broth, and sent to the U.S. Centers for Disease Control and Prevention. DNA extraction was performed on cultures grown from single-colony frozen stocks on blood agar at 37°C overnight before sequencing on the Illumina MiSeq platform, as previously described (3). Default parameters were used for all software, unless otherwise specified.…”