Plasmid-mediated colistin resistance, mediated by the mcr-1 gene, has been identified in Escherichia coli, Salmonella enterica, and other Enterobacteriaceae strains worldwide. The mcr-1 gene was initially described in an E. coli IncI2 plasmid isolated from a pig in China (1). In 2016, the first case of mcr-1 in a U.S. isolate was reported (2,3). So far in the United States, 49 mcr-1-positive isolates, including 47 from human samples, have been reported and are routinely tracked by the CDC (https://www.cdc.gov/drugresistance/biggest-threats/tracking/mcr.html). Here, we report the availability of three whole-genome sequence assemblies generated by PacBio sequencing and corrected with Illumina reads. Additionally, 2017K-0021 was verified using the strain’s whole-genome map (WGM).

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 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. Resistance genes and plasmid replicons were detected using the ResFinder and PlasmidFinder databases, respectively (http://www.genomicepidemiology.org) IncF replicon sequence types were determined as previously described (7).

E. coli strain 2017C-4109 (Table 1) carried genes for serotype O157:H7. Additionally, virulence factors stx₂ (stx_2a and stx_2c), eae, and ehxA were identified. Two plasmids were identified in this isolate, an IncI2 plasmid (pMCR-1) carrying the mcr-1 gene and an IncFII/FIB plasmid (p2017C-4109, replicon sequence type F23:A-:B3) carrying no known resistance genes.

E. coli strain 2017C-4173W12 (Table 1) did not carry a described O serotype gene but carried genes for H2 and afaC, a marker for diffusely adherent E. coli (DAEC) (8). Two plasmids were identified in this isolate, an IncI2 plasmid (pMCR-1_2017C-4173W12) carrying the mcr-1 gene and a second IncFII/FIB plasmid (p2017C-4173W12, replicon sequence type F29:A-:B10), with additional replicons IncQ and Col156, carrying the following resistance genes: bla_TEM-1b, sul1, sul2, strA, strB, aadA5, mphA, and dfrA17.

Salmonella enterica subsp. enterica serovar Enteritidis strain 2017K-0021 (Table 1) carried the expected serotype genes. 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).