We report here Illumina-corrected PacBio whole-genome sequences of an Escherichia coli serotype O157:H7 strain (2017C-4109), an E. coli serotype O[undetermined]:H2 strain (2017C-4173W12), and a Salmonella enterica subsp. enterica serovar Enteritidis strain (2017K-0021), all of which carried the mcr-1 resistance gene on an IncI2 or IncX4 plasmid.
ABSTRACT
We report here Illumina-corrected PacBio whole-genome sequences of an Escherichia coli serotype O157:H7 strain (2017C-4109), an E. coli serotype O[undetermined]:H2 strain (2017C-4173W12), and a Salmonella enterica subsp. enterica serovar Enteritidis strain (2017K-0021), all of which carried the mcr-1 resistance gene on an IncI2 or IncX4 plasmid. We also determined that pMCR-1-CTSe is identical to a previously published plasmid, pMCR-1-CT.
ANNOUNCEMENT
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 (stx2a and stx2c), 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.
TABLE 1.
NCBI/GenBank accession numbers, assembly metrics, and associated plasmids
| Strain | Assignment | NCBI accession no. |
Length (bp) |
GC content (%) |
Complete and circular |
|---|---|---|---|---|---|
| 2017C-4109 | Chromosome | CP030767 | 5,384,880 | 50.5 | Yes |
| pMCR-1 | Plasmid | CP030766 | 59,808 | 42.4 | Yes |
| p2017C-4109 | Plasmid | CP030765 | 93,169 | 47.9 | Yes |
| 2017K-0021 | Chromosome | CP030794 | 4,685,707 | 52.2 | Yes |
| pMCR-1-CTSe | Plasmid | CP030795 | 33,304 | 41.8 | Yes |
| p2017K-0021 | Plasmid | CP030796 | 59,371 | 51.9 | Yes |
| 2017C-4173W12 | Chromosome | CP030768 | 5,300,308 | 50.7 | Yes |
| pMCR-1_2017C-4173W12 | Plasmid | CP030769 | 149,680 | 52.4 | Yes |
| p2017C-4173W12 | Plasmid | CP030770 | 27,128 | 42.5 | No |
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: blaTEM-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).
Data availability.
The whole-genome sequences reported here have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1. The versions described in this paper are the first versions.
ACKNOWLEDGMENTS
This work was funded by federal appropriations to the Centers for Disease Control and Prevention (CDC) through the Advanced Molecular Detection Initiative line item. The findings and conclusions of this article are those of the authors and do not necessarily represent the views of the CDC. Use of trade names is for identification only and does not imply endorsement by the CDC or by the U.S. Department of Health and Human Services.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The whole-genome sequences reported here have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1. The versions described in this paper are the first versions.