Escherichia albertii is an emerging pathogen that is closely related to Escherichia coli and can carry some of the same virulence genes as E. coli. Here, we report the release of Illumina-corrected PacBio sequences for eight E. albertii genomes.
ABSTRACT
Escherichia albertii is an emerging pathogen that is closely related to Escherichia coli and can carry some of the same virulence genes as E. coli. Here, we report the release of Illumina-corrected PacBio sequences for eight E. albertii genomes. Two of these strains carry Shiga toxin 2f.
ANNOUNCEMENT
Escherichia albertii is an emerging pathogen that has been isolated worldwide from humans, birds, animals, and the environment; the resultant isolates that have been described in the literature since 2003 are reviewed here (1). E. albertii strains were implicated in an outbreak of restaurant-associated gastrointestinal disease in Japan (2), and stx2f-positive E. albertii strains have been isolated from a bird and humans (3). Due to the limited number of complete E. albertii genomes publicly available (seven at NCBI as of 11 June 2018), we selected eight diverse strains (all isolated from humans, in different U.S. states, from 1954 to 2014) for PacBio sequencing. Here, we report the release of eight complete circularized E. albertii chromosomes and their associated plasmid sequences. Two of these strains (2012EL-1823B and 2014C-4015) carry an stx2f gene.
Using standard microbial methods, strains were isolated at clinical laboratories as suspected enteric pathogens (4). Strains were received at the Escherichia/Shigella Reference Laboratory, CDC, and checked for purity. For initial identification and confirmation of E. albertii, a multiplex PCR was used to test for the presence of the clpX, lysP, and mdh genes (5). Additional confirmation included rpoB gene-based sequence analysis or a multiplex Escherichia species PCR (6, 7). Strain 2045-54 is an E. albertii strain, but it was originally described as a Shigella boydii strain of serotype 13 by W. H. Ewing (CDC, Atlanta, GA); in 1955, it was sent to the National Collection of Type Cultures (NCTC, Public Health England) and named NCTC 9362 (5).
Strain growth, DNA extraction, sequencing, and assembly were completed as previously described, except where noted (8). A single colony was selected from a streak of a frozen stock of a pure culture for a second streak on blood agar (Becton, Dickinson and Company, USA), and the equivalent of 5 to 6 colonies were selected from the second streak for genomic DNA extraction according to the manufacturer’s protocol (Promega Wizard Genomic DNA purification kit, Promega Corporation, Madison, WI). This DNA extract was used for all sequencing. For Illumina MiSeq sequencing, libraries were prepared with a Nextera XT library prep kit (Illumina, USA) and sequenced following the manufacturer’s protocols (Illumina, USA). For PacBio sequencing, DNA was sheared to 20 kb utilizing needle shearing and used to generate large SMRTbell libraries using the standard 20-kb library protocols of the Pacific Biosciences SMRTbell template prep kit 1.0 (PacBio, Menlo Park, CA). The libraries were further size selected utilizing BluePippin (Sage Scientific, Beverly, MA) with a cutoff size of 10 kb. The finished library was bound to proprietary P6v2 polymerase and sequenced on a PacBio RS II sequencer using C4v2 chemistry for 360-minute movies. Sequence reads were filtered and assembled de novo utilizing the PacBio Hierarchical Genome Assembly Process version 3 and polished using Quiver (9) (minread = 1,000, genome size = 5,000,000). For 06-3542, the assembly was generated using Canu 1.6 (minReadLength = 1,000 -g5m), as it generated a circularized chromosome and plasmid (10). All PacBio sequences were Illumina corrected with unicycler_polish that uses Pilon (11, 12) with default settings.
Table 1 lists the sequence identification (ID) numbers, NCBI accession numbers, GC content, and chromosome and plasmid sizes for each E. albertii strain. A single chromosomal sequence (circular with overlapping ends) was obtained for all strains with a minimum of 64× coverage.
TABLE 1.
Sequence IDs, NCBI accession numbers, GC content, and sizes of E. albertii sequences
| E. albertii sequence ID | Assignment | NCBI accession no. | Coverage (×) | % GC content | Total size (bp) |
|---|---|---|---|---|---|
| 05-3106 | Chromosome | CP030778 | 156.90 | 49.77 | 4,719,735 |
| p05-3106-1 | Plasmid | CP030779 | 71.65 | 44.19 | 56,603 |
| p05-3106-2 | Plasmid | CP030780 | 147.98 | 54.23 | 80,632 |
| 06-3542 | Chromosome | CP034162 | 181.25 | 49.80 | 4,709,095 |
| p06-3542 | Plasmid | CP034163 | 62.44 | 47.31 | 95,683 |
| 07-3866 | Chromosome | CP030781 | 127.69 | 49.77 | 4,940,006 |
| p07-3866 | Plasmid | CP030782 | 62.43 | 48.13 | 104,269 |
| 2010C-3449 | Chromosome | CP034212 | 85.04 | 50.02 | 4,923,641 |
| 2012EL-1823B | Chromosome | CP030783 | 64.97 | 49.66 | 4,809,821 |
| p2012EL-1823B-1 | Plasmid | CP030784 | 26.42 | 51.34 | 81,130 |
| p2012EL-1823B-2 | Plasmid | CP030785 | 20.08 | 47.17 | 100,347 |
| p2012EL-1823B-3 | Plasmid | CP030786 | 35.44 | 44.68 | 105,846 |
| 2013C-4143 | Chromosome | CP030787 | 124.52 | 49.80 | 4,659,709 |
| 2014C-4015 | Chromosome | CP034166 | 84.05 | 49.83 | 4,623,903 |
| p2014C-4015-1 | Plasmid | CP034165 | 20.38 | 44.95 | 63,807 |
| p2014C-4015-2 | Plasmid | CP034164 | 28.70 | 47.37 | 96,264 |
| p2014C-4015-3 | Plasmid | CP034167 | 51.69 | 45.17 | 136,645 |
| NCTC 9362 | Chromosome | CP034213 | 162.95 | 50.15 | 4,551,125 |
| pNCTC 9362 | Plasmid | CP034214 | 30.11 | 52.60 | 40,180 |
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. PacBio (SRX5170195 to SRX5170202) and Illumina (SRR8355575 to SRR8355582) sequencing reads for strains in this study have been deposited in the NCBI Sequence Read Archive (SRA) under the accession numbers listed above.
ACKNOWLEDGMENTS
We are very grateful to Devon Stoneburg, Lisley Garcia-Toledo, Pooja Patel, and Haley Martin for their expert contributions.
This work was funded by federal appropriations to the Centers for Disease Control and Prevention 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 Centers for Disease Control and Prevention. Use of trade names is for identification only and does not imply endorsement by the Centers for Disease Control and Prevention or by the U.S. Department of Health and Human Services.
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Associated Data
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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. PacBio (SRX5170195 to SRX5170202) and Illumina (SRR8355575 to SRR8355582) sequencing reads for strains in this study have been deposited in the NCBI Sequence Read Archive (SRA) under the accession numbers listed above.