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Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis Strain SEJ K. A. Bishop-Lilly,a,b K. G. Frey,a,b H. E. Daligault,c K. W. Davenport,c D. C. Bruce,c P. S. Chain,c S. R. Coyne,d O. Chertkov,c T. Freitas,c* J. Jaissle,c G. I. Koroleva,e J. T. Ladner,e T. D. Minogue,d G. F. Palacios,e C. L. Redden,a,b Y. Xu,c S. L. Johnsonc Naval Medical Research Center (NMRC)–Frederick, Fort Detrick, Maryland, USAa; Henry M. Jackson Foundation, Bethesda, Maryland, USAb; Los Alamos National Laboratory (LANL), Los Alamos, New Mexico, USAc; Diagnostic Systems Division (DSD), United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, USAd; Center for Genome Sciences (CGS), USAMRIID, Fort Detrick, Maryland, USAe * Present address: T. Freitas, Med Fusion, Lewisville, Texas, USA.
Salmonella enterica constitutes a group of enteric pathogens with a broad host range, including humans, reptiles, and birds. S. enterica subsp. enterica is a common cause of inflammatory diarrhea in humans. We present the draft genome of S. enterica subsp. enterica serovar Enteritidis strain SEJ, including a 59-kbp plasmid. Received 12 September 2014 Accepted 16 September 2014 Published 23 October 2014 Citation Bishop-Lilly KA, Frey KG, Daligault HE, Davenport KW, Bruce DC, Chain PS, Coyne SR, Chertkov O, Freitas T, Jaissle J, Koroleva GI, Ladner JT, Minogue TD, Palacios GF, Redden CL, Xu Y, Johnson SL. 2014. Complete genome sequence of Salmonella enterica subsp. enterica serovar Enteritidis strain SEJ. Genome Announc. 2(5):e01084-14. doi: 10.1128/genomeA.01084-14. Copyright © 2014 Bishop-Lilly et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to S. L. Johnson,
[email protected].
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almonella enterica constitutes a group of enteric pathogens with a broad host range, including humans, reptiles, and birds. Of this group, S. enterica subsp. enterica is the predominant pathogen of birds and mammals. Disease manifestations and/or severity can vary by host status and age but a typical manifestation would be inflammatory diarrhea (reviewed in reference 1). Tracking enteric pathogens such as these for epidemiological purposes has traditionally been performed via pulsed-field gel electrophoresis (PFGE); however, for the serovar Enteriditis, phylogenetic analysis based on whole-genome sequence data was recently shown to provide increased resolution (2). Accordingly, there is utility in increasing the number of highquality references available. We present here the draft genome of S. enterica subsp. Enterica serovar Enteritidis strain SEJ, sequenced to 314⫻ total draft coverage. A QIAgen Genome Tip-500 was used to extract high-quality genomic DNA from a purified isolate. Specifically, nucleic acid was extracted from a 100-mL bacterial culture at stationary phase. This draft genome was derived via a combination of Illumina library technologies (1). A 100-bp unpaired library was constructed (312-fold genome coverage) as well as a longinsert paired-end library (7,944 ⫾ 2,066-bp insert and 2-fold genome coverage). The paired-end data were assembled in Newbler (3) and those consensus sequences computationally shredded into 2 kbp overlapping fake reads (shreds). The standard Illumina sequencing data were assembled with VELVET (2) and the consensus sequence computationally shredded into 1.5-kbp overlapping shreds. All data were additionally assembled together in Allpaths (4) and the consensus sequences computationally shredded into 5-kbp overlapping shreds. All of the shreds were integrated using parallel phrap (High Performance Software, LLC). Possible misassemblies were corrected and re-
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peat regions verified using in-house scripts and manual editing in Consed (3–6). By these methods the chromosome and plasmid sequence for this strain were assembled into a single contig each. Annotation was performed using an Ergatis-based (7) workflow with minor manual curation. The S. enterica SEJ chromosome (CP008928) is 4,678,927 bp (52.2% G⫹C content) and encodes 4,341 coding sequences, 21 rRNAs, and 82 tRNAs. The 59,372-bp plasmid (CP008927) has 52.0% G⫹C content and encodes 77 CDSs. This draft genome expands the repertoire of Salmonella whole-genome sequences available for comparative analysis. Nucleotide sequence accession numbers. The NCBI accession no. for the S. enterica SEJ chromosome is CP008928 and for the plasmid is CP008927. ACKNOWLEDGMENTS Funding for this effort was provided by the Defense Threat Reduction Agency’s Joint Science and Technology Office (DTRA J9-CB/ JSTO). This manuscript is approved by the LANL for unlimited release (LAUR-14-26025). The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Navy, Department of Defense, or the US. Government.
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