ABSTRACT
Isolates of Salmonella enterica subsp. enterica serovar Heidelberg are often associated with poultry products and may cause severe human illness. Here, we report the fully assembled genome and plasmid sequences of three S. Heidelberg strains with phage types 9, 29, and 41.
GENOME ANNOUNCEMENT
We present here the closed genome and plasmid sequences of three isolates of Salmonella enterica subsp. enterica serovar Heidelberg from Quebec, Canada, which include one human clinical isolate (12-4374, phage type 41 [PT41]) and two food isolates, one from turkey meat (N13-01290, PT9) and one from chicken meat (SA02DT10168701, PT29). The antimicrobial resistance profile of the turkey isolate includes amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, streptomycin, sulfamethoxazole, and tetracycline, and the profiles of the human and chicken isolates include amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftiofur, and ceftriaxone.
Genomic DNA was extracted using either the Qiagen EZ1 DNA tissue kit (Qiagen, Hilden, Germany), or the EpiCentre MasterPure complete DNA and RNA purification kit (Epicentre, Madison, WI). Sequencing was performed on two platforms: (i) PacBio (at the Innovation Centre, at McGill University and Genome Quebec, Quebec, Canada, using 2 single-molecule real-time [SMRT] cells in an RSII sequencer), which generated 96,807 to 190,337 raw subreads averaging 4,769 to 5,306 bp in length with 92 to 167× coverage, and were assembled into contigs by the Innovation Centre using the HGAP workflow (1); and (ii) the Illumina MiSeq platform (at the Public Health Agency of Canada [PHAC] National Microbiology Laboratory, Winnipeg, Canada) with 2 × 251 paired-end runs after library preparation with the Illumina Nextera XT DNA library preparation kit, achieving 116 to 150× coverage. The Illumina reads were analyzed and quality checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Also, an optical map of the chicken isolate was generated using the restriction enzyme NcoI (OpGen, Inc., Gaithersburg, MD) and used to verify correct the contig assembly. Unweighted pair group method using average linkages (UPGMA) similarity clustering of the restriction fragments in the whole-genome optical map of the chicken isolate with in silico maps of publicly available S. Heidelberg isolates was performed using MapSolver version 2.1.1 (OpGen, Inc.). Genome assemblies were created by using the MIRA assembler version 4.9.3 (2) and by manually checking potential joins using the Gap5 software of the Staden package (3). A comparison of the genome assemblies with the genome optical map and with closely related plasmid sequences found in GenBank, together with the finishing process, produced fully assembled genomes and plasmids. To verify that no plasmids were missed, the nonmatched reads were used to produce de novo assemblies for each data set, and the remaining contigs were subjected to BLASTn searches and analyzed for gene content. The genomes consisted of single-chromosome contigs ranging from 4,751,447 to 4,809,628 bp, with an average G+C content of ~52.18%, and the plasmid contigs ranged from ~2,096 to 236,176 bp, with G+C content ranging from ~41.17 to 55.82%. The genomes and plasmids were annotated with the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) (http://ncbi.nlm.nih.gov/genomes/static/Pipeline.html), identifying an average of ~4,550 coding DNA sequences (CDSs) per genome and ~2 to 270 CDSs per plasmid.
Nucleotide sequence accession numbers.The complete genome sequences of these three isolates of S. Heidelberg and their plasmids (Table 1) have been deposited in GenBank under BioProject number 298211. The GenBank accession numbers are listed in Table 1.
Accession and isolate numbers for the genomes and plasmids of three Salmonella Heidelberg isolates sequenced in this study
ACKNOWLEDGMENTS
Funding was provided by the Genomics Research and Development Initiative (GRDI) of the Government of Canada.
We thank the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) for providing the two food isolate strains (SA02DT10168701 and N13-01290) and the Institut National de Santé Publique du Québec and CIPARS for providing the human isolate (12-4374). Also, we thank the NCBI rapid annotation pipeline team for key genome annotation services, the McGill University and Génome Québec Innovation Centre, and our colleagues at the PHAC National Microbiology Laboratory for assistance with genome sequencing, and Lok Kan Lee for his help with the GenBank submissions.
FOOTNOTES
- Received 4 November 2015.
- Accepted 18 November 2015.
- Published 14 January 2016.
- Copyright © 2016 Labbé et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
