Abstract
Salmonella enterica subsp. enterica serovar Heidelberg is a highly clonal serovar frequently associated with foodborne illness. To facilitate subtyping efforts, we report fully assembled genome sequences of 17 Canadian S. Heidelberg isolates including six pairs of epidemiologically related strains. The plasmid sequences of eight isolates contain several drug resistance genes.
GENOME ANNOUNCEMENT
We present closed genome sequences of 17 Canadian isolates of Salmonella enterica subsp. enterica serovar Heidelberg collected between 2003 and 2014 in Ontario, Quebec, and British Columbia. Twelve isolates comprise six epidemiologically related pairs (Table 1): three pairs from outbreaks in Quebec in 2012, 2013, and 2014 (1); one pair from an outbreak in British Columbia in 2003; and two pairs collected from broiler chicken feces in Ontario in 2013 as part of the Canadian Integrated Program for Antimicrobial Resistance Surveillance. The five remaining isolates are unrelated and include two isolates from retail chicken meat, one from chicken cecal contents collected at a slaughterhouse, as well as two animal clinical isolates.
TABLE 1.
Accession numbers and metadata for the genomes of 17 Salmonella serovar Heidelberg isolates sequenced in this study
| GenBank accession no. | Local reference ID | Pair ID, sourcea | AMR profile (resistance genes in plasmids according to ResFinder 2.0) | PFGE profile (XbaI/BlnI) | Phage type |
|---|---|---|---|---|---|
| CP016565 | AMR588-04-00318 | A, chicken feces | AcAmCeCfCxSt (blaCMY-2) | SHEXAI.0001/SHEBNI.0001 | 29 |
| CP016569 | AMR588-04-00320 | A, chicken feces | AcAmCeCfCxSt (blaCMY-2) | SHEXAI.0001/SHEBNI.0001 | 29 |
| CP016573 | AMR588-04-00435 | B, chicken feces | Susceptible | SHEXAI.0001/SHEBNI.0001 | 19 |
| CP016576 | AMR588-04-00437 | B, chicken feces | Susceptible | SHEXAI.0001/SHEBNI.0001 | 19 |
| CP016507 | SH12-003 | C, human | Susceptible | SHEXAI.0001/SHEBNI.0001 | 19 |
| CP016504 | SH12-007 | C, human | Susceptible | SHEXAI.0001/SHEBNI.0001 | 19 |
| CP016579 | SH13-006 | D, human | Susceptible | SHEXAI.0001/SHEBNI.0001 | 26 |
| CP016586 | SH13-004 | D, human | Susceptible | SHEXAI.0001/SHEBNI.0001 | 26 |
| CP016510 | SH14-028 | E, food | Susceptible | SHEXAI.0001/SHEBNI.0001 | 19 |
| CP016581 | SH14-009 | E, human | GeSt [aac(3)-VIa, aadA1] | SHEXAI.0001/SHEBNI.0001 | 19 |
| CP016561 | A3ES40 | F, food | Susceptible | SHEXAI.0001/SHEBNI.0001 | 26 |
| CP016563 | A3EZ223 | F, human | Susceptible | SHEXAI.0001/SHEBNI.0001 | 26 |
| CP016525 | 09-036813-1A | NA, equine clinical | AmChGeKaSuTm [strB, strA, aac(6′)-IIc, aph(3′)-Ia, blaTEM-1B, QnrB49, ere(A), sul1, dfrA18] | SHEXAI.0014/SHEBNI.0210 | 29 |
| CP016514 | 11-004736-1-7 | NA, bovine clinical | AcAmCeCfCx (blaCMY-2) | SHEXAI.0001/SHEBNI.0001 | 29 |
| CP016530 | SA01AB09084001 | NA, chicken cecal contents | AcAmCeCfCx (blaCMY-2) | SHEXAI.0001/SHEBNI.0001 | 19 |
| CP016521 | SA02DT09004001 | NA, chicken meat | AcAmCeCfCx (blaCMY-2) | SHEXAI.0001/SHEBNI.0001 | 9 |
| CP016517 | CE-R2-11-0435 | NA, chicken meat | Am (blaTEM-1B) | SHEXAI.0001/SHEBNI.0001 | 20 |
Six pairs (A to F) of related strains are shown in paired rows and are from broiler chicken feces collected in 2013 (pairs A and B) and from foodborne illness outbreaks that occurred in 2012 (pair C), 2013 (pair D), 2014 (pair E), and 2003 (pair F). NA, not applicable.
Genomic DNA was extracted using either the EZ1 DNA tissue kit or the DNeasy 96 blood and tissue kit (Qiagen, Hilden, Germany). Sequencing was performed on two platforms: (1) PacBio (using SMRT cells in RSII sequencers [2]), which generated 79,000 to 190,000 raw subreads averaging 4,700 to 11,600 bp with 92 to 222× coverage that were assembled into contigs by the sequencing facilities using the HGAP workflow; (2) and/or Illumina after library preparation with the Illumina Nextera XT DNA library preparation kit, using either Illumina MiSeq with 2 × 251 paired-end runs achieving 47 to 131× coverage, and/or Illumina HiSeq with 2 × 101 paired-end runs achieving 390 to 615× coverage. The Illumina reads were analyzed and quality-checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Genomes were assembled with MIRA assembler version 4.9.3 (3), with the Illumina reads assembled to the PacBio consensus sequence for each isolate to correct errors, and by manually checking potential joins using the Gap5 Software v1.2.14 of the Staden package (4). In contrast with the other strains, the isolates from outbreak C (Table 1) were sequenced with both Illumina HiSeq and Illumina MiSeq and not with PacBio; in this case, the closed genome sequence from strain CFSAN002064 (GenBank accession no. NZ_CP005995) (5) was used for the initial reference assembly of the Illumina reads. Plasmids were assembled as previously described (6). Comparison of the genome assemblies with the genome optical maps of other S. Heidelberg strains found in GenBank (6), together with the finishing process produced fully assembled genomes. The genomes consisted of single chromosomal contigs ranging from 4,747,525 to 4,751,746 bp, with an average G+C content of 52.19%. The genomes were annotated with the National Center for Biotechnology Information (NCBI) Prokaryotic Genomes Annotation Pipeline (PGAP) (http://ncbi.nlm.nih.gov/genomes/static/Pipeline.html), identifying an average of ~4,596 coding DNA sequences (CDS) per genome.
The pulsed-field gel electrophoresis (PFGE) profiles, phage types and antimicrobial resistance profiles of all isolates were determined by established methods (7). Eight of the 17 isolates were drug resistant (Table 1) with plasmid-borne resistance genes. The two strains of pair E (Table 1) had different AMR plasmid content, as has been reported previously for S. Heidelberg (8).
Accession number(s).
The complete genome sequences of these 17 isolates of S. Heidelberg as well as the complete sequences of their 40 plasmids have been deposited in GenBank under BioProject no. 298211 and 305824. The GenBank accession numbers for the genomes are listed in Table 1.
ACKNOWLEDGMENTS
We thank McGill University, Génome Québec Innovation Centre, Montréal, Québec, Canada and Guilin Wang at Yale University, New Haven, Connecticut, United States for PacBio sequencing, Sergio Pereira at The Centre for Applied Genomics at the Hospital for Sick Children, Toronto, Ontario, Canada for the Illumina HiSeq sequencing, and our colleagues Morag Graham and Matthew Walker at the PHAC National Microbiology Laboratory at Winnipeg, Manitoba, Canada for the Illumina MiSeq sequencing. We thank Chad Gill for his work on AMR testing, Elissa Giang for her help proofreading the assemblies, Jonathan Moffat for his help with PCR analysis of plasmids, Joanne MacKinnon for her helpful comments on the manuscript, and Lok Kan Lee for his help with the GenBank submissions.
Funding was provided by the Genomics Research and Development Initiative (GRDI) of the Government of Canada.
Funding Statement
This work was funded by the Genomics Research and Development Initiative (GRDI) of the Government of Canada awarded to Roger P. Johnson.
Footnotes
Citation Labbé G, Ziebell K, Bekal S, Macdonald KA, Parmley EJ, Agunos A, Desruisseau A, Daignault D, Slavic D, Hoang L, Ramsay D, Pollari F, Robertson J, Nash JHE, Johnson RP. 2016. Complete genome sequences of 17 Canadian isolates of Salmonella enterica subsp. enterica serovar Heidelberg from human, animal, and food sources. Genome Announc 4(5):e00990-16. doi:10.1128/genomeA.00990-16
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