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J Bacteriol. Oct 2011; 193(19): 5546–5547.
PMCID: PMC3187440
Genome Sequences of Two Stress-Tolerant Campylobacter jejuni Poultry Strains, 305 and DFVF1099
Monica Takamiya,1 Asli Ozen,2 Morten Rasmussen,3 Thomas Alter,4 Tom Gilbert,3 Dave W. Ussery,2 and Susanne Knøchel1*
1Department of Food Science, Faculty of Life Science, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
2Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark
3Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
4Institute of Food Hygiene, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
*Corresponding author. Mailing address: Department of Food Science, Faculty of Life Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark. Phone: 45-353 33258. Fax: 45-353 33214. E-mail: skn/at/life.ku.dk.
Received July 7, 2011; Accepted July 18, 2011.
Abstract
Campylobacter jejuni is a food-borne pathogen with a high prevalence in poultry meat, which in fresh unfrozen condition is the major source of campylobacteriosis. C. jejuni strains DFVF1099 and 305 are considered tolerant to several environmental stresses (T. Birk et al., J. Food Prot. 73:258–265, 2010; S. L. On et al., Int. J. Med. Microbiol. 296:353–363, 2006). Here, we report the genome sequences of C. jejuni 305 and DFVF1099, a turkey and a chicken isolate, respectively.
The sequences of Campylobacter jejuni poultry strains 305 and DFVF1099 were determined using 454 pyrosequencing technology (454 Life Sciences, Branford, CT) at The Institute of Biology, Faculty of Science (KU-NAT). The chicken isolate DFVF1099 was provided by The Danish Institute for Food and Veterinary Research (DFVF) and showed tolerance to gentle stress (8) (M. Takamiya et al., unpublished data). The turkey isolate 305 was originally isolated from a slaughterhouse (1) and showed tolerance to stresses such as oxygen exposure and acidity (2, 3). Draft assemblies of 305 were based on 71,972 total reads with a 10-fold coverage of the genome. Draft assemblies of DFVF1099 were based on 206,366 total reads with a 30-fold coverage of the genome. The 454 data files were loaded into the CLC Genomics Workbench (CLC Bio, Aarhus, Denmark).
After genome sequence comparisons of 305 and DFVF1099 with published genome sequences to date, the initial assembly of 305 created contigs using C. jejuni NCTC11168 (10) as the scaffold. The C. jejuni 305 genome was found to be 1,808,274 bp long, and it contains 2,243 putative open reading frames (ORFs). For DFVF1099, an initial assembly was performed using C. jejuni 84-25 as the scaffold (GenBank accession number AANT00000000), which created 1,632 contigs with 203,934 matched reads. The C. jejuni DFVF1099 genome was found to be 1,733,857 bp long, and contains 1,997 putative ORFs.
The average G+C content of strains 305 and DFVF1099 is 30.4%, and these strains possess 44 and 43 tRNAs, respectively (7). Both strains contain three rRNA operons (6). C. jejuni strain 305 might contain a pTet plasmid, as revealed by the presence of tetracycline resistance proteins CSS_1767 (TetO) and CSS_2124 (TetR). In contrast, DFVF1099 does not contain plasmids. The number of homopolymeric G tracts (HGTs, defined as tracts of >7 consecutive G residues) was 10 in strain 305 and 20 in DFVF1099 compared to 29 in NCTC11168, 25 in RM1221, and 19 in 81-176 (5, 9, 10). As described earlier (11), the genome of C. jejuni can be changed via hypervariable G tracts, and the length of these regions is an indication of strain stability. C. jejuni 305 has fewer hypervariable G tracts than do other strains, which might indicate that 305 is a stable and reliable strain for in vitro and in vivo experiments.
Proteome homology searching of 305 and DFVF1099 with available sequence data from completed (strains NCTC11168, 81116 [NCTC11828], M1, RM1221, 81-176, 269.97) and ongoing (strains 84-25, 260-94, HB93-13, CF93-6, CG8421, CG8486) C. jejuni sequence projects to date was performed based on a matrix of an all-against-all BLASTP analysis (4). Visualization of protein sequence identity or BLAST matrix, revealed the highest protein sequence homology of DFVF1099 with 84-25 (85.8%) and 305 with CF93-6 (69.6%), respectively (data not shown). Both 84-25 and CF93-6 C. jejuni strains are human clinical isolates.
Nucleotide sequence accession numbers.
The sequences of the C. jejuni strains 305 and DFVF1099 genomes can be accessed under GenBank accession numbers ADHL00000000 and ADHK00000000, respectively.
Acknowledgments
We acknowledge the Danish Directorate for Food, Fisheries and Agriculture, grant number 93S-953-00090, for funding the whole-genome shotgun sequence projects of strains 305 and DFVF1099 and the Institute for Genome Sciences (IGS) Annotation Engine at the University of Maryland School of Medicine.
1. Alter T., Gaull F., Froeb A., Fehlhaber K. 2005. Distribution of Campylobacter jejuni strains at different stages of a turkey slaughter line. Food Microbiol. 22:345–351.
2. Birk T., et al. 2010. Effect of organic acids and marination ingredients on the survival of Campylobacter jejuni on meat. J. Food Prot. 73:258–265. [PubMed]
3. Boysen L., Knøchel S., Rosenquist H. 2007. Survival of Campylobacter jejuni in different gas mixtures. FEMS Microbiol. Lett. 266:152–157. [PubMed]
4. Hallin P. F., Binnewies T. T., Ussery D. W. 2008. The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol. Biosys. 4:363–371. [PubMed]
5. Hofreuter D., et al. 2006. Unique features of a highly pathogenic Campylobacter jejuni strain. Infect. Immun. 74:4694–4707. [PMC free article] [PubMed]
6. Lagesen K., et al. 2007. RNAmmer: consistent and rapid annotation of rRNA genes. Nucleic Acids Res. 35:3100–3108. [PMC free article] [PubMed]
7. Lowe T. M., Eddy S. R. 1997. tRNAscan-SE: A program for improved detection of tRNA genes in genomic sequence. Nucleic Acids Res. 25:955–964. [PMC free article] [PubMed]
8. On S. L., et al. 2006. Numerical analysis of DNA microarray data of Campylobacter jejuni strains correlated with survival, cytolethal distending toxin and haemolysin analyses. Int. J. Med. Microbiol. 296:353–363. [PubMed]
9. Parker C. T., Quiñones B., Miller W. G., Horn S. T., Mandrell R. E. 2006. Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221. J. Clin. Microbiol. 44:4125–4135. [PMC free article] [PubMed]
10. Parkhill J., et al. 2000. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403:665–668. [PubMed]
11. Pearson B. M., et al. 2007. The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). J. Bacteriol. 189:8402–8403. [PMC free article] [PubMed]
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