Evaluation of whole-genome sequencing as a genotyping tool for Campylobacter jejuni in comparison with pulsed-field gel electrophoresis and flaA typing

Poultry Science

Volumn 92, Issue 2, 2013, Pages 573-580

  Pendleton, S ^a   Hanning, I ^a   Biswas, D ^b   Ricke, S C ^c  

^a UNIVERSITY OF TENNESSEE   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

^c UNIVERSITY OF ARKANSAS   (United States)

Author keywords

Campylobacter; FlaA short variable region; Genome; Poultry; Pulsed field gel electrophoresis

Indexed keywords

BACTERIA (MICROORGANISMS); CAMPYLOBACTER; CAMPYLOBACTER JEJUNI;

EID: 84872328659     PISSN: 00325791     EISSN: 15253171     Source Type: Journal    
DOI: 10.3382/ps.2012-02695     Document Type: Article

References (36)

1. Argos, P., M. G. Rossman, U. M. Grau, A. Zuber, G. Frank, and J. D. Trarschin. 1979. Thermal stability and protein structure. Biochemistry 18:5698-5703.
2. Aziz, R., D. Bartels, A. Best, M. DeJongh, T. Disz, R. A. Edwards, K. Formsma, S. Gerdes, E. M. Glass, M. Kubal, F. Meyer, G. J. Olsen, R. Olson, A. L. Osterman, R. Overbeek, L. McNeil, D. Paarmann, T. Paczian, B. Parrello, G. D. Pusch, C. Reich, R. Stevens, O. Vassieva, V. Vonstein, A. Wilke, and O. Zagnitko. 2008. The RAST Server: Rapid annotations using subsystems technology. BMC Genomics 9:75.
3. Berndtson, E., M. Tivemo, and A. Engvall. 1992. Distribution and numbers of Campylobacter in newly slaughtered broiler chickens and hens. Int. J. Food Microbiol. 15:45-50.
4. Centers for Disease Control (CDC). 2011. Investigation Update: Outbreak of Shiga toxin-producing E. coli O104 (STEC O104:H4) Infections Associated with Travel to Germany. Accessed Feb. 12, 2012. http://www.cdc.gov/ecoli/2011/ecoliO104/.
5. Champion, O., S. Al-Jaberi, R. Stabler, and B. Wren. 2008. Comparative genomics of Campylobacter jejuni. Pages 63-71 in Campylobacter. I. Nachamkin, C. Szymanski, and M. Blaser, ed. ASM Press, Washington, DC.
6. Chan, K., D. Elhanafi, and S. Kathariou. 2008. Genomic evidence for interspecies acquisition of chromosomal DNA from Campylobacter jejuni by Campylobacter coli strains of a turkey-associated clonal group (cluster II). Foodborne Pathog. Dis. 5:387-398.
7. Darling, A. C., B. Mau, F. R. Blatter, and N. T. Perna. 2004. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394-1403.
8. Debruyne, L., D. Gevers, and P. Vandamme. 2008. Taxonomy of the Campylobacteraceae. Pages 3-25 in Campylobacter. I. Nachamkin, C. Szymanski, and M. Blaser, ed. ASM Press, Washington, DC.
9. Dorrell, N., J. A. Mangan, K. G. Laing, J. Hinds, D. Linton, H. Al-Ghusein, B. G. Barrell, J. Parkhill, N. G. Stoker, A. V. Karlyshev, P. D. Butcher, and B. W. Wren. 2001. Whole genome comparison of Campylobacter jejuni human isolates using a lowcost microarray reveals extensive genetic diversity. Genome Res. 11:1706-1715.
10. Gonzalez, M., M. Hakkinen, H. Rautelin, and M. Hanninen. 2009. Bovine Campylobacter jejuni strains differ from human and chicken strains in an analysis of certain molecular genetic markers. Appl. Environ. Microbiol. 75:1208-1210.
11. Gu, X., D. Hewestt-Emmett, and W. Li. 1998. Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 102/103:383-391.
12. Hanning, I., D. Biswas, P. Herrera, M. Roesler, and S. Ricke. 2010. Prevalence and characterization of Campylobacter jejuni isolated from pasture flock poultry. J. Food Sci. 75:M496-M502.
13. Harvey, S. 1980. Hippurate hydrolysis by Campylobacter fetus. J. Clin. Microbiol. 11:435-437.
14. Huang, S., T. Luangtongkum, T. Y. Morishita, and Q. Zhang. 2005. Molecular typing of Campylobacter strains using the cmp gene encoding the major outer membrane protein. Foodborne Pathog. Dis. 2:12-23.
15. Huang, W., and G. Marth. 2008. EagleView: A genome assembly viewer for next generation sequencing technologies. Genome Res. 18:1538-1543.
16. Jacobs-Reitsma, W., U. Lyhs, and J. Wagenaar. 2008. Campylobacter in the food supply. Pages 627-644 in Campylobacter. I. Nachamkin, C. Szymanski, and M. Blaser, ed. ASM Press, Washington, DC.
17. Kagawa, Y., N. Nojima, N. Nukiwa, M. Ishizuka, T. Nakajima, T. Yasuhara, T. Tanaka, and T. Oshima. 1984. High guanine plus cytocine content in the third letter of codons of an extreme thermophile. J. Biol. Chem. 259:2956-2960.
18. Laturnus, C., J. Jores, I. Moser, P. Schwerk, and L. Wieler. 2005. Long-term clonal lineages within Campylobacter jejuni O: 2 strains from different geographical regions and hosts. Int. J. Med. Microbiol. 294:521-524.
19. Lee, M., and D. Newell. 2006. Campylobacter in poultry: Filling an ecological niche. Avian Dis. 50:1-9.
20. Lefébure, T., P. D. Bitar, H. Suzuki, and M. Stanhope. 2010. Evolutionary dynamics of complete pan-genomes and the bacterial species concept. Genome Biol. Evol. 2:646-655.
21. Life Technologies Corporation. 2011. Application note: Shiga toxin-producing Escherichia coli. Accessed Feb. 12, 2012. http://www. lifetechnologies.com/content/dam/LifeTech/Documents/PDFs/CO19643-EcoliAppNote-final-hr-v4.pdf.
22. Line, J. E. 2001. Development of a selective differential agar for isolation and enumeration of Campylobacter spp. J. Food Prot. 64:1711-1715.
23. Linton, D., A. J. Lawson, R. J. Owen, and J. Stanley. 1997. PCR detection, identification to species level, and finger printing of Campylobacter jejuni and Campylobacter coli direct from diarrheic samples. J. Clin. Microbiol. 35:2568-2572.
24. Meinersmann, R. J., L. O. Helsel, P. I. Fields, and K. L. Hiett. 1997. Discrimination of Campylobacter jejuni isolates by fla gene sequencing. J. Clin. Microbiol. 35:2810-2814.
25. Miller, W. G. 2008. Comparative genomics of Campylobacter species other than Campylobacter jejuni. Pages 73-95 in Campylobacter. I. Nachamkin, C. Szymanski, and M. Blaser, ed. ASM Press, Washington, DC.
26. Newell, D. G., J. E. Shreeve, M. Toszeghy, G. Domingue, S. Bull, T. Humphrey, and G. Mead. 2001. Changes in carriage of Campylobacter strains by poultry carcasses during processing in abattoirs. Appl. Environ. Microbiol. 67:2636-2640.
27. Overbeek, R., T. Begley, R. M. Butler, J. V. Choudhuri, H. Y. Chuang, M. Cohoon, V. de Crécy-Lagard, N. Diaz, T. Disz, R. Edwards, M. Fonstein, E. D. Frank, S. Gerdes, E. M. Glass, A. Goesmann, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, L. Krause, M. Kubal, N. Larsen, B. Linke, A. C. McHardy, F. Meyer, H. Neuweger, G. Olsen, R. Olson, A. Osterman, V. Portnoy, G. D. Pusch, D. A. Rodionov, C. Rückert, J. Steiner, R. Stevens, I. Thiele, O. Vassieva, Y. Ye, O. Zagnitko, and V. Vonstein. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33:5691-5702.
28. Parker, C., W. G. Miller, S. Horn, and A. J. Lastovica. 2007. Common genomic features of Campylobacter jejuni ssp. Doylei strains distinguish them from C. jejuni ssp. jejuni. BMC Microbiol. 7:50.
29. Parker, C., B. Quinones, W. G. Miller, S. Horn, and R. Mandrell. 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.
30. Parkhill, J., B. W. Wren, K. Mungall, J. M. Ketley, C. Churcher, D. Basham, T. Chillingworth, R. M. Davies, T. Feltwell, S. Holroyd, K. Jagels, A. V. Karlyshev, S. Moule, M. J. Pallen, C. W. Penn, M. A. Quai, M. A. Rajandream, K. M. Rutherford, A. H. van Vliet, S. Whitehead, and B. G. Barrell. 2000. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403:665-668.
31. Poly, F., D. Threadgill, and A. Stinzi. 2005. Genomic diversity in Campylobacter jejuni: Identification of C. jejuni 81-176-specific genes. J. Clin. Microbiol. 43:2330-2338.
32. Poly, F., T. D. R. Tribble, S. Baqar, M. Lorenzo, and P. Guerry. 2007. Genome sequences of a clinical isolate of Campylobacter jejuni from Thailand. Infect. Immun. 75:3425-3433.
33. Ribot, E., C. Fitzgerald, K. Kubota, B. Swaminathan, and T. Barrett. 2001. Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni. J. Clin. Microbiol. 39:1889-1894.
34. Scallan, E., R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, M. A. Widdowson, S. L. Roy, J. L. Jones, and P. M. Griffin. 2011. Foodborne illness acquired in the United States-Major pathogens. Emerg. Infect. Dis. 17:7-15.
35. Stahl, M., and A. Stintzi. 2011. Identification of essential genes in C. jejuni genome highlights hyper-variable plasticity regions. Funct. Integr. Genomics 11:241-257.
36. Stern, N., P. Fedorka-Cray, J. Bailey, N. Cox, S. Craven, K. Hiett, M. Musgrove, S. Ladely, D. Cosby, and G. Mead. 2001. Distribution of Campylobacter spp. in selected U.S. poultry production and processing operations. J. Food Prot. 64:1705-1710.