Characterization of water and wildlife strains as a subgroup of Campylobacter jejuni using DNA microarrays

Environmental Microbiology

Volumn 15, Issue 8, 2013, Pages 2371-2383

  Stabler, Richard A ^a   Larsson, Jonas T ^b   Al Jaberi, Suaad ^a   Nielsen, Eva M ^b   Kay, Emily ^a   Tam, Clarence C ^a   Higgins, Craig D ^a   Rodrigues, Laura C ^a   Richardson, Judith F ^c   O'Brien, Sarah J ^d   Wren, Brendan W ^a  

^a LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^b STATENS SERUM INSTITUT   (Denmark)

^c PUBLIC HEALTH ENGLAND   (United Kingdom)

^d UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); CAMPYLOBACTER JEJUNI;

EID: 84881228604     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12111     Document Type: Article

References (56)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Brandl, M.T., Haxo, A.F., Bates, A.H., and Mandrell, R.E. (2004) Comparison of survival of Campylobacter jejuni in the phyllosphere with that in the rhizosphere of spinach and radish plants. Appl Environ Microbiol 70: 1182-1189.
3. Champion, O.L., Gaunt, M.W., Gundogdu, O., Elmi, A., Witney, A.A., Hinds, J., etal. (2005) Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. Proc Natl Acad Sci USA 102: 16043-16048.
4. Dingle, K.E., Colles, F.M., Wareing, D.R., Ure, R., Fox, A.J., Bolton, F.E., etal. (2001) Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol 39: 14-23.
5. Dingle, K.E., Colles, F.M., Ure, R., Wagenaar, J.A., Duim, B., Bolton, F.J., etal. (2002) Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation. Emerg Infect Dis 8: 949-955.
6. Dorrell, N., Hinchliffe, S.J., and Wren, B.W. (2005) Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol 8: 620-626.
7. Ethelberg, S., Simonsen, J., Gerner-Smidt, P., Olsen, K.E., and Molbak, K. (2005) Spatial distribution and registry-based case-control analysis of Campylobacter infections in Denmark, 1991-2001. Am J Epidemiol 162: 1008-1015.
8. Francisco, A.P., Bugalho, M., Ramirez, M., and Carrico, J.A. (2009) Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics 10: 152.
9. French, N.P., Midwinter, A., Holland, B., Collins-Emerson, J., Pattison, R., Colles, F., and Carter, P. (2009) Molecular epidemiology of Campylobacter jejuni isolates from wild-bird fecal material in children's playgrounds. Appl Environ Microbiol 75: 779-783.
10. Gundogdu, O., Bentley, S.D., Holden, M.T., Parkhill, J., Dorrell, N., and Wren, B.W. (2007) Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics 8: 162.
11. Harris, N.V., Weiss, N.S., and Nolan, C.M. (1986) The role of poultry and meats in the etiology of Campylobacter jejuni/coli enteritis. Am J Public Health 76: 407-411.
12. Hepworth, P.J., Leatherbarrow, H., Hart, C.A., and Winstanley, C. (2007) Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni. BMC Genomics 8: 110.
13. Hepworth, P.J., Ashelford, K.E., Hinds, J., Gould, K.A., Witney, A.A., Williams, N.J., etal. (2011) Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes. Environ Microbiol 13: 1549-1560.
14. Hinchliffe, S.J., Isherwood, K.E., Stabler, R.A., Prentice, M.B., Rakin, A., Nichols, R.A., etal. (2003) Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res 13: 2018-2029.
15. Howard, S.L., Gaunt, M.W., Hinds, J., Witney, A.A., Stabler, R., and Wren, B.W. (2006) Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity. J Bacteriol 188: 3645-3653.
16. Huelsenbeck, J.P., and Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
17. Jensen, A.N., Dalsgaard, A., Baggesen, D.L., and Nielsen, E.M. (2006) The occurrence and characterization of Campylobacter jejuni and C. coli in organic pigs and their outdoor environment. Vet Microbiol 116: 96-105.
18. Jorgensen, F., Ellis-Iversen, J., Rushton, S., Bull, S.A., Harris, S.A., Bryan, S.J., etal. (2011) Influence of season and geography on Campylobacter jejuni and C.coli subtypes in housed broiler flocks reared in Great Britain. Appl Environ Microbiol 77: 3741-3748.
19. Joshua, G.W., Guthrie-Irons, C., Karlyshev, A.V., and Wren, B.W. (2006) Biofilm formation in Campylobacter jejuni. Microbiology 152: 387-396.
20. Kalendar, R., Lee, D., and Schulman, A.H. (2009) FastPCR Software for PCR Primer and Probe Design and Repeat Search. Genes, Genomes and. Genomics 3: 1-14.
21. Karenlampi, R., Rautelin, H., Schonberg-Norio, D., Paulin, L., and Hanninen, M.L. (2007) Longitudinal study of Finnish Campylobacter jejuni and C.coli isolates from humans, using multilocus sequence typing, including comparison with epidemiological data and isolates from poultry and cattle. Appl Environ Microbiol 73: 148-155.
22. Katoh, K., Misawa, K., Kuma, K., and Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066.
23. Katoh, K., Kuma, K., Toh, H., and Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
24. Kemp, R., Leatherbarrow, A.J., Williams, N.J., Hart, C.A., Clough, H.E., Turner, J., etal. (2005) Prevalence and genetic diversity of Campylobacter spp. in environmental water samples from a 100-square-kilometer predominantly dairy farming area. Appl Environ Microbiol 71: 1876-1882.
25. Kim, C.C., Joyce, E.A., Chan, K., and Falkow, S. (2002) Improved analytical methods for microarray-based genome-composition analysis. Genome Biol 3: RESEARCH0065.
26. Kim, J.S., Artymovich, K.A., Hall, D.F., Smith, E.J., Fulton, R., Bell, J., etal. (2012) Passage of Campylobacter jejuni through the chicken reservoir or mice promotes phase variation in contingency genes Cj0045 and Cj0170 that strongly associates with colonization and disease in a mouse model. Microbiology 158 (Part 5): 1304-1316.
27. King, J.Y., Ferrara, R., Tabibiazar, R., Spin, J.M., Chen, M.M., Kuchinsky, A., etal. (2005) Pathway analysis of coronary atherosclerosis. Physiol Genomics 23: 103-118.
28. Kwan, P.S., Birtles, A., Bolton, F.J., French, N.P., Robinson, S.E., Newbold, L.S., etal. (2008a) Longitudinal study of the molecular epidemiology of Campylobacter jejuni in cattle on dairy farms. Appl Environ Microbiol 74: 3626-3633.
29. Kwan, P.S., Barrigas, M., Bolton, F.J., French, N.P., Gowland, P., Kemp, R., etal. (2008b) Molecular epidemiology of Campylobacter jejuni populations in dairy cattle, wildlife, and the environment in a farmland area. Appl Environ Microbiol 74: 5130-5138.
30. McCarthy, N.D., Colles, F.M., Dingle, K.E., Bagnall, M.C., Manning, G., Maiden, M.C., and Falush, D. (2007) Host-associated genetic import in Campylobacter jejuni. Emerg Infect Dis 13: 267-272.
31. Manning, G., Dowson, C.G., Bagnall, M.C., Ahmed, I.H., West, M., and Newell, D.G. (2003) Multilocus sequence typing for comparison of veterinary and human isolates of Campylobacter jejuni. Appl Environ Microbiol 69: 6370-6379.
32. Mellmann, A., Mosters, J., Bartelt, E., Roggentin, P., Ammon, A., Friedrich, A.W., etal. (2004) Sequence-based typing of flaB is a more stable screening tool than typing of flaA for monitoring of Campylobacter populations. J Clin Microbiol 42: 4840-4842.
33. Miller, W.G., On, S.L., Wang, G., Fontanoz, S., Lastovica, A.J., and Mandrell, R.E. (2005) Extended multilocus sequence typing system for Campylobacter coli, C.lari, C.upsaliensis, and C.helveticus. J Clin Microbiol 43: 2315-2329.
34. Moen, B., Oust, A., Langsrud, O., Dorrell, N., Marsden, G.L., Hinds, J., etal. (2005) Explorative multifactor approach for investigating global survival mechanisms of Campylobacter jejuni under environmental conditions. Appl Environ Microbiol 71: 2086-2094.
35. Murphy, C., Carroll, C., and Jordan, K.N. (2005) The effect of different media on the survival and induction of stress responses by Campylobacter jejuni. J Microbiol Methods 62: 161-166.
36. Ogden, I.D., Dallas, J.F., MacRae, M., Rotariu, O., Reay, K.W., Leitch, M., etal. (2009) Campylobacter excreted into the environment by animal sources: prevalence, concentration shed, and host association. Foodborne Pathog Dis 6: 1161-1170.
37. On, S.L., Dorrell, N., Petersen, L., Bang, D.D., Morris, S., Forsythe, S.J., and Wren, B.W. (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.
38. Park, C.E., and Sanders, G.W. (1992) Occurrence of thermotolerant campylobacters in fresh vegetables sold at farmers' outdoor markets and supermarkets. Can J Microbiol 38: 313-316.
39. Pearson, B.M., Pin, C., Wright, J., I'Anson, K., Humphrey, T., and Wells, J.M. (2003) Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. FEBS Lett 554: 224-230.
40. Petersen, L., Nielsen, E.M., Engberg, J., On, S.L., and Dietz, H.H. (2001) Comparison of genotypes and serotypes of Campylobacter jejuni isolated from Danish wild mammals and birds and from broiler flocks and humans. Appl Environ Microbiol 67: 3115-3121.
41. Ronquist, F., and Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
42. Rosef, O., Gondrosen, B., Kapperud, G., and Underdal, B. (1983) Isolation and characterization of Campylobacter jejuni and Campylobacter coli from domestic and wild mammals in Norway. Appl Environ Microbiol 46: 855-859.
43. Rosef, O., Kapperud, G., Lauwers, S., and Gondrosen, B. (1985) Serotyping of Campylobacter jejuni, Campylobacter coli, and Campylobacter laridis from domestic and wild animals. Appl Environ Microbiol 49: 1507-1510.
44. Sails, A.D., Swaminathan, B., and Fields, P.I. (2003) Utility of multilocus sequence typing as an epidemiological tool for investigation of outbreaks of gastroenteritis caused by Campylobacter jejuni. J Clin Microbiol 41: 4733-4739.
45. Sanad, Y.M., Kassem, I.I., Abley, M., Gebreyes, W., Lejeune, J.T., and Rajashekara, G. (2011) Genotypic and phenotypic properties of cattle-associated Campylobacter and their implications to public health in the USA. PLoS ONE 6: e25778.
46. Schonberg-Norio, D., Takkinen, J., Hanninen, M.L., Katila, M.L., Kaukoranta, S.S., Mattila, L., and Rautelin, H. (2004) Swimming and Campylobacter infections. Emerg Infect Dis 10: 1474-1477.
47. Skirrow, M.B. (1977) Campylobacter enteritis: a 'new' disease. Br Med J 2: 9-11.
48. Skirrow, M.B., Fidoe, R.G., and Jones, D.M. (1981) An outbreak of presumptive food-borne Campylobacter enteritis. J Infect 3: 234-236.
49. Stabler, R.A., Gerding, D.N., Songer, J.G., Drudy, D., Brazier, J.S., Trinh, H.T., etal. (2006) Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J Bacteriol 188: 7297-7305.
50. Staden, R. (1996) The Staden sequence analysis package. Mol Biotechnol 5: 233-241.
51. Staden, R., Beal, K.F., and Bonfield, J.K. (2000) The Staden package, 1998. Methods Mol Biol 132: 115-130.
52. Taboada, E.N., Acedillo, R.R., Carrillo, C.D., Findlay, W.A., Medeiros, D.T., Mykytczuk, O.L., etal. (2004) Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J Clin Microbiol 42: 4566-4576.
53. Taboada, E.N., Mackinnon, J.M., Luebbert, C.C., Gannon, V.P., Nash, J.H., and Rahn, K. (2008) Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni. BMC Evol Biol 8: 229.
54. Tam, C.C., Higgins, C.D., Neal, K.R., Rodrigues, L.C., Millership, S.E., and O'Brien, S.J. (2009) Chicken consumption and use of acid-suppressing medications as risk factors for Campylobacter enteritis, England. Emerg Infect Dis 15: 1402-1408.
55. Tam, C.C., Rodrigues, L.C., Viviani, L., Dodds, J.P., Evans, M.R., Hunter, P.R., etal. (2012) Longitudinal study of infectious intestinal disease in the UK (IID2 study): incidence in the community and presenting to general practice. Gut 61: 69-77.
56. Wilson, D.J., Gabriel, E., Leatherbarrow, A.J., Cheesbrough, J., Gee, S., Bolton, E., etal. (2008) Tracing the source of campylobacteriosis. PLoS Genet 4: e1000203.