Genomic characterization of campylobacter jejuni strain M1

PLoS ONE

Volumn 5, Issue 8, 2010, Pages

  Friis, Carsten ^a   Wassenaar, Trudy M ^a,b   Javed, Muhammad A ^c   Snipen, Lars ^a,d   Lagesen, Karin ^a,e,f   Hallin, Peter F ^a   Newell, Diane G ^g,h   Toszeghy, Monique ^g   Ridley, Anne ^g   Manning, Georgina ^c   Ussery, David W ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b Molecular Microbiology and Genomics Consultants   (Germany)

^c NOTTINGHAM TRENT UNIVERSITY   (United Kingdom)

^d NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^e OSLO UNIVERSITY HOSPITAL   (Norway)

^f UNIVERSITY OF OSLO   (Norway)

^g Veterinary Laboratories Agencies   (United Kingdom)

^h Foodborne Zoonoses Consultancy   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM ADHERENCE; BACTERIUM ISOLATION; CAMPYLOBACTER JEJUNI; CHICKEN; CONTROLLED STUDY; GENE CLUSTER; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC TRAIT; GENOME ANALYSIS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA SEQUENCE; STRAIN DIFFERENCE; ANIMAL; ANIMAL DISEASE; BIRD DISEASE; CAMPYLOBACTERIOSIS; CHROMOSOME MAP; CLASSIFICATION; DISEASE TRANSMISSION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY;

CAMPYLOBACTER JEJUNI;

ANIMALS; BACTERIAL PROTEINS; CAMPYLOBACTER INFECTIONS; CAMPYLOBACTER JEJUNI; CHICKENS; CHROMOSOME MAPPING; GENOME, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POULTRY DISEASES;

EID: 77957869924     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012253     Document Type: Article

References (79)

1. Nauta M, Hill A, Rosenquist H, Brynestad S, Fetsch A, et al. (2009) A comparison of risk assessments on Campylobacter in broiler meat. Int J Food Microbiol 129: 107-123.
2. Wagenaar JA, Mevius DJ, Havelaar AH (2006) Campylobacter in primary animal production and control strategies to reduce the burden of human campylobacteriosis. Rev Sci Tech 25: 581-594.
3. Wingstrand A, Neimann J, Engberg J, Nielsen EM, Gerner-Smidt P, et al. (2006) Fresh chicken as main risk factor for campylobacteriosis, Denmark. Emerg Infect Dis 12: 280-285.
4. Jacobs-Reitsma W (2000) Campylobacter in the food supply. In: Nachamkin I, Blaser MJ, eds. Campylobacter. 2nd ed. Washington, D.C: American Society for Microbhioology. pp 467-481.
5. Little CL, Richardson JF, Owen RJ, de Pinna E, Threlfall EJ (2008) Prevalence, characterisation and antimicrobial resistance of Campylobacter and Salmonella in raw poultrymeat in the UK, 2003-2005. Int J Environ Health Res 18: 403-414.
6. Jorgensen F, Bailey R, Williams S, Henderson P, Wareing DR, et al. (2002) Prevalence and numbers of Salmonella and Campylobacter spp. on raw, whole chickens in relation to sampling methods. Int J Food Microbiol 76: 151-164.
7. Wassenaar TM, Fernandez-Astorga A, Alonso R, Marteinsson VT, Magnusson SH, et al. (2009) Comparison of Campylobacter fla-SVR genotypes isolated from humans and poultry in three European regions. Lett Appl Microbiol.
8. Sheppard SK, Dallas JF, MacRae M, McCarthy ND, Sproston EL, et al. (2009) Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6. Int J Food Microbiol 134: 96-103.
9. Miller WG, Englen MD, Kathariou S, Wesley IV, Wang G, et al. (2006) Identification of host-associated alleles by multilocus sequence typing of Campylobacter coli strains from food animals. Microbiology 152: 245-255.
10. Wassenaar TM (1997) Toxin production by Campylobacter spp. Clin Microbiol Rev 10: 466-476.
11. Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, et al. (2004) Genomewide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 279: 20327-20338.
12. Newell DG (2001) Animal models of Campylobacter jejuni colonization and disease and the lessons to be learned from similar Helicobacter pylori models. Symp Ser Soc Appl Microbiol. pp 57S-67S.
13. Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, et al. (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403: 665-668.
14. Gaynor EC, Cawthraw S, Manning G, MacKichan JK, Falkow S, et al. (2004) The genome-sequenced variant of Campylobacter jejuni NCTC 11168 and the original clonal clinical isolate differ markedly in colonization, gene expression, and virulence-associated phenotypes. J Bacteriol 186: 503-517.
15. Black RE, Levine MM, Clements ML, Hughes TP, Blaser MJ (1988) Experimental Campylobacter jejuni infection in humans. J Infect Dis 157: 472-479.
16. Pearson BM, Gaskin DJ, Segers RP, Wells JM, Nuijten PJ, et al. (2007) The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). J Bacteriol 189: 8402-8403.
17. Palmer SR, Gully PR, White JM, Pearson AD, Suckling WG, et al. (1983) Water-borne outbreak of campylobacter gastroenteritis. Lancet 1: 287-290.
18. Poly F, Read T, Tribble DR, Baqar S, Lorenzo M, et al. (2007) Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand. Infect Immun 75: 3425-3433.
19. Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, et al. (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol 3: e15.
20. Medini D, Serruto D, Parkhill J, Relman DA, Donati C, et al. (2008) Microbiology in the post-genomic era. Nat Rev Microbiol 6: 419-430.
21. Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8: 396-401.
22. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15: 589-594.
23. Ayling RD, Woodward MJ, Evans S, Newell DG (1996) Restriction fragment length polymorphism of polymerase chain reaction products applied to the differentiation of poultry campylobacters for epidemiological investigations. Res Vet Sci 60: 168-172.
24. Cell lines were obtained from the European Cell Culture Collection, Health Protection Agency. Porton Down. Salisbury, UK.
25. Konkel ME, Garvis SG, Tipton SL, Anderson DE, Jr., Cieplak W, Jr. (1997) Identification and molecular cloning of a gene encoding a fibronectin-binding protein (CadF) from Campylobacter jejuni. Mol Microbiol 24: 953-963.
26. Monteville MR, Yoon JE, Konkel ME (2003) Maximal adherence and invasion of INT 407 cells by Campylobacter jejuni requires the CadF outer-membrane protein and microfilament reorganization. Microbiology 149: 153-165.
27. Ziprin RL, Young CR, Stanker LH, Hume ME, Konkel ME (1999) The absence of cecal colonization of chicks by a mutant of Campylobacter jejuni not expressing bacterial fibronectin-binding protein. Avian Dis 43: 586-589.
28. Jin S, Joe A, Lynett J, Hani EK, Sherman P, et al. (2001) JlpA, a novel surfaceexposed lipoprotein specific to Campylobacter jejuni, mediates adherence to host epithelial cells. Mol Microbiol 39: 1225-1236.
29. Kervella M, Pages JM, Pei Z, Grollier G, Blaser MJ, et al. (1993) Isolation and characterization of two Campylobacter glycine-extracted proteins that bind to HeLa cell membranes. Infect Immun 61: 3440-3448.
30. Moser I, Schroeder W, Salnikow J (1997) Campylobacter jejuni major outer membrane protein and a 59-kDa protein are involved in binding to fibronectin and INT 407 cell membranes. FEMS Microbiol Lett 157: 233-238.
31. Flanagan RC, Neal-McKinney JM, Dhillon AS, Miller WG, Konkel ME (2009) Examination of Campylobacter jejuni putative adhesins leads to the identification of a new protein, designated FlpA, required for chicken colonization. Infect Immun 77: 2399-2407.
32. Raphael BH MM, Klena JD, Joens LA, Konkel M (2005) Interactions of Campylobacter jejuni with non-professional phagocytic cells. In: Ketley JM KM, ed. Campylobacter: Molecular and Cellular Biology. Norfolk NR: Horizon Bioscience. pp 397-413.
33. Christensen JE, Pacheco SA, Konkel ME (2009) Identification of a Campylobacter jejuni secreted protein required for maximal invasion of host cells. Mol Microbiol.
34. Ashgar SS, Oldfield NJ, Wooldridge KG, Jones MA, Irving GJ, et al. (2007) CapA, an autotransporter protein of Campylobacter jejuni, mediates association with human epithelial cells and colonization of the chicken gut. J Bacteriol 189: 1856-1865.
35. Jensen LJ, Friis C, Ussery DW (1999) Three views of microbial genomes. Res Microbiol 150: 773-777.
36. Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW (2000) A DNA structural atlas for Escherichia coli. J Mol Biol 299: 907-930.
37. Sinden RR, Hashem VI, Rosche WA (1999) DNA-directed mutations. Leading and lagging strand specificity. Ann N Y Acad Sci 870: 173-189.
38. Raskin DM, Seshadri R, Pukatzki SU, Mekalanos JJ (2006) Bacterial genomics and pathogen evolution. Cell 124: 703-714.
39. Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43: 783-791.
40. Snipen L, Almoy T, Ussery DW (2009) Microbial comparative pan-genomics using binomial mixture models. BMC Genomics 10: 385.
41. Lefebure T, Stanhope MJ (2009) Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res 19: 1224-1232.
42. Parker CT, Miller WG, Horn ST, Lastovica AJ (2007) Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni. BMC Microbiol 7: 50.
43. Manning G, Duim B, Wassenaar T, Wagenaar JA, Ridley A, et al. (2001) Evidence for a genetically stable strain of Campylobacter jejuni. Appl Environ Microbiol 67: 1185-1189.
44. Hallin PF, Binnewies TT, Ussery DW (2008) The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst 4: 363-371.
45. Friis C, Wassenaar T, Javed MA, Snipen L, Lagersen K, et al. (2009) Supplementary Section for "Genomic Characterization of Campylobacter jejuni strain M1". Available from: http://www.cbs.dtu.dk/services/GenomeAtlas/Campy_M1/.
46. Hofreuter D, Novik V, Galan JE (2008) Metabolic diversity in Campylobacter jejuni enhances specific tissue colonization. Cell Host Microbe 4: 425-433.
47. Barnes IH, Bagnall MC, Browning DD, Thompson SA, Manning G, et al. (2007) Gamma-glutamyl transpeptidase has a role in the persistent colonization of the avian gut by Campylobacter jejuni. Microb Pathog 43: 198-207.
48. Russell RG, Blaser MJ, Sarmiento JI, Fox J (1989) Experimental Campylobacter jejuni infection in Macaca nemestrina. Infect Immun 57: 1438-1444.
49. Miller WG, Pearson BM, Wells JM, Parker CT, Kapitonov VV, et al. (2005) Diversity within the Campylobacter jejuni type I restriction-modification loci. Microbiology 151: 337-351.
50. Simonsen B (1971) Methods for determining the microbial counts of ready-tocook chicken. World's Poultry Science: 27-368.
51. Newell DG, Shreeve JE, Toszeghy M, Domingue G, Bull S, et al. (2001) Changes in the carriage of Campylobacter strains by poultry carcasses during processing in abattoirs. Appl Environ Microbiol 67: 2636-2640.
52. Skirrow MB (1977) Campylobacter enteritis: a ''new'' disease. Br Med J 2: 9-11.
53. Humphrey T, Mason M, Martin K (1995) The isolation of Campylobacter jejuni from contaminated surfaces and its survival in diluents. Int J Food Microbiol 26: 295-303.
54. Frost JA, Oza AN, Thwaites RT, Rowe B (1998) Serotyping scheme for Campylobacter jejuni and Campylobacter coli based on direct agglutination of heat-stable antigens. J Clin Microbiol 36: 335-339.
55. Gibson J, Lorenz E, Owen RJ (1997) Lineages within Campylobacter jejuni defined by numerical analysis of pulsed-field gel electrophoretic DNA profiles. J Med Microbiol 46: 157-163.
56. Duim B, Wassenaar TM, Rigter A, Wagenaar J (1999) High-resolution genotyping of Campylobacter strains isolated from poultry and humans with amplified fragment length polymorphism fingerprinting. Appl Environ Microbiol 65: 2369-2375.
57. Dingle KE, Colles FM, Falush D, Maiden MC (2005) Sequence typing and comparison of population biology of Campylobacter coli and Campylobacter jejuni. J Clin Microbiol 43: 340-347.
58. Fearnley C, Manning G, Bagnall M, Javed MA, Wassenaar TM, et al. (2008) Identification of hyperinvasive Campylobacter jejuni strains isolated from poultry and human clinical sources. J Med Microbiol 57: 570-580.
59. Abuoun M, Manning G, Cawthraw SA, Ridley A, Ahmed IH, et al. (2005) Cytolethal distending toxin (CDT)-negative Campylobacter jejuni strains and anti-CDT neutralizing antibodies are induced during human infection but not during colonization in chickens. Infect Immun 73: 3053-3062.
60. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, et al. (2002) ARACHNE: a whole-genome shotgun assembler. Genome Res 12: 177-189.
61. Nielsen P, Krogh A (2005) Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 21: 4322-4329.
62. Larsen TS, Krogh A (2003) EasyGene-a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinformatics 4: 21.
63. Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A (2001) On the total number of genes and their length distribution in complete microbial genomes. Trends Genet 17: 425-428.
64. Pruitt KD, Tatusova T, Klimke W, Maglott DR (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 37: D32-36.
65. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
66. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res 33: D154-159.
67. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2008) GenBank. Nucleic Acids Res 36: D25-30.
68. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36: D281-288.
69. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, et al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100-3108.
70. Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33: W686-689.
71. Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW (2005) Genome Update: proteome comparisons. Microbiology 151: 1-4.
72. Ussery DW, Wassenaar TM, Borini S (2009) Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists: Springer.
73. Loytynoja A, Goldman N (2005) An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A 102: 10557-10562.
74. Loytynoja A, Goldman N (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635.
75. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
76. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ''pan-genome''. Proc Natl Acad Sci U S A 102: 13950-13955.
77. Koga M, Gilbert M, Li J, Koike S, Takahashi M, et al. (2005) Antecedent infections in Fisher syndrome: a common pathogenesis of molecular mimicry. Neurology 64: 1605-1611.
78. Poly F, Read TD, Chen YH, Monteiro MA, Serichantalergs O, et al. (2008) Characterization of two Campylobacter jejuni strains for use in volunteer experimental-infection studies. Infect Immun 76: 5655-5667.
79. Miller WG, Wang G, Binnewies TT, Parker CT (2008) The complete genome sequence and analysis of the human pathogen Campylobacter lari. Foodborne Pathog Dis 5: 371-386.