Progressive genome-wide introgression in agricultural Campylobacter coli

Molecular Ecology

Volumn 22, Issue 4, 2013, Pages 1051-1064

  Sheppard, Samuel K ^a,b   Didelot, Xavier ^c   Jolley, Keith A ^a   Darling, Aaron E ^d   Pascoe, Ben ^b   Meric, Guillaume ^b   Kelly, David J ^e   Cody, Alison ^a   Colles, Frances M ^a   Strachan, Norval J C ^f   Ogden, Iain D ^f   Forbes, Ken ^f   French, Nigel P ^g   Carter, Philip ^h   Miller, William G ⁱ   McCarthy, Noel D ^a   Owen, Robert ^j   Litrup, Eva ^k   Egholm, Michael ^l   Affourtit, Jason P ^m   Bentley, Stephen D ⁿ   Parkhill, Julian ⁿ   Maiden, Martin C J ^a   Falush, Daniel ^d   more..

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b SWANSEA UNIVERSITY   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d Western Bank ^*  (United Kingdom)

^e UNIVERSITY OF SHEFFIELD   (United Kingdom)

^f UNIVERSITY OF ABERDEEN   (United Kingdom)

^g MASSEY UNIVERSITY   (New Zealand)

^h INSTITUTE OF ENVIRONMENTAL SCIENCE AND RESEARCH   (New Zealand)

ⁱ U S DEPARTMENT OF AGRICULTURE   (United States)

^j PUBLIC HEALTH ENGLAND   (United Kingdom)

^k STATENS SERUM INSTITUT   (Denmark)

^l PALL CORPORATION   (United States)

^m Ion Torrent   (United States)

ⁿ WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

more..

Author keywords

adaptation; Campylobacter; epistasis; genomics; introgression

Indexed keywords

BACTERIA (MICROORGANISMS); CAMPYLOBACTER; CAMPYLOBACTER COLI; CAMPYLOBACTER JEJUNI;

EID: 84873085208     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12162     Document Type: Article

References (58)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
2. Bisharat N, Cohen DI, Harding RM, et al,. (2005) Hybrid Vibrio vulnificus. Emerging Infectious Diseases, 11, 30-35.
3. Cabello H, Torres A, Celis R, et al,. (1997) Bacterial colonization of distal airways in healthy subjects and chronic lung disease: a bronchoscopic study. European Respiratory Journal, 10, 1137-1144.
4. Caro-Quintero A, Rodriguez-Castano GP, Konstantinidis KT, (2009) Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species. Journal of Bacteriology, 191, 5824-5831.
5. Cohan FM, (2002) Sexual isolation and speciation in bacteria. Genetica, 116, 359-370.
6. Cohan FM, Koeppel AF, (2008) The origins of ecological diversity in prokaryotes. Current Biology, 18, R1024-R1034.
7. Colles FM, Dingle KE, Cody AJ, Maiden MC, (2008) Comparison of Campylobacter populations in wild geese with those in starlings and free-range poultry on the same farm. Applied and Environmental Microbiology, 74, 3583-3590.
8. Consortium(TCSaA) (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437, 69-87.
9. Darling AC, Mau B, Blattner FR, Perna NT, (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research, 14, 1394-1403.
10. Darling AE, Mau B, Perna NT, (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One, 5, e11147.
11. Didelot X, Falush D, (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics, 175, 1251-1266.
12. Didelot X, Achtman M, Parkhill J, Thomson NR, Falush D, (2007) A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination? Genome Research, 17, 61-68.
13. Didelot X, Darling A, Falush D, (2009) Inferring genomic flux in bacteria. Genome Research, 19, 306-317.
14. Doolittle WF, (2008) Microbial evolution: stalking the wild bacterial species. Current Biology, 18, R565-R567.
15. Doolittle WF, Zhaxybayeva O, (2009) On the origin of prokaryotic species. Genome Research, 19, 744-756.
16. Doyle LP, (1948) The etiology of swine dysentrey. American Journal of Veterinary Research, 9, 50-51.
17. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
18. Escherich T, (1886) Beitrage zur Kenntniss der Darmbacterien. III. Ueber das Vorkommen von Vibrionen im Darmcanal und den Stuhlgangen der Sauglinge. (Articles adding to the knowledge of intestinal bacteria. III. On the existence of vibrios in the intestines and feces of babies.). Munchener Med Wochenschrift, 33, 815-817.
19. Falush D, (2009) Toward the use of genomics to study microevolutionary change in bacteria. PLoS Genetics, 5, e1000627.
20. Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
21. Fouts DE, Mongodin EF, Mandrell RE, et al,. (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biology, 3, e15.
22. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW, (2002) Evolutionary rate in the protein interaction network. Science, 296, 750-752.
23. Fraser C, Hanage WP, Spratt BG, (2007) Recombination and the nature of bacterial speciation. Science, 315, 476-480.
24. Gundogdu O, Bentley SD, Holden MT, et al,. (2007) Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics, 8, 162.
25. Hartley-Tassell LE, Shewell LK, Day CJ, et al,. (2010) Identification and characterization of the aspartate chemosensory receptor of Campylobacter jejuni. Molecular Microbiology, 75, 710-730.
26. Jolley K, Maiden M, (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics, 11, 595.
27. Jolley KA, Bliss CM, Bennett JS, et al,. (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology, 158, 1005-1015.
28. Kumar S, Nei M, Dudley J, Tamura K, (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinformatics, 9, 299-306.
29. Lawrence JG, (1999) Gene transfer, speciation, and the evolution of bacterial genomes. Current Opinion in Microbiology, 2, 519-523.
30. Lefebure T, Bitar PD, Suzuki H, Stanhope MJ, (2010) Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biology and Evolution, 2, 646-655.
31. Mayr E, (1970) Multiplication of species. In: Populations, Species, and Evolution: An Abridgment of Animal Species and Evolution (ed., Mayr E,), pp. 253. Belknap Press, Cambridge, MA.
32. Muraoka WT, Zhang Q, (2011) Phenotypic and genotypic evidence for L-fucose utilization by Campylobacter jejuni. Journal of Bacteriology, 193, 1065-1075.
33. Ochman H, Groisman EA, (1994) The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium. EXS, 69, 479-493.
34. Ochman H, Lawrence JG, Groisman EA, (2000) Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299-304.
35. Parkhill J, Wren BW, Mungall K, et al,. (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature, 403, 665-668.
36. Parkhill J, Dougan G, James KD, et al,. (2001) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature, 413, 848-852.
37. Pearson BM, Gaskin DJ, Segers RP, et al,. (2007) The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). Journal of Bacteriology, 189, 8402-8403.
38. Peng Z, Elango N, Wildman DE, Yi SV, (2009) Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation. BMC Genomics, 10, 247.
39. Retchless AC, Lawrence JG, (2010) Phylogenetic incongruence arising from fragmented speciation in enteric bacteria. Proceedings of the National Academy of Sciences of the United States of America, 107, 11453-11458.
40. Rieseberg LH, Raymond O, Rosenthal DM, et al,. (2003) Major ecological transitions in wild sunflowers facilitated by hybridization. Science, 301, 1211-1216.
41. Rosef O, Gondrosen B, Kapperud G, Underdal B, (1983) Isolation and characterization of Campylobacter jejuni and Campylobacter coli from domestic and wild mammals in Norway. Applied and Environmental Microbiology, 46, 855-859.
42. Sebald M, Veron M, (1963) [Base DNA content and classification of vibrios]. Annales de l'Institut Pasteur, 105, 897-910.
43. Sheppard SK, McCarthy ND, Falush D, Maiden MC, (2008) Convergence of Campylobacter species: implications for bacterial evolution. Science, 320, 237-239.
44. Sheppard SK, Dallas JF, Strachan NJ, et al,. (2009) Campylobacter genotyping to determine the source of human infection. Clinical Infectious Diseases, 48, 1072-1078.
45. Sheppard SK, Colles F, Richardson J, et al,. (2010a) Host association of Campylobacter genotypes transcends geographic variation. Applied and Environmental Microbiology, 76, 5269-5277.
46. Sheppard SK, Dallas JF, Wilson DJ, et al,. (2010b) Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland. PLoS One, 5, e15708.
47. Sheppard SK, Maiden MCJ, Falush D, (2010c) Population genetics of Campylobacter. In: Bacterial Population Genetics in Infectious Disease (eds, Robinson DA, Falush D, Feil EJ,), pp. 181-194. Wiley-Blackwell, Hoboken, NJ.
48. Sheppard SK, McCarthy ND, Jolley KA, Maiden MC, (2011) Introgression in the genus Campylobacter: generation and spread of mosaic alleles. Microbiology, 157, 1066-1074.
49. Snipen L, Wassenaar T, Altermann E, et al,. (2012) Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli. Microbial Informatics and Experimentation, 2, 8.
50. Sopwith W, Birtles A, Matthews M, et al,. (2008) Identification of potential environmentally adapted Campylobacter jejuni strain, United Kingdom. Emerging Infectious Diseases, 14, 1769-1773.
51. Stahl M, Friis LM, Nothaft H, et al,. (2011) L-fucose utilization provides Campylobacter jejuni with a competitive advantage. Proceedings of the National Academy of Sciences of the United States of America, 108, 7194-7199.
52. Suerbaum S, Lohrengel M, Sonneveld A, Ruberg F, Kist M, (2001) Allelic diversity and recombination in Campylobacter jejuni. Journal of Bacteriology, 183, 2553-2559.
53. Thakur S, Morrow WE, Funk JA, Bahnson PB, Gebreyes WA, (2006) Molecular epidemiologic investigation of Campylobacter coli in swine production systems, using multilocus sequence typing. Applied and Environmental Microbiology, 72, 5666-5669.
54. Treangen TJ, Darling AE, Achaz G, et al,. (2009) A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6, 180-189.
55. Velayudhan J, Kelly DJ, (2002) Analysis of gluconeogenic and anaplerotic enzymes in Campylobacter jejuni: an essential role for phosphoenolpyruvate carboxykinase. Microbiology, 148, 685-694.
56. Veron M, Chatelain R, (1973) Taxonomic study of the genus Campylobacter and designation of the neotype strain for the type species Campylobacter fetus. International Journal of Systematic Bacteriology, 23, 122-134.
57. Waldenstrom J, Broman T, Carlsson I, et al,. (2002) Prevalence of Campylobacter jejuni, Campylobacter lari, and Campylobacter coli in different ecological guilds and taxa of migrating birds. Applied and Environmental Microbiology, 68, 5911-5917.
58. Waldenstrom J, On SL, Ottvall R, Hasselquist D, Olsen B, (2007) Species diversity of campylobacteria in a wild bird community in Sweden. Journal of Applied Microbiology, 102, 424-432.