The evolution of campylobacter jejuni and campylobacter coli

Cold Spring Harbor Perspectives in Biology

Volumn 7, Issue 8, 2015, Pages

  Sheppard, Samuel K ^a   Maiden, Martin C J ^b  

^a SWANSEA UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AVES; CAMPYLOBACTER; CAMPYLOBACTER COLI; CAMPYLOBACTER JEJUNI; MAMMALIA;

ADAPTATION; CAMPYLOBACTER COLI; CAMPYLOBACTER JEJUNI; GENETIC RECOMBINATION; GENETICS; MOLECULAR EVOLUTION; PHYSIOLOGY;

ADAPTATION, PHYSIOLOGICAL; CAMPYLOBACTER COLI; CAMPYLOBACTER JEJUNI; EVOLUTION, MOLECULAR; RECOMBINATION, GENETIC;

EID: 84940093869     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a018119     Document Type: Article

References (69)

1. Achtman M, Morelli G, Zhu P, Wirth T, Diehl I, Kusecek B, Vogler AJ, Wagner DM, Allender CJ, Easterday WR, et al. 2004. Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci 101: 17837-17842.
2. Allos B. 2001. Campylobacter jejuni infections: Update on emerging issues and trends. Clin Infect Dis 32: 1201-1206.
3. Ammerman AJ, Cavalii-Sforza LL. 1984. The neolithic transition and the genetics of populations in Europe. Princeton University Press, Princeton, NJ.
4. Bayliss CD, Bidmos FA, Anjum A, Manchev VT, Richards RL, Grossier JP, Wooldridge KG, Ketley JM, Barrow PA, Jones MA, et al. 2012. Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonization. Nucleic Acids Res 40: 5876-5889.
5. Buckling A, Brockhurst MA, Travisano M, Rainey PB. 2007. Experimental adaptation to high and low quality environments under different scales of temporal variation. J Evol Biol 20: 296-300.
6. Caro-Quintero A, Rodriguez-Castano GP, Konstantinidis KT. 2009. Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species. J Bacteriol 191: 5824-5831.
7. Carter PE, McTavish SM, Brooks HJ, Campbell D, Collins-Emerson JM, Midwinter AC, French NP. 2009. Novel clonal complexes with an unknown animal reservoir dominate Campylobacter jejuni isolates from river water in New Zealand. Appl Environ Microbiol 75: 6038-6046.
8. Cheng L, Connor TR, Siren J, Aanensen DM, Corander J. 2013. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol 30: 1224-1228.
9. Cody AJ, Clarke L, Bowler IC, Dingle KE. 2010. Ciprofloxacin-resistant campylobacteriosis in the UK. Lancet 376: 1987.
10. Colles FM, Maiden MC. 2012. Campylobacter sequence typing databases: Applications and future prospects. Microbiology 158: 2695-2709.
11. Colles FM, Maiden MC. 2014. Exploring the population dynamics of multiple Campylobacter strains in poultry. Campylobacter ecology and evolution (ed. Sheppard SK, Meric G). Caister Academic, Norfolk, England.
12. Colles FM, Dingle KE, Cody AJ, Maiden MC. 2008a. Comparison of Campylobacter populations in wild geese with those in starlings and free-range poultry on the same farm. Appl Environ Microbiol 74: 3583-3590.
13. Colles FM, Jones TA, McCarthy ND, Sheppard SK, Cody AJ, Dingle KE, Dawkins MS, Maiden MC. 2008b. Campylobacter infection of broiler chickens in a free-range environment. Environ Microbiol 10: 2042-2050.
14. Colles FM, Ali JS, Sheppard SK, McCarthyND, Maiden MC. 2011. Campylobacter populations in wild and domesticated Mallard ducks (Anas platyrhynchos). Environ Microbiol Rep 3: 574-580.
15. Condran GA, Murphy J. 2008. Defining and managing infant mortality: A case study of Philadelphia, 1870-1920. Soc Sci Hist 32: 473-513.
16. Coward C, van Diemen PM, Conlan AJ, Gog JR, StevensMP, Jones MA, Maskell DJ. 2008. Competing isogenic Campylobacter strains exhibit variable population structures in vivo. Appl Environ Microbiol 74: 3857-3867.
17. de Haan CP, Lampen K, Corander J, Hanninen ML. 2013. Multilocus sequence types of environmental Campylobacter jejuni isolates and their similarities to those of human, poultry and bovine C. jejuni isolates. Zoonoses Public Health 60: 125-133.
18. Didelot X, Falush D. 2007. Inference of bacterial microevolution using multilocus sequence data. Genetics 175: 1251-1266.
19. Dingle K, McCarthy N, Cody A, Peto T, Maiden M. 2008. Extended sequence typing of Campylobacter spp., United Kingdom. Emerg Infect Dis 14: 1620-1622.
20. Falush D, Kraft C, Taylor NS, Correa P, Fox JG, Achtman M, Suerbaum S. 2001. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age. Proc Natl Acad Sci 98: 15056-15061.
21. Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray M. 2014. A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens. Genome Med 6: 101.
22. Feng L, Reeves PR, Lan R, Ren Y, Gao C, Zhou Z, Ren Y, Cheng J, Wang W, Wang J, et al. 2008. A recalibrated molecular clock and independent origins for the cholera pandemic clones. PLoS ONE 3: e4053.
23. French NP, Midwinter A, Holland B, Collins-Emerson J, Pattison R, Colles F, Carter P. 2009. Molecular epidemi-ology of Campylobacter jejuni isolates from wild-bird fecal material in children's playgrounds. Appl Environ Microbiol 75: 779-783.
24. French N, Yu S, Biggs P, Holland B, Fearnheard P, Binney B, Fox A, Grove-White D, Leigh JW, Miller W, et al. 2014. Evolution of Campylobacter species in New Zealand Campylobacter ecology and evolution (ed. Sheppard SK). Caister Academic, Norfolk, England.
25. Friedman CJ, Neiman J, Wegener HC, Tauxe RV. 2000. Epidemiology of Campylobacter jejuni infections in the United States and other industrialised nations. In Campylobacter (ed. Nachamkin I, Blaser MJ), pp. 121-138. ASM, Washington, DC.
26. 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.
27. Griekspoor P, Colles FM, McCarthy ND, Hansbro PM, Ashhurst-Smith C, Olsen B, HasselquistD, Maiden MC, Waldenström J. 2013. Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds. Mol Ecol 22: 1463-1472.
28. Hastings R, Colles FM, McCarthy ND, Maiden MC, Sheppard SK. 2011. Campylobacter genotypes from poultry transportation crates indicate a source of contamination and transmission. J Appl Microbiol 110: 266-276.
29. Jerome JP, Mansfield LS. 2014. Within-host evolution of Campylobacter jejuni. In Campylobacter ecology and evolution (ed. Sheppard SK). Caister Academic, Norfolk, England.
30. Jolley KA, Maiden MC. 2014. Using MLST to study bacterial variation: Prospects in the genomic era. Future Microbiol 9: 623-630.
31. Jorgensen F, Ellis-Iversen J, Rushton S, Bull SA, Harris SA, Bryan SJ, Gonzalez A, Humphrey TJ. 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.
32. Kessel AS, Gillespie IA, O'Brien SJ, Adak GK, Humphrey TJ, Ward LR. 2001. General outbreaks of infectious intestinal disease linked with poultry, England and Wales, 1992-1999. Commun Dis Public Health 4: 171-177.
33. Kittl S, Kuhnert P, Hachler H, Korczak BM. 2011. Comparison of genotypes and antibiotic resistance of Campylobacter jejuni isolated from humans and slaughtered chickens in Switzerland. J Appl Microbiol 110: 513-520.
34. Lang P, Lefebure T, WangW, Pavinski Bitar P, Meinersmann RJ, Kaya K, Stanhope MJ. 2010. Expanded multilocus sequence typing and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts. Appl Environ Microbiol 76: 1913-1925.
35. Lefébure T, Bitar PD, Suzuki H, Stanhope MJ. 2010. Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol Evol 2: 646-655.
36. Lenski RE, Mongold JA, Sniegowski PD, Travisano M, Vasi F, Gerrish PJ, Schmidt TM. 1998. Evolution of competitive fitness in experimental populations of E. coli: What makes one genotype a better competitor than another? Antonie Van Leeuwenhoek 73: 35-47.
37. Magnú sson SH, Guðmundsdóttir S, Reynisson E, Rú narsson AR, Harðardóttir H, Gunnarson E, Georgsson F, Reiersen J, Marteinsson VT. 2011. Comparison of Campylobacter jejuni isolates from human, food, veterinary and environmental sources in Iceland using PFGE, MLST and fla-SVR sequencing. J Appl Microbiol 111: 971-981.
38. Maiden M. 2006. Multilocus sequence typing of bacteria. Annu Rev Microbiol 60: 561-588.
39. Maiden M, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, et al. 1998. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci 95: 3140-3145.
40. McCarthy ND, Colles FM, Dingle KE, Bagnall MC, Manning G, Maiden MC, Falush D. 2007. Host-associated genetic import in Campylobacter jejuni. Emerg Infect Dis 13: 267-272.
41. McCorriston J, Hole F. 1991. The ecology of seasonal stress and the origin of agriculture in theNear East. AmAnthropol 93: 46-69.
42. Méric G, Yahara K, Mageiros L, Pascoe B, Maiden MC, Jolley KA, Sheppard SK. 2014. A reference pan-genome approach to comparative bacterial genomics: Identification of novel epidemiological markers in pathogenic Campylobacter. PLoS ONE 9: e92798.
43. Miller WG, Englen MD, Kathariou S, Wesley IV, Wang G, Pittenger-Alley L, Siletz RM, Muraoka W, Fedorka-Cray PJ, Mandrell RE. 2006. Identification of host-associated alleles by multilocus sequence typing of Campylobacter coli strains from food animals. Microbiology 152: 245-255.
44. Müllner P, Collins-Emerson JM, Midwinter AC, Carter P, Spencer SE, van der Logt P, Hathaway S, French NP. 2010. Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry. Appl Environ Microbiol 76: 2145-2154.
45. Neimann J, Engberg J, Molbak K, Wegener HC. 2003. A case-control study of risk factors for sporadic Campylobacter infections in Denmark. Epidemiol Infect 130: 353-366.
46. Ochman H, Wilson AC. 1987. Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes. J Mol Evol 26: 74-86.
47. Perez-Losada M, Crandall KA, Zenilman J, Viscidi RP. 2007. Temporal trends in gonococcal population genetics in a high prevalence urban community. Infect Genet Evol 7: 271-278.
48. Read DS, Woodcock DJ, Strachan NJ, Forbes KJ, Colles FM, Maiden MC, Clifton-Hadley F, Ridley A, Vidal A, Rodgers J, et al. 2013. Evidence for phenotypic plasticity among multihost Campylobacter jejuni and C. coli lineages, obtained using ribosomal multilocus sequence typing and Raman spectroscopy. Appl Environ Microbiol 79: 965-973.
49. Ribot EM, Fitzgerald C, Kubota K, Swaminathan B, Barrett TJ. 2001. Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni. J Clin Microbiol 39: 1889-1894.
50. Roumagnac P, Weill FX, Dolecek C, Baker S, Brisse S, Chinh NT, Le TA, Acosta CJ, Farrar J, Dougan G, et al. 2006. Evolutionary history of Salmonella typhi. Science 314: 1301-1304.
51. Samie A, Obi CL, Barrett LJ, Powell SM, Guerrant RL. 2007. Prevalence of Campylobacter species, Helicobacter pylori and Arcobacter species in stool samples from the Venda region, Limpopo, South Africa: Studies using molecular diagnostic methods. J Infect 54: 558-566.
52. Sears A, Baker MG, Wilson N, Marshall J, Muellner P, Campbell DM, Lake RJ, French NP. 2011. Marked campylobacteriosis decline after interventions aimed at poultry, New Zealand. Emerg Infect Dis 17: 1007-1015.
53. Sheppard SK, McCarthy ND, Falush D, Maiden MC. 2008. Convergence of Campylobacter species: Implications for bacterial evolution. Science 320: 237-239.
54. Sheppard SK, Dallas JF, MacRae M, McCarthyND, Sproston EL, Gormley FJ, Strachan NJ, Ogden ID, Maiden MC, Forbes KJ. 2009a. Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6. Int J Food Microbiol 134: 96-103.
55. Sheppard SK, Dallas JF, Strachan NJ, MacRae M, McCarthy ND, Wilson DJ, Gormley FJ, FalushD, Ogden ID, Maiden MC, et al. 2009b. Campylobacter genotyping to determine the source of human infection. Clin Infect Dis 48: 1072-1078.
56. Sheppard SK, Dallas JF, Wilson DJ, Strachan NJ, McCarthy ND, Jolley KA, Colles FM, Rotariu O, Ogden ID, Forbes KJ, et al. 2010a. Evolution of an agriculture-associated disease causing Campylobacter coli clade: Evidence from national surveillance data in Scotland. PLoS ONE 5: e15708.
57. Sheppard SK, Colles F, Richardson J, Cody AJ, Elson R, Lawson A, Brick G, Meldrum R, Little CL, Owen RJ, et al. 2010b. Host association of Campylobacter genotypes transcends geographic variation. Appl Environ Microbiol 76: 5269-5277.
58. Sheppard SK, Colles FM, McCarthy ND, Strachan NJ, Ogden ID, Forbes KJ, Dallas JF, Maiden MC. 2011a. Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species. Mol Ecol 20: 3484-3490.
59. Sheppard SK, McCarthyND, Jolley KA, Maiden MC. 2011b. Introgression in the genus Campylobacter: Generation and spread of mosaic alleles. Microbiology 157: 1066-1074.
60. Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, Bentley SD, Maiden MC, Parkhill J, Falush D. 2013a. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc Natl Acad Sci 110: 11923-11927.
61. Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJ, et al. 2013b. Progressive genome-wide introgression in agricultural Campylobacter coli. Mol Ecol 22: 1051-1064.
62. Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK, Marttinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR, et al. 2014. Cryptic ecology among host generalist Campylobacter jejuni in domestic animals. Mol Ecol 23: 2442-2451.
63. Sproston EL, Ogden ID, MacRae M, Dallas JF, Sheppard SK, Cody AJ, Colles FM, Wilson MJ, Forbes KJ, Strachan NJ. 2011. Temporal variation and host association in the Campylobacter population in a longitudinal ruminant farm study. Appl Environ Microbiol 77: 6579-6586.
64. Thakur S, Zhao S, McDermott PF, Harbottle H, Abbott J, English L, GebreyesWA, White DG. 2010. Antimicrobial resistance, virulence, and genotypic profile comparison of Campylobacter jejuni and Campylobacter coli isolated from humans and retail meats. Foodborne Pathog Dis 7: 835-844.
65. van Tonder AJ, Mistry S, Bray JE, Hill DM, Cody AJ, Farmer CL, Klugman KP, von Gottberg A, Bentley SD, Parkhill J, et al. 2014. Defining the estimated core genome of bacterial populations using a Bayesian decision model. PLoS Comput Biol 10: e1003788.
66. Wilson DJ, Gabriel E, LeatherbarrowAJ, Cheesbrough J, Gee S, Bolton E, Fox A, Hart CA, Diggle PJ, Fearnhead P. 2009. Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni. Mol Biol Evol 26: 385-397.
67. Wimalarathna HML, Sheppard SK. 2012. Ecological factors that influence genetic structure in Campylobacter coli and Campylobacter jejuni. In Current topics in phylogenetics and phylogeography of terrestrial and aquatic systems (ed. Anamthawat-Jonsson K), pp. 1-12. InTech, Rijeka, Croatia.
68. Wimalarathna HM, Richardson JF, Lawson AJ, Elson R, Meldrum R, Little CL, Maiden MC, McCarthyND, Sheppard SK. 2013. Widespread acquisition of antimicrobial resistance among Campylobacter isolates from UK retail poultry and evidence for clonal expansion of resistant lineages. BMC Microbiol 13: 160.
69. Zvelebil M, Dolukhanov P. 1991. The transition to farming in Eastern and Northern Europe. JWorld Prehist 5: 233-278.