A reference pan-genome approach to comparative bacterial genomics: Identification of novel epidemiological markers in pathogenic Campylobacter

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Méric, Guillaume ^a   Yahara, Koji ^a,b,d   Mageiros, Leonardos ^a   Pascoe, Ben ^a   Maiden, Martin C J ^c   Jolley, Keith A ^c   Sheppard, Samuel K ^a  

^a SWANSEA UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF TOKYO   (Japan)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d KURUME UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; CAMPYLOBACTER; CAMPYLOBACTER COLI; CAMPYLOBACTER JEJUNI; GENE SEGREGATION; GENETIC VARIABILITY; GENOME SIZE; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; CAMPYLOBACTER INFECTIONS; CLASSIFICATION; GENETIC VARIATION; GENETICS; MICROBIOLOGY; PHYLOGENY; PREVALENCE; PROCEDURES;

CAMPYLOBACTER; CAMPYLOBACTER COLI; CAMPYLOBACTER INFECTIONS; CAMPYLOBACTER JEJUNI; GENETIC VARIATION; GENOME, BACTERIAL; GENOMICS; PHYLOGENY; PREVALENCE;

EID: 84899798143     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0092798     Document Type: Article

References (43)

1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252: 1651-1656. (Pubitemid 21917081)
2. Olsvik O, Wahlberg J, Petterson B, Uhlen M, Popovic T, et al. (1993) Use of automated sequencing of polymerase chain reaction-generated amplicons to identify three types of cholera toxin subunit B in Vibrio cholerae O1 strains. J Clin Microbiol 31: 22-25. (Pubitemid 23006572)
3. Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, et al. (2010) Evolution of MRSA during hospital transmission and intercontinental spread. Science 327: 469-474.
4. Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES, et al. (2013) Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. MBio 4.
5. Rohde H, Qin J, Cui Y, Li D, Loman NJ, et al. (2011) Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 365: 718-724.
6. Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, et al. (2013) Progressive genome-wide introgression in agricultural Campylobacter coli. Mol Ecol 22: 1051-1064.
7. Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, et al. (2013) Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc Natl Acad Sci U S A 110: 11923-11927.
8. Young BC, Golubchik T, Batty EM, Fung R, Larner-Svensson H, et al. (2012) Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci U S A 109: 4550-4555.
9. Hall N (2007) Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 210: 1518-1525.
10. Gutacker MM, Mathema B, Soini H, Shashkina E, Kreiswirth BN, et al. (2006) Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites. Journal of Infectious Diseases 193: 121-128. (Pubitemid 43032507)
11. Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, et al. (2010) Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 42: 1140-1143.
12. Zhang W, Qi W, Albert TJ, Motiwala AS, Alland D, et al. (2006) Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms. Genome Research 16: 757-767. (Pubitemid 43830696)
13. Sheppard SK, Jolley KA, Maiden MCJ (2012) A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter. Genes 3: 261-277.
14. Jolley KA, Maiden MC (2010) BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11: 595.
15. Maiden MC, van Rensburg MJ, Bray JE, Earle SG, Ford SA, et al. (2013) MLST revisited: the gene-by-gene approach to bacterial genomics. Nature Reviews Microbiology 11: 728-736.
16. 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.
17. Sheppard SK, Dallas JF, Strachan NJ, MacRae M, McCarthy ND, et al. (2009) Campylobacter genotyping to determine the source of human infection. Clinical Infectious Diseases 48: 1072-1078.
18. Kessel AS, Gillespie IA, O'Brien SJ, Adak GK, Humphrey TJ, et al. (2001) General outbreaks of infectious intestinal disease linked with poultry, England and Wales, 1992-1999. Commun Dis Public Health 4: 171-177.
19. Humphrey T, O'Brien S, Madsen M (2007) Campylobacters as zoonotic pathogens: a food production perspective. Int J Food Microbiol 117: 237-257. (Pubitemid 46978410)
20. Sheppard SK, Colles FM, McCarthy ND, Strachan NJ, Ogden ID, et al. (2011) Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species. Mol Ecol 20: 3484-3490.
21. Sheppard SK, McCarthy ND, Falush D, Maiden MC (2008) Convergence of Campylobacter species: implications for bacterial evolution. Science 320: 237-239. (Pubitemid 351521420)
22. Sheppard SK, McCarthy ND, Jolley KA, Maiden MC (2011) Introgression in the genus Campylobacter: generation and spread of mosaic alleles. Microbiology 157: 1066-1074.
23. Griekspoor P, Colles FM,McCarthy ND, Hansbro PM, Ashhurst-Smith C, et al. (2013) Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds. Mol Ecol 22: 1463-1472.
24. Gripp E, Hlahla D, Didelot X, Kops F, Maurischat S, et al. (2011) Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle. Bmc Genomics 12: 584.
25. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
26. Gundogdu O, Bentley SD, Holden MT, Parkhill J, Dorrell N, et al. (2007) Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. Bmc Genomics 8: 162.
27. Hofreuter D, Tsai J, Watson RO, Novik V, Altman B, et al. (2006) Unique features of a highly pathogenic Campylobacter jejuni strain. Infection and Immunity 74: 4694-4707. (Pubitemid 44157257)
28. Pearson BM, Gaskin DJ, Segers RP, Wells JM, Nuijten PJ, et al. (2007) The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). Journal of Bacteriology 189: 8402-8403. (Pubitemid 350178958)
29. Friis C, Wassenaar TM, Javed MA, Snipen L, Lagesen K, et al. (2010) Genomic characterization of Campylobacter jejuni strain M1. PLoS One 5: e12253.
30. Chen Y, Mukherjee S, Hoffmann M, Kotewicz ML, Young S, et al. (2013) Whole-genome sequencing of gentamicin-resistant Campylobacter coli isolated from U.S. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes. Antimicrob Agents Chemother 57: 5398-5405.
31. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
32. Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.
33. Snipen L, Almoy T, Ussery DW (2009) Microbial comparative pan-genomics using binomial mixture models. Bmc Genomics 10: 385.
34. Biggs PJ, Fearnhead P, Hotter G, Mohan V, Collins-Emerson J, et al. (2011) Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PLoS One 6: e27121.
35. Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, et al. (2008) The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of Bacteriology 190: 6881-6893.
36. Stahl M, Friis LM, Nothaft H, Liu X, Li J, et al. (2011) L-fucose utilization provides Campylobacter jejuni with a competitive advantage. Proc Natl Acad Sci U S A 108: 7194-7199.
37. Sheppard SK, Dallas JF, Wilson DJ, Strachan NJ, McCarthy ND, et al. (2010) Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland. PLoS One 5: e15708.
38. Fraser C, Hanage WP, Spratt BG (2007) Recombination and the nature of bacterial speciation. Science 315: 476-480. (Pubitemid 46175745)
39. Sheppard SK, Colles F, Richardson J, Cody AJ, Elson R, et al. (2010) Host association of Campylobacter genotypes transcends geographic variation. Appl Environ Microbiol 76: 5269-5277.
40. Duncan SH, Holtrop G, Lobley GE, Calder AG, Stewart CS, et al. (2004) Contribution of acetate to butyrate formation by human faecal bacteria. Br J Nutr 91: 915-923. (Pubitemid 38931455)
41. Upton AM, McKinney JD (2007) Role of the methylcitrate cycle in propionate metabolism and detoxification in Mycobacterium smegmatis. Microbiology 153: 3973-3982.
42. Munoz-Elias EJ, Upton AM, Cherian J, McKinney JD (2006) Role of the methylcitrate cycle in Mycobacterium tuberculosis metabolism, intracellular growth, and virulence. Mol Microbiol 60: 1109-1122.
43. de Haan CP, Llarena AK, Revez J, Hanninen ML (2012) Association of Campylobacter jejuni metabolic traits with multilocus sequence types. Appl Environ Microbiol 78: 5550-5554.