Current methods for molecular typing of campylobacter species

Journal of Microbiological Methods

Volumn 95, Issue 1, 2013, Pages 24-31

  Taboada, Eduardo N ^a   Clark, Clifford G ^b   Sproston, Emma L ^c   Carrillo, Catherine D ^d  

^a PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^b PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^c HEALTH CANADA   (Canada)

^d CANADIAN FOOD INSPECTION AGENCY   (Canada)

Author keywords

Campylobacter; Comparative genomic fingerprinting; FlaA short variable region sequence typing; Molecular typing; Multi locus sequence typing; Whole genome sequencing

Indexed keywords

ARTICLE; CAMPYLOBACTER; CAMPYLOBACTER COLI; CAMPYLOBACTER JEJUNI; CAMPYLOBACTERIOSIS; CLUSTER ANALYSIS; DISEASE SURVEILLANCE; EPIDEMIC; GEOGRAPHIC DISTRIBUTION; HUMAN; MICROARRAY COMPARATIVE GENOMIC HYBRIDIZATION; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING; MULTILOCUS SEQUENCE TYPING; NEXT GENERATION SEQUENCING; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; SEQUENCE ANALYSIS; SINGLE LOCUS SEQUENCE TYPING; WHOLE GENOME SEQUENCING;

ANIMALIA; BACTERIA (MICROORGANISMS); CAMPYLOBACTER;

CAMPYLOBACTER; CGF; COMPARATIVE GENOMIC FINGERPRINTING; EMLST; EXTENDED MLST; FLAA RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS; FLAA SHORT VARIABLE REGION SEQUENCE TYPING; FLAA-RFLP; FLAA-SVR; HIGH-RESOLUTION MELTING ANALYSIS; HRM; MCGH; MICROARRAY COMPARATIVE GENOMIC HYBRIDIZATION; MLST; MOLECULAR TYPING; MULTI-LOCUS SEQUENCE TYPING; NEXT-GENERATION SEQUENCING; NGS; PFGE; PULSED FIELD GEL ELECTROPHORESIS; RANDOM AMPLIFICATION OF POLYMORPHIC DNA; RAPD; SINGLE NUCLEOTIDE POLYMORPHISMS; SNPS; WGS; WHOLE GENOME SEQUENCING;

ANIMALS; CAMPYLOBACTER; FOOD MICROBIOLOGY; HUMANS; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING;

EID: 84884143311     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2013.07.007     Document Type: Article

References (127)

1. Aeschbacher M., Piffaretti J.C. Population genetics of human and animal enteric Campylobacter strains. Infect. Immun. 1989, 57:1432-1437.
2. Ahmed M.U., Dunn L., Ivanova E.P. Evaluation of current molecular approaches for genotyping of Campylobacter jejuni strains. Foodborne Pathog. Dis. 2012, 9:375-385.
3. Barrett T.J., Lior H., Green J.H., Khakhria R., Wells J.G., Bell B.P., Greene K.D., Lewis J., Griffin P.M. Laboratory investigation of a multistate food-borne outbreak of Escherichia coli O157:H7 by using pulsed-field gel electrophoresis and phage typing. J. Clin. Microbiol. 1994, 32:3013-3017.
4. Barton C., Ng L.K., Tyler S.D., Clark C.G. Temperate bacteriophages affect pulsed-field gel electrophoresis patterns of Campylobacter jejuni. J. Clin. Microbiol. 2007, 45:386-391.
5. Batz M.B., Hoffmann S., Morris J.G. Ranking the disease burden of 14 pathogens in food sources in the United States using attribution data from outbreak investigations and expert elicitation. J. Food Prot. 2012, 75:1278-1291.
6. Bessell P.R., Rotariu O., Innocent G.T., Smith-Palmer A., Strachan N.J., Forbes K.J., Cowden J.M., Reid S.W., Matthews L. Using sequence data to identify alternative routes and risk of infection: a case-study of Campylobacter in Scotland. BMC Infect. Dis. 2012, 1(12):80.
7. Best E.L., Fox A.J., Frost J.A., Bolton F.J. Real-time single-nucleotide polymorphism profiling using Taqman technology for rapid recognition of Campylobacter jejuni clonal complexes. J. Med. Microbiol. 2005, 54:919-925.
8. Biggs P.J., Fearnhead P., Hotter G., Mohan V., Collins-Emerson J., Kwan E., Besser T.E., Cookson A., Carter P.E., French N.P. Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PLoS One 2011, 6:e27121.
9. Boxrud D., Monson T., Stiles T., Besser J. The role, challenges, and support of pulsenet laboratories in detecting foodborne disease outbreaks. Public Health Rep. 2010, 125(Suppl. 2):57-62.
10. Carrillo C.D., Kruczkiewicz P., Mutschall S., Tudor A., Clark C., Taboada E.N. A framework for assessing the concordance of molecular typing methods and the true strain phylogeny of Campylobacter jejuni and C. coli using draft genome sequence data. Front. Cell. Infect. Microbiol. 2012, 2.
11. Champion O.L., Best E.L., Frost J.A. Comparison of pulsed-field gel electrophoresis and amplified fragment length polymorphism techniques for investigating outbreaks of enteritis due to campylobacters. J. Clin. Microbiol. 2002, 40:2263-2265.
12. Champion O.L., Gaunt M.W., Gundogdu O., Elmi A., Witney A.A., Hinds J., Dorrell N., Wren B.W. Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:16043-16048.
13. Clark C.G., Bryden L., Cuff W.R., Johnson P.L., Jamieson F., Ciebin B., Wang G. Use of the Oxford multilocus sequence typing protocol and sequencing of the flagellin short variable region to characterize isolates from a large outbreak of waterborne Campylobacter sp. strains in Walkerton, Ontario, Canada. J. Clin. Microbiol. 2005, 43:2080-2091.
14. Clark C., Taboada E., Grant C., Blakeston C., Pollari F., Marshall B., Rahn K., Mackinnon J., Daignault D., Pillai D., Ng L.-K. Comparison of molecular typing methods useful for detecting clusters of Campylobacter jejuni and C. coli isolates through routine surveillance. J. Clin. Microbiol. 2012, 50:788-797.
15. Cody A.J., McCarthy N.M., Wimalarathna H.L., Colles F.M., Clark L., Bowler I.C., Maiden M.C., Dingle K.E. A longitudinal 6-year study of the molecular epidemiology of clinical Campylobacter isolates in Oxfordshire, United Kingdom. J. Clin. Microbiol. 2012, 50:3193-3201.
16. Colles F.M., Maiden M.C. Campylobacter sequence typing databases: applications and future prospects. Microbiology 2012, 158:2695-2709.
17. Cooper K.K., Cooper M.A., Zuccolo A., Law B., Joens L.A. Complete genome sequence of Campylobacter jejuni strain S3. J. Bacteriol. 2011, 193:1491-1492.
18. Corcoran D., Quinn T., Cotter L., Whyte P., Fanning S. Antimicrobial resistance profiling and fla-typing of Irish thermophillic Campylobacter spp. of human and poultry origin. Lett. Appl. Microbiol. 2006, 43:560-565.
19. Cornelius A.J., Gilpin B., Carter P., Nicol C., On S.L. Comparison of PCR binary typing (P-BIT), a new approach to epidemiological subtyping of Campylobacter jejuni, with serotyping, pulsed-field gel electrophoresis, and multilocus sequence typing methods. Appl. Environ. Microbiol. 2010, 76:1533-1544.
20. Dingle K.E., Colles F.M., Wareing D.R., Ure R., Fox A.J., Bolton F.E., Bootsma H.J., Willems R.J., Urwin R., Maiden M.C. Multilocus sequence typing system for Campylobacter jejuni. J. Clin. Microbiol. 2001, 39:14-23.
21. Dingle K.E., Colles F.M., Ure R., Wagenaar J.A., Duim B., Bolton F.J., Fox A.J., Wareing D.R., Maiden M.C. Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation. Emerg. Infect. Dis. 2002, 8:949-955.
22. Dingle K.E., Colles F.M., Falush D., Maiden M.C. Sequence typing and comparison of population biology of Campylobacter coli and Campylobacter jejuni. J. Clin. Microbiol. 2005, 43:340-347.
23. Dingle K.E., McCarthy N.D., Cody A.J., Peto T.E., Maiden M.C. Extended sequence typing of Campylobacter spp., United Kingdom. Emerg. Infect. Dis. 2008, 14:1620-1622.
24. Djordjevic S.P., Unicomb L.E., Adamson P.J., Mickan L., Rios R. Clonal complexes of Campylobacter jejuni identified by multilocus sequence typing are reliably predicted by restriction fragment length polymorphism analyses of the flaA gene. J. Clin. Microbiol. 2007, 45:102-108.
25. Dorrell N., Mangan J.A., Laing K.G., Hinds J., Linton D., Al-Ghusein H., Barrell B.G., Parkhill J., Stoker N.G., Karlyshev A.V., Butcher P.D., Wren B.W. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res. 2001, 11:1706-1715.
26. Eberle K.N., Kiess A.S. Phenotypic and genotypic methods for typing Campylobacter jejuni and Campylobacter coli in poultry. Poult. Sci. 2012, 91:255-264.
27. ECDC European centre for disease prevention and control (ECDC). Reporting on 2010 Surveillance Data and 2011 Epidemic Intelligence Data 2013, (Stockholm). ECDC (Ed.).
28. Foley S.L., Lynne A.M., Nayak R. Molecular typing methodologies for microbial source tracking and epidemiological investigations of Gram-negative bacterial foodborne pathogens. Infect. Genet. Evol. 2009, 9:430-440.
29. French N., Barrigas M., Brown P., Ribiero P., Williams N., Leatherbarrow H., Birtles R., Bolton E., Fearnhead P., Fox A. Spatial epidemiology and natural population structure of Campylobacter jejuni colonizing a farmland ecosystem. Environ. Microbiol. 2005, 7:1116-1126.
30. Friesema I.H., Havelaar A.H., Westra P.P., Wagenaar J.A., van Pelt W. Poultry culling and campylobacteriosis reduction among humans, the Netherlands. Emerg. Infect. Dis. 2012, 18:466-468.
31. Friis C., Wassenaar T.M., Javed M.A., Snipen L., Lagesen K., Hallin P.F., Newell D.G., Toszeghy M., Ridley A., Manning G., Ussery D.W. Genomic characterization of Campylobacter jejuni strain M1. PLoS One 2010, 5:e12253.
32. Frost J.A. Current epidemiological issues in human campylobacteriosis. Symposium Series 2001, 85S-95S.
33. Fussing V., Moller Nielsen E., Neimann J., Engberg J. Systematic serotyping and riboprinting of Campylobacter spp. improves surveillance: experiences from two Danish counties. Clin. Microbiol. Infect. 2007, 13:635-642.
34. Gardy J.L., Johnston J.C., Ho Sui S.J., Cook V.J., Shah L., Brodkin E., Rempel S., Moore R., Zhao Y., Holt R., Varhol R., Birol I., Lem M., Sharma M.K., Elwood K., Jones S.J., Brinkman F.S., Brunham R.C., Tang P. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N. Engl. J. Med. 2011, 364:730-739.
35. Gilmour M.W., Graham M., Van Domselaar G., Tyler S., Kent H., Trout-Yakel K.M., Larios O., Allen V., Lee B., Nadon C. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 2010, 11:120.
36. Gilpin B., Cornelius A., Robson B., Boxall N., Ferguson A., Nicol C., Henderson T. Application of pulsed-field gel electrophoresis to identify potential outbreaks of campylobacteriosis in New Zealand. J. Clin. Microbiol. 2006, 44:406-412.
37. Gilpin B., Robson B., Lin S., Scholes P., On S. Pulsed-field gel electrophoresis analysis of more than one clinical isolate of Campylobacter spp. from each of 49 patients in New Zealand. J. Clin. Microbiol. 2012, 50:457-459.
38. Gras M.L., Smid J.H., Wagenaar J.A., de Boer A.G., Havelaar A.H., Friesema I.H., French N.P., Busani L., van Pelt W. Risk factors for campylobacteriosis of chicken, ruminant, and environmental origin: a combined case-control and source attribution analysis. PLoS One 2012, 7:e42599.
39. Greig J.D., Ravel A. Analysis of foodborne outbreak data reported internationally for source attribution. Int. J. Food Microbiol. 2009, 130:77-87.
40. Gripp E., Hlahla D., Didelot X., Kops F., Maurischat S., Tedin K., Alter T., Ellerbroek L., Schreiber K., Schomburg D., Janssen T., Bartholomaus P., Hofreuter D., Woltemate S., Uhr M., Brenneke B., Gruning P., Gerlach G., Wieler L., Suerbaum S., Josenhans C. Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle. BMC Genomics 2011, 12:584.
41. Hanninen M.L., Hakkinen M., Rautelin H. Stability of related human and chicken Campylobacter jejuni genotypes after passage through chick intestine studied by pulsed-field gel electrophoresis. Appl. Environ. Microbiol. 1999, 65:2272-2275.
42. Hannon S.J., Taboada E.N., Russell M.L., Allan B., Waldner C., Wilson H.L., Potter A., Babiuk L., Townsend H.G. Genomics-based molecular epidemiology of Campylobacter jejuni isolates from feedlot cattle and from people in Alberta, Canada. J. Clin. Microbiol. 2009, 47:410-420.
43. Hedberg C.W., Smith K.E., Besser J.M., Boxrud D.J., Hennessy T.W., Bender J.B., Anderson F.A., Osterholm M.T. Limitations of pulsed-field gel electrophoresis for the routine surveillance of Campylobacter infections. J. Infect. Dis. 2001, 184:242-244.
44. Hedberg C.W., Greenblatt J.F., Matyas B.T., Lemmings J., Sharp D.J., Skibicki R.T., Liang A.P. Timeliness of enteric disease surveillance in 6 US states. Emerg. Infect. Dis. 2008, 14:311-313.
45. Hepworth P.J., Ashelford K.E., Hinds J., Gould K.A., Witney A.A., Williams N.J., Leatherbarrow H., French N.P., Birtles R.J., Mendonca C., Dorrell N., Wren B.W., Wigley P., Hall N., Winstanley C. Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes. Environ. Microbiol. 2011, 13:1549-1560.
46. Hofreuter D., Tsai J., Watson R.O., Novik V., Altman B., Benitez M., Clark C., Perbost C., Jarvie T., Du L., Galan J.E. Unique features of a highly pathogenic Campylobacter jejuni strain. Infect. Immun. 2006, 74:4694-4707.
47. Hotter G.S., Li I.H., French N.P. Binary genomotyping using lipooligosaccharide biosynthesis genes distinguishes between Campylobacter jejuni isolates within poultry-associated multilocus sequence types. Epidemiol. Infect. 2010, 138:992-1003.
48. Jerome J.P., Klahn B.D., Bell J.A., Barrick J.E., Brown C.T., Mansfield L.S. Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600. J. Bacteriol. 2012, 194:5707-5708.
49. Jolley K.A., Chan M.S., Maiden M.C. mlstdbNet-distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 2004, 5:86.
50. Jolley K.A., Maiden M.C. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010, 11:595.
51. Kirkpatrick B.D., Tribble D.R. Update on human Campylobacter jejuni infections. Curr. Opin. Gastroenterol. 2011, 27:1-7.
52. Korczak B.M., Zurfluh M., Emler S., Kuhn-Oertli J., Kuhnert P. Multiplex strategy for multilocus sequence typing, fla typing, and genetic determination of antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolates collected in Switzerland. J. Clin. Microbiol. 2009, 47:1996-2007.
53. Kruczkiewicz P., Mutschall S., Barker D., Thomas J., Carrillo C.D., Van Domselaar G., Gannon V.P., Taboada E.N. MIST: a tool for rapid in silico generation of molecular typing data from bacterial genome sequences. Bioinformatics 2013, Barcelona, Spain 2013.
54. Larsen M.V., Cosentino S., Rasmussen S., Friis C., Hasman H., Marvig R.L., Jelsbak L., Sicheritz-Pontén T., Ussery D.W., Aarestrup F.M., Lund O. Multilocus sequence typing of total-genome-sequenced bacteria. J. Clin. Microbiol. 2012, 50:1355-1361.
55. Laing C.R., Zhang Y., Thomas J.E., Gannon V.P. Everything at once: comparative analysis of the genomes of bacterial pathogens. Vet. Microbiol. 2011, 153:13-26.
56. Lefébure T., Bitar P.D., Suzuki H., Stanhope M.J. Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol. Evol. 2010, 2:646-655.
57. Leonard E.E., Takata T., Blaser M.J., Falkow S., Tompkins L.S., Gaynor E.C. Use of an open-reading frame-specific Campylobacter jejuni DNA microarray as a new genotyping tool for studying epidemiologically related isolates. J. Infect. Dis. 2003, 187:691-694.
58. Lévesque S., Michaud S., Arbeit R.D., Frost E.H. High-resolution melting system to perform multilocus sequence typing of Campylobacter jejuni. PLoS One 2011, 6:e16167.
59. Lucchini S., Thompson A., Hinton J.C. Microarrays for microbiologists. Microbiology 2001, 147:1403-1414.
60. Manning G., Dowson C.G., Bagnall M.C., Ahmed I.H., West M., Newell D.G. Multilocus sequence typing for comparison of veterinary and human isolates of Campylobacter jejuni. Appl. Environ. Microbiol. 2003, 69:6370-6379.
61. Marotta F., Zilli K., Tonelli A., Sacchini L., Alessiani A., Migliorati G., Di Giannatale E. Detection and genotyping of Campylobacter jejuni and Campylobacter coli by use of DNA oligonucleotide arrays. Mol. Biotechnol. 2013, 53:182-188.
62. McCarthy N.D., Colles F.M., Dingle K.E., Bagnall M.C., Manning G., Maiden M.C.J., Falush D. Host-associated genetic import in Campylobacter jejuni. Emerg. Infect. Dis. 2007, 13:267-272.
63. Meinersmann R.J., Helsel L.O., Fields P.I., Hiett K.L. Discrimination of Campylobacter jejuni isolates by fla gene sequencing. J. Clin. Microbiol. 1997, 35:2810-2814.
64. Melero B., Juntunen P., Hanninen M.L., Jaime I., Rovira J. Tracing Campylobacter jejuni strains along the poultry meat production chain from farm to retail by pulsed-field gel electrophoresis, and the antimicrobial resistance of isolates. Food Microbiol. 2012, 32:124-128.
65. Merchant-Patel S., Blackall P.J., Templeton J., Price E.P., Tong S.Y., Huygens F., Giffard P.M. Campylobacter jejuni and Campylobacter coli genotyping by high-resolution melting analysis of a flaA fragment. Appl. Environ. Microbiol. 2010, 76:493-499.
66. Michaud S., Menard S., Arbeit R.D. Role of real-time molecular typing in the surveillance of Campylobacter enteritis and comparison of pulsed-field gel electrophoresis profiles from chicken and human isolates. J. Clin. Microbiol. 2005, 43:1105-1111.
67. Miller G., Dunn G.M., Smith-Palmer A., Ogden I.D., Strachan N.J. Human campylobacteriosis in Scotland: seasonality, regional trends and bursts of infection. Epidemiol. Infect. 2004, 132:585-593.
68. Miller R.S., Miller W.G., Behringer M., Hariharan H., Matthew V., Oyarzabal O.A. DNA identification and characterization of Campylobacter jejuni and Campylobacter coli isolated from caecal samples of chickens in Grenada. J. Appl. Microbiol. 2010, 108:1041-1049.
69. Miller W.G., Chapman M.H., Yee E., On S.L., McNulty D.K., Lastovica A.J., Carroll A.M., McNamara E.B., Duffy G., Mandrell R.E. Multilocus sequence typing methods for the emerging Campylobacter species C. hyointestinalis, C. lanienae, C. sputorum, C. concisus, and C. curvus. Front. Cell. Infect. Microbiol. 2012, 2:45.
70. Muellner P., Marshall J.C., Spencer S.E., Noble A.D., Shadbolt T., Collins-Emerson J.M., Midwinter A.C., Carter P.E., Pirie R., Wilson D.J., Campbell D.M., Stevenson M.A., French N.P. Utilizing a combination of molecular and spatial tools to assess the effect of a public health intervention. Prev. Vet. Med. 2011, 102:242-253.
71. Muellner P., Pleydell E., Pirie R., Baker M.G., Campbell D., Carter P.E., French N.P. Molecular-based surveillance of campylobacteriosis in New Zealand-from source attribution to genomic epidemiology. Euro Surveill. 2013, 18.
72. Müllner P., Spencer S.E.F., Wilson D.J., Jones G., Noble A.D., Midwinter A.C., Collins-Emerson J.M., Carter P., Hathaway S., French N.P. Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach. Infect. Genet. Evol. 2009, 9:1311-1319.
73. Müllner P., Collins-Emerson J.M., Midwinter A.C., Carter P., Spencer S.E., van der Logt P., Hathaway S., French N.P. Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry. Appl. Environ. Microbiol. 2010, 76:2145-2154.
74. Müllner P., Shadbolt T., Collins-Emerson J.M., Midwinter A.C., Spencer S.E., Marshall J., Carter P.E., Campbell D.M., Wilson D.J., Hathaway S., Pirie R., French N.P. Molecular and spatial epidemiology of human campylobacteriosis: source association and genotype-related risk factors. Epidemiol. Infect. 2010, 138:1372-1383.
75. Nachamkin I., Bohachick K., Patton C.M. Flagellin gene typing of Campylobacter jejuni by restriction fragment length polymorphism analysis. J. Clin. Microbiol. 1993, 31:1531-1536.
76. Nadeau E., Messier S., Quessy S. Prevalence and comparison of genetic profiles of Campylobacter strains isolated from poultry and sporadic cases of campylobacteriosis in humans. J. Food Prot. 2002, 65:73-78.
77. Nielsen L.N., Sheppard S.K., McCarthy N.D., Maiden M.C., Ingmer H., Krogfelt K.A. MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barré syndrome. J. Appl. Microbiol. 2010, 108:591-599.
78. Oyarzabal O.A., Williams A., Zhou P., Samadpour M. Improved protocol for isolation of Campylobacter spp. from retail broiler meat and use of pulsed field gel electrophoresis for the typing of isolates. J. Microbiol. Methods 2013, (in press). http://www.sciencedirect.com/science/article/pii/S0167701213001024.
79. Parker C.T., Quinones B., Miller W.G., Horn S.T., Mandrell R.E. Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221. J. Clin. Microbiol. 2006, 44:4125-4135.
80. Pearson B.M., Pin C., Wright J., I'Anson K., Humphrey T., Wells J.M. Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. FEBS Lett. 2003, 554:224-230.
81. Pearson B.M., Gaskin D.J., Segers R.P., Wells J.M., Nuijten P.J., van Vliet A.H. The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). J. Bacteriol. 2007, 189:8402-8403.
82. Pebody R.G., Ryan M.J., Wall P.G. Outbreaks of Campylobacter infection: rare events for a common pathogen. Commun. Dis. Rep. CDR Rev. 1997, 7:R33-R37.
83. Pendleton S., Hanning I., Biswas D., Ricke S.C. Evaluation of whole-genome sequencing as a genotyping tool for Campylobacter jejuni in comparison with pulsed-field gel electrophoresis and flaA typing. Poult. Sci. 2013, 92:573-580.
84. Penner J.L., Hennessy J.N. Passive hemagglutination technique for serotyping Campylobacter fetus subsp. jejuni on the basis of soluble heat-stable antigens. J. Clin. Microbiol. 1980, 12:732-737.
85. Pittenger L.G., Englen M.D., Parker C.T., Frye J.G., Quinones B., Horn S.T., Son I., Fedorka-Cray P.J., Harrison M.A. Genotyping Campylobacter jejuni by comparative genome indexing: an evaluation with pulsed-field gel electrophoresis and flaA SVR sequencing. Foodborne Pathog. Dis. 2009, 6:337-349.
86. Poly F., Threadgill D., Stintzi A. Identification of Campylobacter jejuni ATCC 43431-specific genes by whole microbial genome comparisons. J. Bacteriol. 2004, 186:4781-4795.
87. Poly F., Read T., Tribble D.R., Baqar S., Lorenzo M., Guerry P. Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand. Infect. Immun. 2007, 75:3425-3433.
88. Price E.P., Huygens F., Giffard P.M. Fingerprinting of Campylobacter jejuni using resolution-optimized binary gene targets derived from comparative genome hybridization studies. Appl. Environ. Microbiol. 2006, 72:7793-7803.
89. Rasko D.A., Webster D.R., Sahl J.W., Bashir A., Boisen N., Scheutz F., Paxinos E.E., Sebra R., Chin C.S., Iliopoulos D., Klammer A., Peluso P., Lee L., Kislyuk A.O., Bullard J., Kasarskis A., Wang S., Eid J., Rank D., Redman J.C., Steyert S.R., Frimodt-Moller J., Struve C., Petersen A.M., Krogfelt K.A., Nataro J.P., Schadt E.E., Waldor M.K. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N. Engl. J. Med. 2011, 365:709-717.
90. Ravel A., Greig J., Tinga C., Todd E., Campbell G., Cassidy M., Marshall B., Pollari F. Exploring historical Canadian foodborne outbreak data sets for human illness attribution. J. Food Prot. 2009, 72:1963-1976.
91. Reimer A.R., Van Domselaar G., Stroika S., Walker M., Kent H., Tarr C., Talkington D., Rowe L., Olsen-Rasmussen M., Frace M., Sammons S., Dahourou G.A., Boncy J., Smith A.M., Mabon P., Petkau A., Graham M., Gilmour M.W., Gerner-Smidt P., Force V.c.O.G.T. Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa. Emerg. Infect. Dis. 2011, 17:2113-2121.
92. Ribot E.M., Fitzgerald C., Kubota K., Swaminathan B., Barrett T.J. Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni. J. Clin. Microbiol. 2001, 39:1889-1894.
93. Rodin S., Andersson A.F., Wirta V., Eriksson L., Ljungstrom M., Bjorkholm B., Lindmark H., Engstrand L. Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni. BMC Microbiol. 2008, 8:73.
94. Sahin O., Fitzgerald C., Stroika S., Zhao S., Sippy R.J., Kwan P., Plummer P.J., Han J., Yaeger M.J., Zhang Q. Molecular evidence for zoonotic transmission of an emergent, highly pathogenic Campylobacter jejuni clone in the United States. J. Clin. Microbiol. 2012, 50:680-687.
95. Sails A.D., Bala S., Fields P.I. Utility of multilocus sequence typing as an epidemiological tool for investigation of outbreaks of gastroenteritis caused by Campylobacter jejuni. J. Clin. Microbiol. 2003, 41:4733-4739.
96. Schouls L.M., Reulen S., Duim B., Wagenaar J.A., Willems R.J., Dingle K.E., Colles F.M., Van Embden J.D. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J. Clin. Microbiol. 2003, 41:15-26.
97. Schwartz D.C., Cantor C.R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 1984, 37:67-75.
98. Sears A., Baker M.G., Wilson N., Marshall J., Muellner P., Campbell D.M., Lake R.J., French N.P. Marked campylobacteriosis decline after interventions aimed at poultry, New Zealand. Emerg. Infect. Dis. 2011, 17:1007-1015.
99. Sheppard S.K., McCarthy N.D., Falush D., Maiden M.C. Convergence of Campylobacter species: implications for bacterial evolution. Science 2008, 320:237-239.
100. Sheppard S.K., Dallas J.F., MacRae M., McCarthy N.D., Sproston E.L., Gormley F.J., Strachan N.J., Ogden I.D., Maiden M.C., Forbes K.J. Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6. Int. J. Food Microbiol. 2009, 134:96-103.
101. Sheppard S.K., Dallas J.F., Strachan N.J., MacRae M., McCarthy N.D., Wilson D.J., Gormley F.J., Falush D., Ogden I.D., Maiden M.C., Forbes K.J. Campylobacter genotyping to determine the source of human infection. Clin. Infect. Dis. 2009, 48:1072-1078.
102. Sheppard S.K., Colles F., Richardson J., Cody A.J., Elson R., Lawson A., Brick G., Meldrum R., Little C.L., Owen R.J., Maiden M.C., McCarthy N.D. Host association of Campylobacter genotypes transcends geographic variation. Appl. Environ. Microbiol. 2010, 76:5269-5277.
103. Sheppard S.K., McCarthy N.D., Jolley K.A., Maiden M.C. Introgression in the genus Campylobacter: generation and spread of mosaic alleles. Microbiology 2011, 157:1066-1074.
104. Sheppard S.K., Jolley K.A., Maiden M.C.J. A gene-by-gene approach to bacterial population genomics: whole genome MLST of Campylobacter. Genes 2012, 3:261-277.
105. Sheppard S.K., Didelot X., Jolley K.A., Darling A.E., Pascoe B., Meric G., Kelly D.J., Cody A., Colles F.M., Strachan N.J., Ogden I.D., Forbes K., French N.P., Carter P., Miller W.G., McCarthy N.D., Owen R., Litrup E., Egholm M., Affourtit J.P., Bentley S.D., Parkhill J., Maiden M.C., Falush D. Progressive genome-wide introgression in agricultural Campylobacter coli. Mol. Ecol. 2013, 22:1051-1064.
106. Silva J., Leite D., Fernandes M., Mena C., Gibbs P.A., Teixeira P. Campylobacter spp. as a foodborne pathogen: a review. Front. Microbiol. 2011, 2:200.
107. Smith K.E., Besser J.M., Hedberg C.W., Leano F.T., Bender J.B., Wicklund J.H., Johnson B.P., Moore K.A., Osterholm M.T. Quinolone-resistant Campylobacter jejuni infections in Minnesota, 1992-1998. Investigation Team. N. Engl. J. Med. 1999, 340:1525-1532.
108. Sopwith W., Birtles A., Matthews M., Fox A., Gee S., Painter M., Regan M., Syed Q., Bolton E. Campylobacter jejuni multilocus sequence types in humans, Northwest England, 2003-2004. Emerg. Infect. Dis. 2006, 12:1500-1507.
109. Sopwith W., Birtles A., Matthews M., Fox A., Gee S., James S., Kempster J., Painter M., Edwards-Jones V., Osborn K., Regan M., Syed Q., Bolton E. Investigation of food and environmental exposures relating to the epidemiology of Campylobacter coli in humans in Northwest England. Appl. Environ. Microbiol. 2010, 76:129-135.
110. Sproston E.L., Ogden I.D., MacRae M., Dallas J.F., Sheppard S.K., Cody A.J., Colles F.M., Wilson M.J., Forbes K.J., Strachan N.J. Temporal variation and host association in the Campylobacter population in a longitudinal ruminant farm study. Appl. Environ. Microbiol. 2011, 77:6579-6586.
111. Steinbrueckner B., Ruberg F., Kist M. Bacterial genetic fingerprint: a reliable factor in the study of the epidemiology of human Campylobacter enteritis?. J. Clin. Microbiol. 2001, 39:4155-4159.
112. Strachan N.J., Gormley F.J., Rotariu O., Ogden I.D., Miller G., Dunn G.M., Sheppard S.K., Dallas J.F., Reid T.M., Howie H., Maiden M.C., Forbes K.J. Attribution of Campylobacter infections in northeast Scotland to specific sources by use of multilocus sequence typing. J. Infect. Dis. 2009, 199:1205-1208.
113. Suerbaum S., Lohrengel M., Sonnevend A., Ruberg F., Kist M. Allelic diversity and recombination in Campylobacter jejuni. J. Bacteriol. 2001, 183:2553-2559.
114. Swaminathan B., Barrett T.J., Hunter S.B., Tauxe R.V., Force C.D.C.P.T. PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg. Infect. Dis. 2001, 7:382-389.
115. Taboada E.N., Acedillo R.R., Carrillo C.D., Findlay W.A., Medeiros D.T., Mykytczuk O.L., Roberts M.J., Valencia C.A., Farber J.M., Nash J.H. Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J. Clin. Microbiol. 2004, 42:4566-4576.
116. Taboada E.N., Luebbert C.C., Nash J.H.E. Studying bacterial genome dynamics using microarray-based comparative genomic hybridization. Methods Mol. Biol. 2007, 396:223-253.
117. Taboada E.N., Mackinnon J.M., Luebbert C.C., Gannon V.P., Nash J.H., Rahn K. Comparative genomic assessment of Multi-locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni. BMC Evol. Biol. 2008, 8:229.
118. Taboada E.N., Ross S.L., Mutschall S.K., MacKinnon J.M., Roberts M.J., Buchanan C.J., Kruczkiewicz P., Jokinen C., Thomas J.E., Nash J.H., Gannon V.P., Marshall B., Pollari F., Clark C.G. Development and validation of a Comparative Genomic Fingerprinting method for high-resolution genotyping of Campylobacter jejuni. J. Clin. Microbiol. 2012, 50:798-809.
119. Takamiya M., Ozen A., Rasmussen M., Alter T., Gilbert T., Ussery D.W., Knochel S. Genome sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse. Stand. Genomic Sci. 2011, 4:113-122.
120. Takamiya M., Ozen A., Rasmussen M., Alter T., Gilbert T., Ussery D.W., Knochel S. Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099. J. Bacteriol. 2011, 193:5546-5547.
121. Tauxe R.V. Molecular subtyping and the transformation of public health. Foodborne Pathog. Dis. 2006, 3:4-8.
122. Tauxe R.V., Doyle M.P., Kuchenmuller T., Schlundt J., Stein C.E. Evolving public health approaches to the global challenge of foodborne infections. Int. J. Food Microbiol. 2010, 139(Suppl. 1):S16-S28.
123. Taylor E.V., Herman K.M., Ailes E.C., Fitzgerald C., Yoder J.S., Mahon B.E., Tauxe R.V. Common source outbreaks of Campylobacter infection in the USA, 1997-2008. Epidemiol. Infect. 2013, 141:987-996.
124. van Belkum A., Tassios P.T., Dijkshoorn L., Haeggman S., Cookson B., Fry N.K., Fussing V., Green J., Feil E., Gerner-Smidt P., Brisse S., Struelens M., European Society of Clinical, Infectious Diseases Study Group on Epidemiological Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin. Microbiol. Infect. 2007, 13(Suppl. 3):1-46.
125. Wang Y., Taylor D.E. Natural transformation in Campylobacter species. J. Bacteriol. 1990, 172:949-955.
126. Wassenaar T.M., Geilhausen B., Newell D.G. Evidence of genomic instability in Campylobacter jejuni isolated from poultry. Appl. Environ. Microbiol. 1998, 64:1816-1821.
127. Zhang M., He L., Li Q., Sun H., Gu Y., You Y., Meng F., Zhang J. Genomic characterization of the Guillain-Barre syndrome-associated Campylobacter jejuni ICDCCJ07001 Isolate. PLoS One 2010, 5:e15060.