Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni

BMC Microbiology

Volumn 8, Issue , 2008, Pages

  Rodin, Sandra ^a   Andersson, Anders F ^a,b   Wirta, Valtteri ^a   Eriksson, Lena ^a   Ljungström, Marianne ^a   Björkholm, Britta ^c   Lindmark, Hans ^d   Engstrand, Lars ^a,c  

^a SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

^d NATIONAL FOOD ADMINISTRATION   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAMPYLOBACTER JEJUNI; CHICKEN; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; GENE ISOLATION; GENETIC ANALYSIS; GENETIC DIFFERENCE; GENOTYPE; HUMAN; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PULSED FIELD GEL ELECTROPHORESIS; ANIMAL; ANIMAL DISEASE; BACTERIUM IDENTIFICATION; BIRD DISEASE; CLASSIFICATION; DNA SEQUENCE; EVALUATION; GENETICS; GRAM NEGATIVE INFECTION; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; NUCLEIC ACID HYBRIDIZATION;

BACTERIA (MICROORGANISMS); CAMPYLOBACTER JEJUNI;

BACTERIAL DNA;

ANIMALS; BACTERIAL TYPING TECHNIQUES; CAMPYLOBACTER INFECTIONS; CAMPYLOBACTER JEJUNI; CHICKENS; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENOTYPE; HUMANS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POULTRY DISEASES; SEQUENCE ANALYSIS, DNA;

EID: 44349111143     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-8-73     Document Type: Article

References (42)

1. Campylobacter jejuni - an emerging foodborne pathogen. SF Altekruse NJ Stern PI Fields DL Swerdlow, Emerg Infect Dis 1999 5 1 28 35 10081669
2. Campylobacter species and Guillain-Barre syndrome. I Nachamkin BM Allos T Ho, Clin Microbiol Rev 1998 11 3 555 567 9665983
3. Distribution of Campylobacter spp. in selected U.S. poultry production and processing operations. NJ Stern P Fedorka-Cray JS Bailey NA Cox SE Craven KL Hiett MT Musgrove S Ladely D Cosby GC Mead, J Food Prot 2001 64 11 1705 1710 11726147
4. Risk factors for indigenous campylobacter infection: a Swedish case-control study. A Studahl Y Andersson, Epidemiol Infect 2000 125 2 269 275 10.1017/S0950268899004562 11117949
5. Outbreaks of campylobacter infection: rare events for a common pathogen. RG Pebody MJ Ryan PG Wall, Commun Dis Rep CDR Rev 1997 7 3 R33 37 9080726
6. Genotyping of Campylobacter spp. TM Wassenaar DG Newell, Appl Environ Microbiol 2000 66 1 1 9 10618195
7. Genetic Characterization and Antibiotic Resistance of Campylobacter jejuni Isolated from Meats, Water, and Humans in Sweden. H Lindmark B Harbom L Thebo L Andersson G Hedin B Osterman T Lindberg Y Andersson A Westoo E Olsson Engvall, J Clin Microbiol 2004 42 2 700 706 14766839 10.1128/JCM.42.2.700-706. 2004
8. Evaluation of Methods for Subtyping Campylobacter jejuni during an Outbreak Involving a Food Handler. C Fitzgerald LO Helsel MA Nicholson SJ Olsen DL Swerdlow R Flahart J Sexton PI Fields, J Clin Microbiol 2001 39 7 2386 2390 11427543 10.1128/JCM.39.7.2386-2390.2001
9. Evaluation of Phenotypic and Genotypic Methods for Subtyping Campylobacter jejuni Isolates from Humans, Poultry, and Cattle. EM Nielsen J Engberg V Fussing L Petersen C-H Brogren SLW On, J Clin Microbiol 2000 38 10 3800 3810 11015406
10. Clonal complexes of Campylobacter jejuni identified by multilocus sequence typing correlate with strain associations identified by multilocus enzyme electrophoresis. AD Sails B Swaminathan PI Fields, J Clin Microbiol 2003 41 9 4058 4067 12958226 10.1128/JCM.41.9.4058-4067.2003
11. Australian multicentre comparison of subtyping methods for the investigation of Campylobacter infection. LC O'Reilly TJ Inglis L Unicomb, Epidemiol Infect 2006 134 4 768 779 10.1017/S0950268805005777 16436218
12. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. FC Tenover RD Arbeit RV Goering PA Mickelsen BE Murray DH Persing B Swaminathan, J Clin Microbiol 1995 33 9 2233 2239 7494007
13. Exploration of biases that affect the interpretation of restriction fragment patterns produced by pulsed-field gel electrophoresis. RS Singer WM Sischo TE Carpenter, J Clin Microbiol 2004 42 12 5502 5511 15583273 10.1128/JCM.42.12.5502-5511.2004
14. Multilocus sequence typing system for Campylobacter jejuni. KE Dingle FM Colles DR Wareing R Ure AJ Fox FE Bolton HJ Bootsma RJ Willems R Urwin MC Maiden, J Clin Microbiol 2001 39 1 14 23 11136741 10.1128/JCM.39.1.14-23.2001
15. Campylobacter jejuni and Campylobacter coli MLST Home Page. http://pubmlst.org/campylobacter/
16. Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation. KE Dingle FM Colles R Ure JA Wagenaar B Duim FJ Bolton AJ Fox DR Wareing MC Maiden, Emerg Infect Dis 2002 8 9 949 955 12194772
17. Multilocus sequence typing for comparison of veterinary and human isolates of Campylobacter jejuni. G Manning CG Dowson MC Bagnall IH Ahmed M West DG Newell, Appl Environ Microbiol 2003 69 11 6370 6379 14602588 10.1128/AEM.69.11.6370-6379.2003
18. Comparative Genotyping of Campylobacter jejuni by Amplified Fragment Length Polymorphism, Multilocus Sequence Typing, and Short Repeat Sequencing: Strain Diversity, Host Range, and Recombination. LM Schouls S Reulen B Duim JA Wagenaar RJL Willems KE Dingle FM Colles JDA Van Embden, J Clin Microbiol 2003 41 1 15 26 12517820 10.1128/JCM.41.1.15-26.2003
19. Utility of multilocus sequence typing as an epidemiological tool for investigation of outbreaks of gastroenteritis caused by Campylobacter jejuni. AD Sails B Swaminathan PI Fields, J Clin Microbiol 2003 41 10 4733 4739 14532212 10.1128/JCM.41.10.4733-4739.2003
20. Comparison of genetic divergence and fitness between two subclones of Helicobacter pylori. B Bjorkholm A Lundin A Sillen K Guillemin N Salama C Rubio JI Gordon P Falk L Engstrand, Infect Immun 2001 69 12 7832 7838 11705965 10.1128/IAI.69.12.7832-7838.2001
21. Comparative genomics of BCG vaccines by whole-genome DNA microarray. MA Behr MA Wilson WP Gill H Salamon GK Schoolnik S Rane PM Small, Science 1999 284 5419 1520 1523 10.1126/science.284.5419.1520 10348738
22. Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens. MF Anjum S Lucchini A Thompson JC Hinton MJ Woodward, Infect Immun 2003 71 8 4674 4683 12874348 10.1128/IAI.71.8.4674-4683.2003
23. Comparative genomics of closely related salmonellae. RA Edwards GJ Olsen SR Maloy, Trends Microbiol 2002 10 2 94 99 10.1016/S0966-842X(01)02293-4 11827811
24. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. J Parkhill BW Wren K Mungall JM Ketley C Churcher D Basham T Chillingworth RM Davies T Feltwell S Holroyd, Nature 2000 403 6770 665 668 10.1038/35001088 10688204
25. Use of an open-reading frame-specific Campylobacter jejuni DNA microarray as a new genotyping tool for studying epidemiologically related isolates. EE Leonard 2nd T Takata MJ Blaser S Falkow LS Tompkins EC Gaynor, J Infect Dis 2003 187 4 691 694 10.1086/368268 12599089
26. Whole Genome Comparison of Campylobacter jejuni Human Isolates Using a Low-Cost Microarray Reveals Extensive Genetic Diversity. N Dorrell JA Mangan KG Laing J Hinds D Linton H Al-Ghusein BG Barrell J Parkhill NG Stoker AV Karlyshev, Genome Res 2001 11 10 1706 1715 11591647 10.1101/gr.185801
27. Large-Scale Comparative Genomics Meta-Analysis of Campylobacter jejuni Isolates Reveals Low Level of Genome Plasticity. EN Taboada RR Acedillo CD Carrillo WA Findlay DT Medeiros OL Mykytczuk MJ Roberts CA Valencia JM Farber JHE Nash, J Clin Microbiol 2004 42 10 4566 4576 15472310 10.1128/JCM.42.10.4566- 4576.2004
28. Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. BM Pearson C Pin J Wright K I'Anson T Humphrey JM Wells, FEBS Letters 2003 554 1-2 224 230 10.1016/S0014-5793(03)01164-5 14596944
29. Comparative Genomic Analysis of Campylobacter jejuni Strains Reveals Diversity Due to Genomic Elements Similar to Those Present in C. jejuni Strain RM1221. CT Parker B Quinones WG Miller ST Horn RE Mandrell, J Clin Microbiol 2006 44 11 4125 4135 16943349 10.1128/JCM.01231-06
30. Identification of Campylobacter jejuni ATCC 43431-Specific Genes by Whole Microbial Genome Comparisons. F Poly D Threadgill A Stintzi, J Bacteriol 2004 186 14 4781 4795 15231810 10.1128/JB.186.14.4781-4795.2004
31. Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. OL Champion MW Gaunt O Gundogdu A Elmi AA Witney J Hinds N Dorrell BW Wren, Proc Natl Acad Sci USA 2005 102 44 16043 16048 16230626 10.1073/pnas.0503252102
32. Numerical analysis of DNA microarray data of Campylobacter jejuni strains correlated with survival, cytolethal distending toxin and haemolysin analyses. SL On N Dorrell L Petersen DD Bang S Morris SJ Forsythe BW Wren, Int J Med Microbiol 2006 296 6 353 363 10.1016/j.ijmm.2006.03.002 16782402
33. Clusters of Orthologous Groups of proteins. http://www.ncbi.nlm.nih.gov/ COG
34. Fingerprinting of Campylobacter jejuni by using resolution-optimized binary gene targets derived from comparative genome hybridization studies. EP Price F Huygens PM Giffard, Appl Environ Microbiol 2006 72 12 7793 7803 16997982 10.1128/AEM.01338-06
35. PCR detection, identification to species level, and fingerprinting of Campylobacter jejuni and Campylobacter coli direct from diarrheic samples. D Linton AJ Lawson RJ Owen J Stanley, J Clin Microbiol 1997 35 10 2568 2572 9316909
36. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. DE Fouts EF Mongodin RE Mandrell WG Miller DA Rasko J Ravel LM Brinkac RT DeBoy CT Parker SC Daugherty, PLoS Biol 2005 3 1 e15 15660156 10.1371/journal.pbio.0030015
37. Operon OMAD database. http://www.operon.com
38. ArrayExpress microarray data repository. http://www.ebi.ac.uk/ arrayexpress
39. The R project for statistical computing. http://www.r-project.org
40. aroma - An R Object-oriented Microarray Analysis environment. H Bengtsson, http://www.maths.lth.se/publications/
41. Bioconductor: open software development for computational biology and bioinformatics. RC Gentleman VJ Carey DM Bates B Bolstad M Dettling S Dudoit B Ellis L Gautier Y Ge J Gentry, Genome Biol 2004 5 10 R80 15461798 10.1186/gb-2004-5-10-r80
42. The kth-package for microarray data analysis. V Wirta J Lindberg M Gry Björklund D Klevebring, 2004 http://www.biotech.kth.se/molbio/microarray