Rapid Combined Characterization of Microorganism and Host Genotypes using a Single Technology

Helicobacter

Volumn 9, Issue 2, 2004, Pages 138-145

  Hjalmarsson, Sandra ^a   Alderborn, Anders ^b   Fock, Caroline ^a   Muldin, Ingrid ^b   Kling, Helene ^a   Uhlén, Mathias ^c   Engstrand, Lars ^d  

^a UPPSALA UNIVERSITY   (Sweden)

^b BIOTAGE AB   (Sweden)

^c ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^d SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

Author keywords

Biomarkers; Genotyping; Helicobacter pylori; Pyrosequencing

Indexed keywords

BACTERIAL DNA; CAGA PROTEIN; CLARITHROMYCIN; INTERLEUKIN 1BETA; RIBOSOME RNA;

ANIMAL MODEL; ARTICLE; BACTERIAL GENETICS; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; CANCER RISK; DEVICE; DRUG SENSITIVITY; GENETIC ANALYSIS; GENOTYPE; HELICOBACTER INFECTION; HELICOBACTER PYLORI; HUMAN; HUMAN TISSUE; INFECTION; MICROORGANISM; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROGNOSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STOMACH BIOPSY; STOMACH CANCER; TECHNOLOGY;

ANIMALS; ANTI-BACTERIAL AGENTS; ANTIGENS, BACTERIAL; BACTERIAL PROTEINS; BIOPSY; CLARITHROMYCIN; DNA, BACTERIAL; DNA, RIBOSOMAL; DRUG RESISTANCE, BACTERIAL; GASTRIC MUCOSA; GENES, BACTERIAL; GENES, RRNA; GENOMIC ISLANDS; GENOTYPE; HELICOBACTER INFECTIONS; HELICOBACTER PYLORI; HUMANS; INTERLEUKIN-1; MICE; MICE, TRANSGENIC; POINT MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEQUENCE ANALYSIS, DNA; VIRULENCE;

ANIMALIA; BACTERIA (MICROORGANISMS); HELICOBACTER; HELICOBACTER PYLORI; MUS MUSCULUS;

EID: 1942504709     PISSN: 10834389     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1083-4389.2004.00210.x     Document Type: Article

References (29)

1. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Science 1998;281:365.
2. Nordström T, Gharizadeh B, Pourmand N, Nyren P, Ronaghi M. Method enabling fast partial sequencing of cDNA clones. Anal Biochem 2001;292:266-71.
3. Alderborn A, Kristofferson A, Hammerling U. Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res 2000;10:1249-58.
4. Sun YQ, Monstein HJ, Nilsson LE, Petersson F, Borch K. Profiling and identification of eubacteria in the stomach of Mongolian gerbils with and without Helicobacter pylori infection. Helicobacter 2003;8:149-57.
5. Monstein H, Nikpour-Badr S, Jonasson J. Rapid molecular identification and subtyping of Helicobacter pylori by pyrosequencing of the 16S rDNA variable V1 and V3 regions. FEMS Microbiol Lett 2001;199:103-7.
6. Versalovic J, Shortridge D, Kibler K, Griffy MV, Beyer J, Flamm RK, Tanaka SK, Graham DY, Go MF. Mutations in 23S rRNA are associated with clarithromycin resistance in Helicobacter pylori. Antimicrob Agents Chemother 1996;40:477-80.
7. Alarcon T, Domingo D, Lopez-Brea M. Antibiotic resistance problems with Helicobacter pylori. Int J Antimicrob Agents 1999;12:19-26.
8. Censini S, Lange C, Xiang Z, Crabtree JE, Ghiara P, Borodovsky M, Rappuoli R, Covacci A. cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc Natl Acad Sci USA 1996; 93:14648-53.
9. El-Omar EM, Carrington M, Chow WH, et al. Interleukin-1 polymorphisms associated with increased risk of gastric cancer. Nature 2000;404: 398-402 (erratum appears in Nature 2001; 412:99).
10. El-Omar EM, Carrington M, Chow WH, et al. Interleukin-1 polymorphisms associated with increased risk of gastric cancer. Nature 2000;404: 398-402 (erratum appears in Nature 2001; 412:99).
11. Hefler LA, Ludwig E, Lebrecht A, Zeillinger R, Tong-Cacsire D, Koelbl H, Leodolter S, Tempfer CB. Polymorphisms of the interleukin-1 gene cluster and ovarian cancer. J Soc Gynecol Invest 2002;9:386-90.
12. Enroth H, Kraaz W, Engstrand L, Nyren O, Rohan T. Helicobacter pylori strain types and risk of gastric cancer: a case-control study. Cancer Epidemiol Biomarkers Prev 2000;9:981-5.
13. Hulten K, Gibreel A, Skold O, Engstrand L. Macrolide resistance in Helicobacter pylori: mechanism and stability in strains from clarithromycin-treated patients. Antimicrob Agents Chemother 1997;41:2550-3.
14. Björkholm B, Lundin A, Sillen A, Guillemin K, Salama N, Rubio C, Gordon JI, Falk P, Engstrand L. Comparison of genetic divergence and fitness between two subclones of Helicobacter pylori. Infect Immun 2001;69:7832-8.
15. Björkholm B, Befrits R, Jaup B, Engstrand L. Rapid PCR detection of Helicobacter pylori-associated virulence and resistance genes directly from gastric biopsy material. J Clin Microbiol 1998;36:3689-90.
16. Enroth H, Kraaz W, Engstrand L, Nyren O, Rohan T. Helicobacter pylori strain types and risk of gastric cancer: a case-control study. Cancer Epidemiol Biomarkers Prevention 2000;9:981-5.
17. Hulten K, Gibreel A, Sköld O, Engstrand L. Macrolide resistance in Helicobacter pylori: mechanism and stability in strains from clarithromycin-treated patients. Antimicrob Agents Chemother 1997;41:2550-3.
18. Björkholm B, Lundin A, Sillen A, Guillemin K, Salama N, Rubio C, Gordon JI, Falk P, Engstrand L. Comparison of genetic divergence and fitness between two subclones of Helicobacter pylori. Infect Immun 2001;69:7832-8.
19. Björkholm B, Befrits R, Jaup B, Engstrand L. Rapid PCR detection of Helicobacter pylori-associated virulence and resistance genes directly from gastric biopsy material. J Clin Microbiol 1998;36:3689-90.
20. Ronaghi M. Improved performance of pyrosequencing using single-stranded DNA-binding protein. Anal Biochem 2000;286:282-8.
21. Eckloff BW, Podzorski RP, Kline BC, Cockerill FR, 3rd. A comparison of 16S ribosomal DNA sequences from five isolates of Helicobacter pylori. Int J Syst Bacteriol 1994;44:320-3.
22. O'Meara D, Wilbe K, Leitner T, Hejdeman B, Albert J, Lundeberg J. Monitoring resistance to human immunodeficiency virus type 1 protease inhibitors by pyrosequencing. J Clin Microbiol 2001;39:464-73.
23. Gibson JR, Saunders NA, Burke B, Owen RJ. Novel method for rapid determination of clarithromycin sensitivity in Helicobacter pylori. J Clin Microbiol 1999;37:3746-8.
24. Maeda S, Yoshida H, Matsunaga H, Ogura K, Kawamata O, Shiratori Y, Omata M. Detection of clarithromycin-resistant Helicobacter pylori strains by a preferential homoduplex formation assay. J Clin Microbiol 2000;38:210-4.
25. Ge Z, Taylor DE. Rapid polymerase chain reaction screening of Helicobacter pylori chromosomal point mutations. Helicobacter 1997;2:127-31.
26. Alarcon T, Domingo D, Prieto N, Lopez-Brea M. PCR using-3′ -mismatched primers to detect A2142C mutation in 23S rRNA conferring resistance to clarithromycin in Helicobacter pylori clinical isolates. J Clin Microbiol 2000;38:923-5.
27. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, Heiner C, Kent SB, Hood LE. Fluorescence detection in automated DNA sequence analysis. Nature 1986;321:674-9.
28. de Jong R, Altare F, Haagen IA, et al. Severe mycobacterial and Salmonella infections in interleukin-12 receptor-deficient patients. Science 1998;280:1435-8.
29. Marquet S, Abel L, Hillaire D, Dessein H, Kalil J, Feingold J, Weissenbach J, Dessein AJ. Genetic localization of a locus controlling the intensity of infection by Schistosoma mansoni on chromosome 5q31-q33. Nat Genetics 1996;14:181-4.