Automated detection of toxigenic Clostridium difficile in clinical samples: Isothermal tcdB amplification coupled to array-based detection

Journal of Clinical Microbiology

Volumn 50, Issue 8, 2012, Pages 2681-2687

  Hicke, Brian ^a   Pasko, Chris ^a   Groves, Benjamin ^a   Ager, Edward ^b   Corpuz, Maylene ^a   Frech, Georges ^a   Munns, Denton ^a   Smith, Wendy ^a   Warcup, Ashley ^a   Denys, Gerald ^c   Ledeboer, Nathan A ^d   Lindsey, Wes ^a   Owen, Charles ^a   Rea, Larry ^a   Jenison, Robert ^a  

^a Great Basin Scientific   (United States)

^b UNIVERSITY OF NORTH CAROLINA HOSPITALS   (United States)

^c INDIANA UNIVERSITY HEALTH   (United States)

^d MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIUM DETECTION; BIOCHIP; CLOSTRIDIUM DIFFICILE; COLONY FORMING UNIT; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DIAGNOSTIC TEST; ELECTRICAL EQUIPMENT; ELECTROMECHANICAL SYSTEM; ENTEROBACTERIACEAE; FECES CULTURE; GENE AMPLIFICATION; GENE TARGETING; HUMAN; HYBRIDIZATION; IMMUNOASSAY; ISOTHERMAL GENE AMPLIFICATION; LABORATORY AUTOMATION; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENICITY LOCUS; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; TCDB GENE; TOXIGENIC CLOSTRIDIUM DIFFICILE;

AUTOMATION, LABORATORY; BACTERIAL PROTEINS; BACTERIAL TOXINS; BACTERIOLOGICAL TECHNIQUES; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM INFECTIONS; FECES; HUMANS; MICROARRAY ANALYSIS; MOLECULAR DIAGNOSTIC TECHNIQUES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SENSITIVITY AND SPECIFICITY; TIME FACTORS;

CLOSTRIDIUM DIFFICILE; ENTEROBACTERIACEAE;

EID: 84864410151     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00621-12     Document Type: Article

References (35)

1. An L, et al. 2005. Characterization of a thermostable uvrD helicase and its participation in helicase-dependent amplification. J. Biol. Chem. 280:28952-28958. (Pubitemid 41161341)
2. Ballard JD. 2010. Medical microbiology: a toxin contest. Nature 467:665-666.
3. Bartlett JG. 2002. Clinical practice. Antibiotic-associated diarrhea. N. Engl. J. Med. 346:334-339.
4. Bartlett JG, Gerding DN. 2008. Clinical recognition and diagnosis of Clostridium difficile infection. Clin. Infect. Dis. 46(Suppl 1):S12-S18. (Pubitemid 351323661)
5. Bartlett JG, Moon N, Chang TW, Taylor N, Onderdonk AB. 1978. Role of Clostridium difficile in antibiotic-associated pseudomembranous colitis. Gastroenterology 75:778-782. (Pubitemid 9040959)
6. Bauer MP, et al. 2011. Clostridium difficile infection in Europe: a hospital-based survey. Lancet 377:63-73.
7. Bélanger SD, Boissinot M, Clairoux N, Picard FJ, Bergeron MG. 2003. Rapid detection of Clostridium difficile in feces by real-time PCR. J. Clin. Microbiol. 41:730-734. (Pubitemid 36184188)
8. Bouvet PJM, Popoff MR. 2008. Genetic relatedness of Clostridium difficile isolates from various origins determined by triple-locus sequence analysis based on toxin regulatory genes tcdC, tcdR, and cdtR. J. Clin. Microbiol. 46:3703-3713.
9. Braun V, Hundsberger T, Leukel P, Sauerborn M, von Eichel-Streiber C. 1996. Definition of the single integration site of the pathogenicity locus in Clostridium difficile. Gene 181:29-38. (Pubitemid 26418243)
10. Chow WHA, et al. 2008. Application of isothermal helicase-dependent amplification with a disposable detection device in a simple sensitive stool test for toxigenic Clostridium difficile. J. Mol. Diagn. 10:452-458.
11. Dingle KE, et al. 2011. Clinical Clostridium difficile: clonality and pathogenicity locus diversity.PLoSOne6:e19993. doi:10.1371/journal.pone.0019993.
12. Dobosy JR, et al. 2011. RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers.BMCBiotechnol. 11:80. doi:10.1186/1472-6750-11-80.
13. Doseeva V, et al. 2011. Multiplex isothermal helicase-dependent amplification assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. Diagn. Microbiol. Infect. Dis. 71:354-365.
14. Dubberke ER, Reske KA, Olsen MA, McDonald LC, Fraser VJ. 2008. Short- and long-term attributable costs of Clostridium difficile-associated disease in nonsurgical inpatients. Clin. Infect. Dis. 46:497-504. (Pubitemid 351263485)
15. Elliott B, et al. 2011. New types of toxin A-negative, toxin B-positive strains among clinical isolates of Clostridium difficile in Australia. J. Med. Microbiol. 60:1108-1111.
16. Geric Stare BG, Rupnik M. 2010. Clostridium difficile toxinotype XI (A-B-) exhibits unique arrangement of PaLoc and its upstream region. Anaerobe 16:393-395.
17. Gilligan PH. 2008. Is a two-step glutamate dehydrogenase antigencytotoxicity neutralization assay algorithm superior to the premier toxinA and B enzyme immunoassay for laboratory detection of Clostridium difficile? J. Clin. Microbiol. 46:1523-1525. (Pubitemid 351563608)
18. He M, et al. 2010. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc. Natl. Acad. Sci. U. S. A. 107:7527-7532.
19. Johnson M, et al. 2008. NCBI BLAST: a better web interface. Nucleic Acids Res. 36:W5-W9.
20. Kato H, Yokoyama T, Kato H, Arakawa Y. 2005. Rapid and simple method for detecting the toxin B gene of Clostridium difficile in stool specimens by loop-mediated isothermal amplification. J. Clin. Microbiol. 43:6108-6112. (Pubitemid 43100667)
21. Novak-Weekley SM, et al. 2010. Clostridium difficile testing in the clinical laboratory by use of multiple testing algorithms. J. Clin. Microbiol. 48:889-893.
22. Pasko C, et al. 2012. Staph ID/R: a rapid method for determining Staphylococcus species identity and detecting the mecA gene directly from positive blood culture. J. Clin. Microbiol. 50:810-817.
23. Peterson LR, et al. 2007. Detection of toxigenic Clostridium difficile in stool samples by real-time polymerase chain reaction for the diagnosis of C. difficile-associated diarrhea. Clin. Infect. Dis. 45:1152-1160. (Pubitemid 47580313)
24. Peterson LR, et al. 2011. Laboratory testing for Clostridium difficile infection: light at the end of the tunnel. Am. J. Clin. Pathol. 136:372-380.
25. Rupnik M. 2008. Heterogeneity of large clostridial toxins: importance of Clostridium difficile toxinotypes. FEMS Microbiol. Rev. 32:541-555. (Pubitemid 351538749)
26. Rupnik M, et al. 2005. Revised nomenclature of Clostridium difficile toxins and associated genes. J. Med. Microbiol. 54:113-117. (Pubitemid 40867994)
27. Rupnik M, Wilcox MH, Gerding DN. 2009. Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat. Rev. Microbiol. 7:526-536.
28. SantaLucia J, Jr, Allawi HT, Seneviratne PA. 1996. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555-3562. (Pubitemid 26092574)
29. Sebaihia M, et al. 2006. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat. Genet. 38:779-786. (Pubitemid 43980598)
30. Song X, et al. 2008. Rising economic impact of Clostridium difficile-associated disease in adult hospitalized patient population. Infect. Control Hosp. Epidemiol. 29:823-828.
31. Stabler RA, Dawson LF, Phua LTH, Wren BW. 2008. Comparative analysis of BI/NAP1/027 hypervirulent strains reveals novel toxin B-encoding gene (tcdB) sequences. J. Med. Microbiol. 57:771-775. (Pubitemid 351842071)
32. Vallone PM, Butler JM. 2004. Autodimer: a screening tool for primerdimer and hairpin structures. Biotechniques 37:226-231. (Pubitemid 39050463)
33. Vincent M, Xu Y, Kong H. 2004. Helicase-dependent isothermal DNA amplification. EMBO Rep. 5:795-800. (Pubitemid 39199169)
34. von Ahsen N, Oellerich M, Armstrong VW, Schütz E. 1999. Application of a thermodynamic nearest-neighbor model to estimate nucleic acid stability and optimize probe design: prediction of melting points of multiple mutations of apolipoprotein b-3500 and factor V with a hybridization probe genotyping assay on the LightCycler. Clin. Chem. 45:2094-2101.
35. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415. (Pubitemid 37442169)