Rapid detection of sequence variation in Clostridium difficile genes using LATE-PCR with multiple mismatch-tolerant hybridization probes

Journal of Microbiological Methods

Volumn 91, Issue 2, 2012, Pages 269-275

  Pierce, Kenneth E ^a   Khan, Huma ^b,d   Mistry, Rohit ^b,d   Goldenberg, Simon D ^c   French, Gary L ^c   Wangh, Lawrence J ^a  

^a BRANDEIS UNIVERSITY   (United States)

^b Smiths Detection Diagnostics   (United Kingdom)

^c KING'S COLLEGE LONDON   (United Kingdom)

^d Tetricus Science Park   (United Kingdom)

Author keywords

Clostridium difficile; Hybridization probes; Infectious disease diagnosis; LATE PCR; Multiplex PCR

Indexed keywords

SINGLE STRANDED DNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM DETECTION; CDTB GENE; CLOSTRIDIUM DIFFICILE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE FREQUENCY; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; LINEAR AFTER THE EXPONENTIAL POLYMERASE CHAIN REACTION; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STOP CODON; TCDA GENE; TCDB GENE; TCDC GENE; THERMODYNAMICS;

ADP RIBOSE TRANSFERASES; BACTERIAL PROTEINS; BACTERIAL TOXINS; CLOSTRIDIUM DIFFICILE; DNA, BACTERIAL; ENTEROTOXINS; MOLECULAR TYPING; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; REPRESSOR PROTEINS; TEMPERATURE;

EID: 84867830461     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.08.018     Document Type: Article

References (27)

1. Babady N.E., Stiles J., Ruggiero P., Khosa P., Huang D., Shuptar S., Kamboj M., Kiehm T.E. Evaluation of the Cepheid Xpert Clostridium difficile Epi assay for diagnosis of Clostridium difficile infection and typing of the NAP1 strain at a cancer hospital. J. Clin. Microbiol. 2010, 48:4519-4524.
2. Carter G.P., Douce G.R., Govind R., Howarth P.M., Mackin K.E., Spencer J., Buckley A.M., Antunes A., Kotsanas D., Jenkin G.A., Dupuy B., Rood J.I., Lyras D. The anti-sigma factor TcdC modulates hypervirulence in an epidemic BI/NAP1/027 clinical isolate of Clostridium difficile. PLoS Pathog. 2011, 7:e1002317.
3. Cartman S.T., Kelly M.L., Heeg D., Heap J.T., Minton N.P. Precise manipulation of the Clostridium difficile chromosome reveals a lack of association between tcdC genotype and toxin production. Appl. Environ. Microbiol. 2012, 78:4683-4690.
4. Chapin K.C., Dickenson R.A., Wu F., Andrea S.B. Comparison of five assays for detection of Clostridium difficile toxin. J. Mol. Diagn. 2011, 13:395-400.
5. Curry S.R., Marsh J.W., Muto C.A., O'Leary M.M., Pasculle A.W., Harrison L.H. tcdC Genotypes associated with severe TcdC truncation in an epidemic clone and other strains of Clostridium difficile. J. Clin. Microbiol. 2007, 45:215-221.
6. Geric B., Carman R.J., Rupnik M., Genheimer C.W., Sambol S.P., Lyerly D.M., Gerding D.N., Johnson S. Binary toxin-producing, large clostridial toxin-negative Clostridium difficile strains are enterotoxic but do not cause disease in hamsters. J. Infect. Dis. 2006, 193:1143-1150.
7. Goldenberg S.D., French G.L. Lack of association of tcdC type and binary toxin status with disease severity and outcome intoxigenic Clostridium difficile. J. Infect. 2011, 62:355-362.
8. Gonçalves C., Decré D., Barbut F., Burghoffer B., Petit J.-C. Prevalence and characterization of a binary toxin (actin-specificADP-ribosyltransferase) from Clostridium difficile. J. Clin. Microbiol. 2004, 42:1933-1939.
9. Goorhuis A., Bakker D., Corver J., Debast S.B., Harmanus C., Notermans D.W., Bergwerff A.A., Dekker F.W., Kuijper E.J. Emergence of Clostridium difficile infection due to a new hypervirulent strain, polymerase chain reaction ribotype 078. Clin. Infect. Dis. 2008, 47:1162-1170.
10. Karre T., Sloan L., Patel R., Mandrekar J., Rosenblatt J. Comparison of two commercial molecular assays to a laboratory-developed molecular assay for diagnosis of Clostridium difficile infection. J. Clin. Microbiol. 2010, 49:725-727.
11. Killgore G., Thompson A., Johnson S., Brazier J., Kuijper E., Pepin J., Frost E.H., Savelkoul P., Nicholson B., van den Berg R.J., Kato H., Sambol S.P., Zukowski W., Woods C., Limbago B., Gerding D.N., McDonald L.C. Comparison of seven techniques for typing international epidemic strains of Clostridium difficile: restriction endonuclease analysis, pulsed-field gel electrophoresis, PCR ribotyping, multilocus sequence typing, multilocus variable-number tandem-repeat analysis, amplified fragment length polymorphism, and surface layer protein A gene sequence typing. J. Clin. Microbiol. 2008, 46:431-437.
12. Matamouros S., England P., Dupuy B. Clostridium difficile toxin expression is inhibited by the novel regulator TcdC. Mol. Microbiol. 2007, 64:1274-1288.
13. McDonald L.C., Killgore G.E., Thompson A., Owens R.C., Kazakova S.V., Sambol S.P., Johnson S., Gerding D.N. An epidemic, toxin gene-variant strain of Clostridium difficile. N. Engl. J. Med. 2005, 353:2433-2441.
14. Persson S., Jensen J.N., Olsen K.E. Multiplex PCR method for detection of Clostridium difficile tcdA, tcdB, cdtA, and cdtB and internal in-frame deletion of tcdC. J. Clin. Microbiol. 2011, 49:4299-4300.
15. Petrella L.A., Sambol S.P., Cheknis A., Nagaro K., Kean Y., Sears P.S., Babakhani F., Johnson S., Gerding D.N. Decreased cure and increased recurrence rates for Clostridium difficile infection caused by the epidemic C. difficile BI strain. Clin. Infect. Dis. 2012, 55:351-357.
16. Pierce K.E., Sanchez J.A., Rice J.E., Wangh L.J. Linear-After-The-Exponential (LATE)-PCR: optimizing primer design for high yields of specific single-stranded DNA and improved real-time detection. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:8609-8614.
17. Rice J.E., Sanchez J.A., Pierce K.E., Reis A.H., Osborne A., Wangh L.J. Monoplex/multiplex linear-after-the-exponential-PCR assays combined with PrimeSafe and Dilute-'N'-Go sequencing. Nat. Protoc. 2007, 2:2429-2438.
18. Rice, J.E., Reis, A.H. Jr., Rice, L.M., Carver-Brown, R.K., Wangh, L.J., in press. Fluorescent Signatures for Variable DNA Sequences. Nucleic Acids Res. http://dx.doi.org/10.1093/nar/gks731.
19. Rupnik M., Kato N., Grabnar M., Kato H. New types of toxin A-negative, toxin B-positive strains among Clostridium difficile isolates from Asia. J. Clin. Microbiol. 2003, 41:1118-1125.
20. Sanchez J.A., Pierce K.E., Rice J.E., Wangh L.J. Linear-After-The-Exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:1933-1938.
21. Sanchez J.A., Abramowitz J.D., Salk J.J., Reis A.H., Rice J.E., Pierce K.E., Wangh L.J. Two-temperature LATE-PCR endpoint genotyping. BMC Biotechnol. 2006, 6:44.
22. Sebaihia M., Wren B.W., Mullany P., Fairweather N.F., Minton N., Stabler R., Thomson N.R., Roberts A.P., Cerdeño-Tárraga A.M., Wang H., Holden M.T., Wright A., Churcher C., Quail M.A., Baker S., Bason N., Brooks K., Chillingworth T., Cronin A., Davis P., Dowd L., Fraser A., Feltwell T., Hance Z., Holroyd S., Jagels K., Moule S., Mungall K., Price C., Rabbinowitsch E., Sharp S., Simmonds M., Stevens K., Unwin L., Whithead S., Dupuy B., Dougan G., Barrell B., Parkhill J. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat. Genet. 2006, 38:779-786.
23. Sirard S., Valiquette L., Fortier L.C. Lack of association between clinical outcome of Clostridium difficile infections, strain type, and virulence-associated phenotypes. J. Clin. Microbiol. 2011, 49:4040-4046.
24. Spigaglia P., Mastrantonio P. Molecular analysis of the pathogenicity locus and polymorphism in the putative negative regulator of toxin production (TcdC) among Clostridium difficile clinical isolates. J. Clin. Microbiol. 2002, 40:3470-3475.
25. Stare B.G., Delmée M., Rupnik M. Variant forms of the binary toxin CDT locus and tcdC gene in Clostridium difficile strains. J. Med. Microbiol. 2007, 56:329-335.
26. Stubbs S., Rupnik M., Gibert M., Brazier J., Duerden B., Popoff M. Production of actin-specific ADP-ribosyltransferase (binary toxin) by strains of Clostridium difficile. FEMS Microbiol. Lett. 2000, 186:307-312.
27. Zidarič V., Kevorkijan B.K., Oresic N., Janezic S., Rupnik M. Comparison of two commercial molecular tests for the detection of Clostridium difficile in the routine diagnostic laboratory. J. Med. Microbiol. 2011, 60:1131-1136.