Challenges for standardization of Clostridium difficile typing methods

Journal of Clinical Microbiology

Volumn 51, Issue 9, 2013, Pages 2810-2814

  Huber, Charlotte A ^a   Foster, Niki F ^b   Riley, Thomas V ^b   Paterson, David L ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM EXAMINATION; BACTERIUM IDENTIFICATION; CLOSTRIDIUM DIFFICILE; GENOME ANALYSIS; INTERMETHOD COMPARISON; INVESTIGATIVE PROCEDURES; MEDICAL DEVICE; MULTILOCUS SEQUENCE TYPING; MULTILOCUS VARIABLE NUMBER TANDEM REPEAT ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION RIBOTYPING; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; REPETITIVE ELEMENT POLYMERASE CHAIN REACTION; RESTRICTION MAPPING; REVIEW; RIBOTYPING; SEQUENCE ANALYSIS; SEROTYPING; STANDARDIZATION; SUFACE LAYER PROTEIN A ENCODING GENE; TOXINOTYPING; TYPING METHOD; WHOLE GENOME SEQUENCING;

CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM INFECTIONS; HUMANS; MOLECULAR EPIDEMIOLOGY; RIBOTYPING;

EID: 84882778202     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00143-13     Document Type: Review

References (30)

1. Jones AM, Kuijper EJ, Wilcox MH. 2013. Clostridium difficile: a European perspective. J. Infect. 66:115-128.
2. Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, Thomson NR, Roberts AP, Cerdeno-Tarraga AM, Wang H, Holden MT, Wright A, Churcher C, Quail MA, 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. 2006. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat. Genet. 38:779-786.
3. He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, Holt KE, Seth-Smith HM, Quail MA, Rance R, Brooks K, Churcher C, Harris D, Bentley SD, Burrows C, Clark L, Corton C, Murray V, Rose G, Thurston S, van Tonder A, Walker D, Wren BW, Dougan G, Parkhill J. 2010. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc. Natl. Acad. Sci. U. S. A. 107:7527-7532.
4. Stabler RA, Gerding DN, Songer JG, Drudy D, Brazier JS, Trinh HT, Witney AA, Hinds J, Wren BW. 2006. Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J. Bacteriol. 188:7297-7305.
5. Clements AC, Magalhaes RJ, Tatem AJ, Paterson DL, Riley TV. 2010. Clostridium difficile PCR ribotype 027: assessing the risks of further worldwide spread. Lancet Infect. Dis. 10:395-404.
6. Walk ST, Micic D, Jain R, Lo ES, Trivedi I, Liu EW, Almassalha LM, Ewing SA, Ring C, Galecki AT, Rogers MAM, Washer L, Newton DW, Malani PN, Young VB, Aronoff DM. 2012. Clostridium difficile ribotype does not predict severe infection. Clin. Infect. Dis. 55:1661-1668.
7. McDonald LC. 2013. Virulence and clinical outcomes in Clostridium difficile infection: a complex business. Clin. Infect. Dis. 56:906-907.
8. Bauer MP, Notermans DW, van Benthem BH, Brazier JS, Wilcox MH, Rupnik M, Monnet DL, van Dissel JT, Kuijper EJ; ECDIS Study Group. 2011. Clostridium difficile infection in Europe: a hospital-based survey. Lancet 377:63-73.
9. Valiente E, Dawson LF, Cairns MD, Stabler RA, Wren BW. 2012. Emergence of new PCR ribotypes from the hypervirulent Clostridium difficile 027 lineage. J. Med. Microbiol. 61:49-56.
10. Killgore G, Thompson A, Johnson S, Brazier J, Kuijper E, Pepin J, Frost EH, Savelkoul P, Nicholson B, van den Berg RJ, Kato H, Sambol SP, Zukowski W, Woods C, Limbago B, Gerding DN, McDonald LC. 2008. 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. 46:431-437.
11. Karjalainen T, Saumier N, Barc MC, Delmee M, Collignon A. 2002. Clostridium difficile genotyping based on slpA variable region in S-layer gene sequence: an alternative to serotyping. J. Clin. Microbiol. 40:2452-2458.
12. Dingle KE, Didelot X, Ansari MA, Eyre DW, Vaughan A, Griffiths D, Ip CL, Batty EM, Golubchik T, Bowden R, Jolley KA, Hood DW, Fawley WN, Walker AS, Peto TE, Wilcox MH, Crook DW. 2013. Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large scale whole genome sequencing. J. Infect. Dis. 207:675-686.
13. Clabots CR, Johnson S, Bettin KM, Mathie PA, Mulligan ME, Schaberg DR, Peterson LR, Gerding DN. 1993. Development of a rapid and efficient restriction endonuclease analysis typing system for Clostridium difficile and correlation with other typing systems. J. Clin. Microbiol. 31: 1870-1875.
14. Kuijper EJ, Oudbier JH, Stuifbergen WN, Jansz A, Zanen HC. 1987. Application of whole-cell DNA restriction endonuclease profiles to the epidemiology of Clostridium difficile-induced diarrhea. J. Clin. Microbiol. 25:751-753.
15. Janezic S, Rupnik M. 2010. Molecular typing methods for Clostridium difficile: pulsed-field gel electrophoresis and PCR ribotyping. Methods Mol. Biol. 646:55-65.
16. Alonso R, Martin A, Pelaez T, Marin M, Rodriguez-Creixems M, Bouza E. 2005. An improved protocol for pulsed-field gel electrophoresis typing of Clostridium difficile. J. Med. Microbiol. 54:155-157.
17. Griffiths D, Fawley W, Kachrimanidou M, Bowden R, Crook DW, Fung R, Golubchik T, Harding RM, Jeffery KJ, Jolley KA, Kirton R, Peto TE, Rees G, Stoesser N, Vaughan A, Walker AS, Young BC, Wilcox M, Dingle KE. 2010. Multilocus sequence typing of Clostridium difficile. J. Clin. Microbiol. 48:770-778.
18. Kuijper EJ, van d Brazier BRJJS. 2009. Comparison of molecular typing methods applied to Clostridium difficile. Methods Mol. Biol. 551:159-171.
19. Eckert C, Van BJ, Spigaglia P, Burghoffer B, Delmee M, Mastrantonio P, Barbut F. 2011. Comparison of a commercially available repetitiveelement PCR system (DiversiLab) with PCR ribotyping for typing of Clostridium difficile strains. J. Clin. Microbiol. 49:3352-3354.
20. 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.
21. O'Neill GL, Ogunsola FT, Brazier JS, Duerden BI. 1996. Modification of a PCR ribotyping method for application as a routine typing scheme for Clostridium difficile. Anaerobe 2:205-209.
22. Sadeghifard N, Gürtler V, Beer M, Seviour RJ. 2006. The mosaic nature of intergenic 16S-23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains. Appl. Environ. Microbiol. 72:7311-7323.
23. Gürtler V. 1993. Typing of Clostridium difficile strains by PCRamplification of variable length 16S-23S rDNA spacer regions. J. Gen. Microbiol. 139:3089-3097.
24. Indra A, Huhulescu S, Schneeweis M, Hasenberger P, Kernbichler S, Fiedler A, Wewalka G, Allerberger F, Kuijper EJ. 2008. Characterization of Clostridium difficile isolates using capillary gel electrophoresis-based PCR ribotyping. J. Med. Microbiol. 57:1377-1382.
25. Xiao M, Kong F, Jin P, Wang Q, Xiao K, Jeoffreys N, James G, Gilbert GL. 2012. Comparison of two capillary gel electrophoresis systems for Clostridium difficile ribotyping, using a panel of ribotype 027 isolates and whole-genome sequences as a reference standard. J. Clin. Microbiol. 50: 2755-2760.
26. Manzoor SE, Tanner HE, Marriott CL, Brazier JS, Hardy KJ, Platt S, Hawkey PM. 2011. Extended multilocus variable-number tandem-repeat analysis of Clostridium difficile correlates exactly with ribotyping and enables identification of hospital transmission. J. Clin. Microbiol. 49:3523-3530.
27. Hardy K, Manzoor S, Marriott C, Parsons H, Waddington C, Gossain S, Szczepura A, Stallard N, Hawkey PM. 2012. Utilizing rapid multiplelocus variable-number tandem-repeat analysis typing to aid control of hospital-acquired Clostridium difficile infection: a multicenter study. J. Clin. Microbiol. 50:3244-3248.
28. He M, Miyajima F, Roberts P, Ellison L, Pickard DJ, Martin MJ, Connor TR, Harris SR, Fairley D, Bamford KB, D'Arc S, Brazier J, Brown D, Coia JE, Douce G, Gerding D, Kim HJ, Koh TH, Kato H, Senoh M, Louie T, Michell S, Butt E, Peacock SJ, Brown NM, Riley T, Songer G, Wilcox M, Pirmohamed M, Kuijper E, Hawkey P, Wren BW, Dougan G, Parkhill J, Lawley TD. 2013. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat. Genet. 45:109-113.
29. Bidet P, Barbut F, Lalande V, Burghoffer B, Petit JC. 1999. Development of a new PCR-ribotyping method for Clostridium difficile based on ribosomal RNA gene sequencing. FEMS Microbiol. Lett. 175:261-266.
30. Janezic S, Indra A, Allerberger F, Rupnik M. 2011. Use of different molecular typing methods for the study of heterogeneity within Clostridium difficile toxinotypes V and III. J. Med. Microbiol. 60:1101-1107.