Macro and micro diversity of Clostridium difficile isolates from diverse sources and geographical locations

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Stabler, Richard A ^a   Dawson, Lisa F ^a   Valiente, Esmeralda ^a   Cairns, Michelle D ^a,b,c   Martin, Melissa J ^a   Donahue, Elizabeth H ^a   Riley, Thomas V ^d   Songer, J Glenn ^e   Kuijper, Ed J ^f   Dingle, Kate E ^g   Wren, Brendan W ^a  

^a LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^b ROYAL LONDON HOSPITAL   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^e IOWA STATE UNIVERSITY   (United States)

^f LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^g UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; AUSTRALIA; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CLADISTICS; CLOSTRIDIUM DIFFICILE; EUROPE; FOOD; GENETIC VARIABILITY; GEOGRAPHICAL VARIATION (SPECIES); HOST; HUMAN; MICROBIAL DIVERSITY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NORTH AMERICA; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; RIBOTYPING; ANIMAL; BIODIVERSITY; CELL LINEAGE; CLUSTER ANALYSIS; DNA SEQUENCE; DOG; GENETICS; GENOMICS; GEOGRAPHY; HORSE; MOLECULAR EVOLUTION; MOUSE; MUTATION; PHYLOGENY; PHYSIOLOGY; SWINE;

ANIMALIA; CLOSTRIDIUM DIFFICILE;

ALLELES; ANIMALS; BACTERIAL TYPING TECHNIQUES; BIODIVERSITY; CELL LINEAGE; CLOSTRIDIUM DIFFICILE; CLUSTER ANALYSIS; DOGS; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOMICS; GEOGRAPHY; HORSES; HUMANS; MICE; MUTATION; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SWINE;

EID: 84857763473     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031559     Document Type: Article

References (51)

1. Johnson S, Gerding DN, (1998) Clostridium difficile-associated diarrhea. Clin Infect Dis 26: 1027-1034; quiz 1035-1026.
2. Songer JG, (2004) The emergence of Clostridium difficile as a pathogen of food animals. Anim Health Res Rev 5: 321-326.
3. Bartlett JG, Moon N, Chang TW, Taylor N, Onderdonk AB, (1978) Role of Clostridium difficile in antibiotic-associated pseudomembranous colitis. Gastroenterology 75: 778-782.
4. Bartlett JG, (2008) Historical perspectives on studies of Clostridium difficile and C. difficile infection. Clin Infect Dis 46 (Suppl 1): S4-11.
5. George RH, Symonds JM, Dimock F, Brown JD, Arabi Y, et al. (1978) Identification of Clostridium difficile as a cause of pseudomembranous colitis. Br Med J 1: 695.
6. Kuijper EJ, Coignard B, Tull P, (2006) Emergence of Clostridium difficile-associated disease in North America and Europe. Clin Microbiol Infect 12 (Suppl 6): 2-18.
7. Health Protection Agency (2011) Clostridium difficile Ribotyping Network (CDRN) for England and Northern Ireland 2009/2010 report.
8. Bauer MP, Notermans DW, van Benthem BH, Brazier JS, Wilcox MH, et al. (2011) Clostridium difficile infection in Europe: a hospital-based survey. Lancet 377: 63-73.
9. Hensgens MP, Goorhuis A, Notermans DW, van Benthem BH, Kuijper EJ, (2009) Decrease of hypervirulent Clostridium difficile PCR ribotype 027 in the Netherlands. Euro Surveill 14.
10. Burns K, Morris-Downes M, Fawley WN, Smyth E, Wilcox MH, et al. (2010) Infection due to C. difficile ribotype 078: first report of cases in the Republic of Ireland. J Hosp Infect 75: 287-291.
11. Jhung MA, Thompson AD, Killgore GE, Zukowski WE, Songer G, et al. (2008) Toxinotype V Clostridium difficile in humans and food animals. Emerg Infect Dis 14: 1039-1045.
12. Goorhuis A, Bakker D, Corver J, Debast SB, Harmanus C, et al. (2008) Emergence of Clostridium difficile infection due to a new hypervirulent strain, polymerase chain reaction ribotype 078. Clin Infect Dis 47: 1162-1170.
13. He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, et al. (2010) Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A 107: 7527-7532.
14. Huang H, Fang H, Weintraub A, Nord CE, (2009) Distinct ribotypes and rates of antimicrobial drug resistance in Clostridium difficile from Shanghai and Stockholm. Clin Microbiol Infect 15: 1170-1173.
15. Kim H, Jeong SH, Roh KH, Hong SG, Kim JW, et al. (2010) Investigation of toxin gene diversity, molecular epidemiology, and antimicrobial resistance of Clostridium difficile isolated from 12 hospitals in South Korea. Korean J Lab Med 30: 491-497.
16. Drudy D, Harnedy N, Fanning S, Hannan M, Kyne L, (2007) Emergence and control of fluoroquinolone-resistant, toxin A-negative, toxin B-positive Clostridium difficile. Infect Control Hosp Epidemiol 28: 932-940.
17. Kuijper EJ, de Weerdt J, Kato H, Kato N, van Dam AP, et al. (2001) Nosocomial outbreak of Clostridium difficile-associated diarrhoea due to a clindamycin-resistant enterotoxin A-negative strain. Eur J Clin Microbiol Infect Dis 20: 528-534.
18. Griffiths D, Fawley W, Kachrimanidou M, Bowden R, Crook DW, et al. (2010) Multilocus sequence typing of Clostridium difficile. J Clin Microbiol 48: 770-778.
19. Stabler RA, Gerding DN, Songer JG, Drudy D, Brazier JS, et al. (2006) Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J Bacteriol 188: 7297-7305.
20. Lemee L, Dhalluin A, Pestel-Caron M, Lemeland JF, Pons JL, (2004) Multilocus sequence typing analysis of human and animal Clostridium difficile isolates of various toxigenic types. J Clin Microbiol 42: 2609-2617.
21. Lemee L, Bourgeois I, Ruffin E, Collignon A, Lemeland JF, et al. (2005) Multilocus sequence analysis and comparative evolution of virulence-associated genes and housekeeping genes of Clostridium difficile. Microbiology 151: 3171-3180.
22. Dingle KE, Griffiths D, Didelot X, Evans J, Vaughan A, et al. (2011) Clinical Clostridium difficile: Clonality and Pathogenicity Locus Diversity. PLoS One 6: e19993.
23. Keel K, Brazier JS, Post KW, Weese S, Songer JG, (2007) Prevalence of PCR ribotypes among Clostridium difficile isolates from pigs, calves, and other species. J Clin Microbiol 45: 1963-1964.
24. Bakri MM, Brown DJ, Butcher JP, Sutherland AD, (2009) Clostridium difficile in ready-to-eat salads, Scotland. Emerg Infect Dis 15: 817-818.
25. al Saif N, Brazier JS, (1996) The distribution of Clostridium difficile in the environment of South Wales. J Med Microbiol 45: 133-137.
26. Metcalf DS, Costa MC, Dew WM, Weese JS, (2010) Clostridium difficile in vegetables, Canada. Lett Appl Microbiol 51: 600-602.
27. Dial S, Delaney JA, Barkun AN, Suissa S, (2005) Use of gastric acid-suppressive agents and the risk of community-acquired Clostridium difficile-associated disease. JAMA 294: 2989-2995.
28. Gould LH, Limbago B, (2010) Clostridium difficile in food and domestic animals: a new foodborne pathogen? Clin Infect Dis 51: 577-582.
29. Rupnik M, Kato N, Grabnar M, Kato H, (2003) New types of toxin A-negative, toxin B-positive strains among Clostridium difficile isolates from Asia. J Clin Microbiol 41: 1118-1125.
30. Rupnik M, Avesani V, Janc M, von Eichel-Streiber C, Delmee M, (1998) A novel toxinotyping scheme and correlation of toxinotypes with serogroups of Clostridium difficile isolates. J Clin Microbiol 36: 2240-2247.
31. Stabler RA, Dawson LF, Phua LT, 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.
32. Spigaglia P, Barbanti F, Dionisi AM, Mastrantonio P, (2010) Clostridium difficile isolates resistant to fluoroquinolones in Italy: emergence of PCR ribotype 018. J Clin Microbiol 48: 2892-2896.
33. Rupnik M, Brazier JS, Duerden BI, Grabnar M, Stubbs SL, (2001) Comparison of toxinotyping and PCR ribotyping of Clostridium difficile strains and description of novel toxinotypes. Microbiology 147: 439-447.
34. Knetsch CW, Hensgens MP, Harmanus C, van der Bijl MW, Savelkoul PH, et al. (2011) Genetic markers for Clostridium difficile lineages linked to hypervirulence. Microbiology.
35. Stabler RA, He M, Dawson L, Martin M, Valiente E, et al. (2009) Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol 10: R102.
36. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
37. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
38. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
39. Stubbs SL, Brazier JS, O'Neill GL, Duerden BI, (1999) PCR targeted to the 16S-23S rRNA gene intergenic spacer region of Clostridium difficile and construction of a library consisting of 116 different PCR ribotypes. J Clin Microbiol 37: 461-463.
40. Elliott B, Reed R, Chang BJ, Riley TV, (2009) Bacteremia with a large clostridial toxin-negative, binary toxin-positive strain of Clostridium difficile. Anaerobe 15: 249-251.
41. Solomon K, Murray S, Scott L, McDermott S, Drudy D, et al. (2011) An investigation of the subtype diversity of clinical isolates of Irish Clostridium difficile ribotypes 027 and 078 by repetitive-extragenic palindromic PCR. J Med Microbiol 60: 1080-1087.
42. Castillo-Ramirez S, Harris SR, Holden MT, He M, Parkhill J, et al. (2011) The impact of recombination on dN/dS within recently emerged bacterial clones. PLoS Pathog 7: e1002129.
43. Popoff MR, Rubin EJ, Gill DM, Boquet P, (1988) Actin-specific ADP-ribosyltransferase produced by a Clostridium difficile strain. Infect Immun 56: 2299-2306.
44. Tenover FC, Akerlund T, Gerding DN, Goering RV, Bostrom T, et al. (2011) Comparison of Strain Typing Results for Clostridium difficile Isolates from North America. J Clin Microbiol 49: 1831-1837.
45. Indra A, Blaschitz M, Kernbichler S, Reischl U, Wewalka G, et al. (2010) Mechanisms behind variation in the Clostridium difficile 16S-23S rRNA intergenic spacer region. J Med Microbiol 59: 1317-1323.
46. Nyc O, Pituch H, Matejkova J, Obuch-Woszczatynski P, Kuijper EJ, (2011) Clostridium difficile PCR ribotype 176 in the Czech Republic and Poland. Lancet 377: 1407.
47. van den Berg RJ, Schaap I, Templeton KE, Klaassen CH, Kuijper EJ, (2007) Typing and subtyping of Clostridium difficile isolates by using multiple-locus variable-number tandem-repeat analysis. J Clin Microbiol 45: 1024-1028.
48. Valiente E, Dawson LF, Cairns MD, Stabler RA, Wren BW, (2011) Emergence of new PCR-ribotypes from the hypervirulent Clostridium difficile 027 lineage. J Med Microbiol.
49. Weese JS, (2010) Clostridium difficile in food-innocent bystander or serious threat? Clin Microbiol Infect 16: 3-10.
50. Elliott B, Squire MM, Thean S, Chang BJ, Brazier JS, 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.
51. von Eichel-Streiber C, Zec-Pirnat I, Grabnar M, Rupnik M, (1999) A nonsense mutation abrogates production of a functional enterotoxin A in Clostridium difficile toxinotype VIII strains of serogroups F and X. FEMS Microbiol Lett 178: 163-168.