Clostridium botulinum group III: A group with dual identity shaped by plasmids, phages and mobile elements

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Skarin, Hanna ^a,b   Håfström, Therese ^a   Westerberg, Josefina ^a   Segerman, Bo ^a  

^a NATIONAL VETERINARY INSTITUTE   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; CLOSTRIDIUM BOTULINUM; CONTROLLED STUDY; DNA BASE COMPOSITION; GENE IDENTIFICATION; GENETIC DRIFT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; REPLICON; TRANSPOSON; BACTERIOPHAGE; BOTULISM; CLASSIFICATION; GENETICS; HUMAN; INTERSPERSED REPEAT; MICROBIOLOGY; MOLECULAR EVOLUTION; PLASMID; SPECIES DIFFERENCE; VIROLOGY;

ANIMALIA; CLOSTRIDIUM BOTULINUM;

BACTERIOPHAGES; BASE SEQUENCE; BOTULISM; CLOSTRIDIUM BOTULINUM; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; HUMANS; INTERSPERSED REPETITIVE SEQUENCES; PHYLOGENY; PLASMIDS; SPECIES SPECIFICITY;

EID: 79953870583     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-185     Document Type: Article

References (43)

1. Arnon SS, Schechter R, Inglesby TV, Henderson DA, Bartlett JG, Ascher MS, Eitzen E, Fine AD, Hauer J, Layton M, et al. Botulinum toxin as a biological weapon: medical and public health management. JAMA 2001, 285:1059-1070. 10.1001/jama.285.8.1059, 11209178.
2. Skarin H, Lindberg A, Blomqvist G, Aspan A, Baverud V. Molecular characterisation and comparison of Clostridium botulinum type C avian strains. Avian Pathol 2010, 39:511-518. 10.1080/03079457.2010.526923, 21154062.
3. Hatheway CL. Toxigenic clostridia. Clin Microbiol Rev 1990, 3:66-98. 358141, 2404569.
4. Collins MD, East AK. Phylogeny and taxonomy of the food-borne pathogen Clostridium botulinum and its neurotoxins. J Appl Microbiol 1998, 84:5-17. 10.1046/j.1365-2672.1997.00313.x, 15244052.
5. Hill KK, Smith TJ, Helma CH, Ticknor LO, Foley BT, Svensson RT, Brown JL, Johnson EA, Smith LA, Okinaka RT, et al. Genetic diversity among Botulinum Neurotoxin-producing clostridial strains. J Bacteriol 2007, 189:818-832. 10.1128/JB.01180-06, 1797315, 17114256.
6. Sasaki Y, Takikawa N, Kojima A, Norimatsu M, Suzuki S, Tamura Y. Phylogenetic positions of Clostridium novyi and Clostridium haemolyticum based on 16S rDNA sequences. Int J Syst Evol Microbiol 2001, 51:901-904.
7. Oguma K. The stability of toxigenicity in Clostridium botulinum types C and D. J Gen Microbiol 1976, 92:67-75.
8. Moriishi K, Koura M, Fujii N, Fujinaga Y, Inoue K, Syuto B, Oguma K. Molecular cloning of the gene encoding the mosaic neurotoxin, composed of parts of botulinum neurotoxin types C1 and D, and PCR detection of this gene from Clostridium botulinum type C organisms. Appl Environ Microbiol 1996, 62:662-667. 167833, 8593068.
9. Takeda M, Tsukamoto K, Kohda T, Matsui M, Mukamoto M, Kozaki S. Characterization of the neurotoxin produced by isolates associated with avian botulism. Avian Dis 2005, 49:376-381. 10.1637/7347-022305R1.1, 16252491.
10. Miyazaki S, Sakaguchi G. Experimental botulism in chickens: the cecum as the site of production and absorption of botulinum toxin. Jpn J Med Sci Biol 1978, 31:1-15.
11. Sakaguchi Y, Hayashi T, Yamamoto Y, Nakayama K, Zhang K, Ma S, Arimitsu H, Oguma K. Molecular analysis of an extrachromosomal element containing the C2 toxin gene discovered in Clostridium botulinum type C. J Bacteriol 2009, 191:3282-3291. 10.1128/JB.01797-08, 2687166, 19270093.
12. Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, Thomson NR, Roberts AP, Cerdeno-Tarraga AM, Wang H, et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 2006, 38:779-786. 10.1038/ng1830, 16804543.
13. Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, Shiba T, Ogasawara N, Hattori M, Kuhara S, Hayashi H. Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci USA 2002, 99:996-1001. 10.1073/pnas.022493799, 117419, 11792842.
14. Bettegowda C, Huang X, Lin J, Cheong I, Kohli M, Szabo SA, Zhang X, Diaz LA, Velculescu VE, Parmigiani G, et al. The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT. Nat Biotechnol 2006, 24:1573-1580. 10.1038/nbt1256, 17115055.
15. Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR, Crossman L, et al. Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Genome Res 2007, 17:1082-1092. 10.1101/gr.6282807, 1899119, 17519437.
16. Smith TJ, Hill KK, Foley BT, Detter JC, Munk AC, Bruce DC, Doggett NA, Smith LA, Marks JD, Xie G, Brettin TS. Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3,/Ba4 and/B1 clusters are located within plasmids. PLoS One 2007, 2:e1271. 10.1371/journal.pone.0001271, 2092393, 18060065.
17. Sakaguchi Y, Hayashi T, Kurokawa K, Nakayama K, Oshima K, Fujinaga Y, Ohnishi M, Ohtsubo E, Hattori M, Oguma K. The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny. Proc Natl Acad Sci USA 2005, 102:17472-17477. 10.1073/pnas.0505503102, 1283531, 16287978.
18. Dinter VZ, Kull KE. Ergänzende Untersuchungen über den Botulismus beim Nerz. Nord Vet Med 1951, 3:297-311.
19. Carter AT, Paul CJ, Mason DR, Twine SM, Alston MJ, Logan SM, Austin JW, Peck MW. Independent evolution of neurotoxin and flagellar genetic loci in proteolytic Clostridium botulinum. BMC Genomics 2009, 10:115. 10.1186/1471-2164-10-115, 2674064, 19298644.
20. Segerman B, De Medici D, Ehling Schulz M, Fach P, Fenicia L, Fricker M, Wielinga P, Van Rotterdam B, Knutsson R. Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain. Int J Food Microbiol
21. Eisen JA, Heidelberg JF, White O, Salzberg SL. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol 2000, 1:RESEARCH0011. 10.1186/gb-2000-1-6-research0011, 16139, 11178265.
22. Tillier ER, Collins RA. Genome rearrangement by replication-directed translocation. Nat Genet 2000, 26:195-197. 10.1038/79918, 11017076.
23. Marshall KM, Bradshaw M, Johnson EA. Conjugative botulinum neurotoxin-encoding plasmids in Clostridium botulinum. PLoS One 2010, 5:e11087. 10.1371/journal.pone.0011087, 2884020, 20552020.
24. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010, 327:167-170. 10.1126/science.1179555, 20056882.
25. Maksymowych AB, Reinhard M, Malizio CJ, Goodnough MC, Johnson EA, Simpson LL. Pure botulinum neurotoxin is absorbed from the stomach and small intestine and produces peripheral neuromuscular blockade. Infect Immun 1999, 67:4708-4712. 96798, 10456920.
26. Amimoto K, Sasaki Y, Fukuyama S, Tamura Y. Genetic variation and cross-reactivity of Clostridium septicum alpha-toxin. Vet Microbiol 2006, 114:51-59. 10.1016/j.vetmic.2005.10.039, 16337096.
27. Manabe S, Nariya H, Miyata S, Tanaka H, Minami J, Suzuki M, Taniguchi Y, Okabe A. Purification and characterization of a clostripain-like protease from a recombinant Clostridium perfringens culture. Microbiology 2010, 156:561-569. 10.1099/mic.0.031609-0, 19850615.
28. Sterthoff C, Lang AE, Schwan C, Tauch A, Aktories K. Functional characterization of an extended binding component of the actin-ADP-ribosylating C2 toxin detected in Clostridium botulinum strain (C) 2300. Infect Immun 2010, 78:1468-1474. 10.1128/IAI.01351-09, 2849413, 20145093.
29. Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM, et al. Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Res 2006, 16:1031-1040. 10.1101/gr.5238106, 1524862, 16825665.
30. Liyanage H, Holcroft P, Evans VJ, Keis S, Wilkinson SR, Kashket ER, Young M. A new insertion sequence, ISCb1, from Clostridium beijernickii NCIMB 8052. J Mol Microbiol Biotechnol 2000, 2:107-113.
31. Hill KK, Xie G, Foley BT, Smith TJ, Munk AC, Bruce D, Smith LA, Brettin TS, Detter JC. Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. BMC Biol 2009, 7:66. 10.1186/1741-7007-7-66, 2764570, 19804621.
32. Schmid S, Seitz T, Haas D. Cointegrase, a naturally occurring, truncated form of IS21 transposase, catalyzes replicon fusion rather than simple insertion of IS21. J Mol Biol 1998, 282:571-583. 10.1006/jmbi.1998.2041, 9737923.
33. Song H, Hwang J, Yi H, Ulrich RL, Yu Y, Nierman WC, Kim HS. The early stage of bacterial genome-reductive evolution in the host. PLoS Pathog 2010, 6:e1000922. 10.1371/journal.ppat.1000922, 2877748, 20523904.
34. Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998, 8:195-202.
35. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12. 10.1186/gb-2004-5-2-r12, 395750, 14759262.
36. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics 2005, 21:3422-3423. 10.1093/bioinformatics/bti553, 15976072.
37. Barton BM, Harding GP, Zuccarelli AJ. A general method for detecting and sizing large plasmids. Anal Biochem 1995, 226:235-240. 10.1006/abio.1995.1220, 7793624.
38. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27:4636-4641. 10.1093/nar/27.23.4636, 148753, 10556321.
39. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:944-945. 10.1093/bioinformatics/16.10.944, 11120685.
40. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009, 25:119-120. 10.1093/bioinformatics/btn578, 2612626,2612626, 18990721.
41. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964. 10.1093/nar/25.5.955, 146525, 9023104.
42. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007, 35:W52-57. 10.1093/nar/gkm360, 1933234, 17537822.
43. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.