TY - JOUR AU - Uzal, F. A. AU - Freedman, J. C. AU - Shrestha, A. AU - Theoret, J. R. AU - Garcia, J. AU - Awad, M. M. PY - 2014 DA - 2014// TI - Towards an understanding of the role of Clostridium perfringens toxins in human and animal disease JO - Future Microbiol VL - 9 UR - https://doi.org/10.2217/fmb.13.168 DO - 10.2217/fmb.13.168 ID - Uzal2014 ER - TY - JOUR AU - Li, J. AU - Adams, V. AU - Bannam, T. L. AU - Miyamoto, K. AU - Garcia, J. P. AU - Uzal, F. A. PY - 2013 DA - 2013// TI - Toxin plasmids of Clostridium perfringens JO - Microbiol Mol Biol Rev VL - 77 UR - https://doi.org/10.1128/MMBR.00062-12 DO - 10.1128/MMBR.00062-12 ID - Li2013 ER - TY - JOUR AU - Parreira, V. R. AU - Costa, M. AU - Eikmeyer, F. AU - Blom, J. AU - Prescott, J. F. PY - 2012 DA - 2012// TI - Sequence of two plasmids from Clostridium perfringens chicken necrotic enteritis isolates and comparison with C. perfringens conjugative plasmids JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0049753 DO - 10.1371/journal.pone.0049753 ID - Parreira2012 ER - TY - JOUR AU - Sayeed, S. AU - Li, J. AU - McClane, B. A. PY - 2007 DA - 2007// TI - Virulence plasmid diversity in Clostridium perfringens type D isolates JO - Infect Immun VL - 75 UR - https://doi.org/10.1128/IAI.02014-06 DO - 10.1128/IAI.02014-06 ID - Sayeed2007 ER - TY - JOUR AU - Bueschel, D. M. AU - Jost, B. H. AU - Billington, S. J. AU - Trinh, H. T. AU - Songer, J. G. PY - 2003 DA - 2003// TI - Prevalence of cpb2, encoding beta2 toxin, in Clostridium perfringens field isolates: correlation of genotype with phenotype JO - Vet Microbiol VL - 94 UR - https://doi.org/10.1016/S0378-1135(03)00081-6 DO - 10.1016/S0378-1135(03)00081-6 ID - Bueschel2003 ER - TY - JOUR AU - Garmory, H. S. AU - Chanter, N. AU - French, N. P. AU - Bueschel, D. AU - Songer, J. G. AU - Titball, R. W. PY - 2000 DA - 2000// TI - Occurrence of Clostridium perfringens beta2-toxin amongst animals, determined using genotyping and subtyping PCR assays JO - Epidemiol Infect VL - 124 UR - https://doi.org/10.1017/S0950268899003295 DO - 10.1017/S0950268899003295 ID - Garmory2000 ER - TY - JOUR AU - Bannam, T. L. AU - Yan, X. -. X. AU - Harrison, P. F. AU - Seemann, T. AU - Keyburn, A. L. AU - Stubenrauch, C. PY - 2011 DA - 2011// TI - Necrotic enteritis-derived Clostridium perfringens strain with three closely related independently conjugative toxin and antibiotic resistance plasmids JO - MBio VL - 2 UR - https://doi.org/10.1128/mBio.00190-11 DO - 10.1128/mBio.00190-11 ID - Bannam2011 ER - TY - STD TI - Adams V, Li J, Wisniewski JA, Uzal FA, Moore RJ, McClane BA, et al. Virulence plasmids of spore-forming bacteria. Microbiol Spectr. 2014;2:PLAS-0024-2014. ID - ref8 ER - TY - JOUR AU - Freedman, J. C. AU - Theoret, J. R. AU - Wisniewski, J. A. AU - Uzal, F. A. AU - Rood, J. I. AU - McClane, B. A. PY - 2015 DA - 2015// TI - Clostridium perfringens type A–E toxin plasmids JO - Res Microbiol VL - 166 UR - https://doi.org/10.1016/j.resmic.2014.09.004 DO - 10.1016/j.resmic.2014.09.004 ID - Freedman2015 ER - TY - JOUR AU - Keyburn, A. L. AU - Boyce, J. D. AU - Vaz, P. AU - Bannam, T. L. AU - Ford, M. E. AU - Parker, D. PY - 2008 DA - 2008// TI - NetB, a new toxin that is associated with avian necrotic enteritis caused by Clostridium perfringens JO - PLoS Pathog VL - 4 UR - https://doi.org/10.1371/journal.ppat.0040026 DO - 10.1371/journal.ppat.0040026 ID - Keyburn2008 ER - TY - JOUR AU - Nowell, V. J. AU - Kropinski, A. M. AU - Songer, J. G. AU - MacInnes, J. I. AU - Parreira, V. R. AU - Prescott, J. F. PY - 2012 DA - 2012// TI - Genome sequencing and analysis of a type a Clostridium perfringens isolate from a case of bovine clostridial abomasitis JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0032271 DO - 10.1371/journal.pone.0032271 ID - Nowell2012 ER - TY - STD TI - Wong YM, Juan JC, Gan HM, Austin CM. Draft genome sequence of Clostridium perfringens strain JJC, a highly efficient hydrogen producer isolated from landfill leachate sludge. Genome Announc. 2014;2:​e00064–14. ID - ref12 ER - TY - JOUR AU - Johansson, A. AU - Aspan, A. AU - Bagge, E. AU - Båverud, V. AU - Engström, B. E. AU - Johansson, K. -. E. PY - 2006 DA - 2006// TI - Genetic diversity of Clostridium perfringens type a isolates from animals, food poisoning outbreaks and sludge JO - BMC Microbiol VL - 6 UR - https://doi.org/10.1186/1471-2180-6-47 DO - 10.1186/1471-2180-6-47 ID - Johansson2006 ER - TY - JOUR AU - Myers, G. S. A. AU - Rasko, D. A. AU - Cheung, J. K. AU - Ravel, J. AU - Seshadri, R. AU - DeBoy, R. T. PY - 2006 DA - 2006// TI - Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.5238106 DO - 10.1101/gr.5238106 ID - Myers2006 ER - TY - JOUR AU - Chalmers, G. AU - Bruce, H. L. AU - Hunter, D. B. AU - Parreira, V. R. AU - Kulkarni, R. R. AU - Jiang, Y. -. F. PY - 2008 DA - 2008// TI - Multilocus sequence typing analysis of Clostridium perfringens isolates from necrotic enteritis outbreaks in broiler chicken populations JO - J Clin Microbiol VL - 46 UR - https://doi.org/10.1128/JCM.01548-08 DO - 10.1128/JCM.01548-08 ID - Chalmers2008 ER - TY - STD TI - Chalmers G, Martin SW, Hunter DB, Prescott JF, Weber LJ, Boerlin P. Genetic diversity of Clostridium perfringens isolated from healthy broiler chickens at a commercial farm. Vet Microbiol. 2008;127:116–27. ID - ref16 ER - TY - JOUR AU - Nauerby, B. AU - Pedersen, K. AU - Madsen, M. PY - 2003 DA - 2003// TI - Analysis by pulsed-field gel electrophoresis of the genetic diversity among Clostridium perfringens isolates from chickens JO - Vet Microbiol VL - 94 UR - https://doi.org/10.1016/S0378-1135(03)00118-4 DO - 10.1016/S0378-1135(03)00118-4 ID - Nauerby2003 ER - TY - JOUR AU - Hassan, K. A. AU - Elbourne, L. D. H. AU - Tetu, S. G. AU - Melville, S. B. AU - Rood, J. I. AU - Paulsen, I. T. PY - 2015 DA - 2015// TI - Genomic analyses of Clostridium perfringens isolates from five toxinotypes JO - Res Microbiol VL - 166 UR - https://doi.org/10.1016/j.resmic.2014.10.003 DO - 10.1016/j.resmic.2014.10.003 ID - Hassan2015 ER - TY - JOUR AU - Parish, W. E. PY - 1961 DA - 1961// TI - Necrotic enteritis in the fowl (Gallus Gallus Domesticus). I. Histopathology of the disease and isolation of a strain of Clostridium welchii JO - J Comp Pathol Ther VL - 71 UR - https://doi.org/10.1016/S0368-1742(61)80043-X DO - 10.1016/S0368-1742(61)80043-X ID - Parish1961 ER - TY - JOUR AU - Songer, J. G. PY - 1996 DA - 1996// TI - Clostridial enteric diseases of domestic animals JO - Clin Microbiol Rev VL - 9 UR - https://doi.org/10.1128/CMR.9.2.216 DO - 10.1128/CMR.9.2.216 ID - Songer1996 ER - TY - JOUR AU - Lovland, A. AU - Kaldhusdal, M. PY - 2001 DA - 2001// TI - Severely impaired production performance in broiler flocks with high incidence of Clostridium perfringens-associated hepatitis JO - Avian Pathol. VL - 30 UR - https://doi.org/10.1080/03079450020023230 DO - 10.1080/03079450020023230 ID - Lovland2001 ER - TY - JOUR AU - Lepp, D. AU - Roxas, B. AU - Parreira, V. R. AU - Marri, P. R. AU - Rosey, E. L. AU - Gong, J. PY - 2010 DA - 2010// TI - Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0010795 DO - 10.1371/journal.pone.0010795 ID - Lepp2010 ER - TY - JOUR AU - Lepp, D. AU - Gong, J. AU - Songer, J. G. AU - Boerlin, P. AU - Parreira, V. R. AU - Prescott, J. F. PY - 2013 DA - 2013// TI - Identification of accessory genome regions in poultry Clostridium perfringens isolates carrying the netB plasmid JO - J Bacteriol VL - 195 UR - https://doi.org/10.1128/JB.01032-12 DO - 10.1128/JB.01032-12 ID - Lepp2013 ER - TY - JOUR AU - Keyburn, A. L. AU - Bannam, T. L. AU - Moore, R. J. AU - Rood, J. I. PY - 2010 DA - 2010// TI - NetB, a pore-forming toxin from necrotic enteritis strains of Clostridium perfringens JO - Toxins VL - 2 UR - https://doi.org/10.3390/toxins2071913 DO - 10.3390/toxins2071913 ID - Keyburn2010 ER - TY - JOUR AU - Keyburn, A. L. AU - Yan, X. -. X. AU - Bannam, T. L. AU - Van Immerseel, F. AU - Rood, J. I. AU - Moore, R. J. PY - 2010 DA - 2010// TI - Association between avian necrotic enteritis and Clostridium perfringens strains expressing NetB toxin JO - Vet Res VL - 41 UR - https://doi.org/10.1051/vetres/2009069 DO - 10.1051/vetres/2009069 ID - Keyburn2010 ER - TY - JOUR AU - Coursodon, C. F. AU - Glock, R. D. AU - Moore, K. L. AU - Cooper, K. K. AU - Songer, J. G. PY - 2012 DA - 2012// TI - TpeL-producing strains of Clostridium perfringens type a are highly virulent for broiler chicks JO - Anaerobe VL - 18 UR - https://doi.org/10.1016/j.anaerobe.2011.10.001 DO - 10.1016/j.anaerobe.2011.10.001 ID - Coursodon2012 ER - TY - JOUR AU - Allaart, J. G. AU - de, B. N. D. AU - van, A. A. J. A. M. AU - Fabri, T. H. F. AU - Gröne, A. PY - 2012 DA - 2012// TI - NetB-producing and beta2-producing Clostridium perfringens associated with subclinical necrotic enteritis in laying hens in the Netherlands JO - Avian Pathol VL - 41 UR - https://doi.org/10.1080/03079457.2012.729809 DO - 10.1080/03079457.2012.729809 ID - Allaart2012 ER - TY - JOUR AU - Han, X. AU - Du, X. -. D. AU - Southey, L. AU - Bulach, D. M. AU - Seemann, T. AU - Yan, X. -. X. PY - 2015 DA - 2015// TI - Functional analysis of a bacitracin resistance determinant located on ICECp1, a novel Tn916-like element from a conjugative plasmid in Clostridium perfringens JO - Antimicrob Agents Chemother VL - 59 UR - https://doi.org/10.1128/AAC.01643-15 DO - 10.1128/AAC.01643-15 ID - Han2015 ER - TY - JOUR AU - Edgar, R. C. PY - 2010 DA - 2010// TI - Search and clustering orders of magnitude faster than BLAST JO - Bioinforma. VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq461 DO - 10.1093/bioinformatics/btq461 ID - Edgar2010 ER - TY - JOUR AU - Wade, B. AU - Keyburn, A. AU - Haring, V. AU - Ford, M. AU - Rood, J. AU - Moore, R. PY - 2016 DA - 2016// TI - The adherent abilities of Clostridium perfringens strains are critical for the pathogenesis of avian necrotic enteritis JO - Vet Microbiol VL - 197 UR - https://doi.org/10.1016/j.vetmic.2016.10.028 DO - 10.1016/j.vetmic.2016.10.028 ID - Wade2016 ER - TY - JOUR AU - Wade, B. AU - Keyburn, A. L. AU - Seemann, T. AU - Rood, J. I. AU - Moore, R. J. PY - 2015 DA - 2015// TI - Binding of Clostridium perfringens to collagen correlates with the ability to cause necrotic enteritis in chickens JO - Vet Microbiol VL - 180 UR - https://doi.org/10.1016/j.vetmic.2015.09.019 DO - 10.1016/j.vetmic.2015.09.019 ID - Wade2015 ER - TY - JOUR AU - Timbermont, L. AU - De Smet, L. AU - Van Nieuwerburgh, F. AU - Parreira, V. R. AU - Van Driessche, G. AU - Haesebrouck, F. PY - 2014 DA - 2014// TI - Perfrin, a novel bacteriocin associated with netB positive Clostridium perfringens strains from broilers with necrotic enteritis JO - Vet Res VL - 45 UR - https://doi.org/10.1186/1297-9716-45-40 DO - 10.1186/1297-9716-45-40 ID - Timbermont2014 ER - TY - JOUR AU - Stamatakis, A. PY - 2014 DA - 2014// TI - RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu033 DO - 10.1093/bioinformatics/btu033 ID - Stamatakis2014 ER - TY - JOUR AU - Neumann, A. P. AU - Rehberger, T. G. PY - 2009 DA - 2009// TI - MLST analysis reveals a highly conserved core genome among poultry isolates of Clostridium septicum JO - Anaerobe VL - 15 UR - https://doi.org/10.1016/j.anaerobe.2009.01.005 DO - 10.1016/j.anaerobe.2009.01.005 ID - Neumann2009 ER - TY - JOUR AU - Gholamiandekhordi, A. R. AU - Ducatelle, R. AU - Heyndrickx, M. AU - Haesebrouck, F. AU - Van Immerseel, F. PY - 2006 DA - 2006// TI - Molecular and phenotypical characterization of Clostridium perfringens isolates from poultry flocks with different disease status JO - Vet Microbiol VL - 113 UR - https://doi.org/10.1016/j.vetmic.2005.10.023 DO - 10.1016/j.vetmic.2005.10.023 ID - Gholamiandekhordi2006 ER - TY - JOUR AU - Hughes, M. L. AU - Poon, R. AU - Adams, V. AU - Sayeed, S. AU - Saputo, J. AU - Uzal, F. A. PY - 2007 DA - 2007// TI - Epsilon-toxin plasmids of Clostridium perfringens type D are conjugative JO - J Bacteriol VL - 189 UR - https://doi.org/10.1128/JB.00767-07 DO - 10.1128/JB.00767-07 ID - Hughes2007 ER - TY - JOUR AU - Brynestad, S. AU - Sarker, M. R. AU - McClane, B. A. AU - Granum, P. E. AU - Rood, J. I. PY - 2001 DA - 2001// TI - Enterotoxin plasmid from Clostridium perfringens is conjugative JO - Infect Immun VL - 69 UR - https://doi.org/10.1128/IAI.69.5.3483-3487.2001 DO - 10.1128/IAI.69.5.3483-3487.2001 ID - Brynestad2001 ER - TY - JOUR AU - Crespo, R. AU - Fisher, D. J. AU - Shivaprasad, H. L. AU - Fernández-Miyakawa, M. E. AU - Uzal, F. A. PY - 2007 DA - 2007// TI - Toxinotypes of Clostridium perfringens isolated from sick and healthy avian species JO - J Vet Diagn Investig VL - 19 UR - https://doi.org/10.1177/104063870701900321 DO - 10.1177/104063870701900321 ID - Crespo2007 ER - TY - JOUR AU - Brady, J. AU - Hernandez-Doria, J. D. AU - Bennett, C. AU - Guenter, W. AU - House, J. D. AU - Rodriguez-Lecompte, J. C. PY - 2010 DA - 2010// TI - Toxinotyping of necrotic enteritis-producing and commensal isolates of Clostridium perfringens from chickens fed organic diets JO - Avian Pathol. VL - 39 UR - https://doi.org/10.1080/03079457.2010.521141 DO - 10.1080/03079457.2010.521141 ID - Brady2010 ER - TY - JOUR AU - Park, J. Y. AU - Kim, S. AU - Oh, J. Y. AU - Kim, H. R. AU - Jang, I. AU - Lee, H. S. PY - 2015 DA - 2015// TI - Characterization of Clostridium perfringens isolates obtained from 2010 to 2012 from chickens with necrotic enteritis in Korea JO - Poult Sci VL - 94 UR - https://doi.org/10.3382/ps/pev037 DO - 10.3382/ps/pev037 ID - Park2015 ER - TY - JOUR AU - Engström, B. E. AU - Johansson, A. AU - Aspan, A. AU - Kaldhusdal, M. PY - 2012 DA - 2012// TI - Genetic relatedness and netB prevalence among environmental Clostridium perfringens strains associated with a broiler flock affected by mild necrotic enteritis JO - Vet Microbiol VL - 159 UR - https://doi.org/10.1016/j.vetmic.2012.03.024 DO - 10.1016/j.vetmic.2012.03.024 ID - Engström2012 ER - TY - JOUR AU - Martin, T. G. AU - Smyth, J. A. PY - 2010 DA - 2010// TI - The ability of disease and non-disease producing strains of Clostridium perfringens from chickens to adhere to extracellular matrix molecules and Caco-2 cells JO - Anaerobe VL - 16 UR - https://doi.org/10.1016/j.anaerobe.2010.07.003 DO - 10.1016/j.anaerobe.2010.07.003 ID - Martin2010 ER - TY - JOUR AU - Barbara, A. J. AU - Trinh, H. T. AU - Glock, R. D. AU - Glenn Songer, J. PY - 2008 DA - 2008// TI - Necrotic enteritis-producing strains of Clostridium perfringens displace non-necrotic enteritis strains from the gut of chicks JO - Vet Microbiol VL - 126 UR - https://doi.org/10.1016/j.vetmic.2007.07.019 DO - 10.1016/j.vetmic.2007.07.019 ID - Barbara2008 ER - TY - JOUR AU - Ronco, T. AU - Stegger, M. AU - Ng, K. L. AU - Lilje, B. AU - Lyhs, U. AU - Andersen, P. S. PY - 2017 DA - 2017// TI - Genome analysis of Clostridium perfringens isolates from healthy and necrotic enteritis infected chickens and turkeys JO - BMC Res Notes VL - 10 UR - https://doi.org/10.1186/s13104-017-2594-9 DO - 10.1186/s13104-017-2594-9 ID - Ronco2017 ER - TY - JOUR AU - Yother, J. PY - 2011 DA - 2011// TI - Capsules of Streptococcus pneumoniae and other bacteria: paradigms for polysaccharide biosynthesis and regulation JO - Annu Rev Microbiol VL - 65 UR - https://doi.org/10.1146/annurev.micro.62.081307.162944 DO - 10.1146/annurev.micro.62.081307.162944 ID - Yother2011 ER - TY - JOUR AU - Bentley, S. D. AU - Aanensen, D. M. AU - Mavroidi, A. AU - Saunders, D. AU - Rabbinowitsch, E. AU - Collins, M. PY - 2006 DA - 2006// TI - Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes JO - PLoS Genet VL - 2 UR - https://doi.org/10.1371/journal.pgen.0020031 DO - 10.1371/journal.pgen.0020031 ID - Bentley2006 ER - TY - JOUR AU - Seo, N. AU - Tamai, K. AU - Nishida, S. PY - 1969 DA - 1969// TI - Criteria for identification of Clostridium perfringens. 5. Capsule formation and urease production JO - Igaku To Seibutsugaku VL - 79 ID - Seo1969 ER - TY - JOUR AU - Baine, H. AU - Cherniak, R. PY - 1971 DA - 1971// TI - Capsular polysaccharides of Clostridium perfringens Hobbs 5 JO - Biochemistry (Mosc) VL - 10 ID - Baine1971 ER - TY - JOUR AU - Cherniak, R. AU - Frederick, H. M. PY - 1977 DA - 1977// TI - Capsular polysaccharide of Clostridium perfringens Hobbs 9 JO - Infect Immun VL - 15 ID - Cherniak1977 ER - TY - JOUR AU - Sheng, S. AU - Cherniak, R. PY - 1997 DA - 1997// TI - Structure of the capsular polysaccharide of Clostridium perfringens Hobbs 10 determined by NMR spectroscopy JO - Carbohydr Res VL - 305 UR - https://doi.org/10.1016/S0008-6215(97)00280-2 DO - 10.1016/S0008-6215(97)00280-2 ID - Sheng1997 ER - TY - JOUR AU - Stringer, M. F. AU - Turnbull, P. C. AU - Hughes, J. A. AU - Hobbs, B. C. PY - 1976 DA - 1976// TI - An international serotyping system for Clostridium perfringens (welchii) type a in the near future JO - Dev Biol Stand VL - 32 ID - Stringer1976 ER - TY - JOUR AU - Vinogradov, E. AU - Aubry, A. AU - Logan, S. M. PY - 2017 DA - 2017// TI - Structural characterization of wall and lipidated polysaccharides from Clostridium perfringens ATCC 13124 JO - Carbohydr Res VL - 448 UR - https://doi.org/10.1016/j.carres.2017.06.003 DO - 10.1016/j.carres.2017.06.003 ID - Vinogradov2017 ER - TY - JOUR AU - Henderson, D. W. PY - 1940 DA - 1940// TI - The somatic antigens of the Cl. welchii group of organisms JO - J Hyg VL - 40 UR - https://doi.org/10.1017/S002217240002800X DO - 10.1017/S002217240002800X ID - Henderson1940 ER - TY - STD TI - Chaguza C, Andam CP, Harris SR, Cornick JE, Yang M, Bricio-Moreno L, et al. Recombination in Streptococcus pneumoniae lineages increase with carriage duration and size of the polysaccharide capsule. MBio. 2016;7:​e01053–16. ID - ref54 ER - TY - JOUR AU - O’Riordan, K. AU - Lee, J. C. PY - 2004 DA - 2004// TI - Staphylococcus aureus capsular polysaccharides JO - Clin Microbiol Rev VL - 17 UR - https://doi.org/10.1128/CMR.17.1.218-234.2004 DO - 10.1128/CMR.17.1.218-234.2004 ID - O’Riordan2004 ER - TY - JOUR AU - Caimano, M. J. AU - Hardy, G. G. AU - Yother, J. PY - 1998 DA - 1998// TI - Capsule genetics in Streptococcus pneumoniae and a possible role for transposition in the generation of the type 3 locus JO - Microb Drug Resist VL - 4 UR - https://doi.org/10.1089/mdr.1998.4.11 DO - 10.1089/mdr.1998.4.11 ID - Caimano1998 ER - TY - JOUR AU - Smith, H. E. AU - Damman, M. AU - van der Velde, J. AU - Wagenaar, F. AU - Wisselink, H. J. AU - Stockhofe-Zurwieden, N. PY - 1999 DA - 1999// TI - Identification and characterization of the cps locus of Streptococcus suis serotype 2: the capsule protects against phagocytosis and is an important virulence factor JO - Infect Immun VL - 67 ID - Smith1999 ER - TY - JOUR AU - Prescott, J. F. AU - Parreira, V. R. AU - Mehdizadeh Gohari, I. AU - Lepp, D. AU - Gong, J. PY - 2016 DA - 2016// TI - The pathogenesis of necrotic enteritis in chickens: what we know and what we need to know: a review JO - Avian Pathol. VL - 45 UR - https://doi.org/10.1080/03079457.2016.1139688 DO - 10.1080/03079457.2016.1139688 ID - Prescott2016 ER - TY - JOUR AU - Timbermont, L. AU - Lanckriet, A. AU - Pasmans, F. AU - Haesebrouck, F. AU - Ducatelle, R. AU - Van Immerseel, F. PY - 2009 DA - 2009// TI - Intra-species growth-inhibition by Clostridium perfringens is a possible virulence trait in necrotic enteritis in broilers JO - Vet Microbiol VL - 137 UR - https://doi.org/10.1016/j.vetmic.2009.01.017 DO - 10.1016/j.vetmic.2009.01.017 ID - Timbermont2009 ER - TY - JOUR AU - Simmons, M. AU - Donovan, D. M. AU - Siragusa, G. R. AU - Seal, B. S. PY - 2010 DA - 2010// TI - Recombinant expression of two bacteriophage proteins that lyse Clostridium perfringens and share identical sequences in the C-terminal cell wall binding domain of the molecules but are dissimilar in their N-terminal active domains JO - J Agric Food Chem VL - 58 UR - https://doi.org/10.1021/jf101387v DO - 10.1021/jf101387v ID - Simmons2010 ER - TY - JOUR AU - Boyd, E. F. AU - Brüssow, H. PY - 2002 DA - 2002// TI - Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved JO - Trends Microbiol VL - 10 UR - https://doi.org/10.1016/S0966-842X(02)02459-9 DO - 10.1016/S0966-842X(02)02459-9 ID - Boyd2002 ER - TY - JOUR AU - Baba, T. AU - Takeuchi, F. AU - Kuroda, M. AU - Yuzawa, H. AU - Aoki, K. AU - Oguchi, A. PY - 2002 DA - 2002// TI - Genome and virulence determinants of high virulence community-acquired MRSA JO - Lancet VL - 359 UR - https://doi.org/10.1016/S0140-6736(02)08713-5 DO - 10.1016/S0140-6736(02)08713-5 ID - Baba2002 ER - TY - JOUR AU - Smoot, L. M. AU - McCormick, J. K. AU - Smoot, J. C. AU - Hoe, N. P. AU - Strickland, I. AU - Cole, R. L. PY - 2002 DA - 2002// TI - Characterization of two novel pyrogenic toxin superantigens made by an acute rheumatic fever clone of Streptococcus pyogenes associated with multiple disease outbreaks JO - Infect Immun VL - 70 UR - https://doi.org/10.1128/IAI.70.12.7095-7104.2002 DO - 10.1128/IAI.70.12.7095-7104.2002 ID - Smoot2002 ER - TY - JOUR AU - Kim, K. -. P. AU - Born, Y. AU - Lurz, R. AU - Eichenseher, F. AU - Zimmer, M. AU - Loessner, M. J. PY - 2012 DA - 2012// TI - Inducible Clostridium perfringens bacteriophages ΦS9 and ΦS63 JO - Bacteriophage VL - 2 UR - https://doi.org/10.4161/bact.21363 DO - 10.4161/bact.21363 ID - Kim2012 ER - TY - JOUR AU - Zimmer, M. AU - Scherer, S. AU - Loessner, M. J. PY - 2002 DA - 2002// TI - Genomic analysis of Clostridium perfringens bacteriophage φ3626, which integrates into guaA and possibly affects sporulation JO - J Bacteriol VL - 184 UR - https://doi.org/10.1128/JB.184.16.4359-4368.2002 DO - 10.1128/JB.184.16.4359-4368.2002 ID - Zimmer2002 ER - TY - JOUR AU - Shimizu, T. AU - Ohtani, K. AU - Hirakawa, H. AU - Ohshima, K. AU - Yamashita, A. AU - Shiba, T. PY - 2002 DA - 2002// TI - Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater JO - Proc Natl Acad Sci VL - 99 UR - https://doi.org/10.1073/pnas.022493799 DO - 10.1073/pnas.022493799 ID - Shimizu2002 ER - TY - JOUR AU - Lucchini, S. AU - Desiere, F. AU - Brüssow, H. PY - 1999 DA - 1999// TI - Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria JO - Virology VL - 263 UR - https://doi.org/10.1006/viro.1999.9959 DO - 10.1006/viro.1999.9959 ID - Lucchini1999 ER - TY - JOUR AU - Gervasi, T. AU - Curto, R. L. AU - Narbad, A. AU - Mayer, M. J. PY - 2013 DA - 2013// TI - Complete genome sequence of ΦCP51, a temperate bacteriophage of Clostridium perfringens JO - Arch Virol VL - 158 UR - https://doi.org/10.1007/s00705-013-1647-1 DO - 10.1007/s00705-013-1647-1 ID - Gervasi2013 ER - TY - JOUR AU - Morales, C. A. AU - Oakley, B. B. AU - Garrish, J. K. AU - Siragusa, G. R. AU - Ard, M. B. AU - Seal, B. S. PY - 2012 DA - 2012// TI - Complete genome sequence of the podoviral bacteriophage ΦCP24R, which is virulent for Clostridium perfringens JO - Arch Virol VL - 157 UR - https://doi.org/10.1007/s00705-011-1218-2 DO - 10.1007/s00705-011-1218-2 ID - Morales2012 ER - TY - JOUR AU - Ronco, T. AU - Stegger, M. AU - Ng, K. L. AU - Lilje, B. AU - Lyhs, U. AU - Andersen, P. S. AU - Pedersen, K. PY - 2017 DA - 2017// TI - Genome analysis of Clostridium perfringens isolates from healthy and necrotic enteritis infected chickens and turkeys JO - BMC Res Notes VL - 10 UR - https://doi.org/10.1186/s13104-017-2594-9 DO - 10.1186/s13104-017-2594-9 ID - Ronco2017 ER - TY - JOUR AU - Karasov, W. H. AU - Douglas, A. E. PY - 2013 DA - 2013// TI - Comparative digestive physiology JO - Compr Physiol VL - 3 ID - Karasov2013 ER - TY - JOUR AU - Aronesty, E. PY - 2013 DA - 2013// TI - Comparison of sequencing utlitity programs JO - Open Bioinform J VL - 7 UR - https://doi.org/10.2174/1875036201307010001 DO - 10.2174/1875036201307010001 ID - Aronesty2013 ER - TY - JOUR AU - Peng, Y. AU - Leung, H. C. M. AU - Yiu, S. M. AU - Chin, F. Y. L. PY - 2012 DA - 2012// TI - IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth JO - Bioinforma. VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts174 DO - 10.1093/bioinformatics/bts174 ID - Peng2012 ER - TY - JOUR AU - Koren, S. AU - Walenz, B. P. AU - Berlin, K. AU - Miller, J. R. AU - Bergman, N. H. AU - Canu, P. A. M. PY - 2017 DA - 2017// TI - Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.215087.116 DO - 10.1101/gr.215087.116 ID - Koren2017 ER - TY - JOUR AU - Walker, B. J. AU - Abeel, T. AU - Shea, T. AU - Priest, M. AU - Abouelliel, A. AU - Sakthikumar, S. PY - 2014 DA - 2014// TI - Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0112963 DO - 10.1371/journal.pone.0112963 ID - Walker2014 ER - TY - JOUR AU - Treangen, T. J. AU - Ondov, B. D. AU - Koren, S. AU - Phillippy, A. M. PY - 2014 DA - 2014// TI - The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0524-x DO - 10.1186/s13059-014-0524-x ID - Treangen2014 ER - TY - JOUR AU - Seemann, T. PY - 2014 DA - 2014// TI - Prokka: rapid prokaryotic genome annotation JO - Bioinforma VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu153 DO - 10.1093/bioinformatics/btu153 ID - Seemann2014 ER - TY - BOOK AU - Sayers, E. PY - 2010 DA - 2010// TI - Entrez Programming Utilities Help ID - Sayers2010 ER - TY - JOUR AU - Chaudhari, N. M. AU - Gupta, V. K. AU - Dutta, C. PY - 2016 DA - 2016// TI - BPGA- an ultra-fast pan-genome analysis pipeline JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep24373 DO - 10.1038/srep24373 ID - Chaudhari2016 ER - TY - JOUR AU - Zhou, Y. AU - Liang, Y. AU - Lynch, K. H. AU - Dennis, J. J. AU - Wishart, D. S. PY - 2011 DA - 2011// TI - PHAST: a fast phage search tool JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr485 DO - 10.1093/nar/gkr485 ID - Zhou2011 ER - TY - JOUR AU - Roach, D. J. AU - Burton, J. N. AU - Lee, C. AU - Stackhouse, B. AU - Butler-Wu, S. M. AU - Cookson, B. T. PY - 2015 DA - 2015// TI - A year of infection in the intensive care unit: prospective whole genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel microbiota JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1005413 DO - 10.1371/journal.pgen.1005413 ID - Roach2015 ER - TY - JOUR AU - Sheedy, S. A. AU - Ingham, A. B. AU - Rood, J. I. AU - Moore, R. J. PY - 2004 DA - 2004// TI - Highly conserved alpha-toxin sequences of avian isolates of Clostridium perfringens JO - J Clin Microbiol VL - 42 UR - https://doi.org/10.1128/JCM.42.3.1345-1347.2003 DO - 10.1128/JCM.42.3.1345-1347.2003 ID - Sheedy2004 ER - TY - JOUR AU - Mehdizadeh Gohari, I. AU - Kropinski, A. M. AU - Weese, S. J. AU - Parreira, V. R. AU - Whitehead, A. E. AU - Boerlin, P. PY - 2016 DA - 2016// TI - Plasmid characterization and chromosome analysis of two netF+ Clostridium perfringens isolates associated with foal and canine necrotizing enteritis JO - PLoS One VL - 11 UR - https://doi.org/10.1371/journal.pone.0148344 DO - 10.1371/journal.pone.0148344 ID - Mehdizadeh Gohari2016 ER - TY - JOUR AU - Stanley, D. AU - Keyburn, A. L. AU - Denman, S. E. AU - Moore, R. J. PY - 2012 DA - 2012// TI - Changes in the caecal microflora of chickens following Clostridium perfringens challenge to induce necrotic enteritis JO - Vet Microbiol VL - 159 UR - https://doi.org/10.1016/j.vetmic.2012.03.032 DO - 10.1016/j.vetmic.2012.03.032 ID - Stanley2012 ER -