2,191
Views
4
CrossRef citations to date
0
Altmetric
Research Paper

Complete genome sequence of the Clostridium difficile LCL126

, , , &
Pages 745-754 | Received 09 Jan 2021, Accepted 19 Feb 2021, Published online: 25 Apr 2021

References

  • Rineh A, Kelso MJ, Vatansever F, et al. Clostridium difficile infection: molecular pathogenesis and novel therapeutics. Expert Review of Anti-infective Therapy. 2014;12(1):131–150.
  • Cao H, Wong S, Yam W, et al. Genomic investigation of a sequence type 67 Clostridium difficile causing community-acquired fulminant colitis in Hong Kong. Int J Med Microbiol. 2019;309(5):270–273.
  • Monot M, Eckert C, Lemire A, et al. Clostridium difficile: new insights into the evolution of the pathogenicity locus. Sci Rep. 2015;5(1):15023.
  • Marvaud JC, Quevedo-Torres S, Eckert C, et al. Virulence of new variant strains of Clostridium difficile producing only toxin A or binary toxin in the hamster model. Microbes Infect. 2019;32:100590.
  • Alcala L, Reigadas E, Marín M, et al. Impact of clinical awareness and diagnostic tests on the underdiagnosis of Clostridium difficile infection. Eur J Clin Microbiol Infect Dis. 2015;34:1515–1525.
  • Solomon SL, Oliver KB. Antibiotic resistance threats in the United States: stepping back from the brink. Am Fam Physician. 2014;89:938.
  • Dupuy B, Matamouros S. Regulation of toxin and bacteriocin synthesis in Clostridium species by a new subgroup of RNA polymerase σ-factors. Res Microbiol. 2006;157:201–205.
  • Knight DR, Elliott B, Chang BJ, et al. Diversity and evolution in the genome of Clostridium difficile. Clin Microbiol Rev. 2015;28:721–741.
  • Mani N, Dupuy B. Regulation of toxin synthesis in Clostridium difficile by an alternative RNA polymerase sigma factor. P Nat Acad Sci. 2001;98:5844–5849.
  • Wang S, Hong W, Dong S, et al. Genome engineering of Clostridium difficile using the CRISPR-Cas9 system. Clin Microbiol Infect. 2018;24:1095–1099.
  • Bouillaut L, Dubois T, Sonenshein A, et al. Integration of metabolism and virulence in Clostridium difficile. Res Microbiol. 2015;166:375–383.
  • Sim JHC, Truong C, Minot SS, et al. Determining the cause of recurrent Clostridium difficile infection using whole genome sequencing. Diagn Micr Infec Dis. 2017;87(1):11–16.
  • Zeng Z, Zhao H, Dorr MB, et al. Bezlotoxumab for prevention of Clostridium difficile infection recurrence: distinguishing relapse from reinfection with whole genome sequencing. Anaerobe. 2019;61:102137.
  • Quesada-Gómez C, Murillo T, Arce G, et al. Proteogenomic analysis of the Clostridium difficile exoproteome reveals a correlation between phylogenetic distribution and virulence potential. Anaerobe. 2020;62:102151.
  • Li Z, Liu X, Zhao J, et al. Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile. J Microbiol Methods. 2018;147:50–55.
  • Riedel T, Wittmann J, Bunk B, et al. A Clostridioides difficile bacteriophage genome encodes functional binary toxin-associated genes. J Biotechnol. 2017;250:23–28.
  • Lim HJ, Lee EH, Yoon Y, et al. Portable lysis apparatus for rapid single‐step DNA extraction of Bacillus. Portable lysis apparatus for rapid single‐step dna extraction of bacillus subtilis. J Appl Microbiol. 2016;120:379–387.
  • Reiner J, Pisani L, Qiao W, et al. Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of aBardet–Biedl Syndrome 9(BBS9) deletion. Npj Genom Med. 2018;3.
  • Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Nucleic Acids Res. 2001;29:2607–2618.
  • Hsiao W, Wan I, Jones SJ, et al. IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics. 2003;19:418–420.
  • Minoru M, Susumu G, Shuichi K, et al. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004;32:277–280.
  • Minoru M, Susumu G, Masahiro H, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34:354–357.
  • Galperin MY, Makarova KS, Wolf YI, et al. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2015;43:261–269.
  • Cantarel BL, Coutinho PM, Corinne R, et al. EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 2009;37:233–238.
  • Petersen TN, Brunak S, Heijne G, et al. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–786.
  • Valerie E, Thomas N, Alexander P, et al. DB—updates and novel features for a better annotation of bacterial secreted proteins and type III, IV, VI secretion systems. Nucleic Acids Res. 2016;44:669–674.
  • Martin U, Rashmi P, Arathi R, et al. Interactions database (PHI-base): additions and future developments. Nucleic Acids Res. 2015;43:645–655.
  • Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S, Marra M. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;1:1639–1645.
  • Holt K, Seth-Smith H, Quail M, et al. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci. 2010;107:7527–7532.
  • Forgetta V, Oughton MT, Marquis P, et al. Fourteen-genome comparison identifies DNA markers for severedisease- associated strains of Clostridium difficile. J Clin Microbiol. 2011;49:2230–2238.
  • Xu P, Zhang X, Su H, et al. Genome-wide analysis of PYL-PP2C-SnRK2s family in Camellia sinensis. Bioengineered. 2020;11:103–115.
  • Kuehne S, Minton N. ClosTron-mediated engineering of Clostridium. Bioengineered. 2012;3:247–254.
  • Andres-Lasheras S, Bolea R, Mainar-Jaime R, et al. Presence of Clostridium difficile in pig faecal samples and wild animal species associated with pig farms. J Appl Microbiol. 2017;122:462–472.
  • Kang Z, Zhang J, Jin P, et al. Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes. Bioengineered. 2015;6:136–140.
  • Sheehan D, O’Sullivan S. Online homology modelling as a means of bridging the sequence-structure gap. Bioengineered. 2011;2:299–305.
  • Janoir C. Virulence factors of Clostridium difficile and their role during infection. Anaerobe. 2016;37:13–24.
  • Tan Y, Yang X, Pei M, et al. A genome-wide survey of interaction between rice and Magnaporthe oryzae via microarray analysis. Bioengineered. 2021;12:108–116.