Hensgens MPM, Keessen EC, Squire MM, Riley TV, Koene MGJ, de Boer E, et al. Clostridium difficile infection in the community: a zoonotic disease? Clin Microbiol Infect. 2012;18:635–45.
Article
CAS
PubMed
Google Scholar
Barbut F, Lalande V, Beaugerie L, Eckert C. Clostridium difficile-associated diarrhea. Hepato-Gastro. 2013;20:111–22.
Hryckowian AJ, Pruss KM, Sonnenburg JL. The emerging metabolic view of Clostridium difficile pathogenesis. Curr Opin Microbiol. Elsevier Ltd. 2017;35:42–7.
Article
CAS
PubMed
Google Scholar
Miller BA, Chen LF, Sexton DJ, Anderson DJ. Comparison of the burdens of hospital-onset, healthcare facility-associated Clostridium difficile infection and of healthcare-associated infection due to methicillin-resistant Staphylococcus aureus in community hospitals. Infect Control Hosp Epidemiol. 2011;32:387–90.
Article
PubMed
Google Scholar
Balabanova Y, Gilsdorf A, Buda S, Burger R, Eckmanns T, Gärtner B, et al. Communicable diseases prioritized for surveillance and epidemiological research: results of a standardized prioritization procedure in Germany, 2011. PLoS One. 2011;6:1–7.
Google Scholar
Wilcox MH. Overcoming barriers to effective recognition and diagnosis of Clostridium difficile infection. Clin Microbiol Infect. European Society of Clinical Microbiology and Infectious Diseases. 2012;18:13–20.
Article
PubMed
Google Scholar
Knight DR, Elliott B, Chang BJ, Perkins TT, Riley TV. Diversity and evolution in the genome of Clostridium difficile. Clin Microbiol Rev. 2015;28:721–41.
Article
PubMed
PubMed Central
Google Scholar
Lessa FC, Gould CV, Clifford McDonald L. Current status of Clostridium difficile infection epidemiology. Clin Infect Dis. 2012;55:65–70.
Article
Google Scholar
Ghose C. Clostridium difficile infection in the twenty-first century. Emerg Microbes Infect. 2013;2:e62.
Article
PubMed
PubMed Central
Google Scholar
Steglich M, Nitsche A, von Müller L, Herrmann M, Kohl TA, Niemann S, et al. Tracing the spread of Clostridium difficile ribotype 027 in Germany based on bacterial genome sequences. PLoS One. 2015;10:e0139811.
Article
PubMed
PubMed Central
Google Scholar
Masri L, Branca A, Sheppard AE, Papkou A, Laehnemann D, Guenther PS, et al. Host–pathogen coevolution: the selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biol. 2015;13:e1002169.
Article
PubMed
PubMed Central
Google Scholar
Zdziarski J, Brzuszkiewicz E, Wullt B, Liesegang H, Biran D, Voigt B, et al. Host imprints on bacterial genomes--rapid, divergent evolution in individual patients. PLoS Pathog. 2010;6:e1001078.
Article
PubMed
PubMed Central
Google Scholar
Zhang L, Dong D, Jiang C, Li Z, Wang X, Peng Y. Insight into alteration of gut microbiota in Clostridium difficile infection and asymptomatic C. difficile colonization. Anaerobe. 2015;34:1–7.
Article
PubMed
Google Scholar
He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, et al. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A. 2010;107:7527–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet. 2006;38:779–86.
Article
PubMed
Google Scholar
Stabler RA, Dawson LF, Phua LTH, Wren BW. Comparative analysis of BI/NAP1/027 hypervirulent strains reveals novel toxin B-encoding gene (tcdB) sequences. J Med Microbiol. 2008;57:771–5.
Article
CAS
PubMed
Google Scholar
Braun V, Hundsberger T, Leukel P, Sauerborn M, Von Eichel-Streiber C. Definition of the single integration site of the pathogenicity locus in Clostridium difficile. Gene. 1996;181:29–38.
Article
CAS
PubMed
Google Scholar
Mullany P, Allan E, Roberts AP. Mobile genetic elements in Clostridium difficile and their role in genome function. Res Microbiol. Elsevier Masson SAS. 2015;166:361–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer F-D, et al. Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia Coli (EAHEC). Arch Microbiol. 2011;193:883–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eyre DW, Cule ML, Griffiths D, Crook DW, Peto TEA, Walker AS, et al. Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. PLoS Comput Biol. 2013;9:e1003059.
Article
CAS
PubMed
PubMed Central
Google Scholar
Balmer O, Tanner M. Prevalence and implications of multiple-strain infections. Lancet Infect Dis. 2011;11:868–78.
Article
PubMed
Google Scholar
Burns DA, Heeg D, Cartman ST, Minton NP. Reconsidering the Sporulation characteristics of Hypervirulent Clostridium difficile BI/NAP1/027. PLoS One. 2011;6:e24894.
Article
CAS
PubMed
PubMed Central
Google Scholar
Riedel T, Bunk B, Thuermer A, Sproer C, Brzuszkiewicz EB, et al. Genome Resequencing of the virulent and multidrug-resistant reference strain Clostridium difficile 630. Genome Announc. 2015;3:15–6.
Google Scholar
Riedel T, Bunk B, Wittmann J, Thürmer A, Spröer C, Gronow S, et al. Complete genome sequence of the Clostridium difficile type strain DSM 1296T. Genome Announc. 2015;3:3–4.
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Article
CAS
PubMed
Google Scholar
Dannheim H, Riedel T, Neumann-Schaal M, Bunk B, Schober I, Spröer C, et al. Manual curation and reannotation of the genomes of Clostridium difficile 630Δerm and C. difficile 630. J Med Microbiol. Microbiology Society. 2017;66:286–93.
Article
PubMed
Google Scholar
Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics. BioMed Central Ltd. 2011;12:124.
Article
PubMed
PubMed Central
Google Scholar
Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA. BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. BioMed Central Ltd. 2011;12:402.
Article
CAS
PubMed
PubMed Central
Google Scholar
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5:e11147.
Article
PubMed
PubMed Central
Google Scholar
Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, et al. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res. 2015;43:104–8.
Article
Google Scholar
Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrell BG, et al. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics. 2008;24:2672–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sahl JW, Matalka MN, Rasko DA. Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments. Appl Environ Microbiol. 2012;78:4884–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12.
Article
PubMed
PubMed Central
Google Scholar
Rupnik M, Brazier JS, Duerden BI, Grabnar M, Stubbs SLJ. Comparison of toxinotyping and PCR ribotyping of Clostridium difficile strains and description of novel toxinotypes. Microbiology. 2001;147:439–47.
Article
CAS
PubMed
Google Scholar
Aslam S, Hamill RJ, Musher DM. Treatment of Clostridium difficile-associated disease: old therapies and new strategies. Lancet Infect Dis. 2005;5:549–57.
Article
CAS
PubMed
Google Scholar
Crowther GS, Chilton CH, Todhunter SL, Nicholson S, Freeman J, Wilcox MH. Recurrence of dual-strain Clostridium difficile infection in an in vitro human gut model. J Antimicrob Chemother. 2015;70:2316–21.
Article
CAS
PubMed
Google Scholar
Brüggemann H, Brzuszkiewicz E, Chapeton-Montes D, Plourde L, Speck D. Genomics of Clostridium tetani. Res Microbiol. 2015;166:326–31.
Article
PubMed
Google Scholar
Carman RJ, Genheimer CW, Rafii F, Park M, Hiltonsmith MF, Lyerly DM. Diversity of moxifloxacin resistance during a nosocomial outbreak of a predominantly ribotype ARU 027 Clostridium difficile diarrhea. Anaerobe. 2009;15:244–8.
Article
CAS
PubMed
Google Scholar
Drudy D, Kyne L, O’Mahony R, Fanning S. gyrA mutations fluoroquinoloneresistant Clostridium difficile PCR-027 [3]. Emerg Infect Dis. 2007;13:504–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walkty A, Boyd DA, Gravel D, Hutchinson J, McGeer A, Moore D, et al. Molecular characterization of moxifloxacin resistance from Canadian Clostridium difficile clinical isolates. Diagn Microbiol Infect Dis. Elsevier B.V. 2010;66:419–24.
Article
CAS
PubMed
Google Scholar
Hargreaves KR, Otieno JR, Thanki A, Blades MJ, Millard AD, Browne HP, et al. As clear as mud? Determining the diversity and prevalence of prophages in the draft genomes of estuarine isolates of Clostridium difficile. Genome Biol Evol. 2015;7:1842–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wiedenbeck J, Cohan FM. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev. 2011;35:957–76.
Article
CAS
PubMed
Google Scholar
Castillo-Ramírez S, Harris SR, Holden MTG, He M, Parkhill J, Bentley SD, et al. The impact of recombination on dN/dS within recently emerged bacterial clones. PLoS Pathog. 2011;7:e1002129.
Article
PubMed
PubMed Central
Google Scholar
Johnson RC. Site-specific DNA inversion by serine Recombinases. 2014;1–36.
Anjuwon-Foster BR, Tamayo R, Browne H, Leung W, Frank J, Schmitz A. A genetic switch controls the production of flagella and toxins in Clostridium difficile. PLoS Genet. Kearns DB, editor. John Wiley & Sons, Inc. 2017;13:e1006701.
Article
PubMed
PubMed Central
Google Scholar
Emerson JE, Reynolds CB, Fagan RP, Shaw HA, Goulding D, Fairweather NF. A novel genetic switch controls phase variable expression of CwpV, a Clostridium difficile cell wall protein. Mol Microbiol. 2009;74:541–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tasteyre A, Karjalainen T, Avesani V, Delmée M, Collignon A, Bourlioux P, et al. Phenotypic and genotypic diversity of the flagellin gene (fliC) among Clostridium difficile isolates from different serogroups. J Clin Microbiol. 2000;38:3179–86.
CAS
PubMed
PubMed Central
Google Scholar
Stabler RA, He M, Dawson L, Martin M, Valiente E, Corton C, et al. Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol. 2009;10:R102.
Article
PubMed
PubMed Central
Google Scholar
Stevenson E, Minton NP, Kuehne SA. The role of flagella in Clostridium difficile pathogenicity. Trends Microbiol. Elsevier Ltd. 2015;23:275–82.
Article
CAS
PubMed
Google Scholar
Hargreaves KR, Thanki AM, Jose BR, Oggioni MR, MRJ C. Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078. BMC Genomics. 2016;17:1020. 2.
Article
Google Scholar