{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T11:32:46Z","timestamp":1790681566696,"version":"4.1.0"},"reference-count":129,"publisher":"Frontiers Media SA","funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP150104670"],"award-info":[{"award-number":["DP150104670"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2016.02138","type":"journal-article","created":{"date-parts":[[2017,1,11]],"date-time":"2017-01-11T03:32:34Z","timestamp":1484105554000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":112,"title":["Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission"],"prefix":"10.3389","volume":"7","author":[{"given":"Daniel R.","family":"Knight","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele M.","family":"Squire","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deirdre A.","family":"Collins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas V.","family":"Riley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2017,1,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"2716","DOI":"10.1128\/AAC.49.7.2716-2719.2005","article-title":"New lnu(C) gene conferring resistance to lincomycin by nucleotidylation in Streptococcus agalactiae UCN36","volume":"49","author":"Achard","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"B2","author":"ACSQHC","year":"2015","journal-title":"Antimicrobial Prescribing Practice in Australian Hospitals: Results of the 2014 National Antimicrobial Prescribing Survey. Australian Commission on Safety and Quality in Health Care Sydney, NSW"},{"key":"B3","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1111\/mmi.12299","article-title":"The functional vanGCd cluster of Clostridium difficile does not confer vancomycin resistance","volume":"89","author":"Ammam","year":"2013","journal-title":"Mol. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: a better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucl. Acids Res."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1968","DOI":"10.1093\/bioinformatics\/btp347","article-title":"ABACAS: algorithm-based automatic contiguation of assembled sequences","volume":"25","author":"Assefa","year":"2009","journal-title":"Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"B8","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1046\/j.1198-743x.2001.00289.x","article-title":"Epidemiology of Clostridium difficile-associated infections","volume":"7","author":"Barbut","year":"2001","journal-title":"Clin. Microbiol. Infect."},{"key":"B10","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1099\/jmm.0.029553-0","article-title":"Role of fibronectin-binding protein A in Clostridium difficile intestinal colonization","volume":"60","author":"Barketi-Klai","year":"2011","journal-title":"J. Med. Microbiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/S0140-6736(10)61266-4","article-title":"Clostridium difficile infection in Europe: a hospital-based survey","volume":"377","author":"Bauer","year":"2011","journal-title":"Lancet"},{"key":"B12","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1007\/s40121-016-0117-y","article-title":"Epidemiology and risk factors for community-associated Clostridium difficile infection: a narrative review","volume":"5","author":"Bloomfield","year":"2016","journal-title":"Infect. Dis. Ther."},{"key":"B13","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B14","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1016\/j.vetmic.2012.05.014","article-title":"Vermin on pig farms are vectors for Clostridium difficile PCR ribotypes 078 and 045","volume":"160","author":"Burt","year":"2012","journal-title":"Vet. Microbiol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","article-title":"Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data","volume":"28","author":"Carver","year":"2012","journal-title":"Bioinformatics"},{"key":"B16","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"B17","first-page":"11","article-title":"The conjugative transposon Tn916 of Enterococcus faecalis: structural analysis and some key factors involved in movement","volume":"85","author":"Clewell","year":"1995","journal-title":"Dev. Biol. Stand."},{"key":"B18","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1086\/651706","article-title":"Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA)","volume":"31","author":"Cohen","year":"2010","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1093\/bioinformatics\/btu661","article-title":"A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data","volume":"31","author":"Coil","year":"2015","journal-title":"Bioinformatics"},{"key":"B20","article-title":"Laboratory-based surveillance of Clostridium difficile strains circulating in the Australian healthcare setting in 2012","author":"Collins","year":"in press","journal-title":"Pathology"},{"key":"B21","doi-asserted-by":"publisher","first-page":"7696","DOI":"10.1128\/AEM.02411-13","article-title":"GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis","volume":"79","author":"Contreras-Moreira","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B23","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1128\/JCM.01599-06","article-title":"tcdC genotypes associated with severe TcdC truncation in an epidemic clone and other strains of Clostridium difficile","volume":"45","author":"Curry","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"e01237","DOI":"10.1128\/mBio.01237-16","article-title":"Accessory gene regulator-1 locus is essential for virulence and pathogenesis of Clostridium difficile","volume":"7","author":"Darkoh","year":"2016","journal-title":"MBio"},{"key":"B26","doi-asserted-by":"publisher","first-page":"e1004041","DOI":"10.1371\/journal.pcbi.1004041","article-title":"ClonalFrameML: efficient inference of recombination in whole bacterial genomes","volume":"11","author":"Didelot","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"R118","DOI":"10.1186\/gb-2012-13-12-r118","article-title":"Microevolutionary analysis of Clostridium difficile genomes to investigate transmission","volume":"13","author":"Didelot","year":"2012","journal-title":"Genome Biol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1093\/infdis\/jis734","article-title":"Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing","volume":"207","author":"Dingle","year":"2013","journal-title":"J. Infect. Dis."},{"key":"B29","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1093\/gbe\/evt204","article-title":"Evolutionary history of the Clostridium difficile pathogenicity locus","volume":"6","author":"Dingle","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"e19993","DOI":"10.1371\/journal.pone.0019993","article-title":"Clinical Clostridium difficile: clonality and pathogenicity locus diversity","volume":"6","author":"Dingle","year":"2011","journal-title":"PLoS ONE"},{"key":"B31","doi-asserted-by":"publisher","first-page":"608","DOI":"10.3201\/eid2204.150455","article-title":"Quantifying transmission of Clostridium difficile within and outside healthcare settings","volume":"22","author":"Durham","year":"2016","journal-title":"Emer. Infect. Dis."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1193","DOI":"10.1586\/14787210.2013.845987","article-title":"Clostridium difficile surveillance: harnessing new technologies to control transmission","volume":"11","author":"Eyre","year":"2013","journal-title":"Expert Rev. Anti Infect. Ther."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1056\/NEJMoa1216064","article-title":"Diverse sources of C. difficile infection identified on whole-genome sequencing","volume":"369","author":"Eyre","year":"2013","journal-title":"N.Engl. J. Med."},{"key":"B35","doi-asserted-by":"publisher","first-page":"e001124","DOI":"10.1136\/bmjopen-2012-001124","article-title":"A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance","volume":"2","author":"Eyre","year":"2012","journal-title":"BMJ Open"},{"key":"B36","doi-asserted-by":"publisher","first-page":"21059","DOI":"10.2807\/1560-7917.ES2015.20.10.21059","article-title":"Emergence and spread of predominantly community-onset Clostridium difficile PCR ribotype 244 infection in Australia, 2010 to 2012","volume":"20","author":"Eyre","year":"2015","journal-title":"Euro Surveill."},{"key":"B37","doi-asserted-by":"publisher","first-page":"2230","DOI":"10.1128\/JCM.00391-11","article-title":"Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile","volume":"49","author":"Forgetta","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1002\/nmi2.43","article-title":"Epidemiology of Clostridium difficile infection in two tertiary-care hospitals in Perth, Western Australia: a cross-sectional study","volume":"2","author":"Foster","year":"2014","journal-title":"New Microb. New Infect."},{"key":"B39","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1016\/j.cmi.2014.09.017","article-title":"Pan-European longitudinal surveillance of antibiotic resistance among prevalent Clostridium difficile ribotypes","volume":"21","author":"Freeman","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"B40","doi-asserted-by":"publisher","first-page":"15","DOI":"10.4161\/gmic.26854","article-title":"Clostridium difficile binary toxin CDT: mechanism, epidemiology, and potential clinical importance","volume":"5","author":"Gerding","year":"2014","journal-title":"Gut Microbes"},{"key":"B41","doi-asserted-by":"publisher","first-page":"e00840","DOI":"10.1128\/mBio.00840-13","article-title":"Phage \u03a6C2 mediates transduction of Tn6215, encoding erythromycin resistance, between Clostridium difficile strains","volume":"4","author":"Goh","year":"2013","journal-title":"MBio"},{"key":"B42","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1128\/JCM.01796-09","article-title":"Multilocus sequence typing of Clostridium difficile","volume":"48","author":"Griffiths","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/978-1-59745-251-9_6","article-title":"Estimating maximum likelihood phylogenies with PhyML","volume":"537","author":"Guindon","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B45","doi-asserted-by":"publisher","first-page":"184","DOI":"10.3389\/fmicb.2014.00184","article-title":"Clostridium difficile phages: still difficult?","volume":"5","author":"Hargreaves","year":"2014","journal-title":"Front. Microbiol."},{"key":"B46","doi-asserted-by":"publisher","first-page":"e85131","DOI":"10.1371\/journal.pone.0085131","article-title":"What does the talking?: quorum sensing signalling genes discovered in a bacteriophage genome","volume":"9","author":"Hargreaves","year":"2014","journal-title":"PLoS ONE"},{"key":"B47","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1126\/science.1182395","article-title":"Evolution of MRSA during hospital transmission and intercontinental spread","volume":"327","author":"Harris","year":"2010","journal-title":"Science"},{"key":"B48","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1038\/ng.2478","article-title":"Emergence and global spread of epidemic healthcare-associated Clostridium difficile","volume":"45","author":"He","year":"2013","journal-title":"Nat. Genet."},{"key":"B49","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1099\/00221287-147-1-87","article-title":"GroEL (Hsp60) of Clostridium difficile is involved in cell adherence","volume":"147","author":"Hennequin","year":"2001","journal-title":"Microbiology"},{"key":"B50","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1111\/j.1469-0691.2012.03853.x","article-title":"Clostridium difficile infection in the community: a zoonotic disease?","volume":"18","author":"Hensgens","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"B51","doi-asserted-by":"publisher","first-page":"8186","DOI":"10.1128\/JB.00690-07","article-title":"Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome","volume":"189","author":"Hiller","year":"2007","journal-title":"J. Bacteriol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1016\/j.vetmic.2010.10.013","article-title":"Acquisition of Clostridium difficile by piglets","volume":"149","author":"Hopman","year":"2011","journal-title":"Vet. Microbiol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13073-014-0090-6","article-title":"SRST2: rapid genomic surveillance for public health and hospital microbiology labs","volume":"6","author":"Inouye","year":"2014","journal-title":"Genome Med."},{"key":"B54","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1186\/1471-2180-14-173","article-title":"International Clostridium difficile animal strain collection and large diversity of animal associated strains","volume":"14","author":"Janezic","year":"2014","journal-title":"BMC Microbiol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"3881","DOI":"10.1128\/JB.00222-09","article-title":"Microarray identification of Clostridium difficile core components and divergent regions associated with host origin","volume":"191","author":"Janvilisri","year":"2009","journal-title":"J. Bacteriol."},{"key":"B56","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: scalable analysis of bacterial genome variation at the population level","volume":"11","author":"Jolley","year":"2010","journal-title":"BMC Bioinform."},{"key":"B57","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1111\/j.1751-0813.2009.00430.x","article-title":"Antimicrobial use in the Australian pig industry: results of a national survey","volume":"87","author":"Jordan","year":"2009","journal-title":"Aust. Vet. J."},{"key":"B58","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J. Mol. Biol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"B60","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1016\/j.envres.2011.09.014","article-title":"Aerial dissemination of Clostridium difficile on a pig farm and its environment","volume":"111","author":"Keessen","year":"2011","journal-title":"Environ. Res."},{"key":"B61","doi-asserted-by":"publisher","first-page":"30","DOI":"10.2807\/1560-7917.ES2014.19.45.20954","article-title":"Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011","volume":"19","author":"Knetsch","year":"2014","journal-title":"Euro Surveill."},{"key":"B62","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.1016\/j.meegid.2012.06.003","article-title":"Comparative analysis of an expanded Clostridium difficile reference strain collection reveals genetic diversity and evolution through six lineages","volume":"12","author":"Knetsch","year":"2012","journal-title":"Infect. Genet. Evol."},{"key":"B63","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1128\/CMR.00127-14","article-title":"Diversity and evolution in the genome of Clostridium difficile","volume":"28","author":"Knight","year":"2015a","journal-title":"Clin. Microbiol. Rev."},{"key":"B64","doi-asserted-by":"publisher","first-page":"2992","DOI":"10.1093\/jac\/dkv220","article-title":"Surveillance for antimicrobial resistance in Australian isolates of Clostridium difficile, 2013-14","volume":"70","author":"Knight","year":"2015b","journal-title":"J. Antimicrob. Chemother."},{"key":"B65","doi-asserted-by":"publisher","first-page":"266.e261","DOI":"10.1016\/j.cmi.2015.11.017","article-title":"Contamination of Australian newborn calf carcasses at slaughter with Clostridium difficile","volume":"22","author":"Knight","year":"2016","journal-title":"Clin. Microbiol. Infect."},{"key":"B66","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1128\/AEM.03032-14","article-title":"Nationwide surveillance study of Clostridium difficile in Australian neonatal pigs shows high prevalence and heterogeneity of PCR ribotypes","volume":"81","author":"Knight","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"B67","doi-asserted-by":"publisher","first-page":"2630","DOI":"10.1128\/AEM.03951-12","article-title":"Cross-sectional study reveals high prevalence of Clostridium difficile non-PCR ribotype 078 strains in Australian veal calves at slaughter","volume":"79","author":"Knight","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"4668","DOI":"10.1128\/jb.173.15.4668-4674.1991","article-title":"Expression of the iap gene coding for protein p60 of Listeria monocytogenes is controlled on the posttranscriptional level","volume":"173","author":"K\u00f6hler","year":"1991","journal-title":"J. Bacteriol."},{"key":"B69","doi-asserted-by":"publisher","first-page":"3733","DOI":"10.1093\/bioinformatics\/btv465","article-title":"GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments","volume":"31","author":"Kosugi","year":"2015","journal-title":"Bioinformatics"},{"key":"B70","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/nature09397","article-title":"The role of toxin A and toxin B in Clostridium difficile infection","volume":"467","author":"Kuehne","year":"2010","journal-title":"Nature"},{"key":"B71","doi-asserted-by":"publisher","first-page":"e86535","DOI":"10.1371\/journal.pone.0086535","article-title":"Sequence similarity of Clostridium difficile strains by analysis of conserved genes and genome content is reflected by their ribotype affiliation","volume":"9","author":"Kurka","year":"2014","journal-title":"PLoS ONE"},{"key":"B72","doi-asserted-by":"publisher","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"B73","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.femsle.2004.07.022","article-title":"The cme gene of Clostridium difficile confers multidrug resistance in Enterococcus faecalis","volume":"238","author":"Lebel","year":"2004","journal-title":"FEMS Microbiol. Lett."},{"key":"B74","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1056\/NEJMoa1408913","article-title":"Burden of Clostridium difficile infection in the United States","volume":"372","author":"Lessa","year":"2015","journal-title":"N.Engl. J. Med."},{"key":"B75","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B76","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1128\/JB.01021-13","article-title":"Comparative analysis of the full genome of the Helicobacter pylori isolate, Sahul64, identifies genes of high divergence","volume":"196","author":"Lu","year":"2013","journal-title":"J. Bacteriol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.jhin.2015.01.021","article-title":"Whole-genome sequencing improves discrimination of relapse from reinfection and identifies transmission events among patients with recurrent Clostridium difficile infections","volume":"90","author":"Mac Aog\u00e1in","year":"2015","journal-title":"J. Hosp. Infect."},{"key":"B78","first-page":"117","article-title":"Antimicrobial resistance in enteric pathogens isolated from Minnesota pigs from 1995 to 2004","volume":"75","author":"Malik","year":"2011","journal-title":"Can. J. Vet. Res."},{"key":"B79","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1111\/j.1472-765X.2010.02933.x","article-title":"Clostridium difficile in vegetables, Canada","volume":"51","author":"Metcalf","year":"2010","journal-title":"Lett. Appl. Microbiol."},{"key":"B80","doi-asserted-by":"publisher","first-page":"1028","DOI":"10.1089\/cmb.2006.13.1028","article-title":"A fast and symmetric DUST implementation to mask low-complexity DNA sequences","volume":"13","author":"Morgulis","year":"2006","journal-title":"J. Comput. Biol."},{"key":"B81","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1016\/j.resmic.2014.12.005","article-title":"Mobile genetic elements in Clostridium difficile and their role in genome function","volume":"166","author":"Mullany","year":"2015","journal-title":"Res. Microbiol."},{"key":"B82","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/0378-1119(96)00511-2","article-title":"A group II intron in a conjugative transposon from the gram-positive bacterium, Clostridium difficile","volume":"174","author":"Mullany","year":"1996","journal-title":"Gene"},{"key":"B83","doi-asserted-by":"publisher","first-page":"2813","DOI":"10.1128\/AAC.00342-08","article-title":"Rifampin and rifaximin resistance in clinical isolates of Clostridium difficile","volume":"52","author":"O'Connor","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"B84","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1186\/1471-2164-15-737","article-title":"Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt","volume":"15","author":"Ozer","year":"2014","journal-title":"BMC Genomics"},{"key":"B85","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"B86","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-15-160","article-title":"Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism","volume":"15","author":"Pettit","year":"2014","journal-title":"BMC Genomics"},{"key":"B87","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.str.2014.11.018","article-title":"Structural and evolutionary analyses show unique stabilization strategies in the type IV pili of Clostridium difficile","volume":"23","author":"Piepenbrink","year":"2015","journal-title":"Structure"},{"key":"B88","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1111\/j.1469-0691.2009.03077.x","article-title":"Impact of an intervention to control Clostridium difficile infection on hospital-and community-onset disease; an interrupted time series analysis","volume":"16","author":"Price","year":"2010","journal-title":"Clin. Microbiol. Infect."},{"key":"B89","author":"Rambaut","year":"2007","journal-title":"FigTree, A Graphical Viewer of Phylogenetic Trees"},{"key":"B90","doi-asserted-by":"publisher","first-page":"6881","DOI":"10.1128\/JB.00619-08","article-title":"The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates","volume":"190","author":"Rasko","year":"2008","journal-title":"J. Bacteriol."},{"key":"B91","doi-asserted-by":"crossref","first-page":"661","DOI":"10.5694\/j.1326-5377.2009.tb02630.x","article-title":"Is Clostridium difficile a threat to Australia's biosecurity?","volume":"190","author":"Riley","year":"2009","journal-title":"Med. J. Aust."},{"key":"B92","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/bs.ampbs.2014.08.002","article-title":"The impact of horizontal gene transfer on the biology of Clostridium difficile","volume":"65","author":"Roberts","year":"2014","journal-title":"Adv. Microb. Physiol."},{"key":"B93","doi-asserted-by":"publisher","first-page":"856","DOI":"10.1111\/j.1574-6976.2011.00283.x","article-title":"Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance","volume":"35","author":"Roberts","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"B94","doi-asserted-by":"publisher","first-page":"1296","DOI":"10.1128\/JB.183.4.1296-1299.2001","article-title":"Demonstration that the group II intron from the clostridial conjugative transposon Tn5397 undergoes splicing in vivo","volume":"183","author":"Roberts","year":"2001","journal-title":"J. Bacteriol."},{"key":"B95","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1128\/AEM.41.4.950-955.1981","article-title":"Characterization of the cecal bacteria of normal pigs","volume":"41","author":"Robinson","year":"1981","journal-title":"Appl. Environ. Microbiol."},{"key":"B96","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1016\/S0140-6736(15)00730-8","article-title":"Animal production and antimicrobial resistance in the clinic","volume":"387","author":"Robinson","year":"2016","journal-title":"Lancet"},{"key":"B97","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/5584_2016_27","article-title":"Clostridium difficile in food and animals: a comprehensive review","volume":"932","author":"Rodriguez","year":"2016","journal-title":"Adv. Exp. Med. Biol."},{"key":"B98","doi-asserted-by":"publisher","first-page":"158601","DOI":"10.1155\/2014\/158601","article-title":"Clostridium difficile with moxifloxacin\/clindamycin resistance in vegetables in Ohio, USA, and prevalence meta-analysis","volume":"2014","author":"Rodriguez-Palacios","year":"2014","journal-title":"J. Pathog."},{"key":"B99","doi-asserted-by":"publisher","first-page":"6643","DOI":"10.1128\/AEM.01379-12","article-title":"Toxigenic Clostridium difficile PCR ribotypes from wastewater treatment plants in southern Switzerland","volume":"78","author":"Romano","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"B100","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/S1043-4526(10)60003-4","article-title":"Clostridium difficile: its potential as a source of foodborne disease","volume":"60","author":"Rupnik","year":"2010","journal-title":"Adv. Food Nutr. Res."},{"key":"B101","doi-asserted-by":"publisher","first-page":"e15147","DOI":"10.1371\/journal.pone.0015147","article-title":"Analysis of ultra low genome conservation in Clostridium difficile","volume":"5","author":"Scaria","year":"2010","journal-title":"PLoS ONE"},{"key":"B102","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/1471-2431-14-28","article-title":"Severe clinical outcome is uncommon in Clostridium difficile infection in children: a retrospective cohort study","volume":"14","author":"Schwartz","year":"2014","journal-title":"BMC Pediatr."},{"key":"B103","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1038\/ng1830","article-title":"The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome","volume":"38","author":"Sebaihia","year":"2006","journal-title":"Nat. Genet."},{"key":"B104","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B105","doi-asserted-by":"publisher","first-page":"6027","DOI":"10.1128\/AEM.01311-12","article-title":"Prophage carriage and diversity within clinically relevant strains of Clostridium difficile","volume":"78","author":"Shan","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"B106","doi-asserted-by":"publisher","first-page":"272","DOI":"10.5694\/mja13.11153","article-title":"Increasing incidence of Clostridium difficile infection, Australia, 2011-2012","volume":"200","author":"Slimings","year":"2014","journal-title":"Med. J. Aust."},{"key":"B107","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1177\/2049936115622891","article-title":"Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection","volume":"3","author":"Spigaglia","year":"2016","journal-title":"Ther. Adv. Infect. Dis."},{"key":"B108","doi-asserted-by":"publisher","first-page":"5142","DOI":"10.1128\/AAC.49.12.5142-5145.2005","article-title":"Horizontal transfer of erythromycin resistance from Clostridium difficile to Butyrivibrio fibrisolvens","volume":"49","author":"Spigaglia","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"B109","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1128\/AAC.00957-07","article-title":"Tetracycline resistance gene tet(W) in the pathogenic bacterium Clostridium difficile","volume":"52","author":"Spigaglia","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"B110","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1007\/82_2012_237","article-title":"Clostridium difficile infection in humans and piglets: a \u2018One Health\u2019 opportunity","volume":"365","author":"Squire","year":"2013","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"B111","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1071\/ma15040","article-title":"Community-acquired Clostridium difficile infection and Australian food animals","volume":"36","author":"Squire","year":"2015","journal-title":"Microbiol. Aus."},{"key":"B112","first-page":"215","article-title":"Detection of Clostridium difficile after treatment in a two-stage pond system","volume-title":"Proceedings of 13th Biannual Conference of the Australian Pig Science Association (APSA), Vol. 8, Manipulating Pig Production","author":"Squire","year":"2011"},{"key":"B113","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"B114","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1016\/j.tim.2015.01.004","article-title":"The role of flagella in Clostridium difficile pathogenicity","volume":"23","author":"Stevenson","year":"2015","journal-title":"Trends Microbiol."},{"key":"B115","doi-asserted-by":"publisher","first-page":"e0164504","DOI":"10.1371\/journal.pone.0164504","article-title":"More than 50% of Clostridium difficile isolates from pet dogs in Flagstaff, USA, carry toxigenic genotypes","volume":"11","author":"Stone","year":"2016","journal-title":"PLoS ONE"},{"key":"B116","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","article-title":"Easyfig: a genome comparison visualizer","volume":"27","author":"Sullivan","year":"2011","journal-title":"Bioinformatics"},{"key":"B117","doi-asserted-by":"publisher","first-page":"2725","DOI":"10.1093\/molbev\/mst197","article-title":"MEGA6: molecular evolutionary genetics analysis version 6.0","volume":"30","author":"Tamura","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"B118","doi-asserted-by":"publisher","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B119","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","article-title":"Comparative genomics: the bacterial pan-genome","volume":"11","author":"Tettelin","year":"2008","journal-title":"Curr. Opin. Microbiol."},{"key":"B120","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.1086\/342691","article-title":"Clostridium difficile-associated diarrhea: epidemiological data from Western Australia associated with a modified antibiotic policy","volume":"35","author":"Thomas","year":"2002","journal-title":"Clin. Infect. Dis."},{"key":"B121","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0524-x","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes","volume":"15","author":"Treangen","year":"2014","journal-title":"Genome Biol."},{"key":"B122","doi-asserted-by":"publisher","first-page":"5649","DOI":"10.1073\/pnas.1503141112","article-title":"Global trends in antimicrobial use in food animals","volume":"112","author":"Van Boeckel","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B123","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.mib.2014.11.016","article-title":"Ten years of pan-genome analyses","volume":"23","author":"Vernikos","year":"2015","journal-title":"Curr. Opin. Microbiol."},{"key":"B124","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1128\/AEM.01331-08","article-title":"Survey of wastewater indicators and human pathogen genomes in biosolids produced by class A and class B stabilization treatments","volume":"75","author":"Viau","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"B125","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1089\/mdr.2014.0015","article-title":"Inter- and intraspecies transfer of a Clostridium difficile conjugative transposon conferring resistance to MLSB","volume":"20","author":"Wasels","year":"2014","journal-title":"Microb. Drug Resist."},{"key":"B126","doi-asserted-by":"publisher","first-page":"17020","DOI":"10.1073\/pnas.252529799","article-title":"Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli","volume":"99","author":"Welch","year":"2002","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B127","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1111\/jam.13018","article-title":"Persistence of Clostridium difficile in wastewater treatment-derived biosolids during land application or windrow composting","volume":"120","author":"Xu","year":"2016","journal-title":"J. Appl. Microbiol."},{"key":"B128","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1111\/jam.12575","article-title":"Fate of Clostridium difficile during wastewater treatment and incidence in Southern Ontario watersheds","volume":"117","author":"Xu","year":"2014","journal-title":"J. Appl. Microbiol."},{"key":"B129","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1093\/bioinformatics\/btu017","article-title":"PanGP: a tool for quickly analyzing bacterial pan-genome profile","volume":"30","author":"Zhao","year":"2014","journal-title":"Bioinformatics"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fmicb.2016.02138\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,28]],"date-time":"2020-09-28T21:09:01Z","timestamp":1601327341000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fmicb.2016.02138\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,1,11]]},"references-count":129,"URL":"https:\/\/doi.org\/10.3389\/fmicb.2016.02138","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,11]]}}}