References
- Bartlett JG. Clinical practice. antibiotic-associated diarrhea. N Engl J Med. 2002;346:334–339. DOI:https://doi.org/10.1056/NEJMcp011603.
- Bartlett JG, Gerding DN. Clinical recognition and diagnosis of Clostridium difficile infection. Clin Infect Dis. 2008;46(Suppl 1):S12–S18. DOI:https://doi.org/10.1086/521863.
- Barbut F, Petit JC. Epidemiology of Clostridium difficile-associated infections. Clin Microbiol Infect. 2001;7:405–410. DOI:https://doi.org/10.1046/j.1198-743x.2001.00289.x.
- Khanna S, Pardi DS, Aronson SL, et al. The epidemiology of community-acquired Clostridium difficile infection: a population-based study. Am J Gastroenterol. 2012;107:89–95. DOI:https://doi.org/10.1038/ajg.2011.398.
- Worth LJ, Spelman T, Bull AL, et al. Epidemiology of Clostridium difficile infections in Australia: enhanced surveillance to evaluate time trends and severity of illness in Victoria, 2010-2014. J Hosp Infect. 2016;93:280–285. DOI:https://doi.org/10.1016/j.jhin.2016.03.014.
- Riggs MM, Sethi AK, Zabarsky TF, et al. Asymptomatic carriers are a potential source for transmission of epidemic and nonepidemic Clostridium difficile strains among long-term care facility residents. Clin Infect Dis. 2007;45:992–998. DOI:https://doi.org/10.1086/521854.
- Eyre DW, Cule ML, Wilson DJ, et al. Diverse sources of C. difficile infection identified on whole-genome sequencing. N Engl J Med. 2013;369:1195–1205. DOI:https://doi.org/10.1056/NEJMoa1216064.
- Curry SR, Muto CA, Schlackman JL, et al. Use of multilocus variable number of tandem repeats analysis genotyping to determine the role of asymptomatic carriers in Clostridium difficile transmission. Clin Infect Dis. 2013;57:1094–1102. DOI:https://doi.org/10.1093/cid/cit475.
- Baron SW, Ostrowsky BE, Nori P, et al. Screening of Clostridioides difficile carriers in an urban academic medical center: understanding implications of disease. Infect Control Hosp Epidemiol. 2020;41:149–153. DOI:https://doi.org/10.1017/ice.2019.309.
- Mi H, Bao R, Xiao Y, et al. Colonization of toxigenic Clostridium difficile Among intensive care unit patients: A multi-centre cross-sectional study. Front Cell Infect Microbiol. 2020;10:12. DOI:https://doi.org/10.3389/fcimb.2020.00012.
- Heise J, Witt P, Maneck C, et al. Prevalence and phylogenetic relationship of Clostridioides difficile strains in fresh poultry meat samples processed in different cutting plants. Int J Food Microbiol. 2021;339:109032. DOI:https://doi.org/10.1016/j.ijfoodmicro.2020.109032.
- Warriner K, Xu C, Habash M, et al. Dissemination of Clostridium difficile in food and the environment: significant sources of C. difficile community-acquired infection? J Appl Microbiol. 2017;122:542–553. DOI:https://doi.org/10.1111/jam.13338.
- Lim SC, Knight DR, Riley TV. Clostridium difficile and One health. Clin Microbiol Infect. 2020;26:857–863. DOI:https://doi.org/10.1016/j.cmi.2019.10.023.
- Knight DR, Riley TV. Genomic delineation of Zoonotic origins of Clostridium difficile. Front Public Health. 2019;7:164. DOI:https://doi.org/10.3389/fpubh.2019.00164.
- Werner A, Molling P, Fagerstrom A, et al. Whole genome sequencing of Clostridioides difficile PCR ribotype 046 suggests transmission between pigs and humans. PLoS One. 2020;15:e0244227. DOI:https://doi.org/10.1371/journal.pone.0244227.
- Wu YC, Chen CM, Kuo CJ, et al. Prevalence and molecular characterization of Clostridium difficile isolates from a pig slaughterhouse, pork, and humans in Taiwan. Int J Food Microbiol. 2017;242:37–44. DOI:https://doi.org/10.1016/j.ijfoodmicro.2016.11.010.
- Zhang WZ, Li WG, Liu YQ, et al. The molecular characters and antibiotic resistance of Clostridioides difficile from economic animals in China. BMC Microbiol. 2020;20:70. DOI:https://doi.org/10.1186/s12866-020-01757-z.
- Debast SB, Bauer MP, Kuijper EJ, et al. European society of Clinical microbiology and Infectious Diseases: update of the treatment guidance document for Clostridium difficile infection. Clin Microbiol Infect. 2014;20(Suppl 2):1–26. DOI:https://doi.org/10.1111/1469-0691.12418.
- Chen YB, Gu SL, Shen P, et al. Molecular epidemiology and antimicrobial susceptibility of Clostridium difficile isolated from hospitals during a 4-year period in China. J Med Microbiol. 2018;67:52–59. DOI:https://doi.org/10.1099/jmm.0.000646.
- Lv T, Chen Y, Guo L, et al. Whole genome analysis reveals new insights into the molecular characteristics of Clostridioides difficile NAP1/BI/027/ST1 clinical isolates in the People's Republic of China. Infect Drug Resist. 2019;12:1783–1794. DOI:https://doi.org/10.2147/IDR.S203238.
- Monot M, Eckert C, Lemire A, et al. Clostridium difficile: New insights into the Evolution of the pathogenicity locus. Sci Rep. 2015;5:15023. DOI:https://doi.org/10.1038/srep15023.
- Jin D, Luo Y, Huang C, et al. Molecular epidemiology of Clostridium difficile infection in hospitalized patients in eastern China. J Clin Microbiol. 2017;55:801–810. DOI:https://doi.org/10.1128/JCM.01898-16.
- Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. DOI:https://doi.org/10.1093/bioinformatics/btu170.
- Nurk S, Bankevich A, Antipov D, et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013;20:714–737. DOI:https://doi.org/10.1089/cmb.2013.0084.
- Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. DOI:https://doi.org/10.12688/wellcomeopenres.14826.1.
- Knight DR, Kullin B, Androga GO, et al. Evolutionary and genomic insights into Clostridioides difficile sequence type 11: a diverse Zoonotic and antimicrobial-resistant lineage of global One Health importance. mBio. 2019;10. DOI:https://doi.org/10.1128/mBio.00446-19.
- Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–2069. DOI:https://doi.org/10.1093/bioinformatics/btu153.
- Croucher NJ, Page AJ, Connor TR, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using gubbins. Nucleic Acids Res. 2015;43:e15), DOI:https://doi.org/10.1093/nar/gku1196.
- Silva M, Machado MP, Silva DN, et al. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom. 2018;4. DOI:https://doi.org/10.1099/mgen.0.000166.
- Tamura K, Stecher G, Kumar S. MEGA11: molecular Evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38:3022–7. DOI:https://doi.org/10.1093/molbev/msab120.
- Letunic I, Bork P. Interactive Tree of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 2011;39:W475–W478. DOI:https://doi.org/10.1093/nar/gkr201.
- Nascimento M, Sousa A, Ramirez M, et al. PHYLOViz 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. Bioinformatics. 2017;33:128–129. DOI:https://doi.org/10.1093/bioinformatics/btw582.
- Ruan Z, Feng Y. BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. Nucleic Acids Res. 2016;44:D682–D687. DOI:https://doi.org/10.1093/nar/gkv1004.
- Knight DR, Squire MM, Collins DA, et al. 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. Front Microbiol. 2016;7:2138. DOI:https://doi.org/10.3389/fmicb.2016.02138.
- Carattoli A, Zankari E, Garcia-Fernandez A, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58:3895–3903. DOI:https://doi.org/10.1128/AAC.02412-14.
- Shen E, Zhu K, Li D, et al. Subtyping analysis reveals new variants and accelerated evolution of Clostridioides difficile toxin B. Commun Biol. 2020;3:347. DOI:https://doi.org/10.1038/s42003-020-1078-y.
- Chitnis AS, Holzbauer SM, Belflower RM, et al. Epidemiology of community-associated Clostridium difficile infection, 2009 through 2011. JAMA Intern Med. 2013;173:1359–1367. DOI:https://doi.org/10.1001/jamainternmed.2013.7056.
- Gonzalez-Orta M, Saldana C, Ng-Wong Y, et al. Are many patients diagnosed With healthcare-associated Clostridioides difficile infections colonized With the infecting strain on admission? Clin Infect Dis. 2019;69:1801–1804. DOI:https://doi.org/10.1093/cid/ciz189.
- Ofori E, Ramai D, Dhawan M, et al. Community-acquired Clostridium difficile: epidemiology, ribotype, risk factors, hospital and intensive care unit outcomes, and current and emerging therapies. J Hosp Infect. 2018;99:436–442. DOI:https://doi.org/10.1016/j.jhin.2018.01.015.
- Keessen EC, Harmanus C, Dohmen W, et al. Clostridium difficile infection associated with pig farms. Emerg Infect Dis. 2013;19:1032–1034. DOI:https://doi.org/10.3201/eid1906.121645.
- Davies KA, Ashwin H, Longshaw CM, et al. Diversity of Clostridium difficile PCR ribotypes in Europe: results from the european, multicentre, prospective, biannual, point-prevalence study of Clostridium difficile infection in hospitalised patients with diarrhoea (EUCLID), 2012 and 2013. Euro Surveill. 2016: 21. DOI:https://doi.org/10.2807/1560-7917.ES.2016.21.29.30294.
- Luo Y, Cheong E, Bian Q, et al. Different molecular characteristics and antimicrobial resistance profiles of Clostridium difficile in the Asia-Pacific region. Emerg Microbes Infect. 2019;8:1553–1562. DOI:https://doi.org/10.1080/22221751.2019.1682472.
- Berger FK, Mellmann A, Bischoff M, et al. Molecular epidemiology and antimicrobial resistance of Clostridioides difficile detected in chicken, soil and human samples from Zimbabwe. Int J Infect Dis. 2020;96:82–87. DOI:https://doi.org/10.1016/j.ijid.2020.04.026.
- Frentrup M, Thiel N, Junker V, et al. Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile. Environ Microbiol. 2021. DOI:https://doi.org/10.1111/1462-2920.15601.
- Lim SC, Foster NF, Elliott B, et al. High prevalence of Clostridium difficile on retail root vegetables, western Australia. J Appl Microbiol. 2018;124:585–590. DOI:https://doi.org/10.1111/jam.13653.
- Bloomfield LE, Riley TV. Epidemiology and Risk factors for community-associated Clostridium difficile infection: A narrative review. Infect Dis Ther. 2016;5:231–251. DOI:https://doi.org/10.1007/s40121-016-0117-y.
- Pepin J, Gonzales M, Valiquette L. Risk of secondary cases of Clostridium difficile infection among household contacts of index cases. J Infect. 2012;64:387–390. DOI:https://doi.org/10.1016/j.jinf.2011.12.011.
- Halstead FD, Ravi A, Thomson N, et al. Whole genome sequencing of toxigenic Clostridium difficile in asymptomatic carriers: insights into possible role in transmission. J Hosp Infect. 2019;102:125–134. DOI:https://doi.org/10.1016/j.jhin.2018.10.012.
- Sheth PM, Douchant K, Uyanwune Y, et al. Evidence of transmission of Clostridium difficile in asymptomatic patients following admission screening in a tertiary care hospital. PLoS One. 2019;14:e0207138. DOI:https://doi.org/10.1371/journal.pone.0207138.