Genomic Epidemiology and Antimicrobial Resistance Profiles of Clostridioides difficile from Multi-Hospitals in a City in Eastern China

References

• Ramai D, Noorani A, Ofosu A, et al. Practice measures for controlling and preventing hospital associated Clostridium difficile infections. Hosp Pract. 2019;47(3):123–129. doi:10.1080/21548331.2019.1627851
   PubMedGoogle Scholar
• Evans CT, Safdar N. Current trends in the epidemiology and outcomes of clostridium difficile infection. Clin Infect Dis. 2015;60(Suppl 2):S66–S71. doi:10.1093/cid/civ140
   PubMedGoogle Scholar
• Costa DVS, Pham NVS, Hays RA, et al. Influence of binary toxin gene detection and decreased susceptibility to antibiotics among Clostridioides difficile strains on disease severity: a single-center study. Antimicrob Agents Chemother. 2022;66(8):e0048922. doi:10.1128/aac.00489-22
   PubMed Web of Science ®Google Scholar
• Rodriguez C, Van Broeck J, Taminiau B, et al. Clostridium difficile infection: early history, diagnosis and molecular strain typing methods. Microb Pathog. 2016;97:59–78. doi:10.1016/j.micpath.2016.05.018
   PubMed Web of Science ®Google Scholar
• Lessa FC, Mu Y, Bamberg WM, et al. Burden of Clostridium difficile infection in the United States. N Engl J Med. 2015;372(9):825–834. doi:10.1056/NEJMoa1408913
   PubMed Web of Science ®Google Scholar
• Zarb P, Coignard B, Griskeviciene J, et al. The European Centre for Disease Prevention and Control (ECDC) pilot point prevalence survey of healthcare-associated infections and antimicrobial use. Euro Surveill. 2012;17(46). doi:10.2807/ese.17.46.20316-en
   PubMedGoogle Scholar
• 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 Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing.), 2012 and 2013. Euro Surveill. 2016;21:29.
   Google Scholar
• Wiuff C, Banks AL, Fitzpatrick F, Cottom L. The need for European surveillance of CDI. Adv Exp Med Biol. 2018;1050:13–25.
   PubMed Web of Science ®Google Scholar
• Tang C, Cui L, Xu Y, et al. The incidence and drug resistance of Clostridium difficile infection in Mainland China: a systematic review and meta-analysis. Sci Rep. 2016;6(1):37865. doi:10.1038/srep37865
   PubMedGoogle Scholar
• Zhou Y, Mao L, Yu J, et al. Epidemiology of Clostridium difficile infection in hospitalized adults and the first isolation of C. difficile PCR ribotype 027 in central China. BMC Infect Dis. 2019;19(1):1. doi:10.1186/s12879-019-3841-6
   PubMedGoogle Scholar
• Jia H, Du P, Yang H, et al. Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing. BMC Genomics. 2016;17(1):405. doi:10.1186/s12864-016-2708-0
   PubMedGoogle Scholar
• Forde BM, Bergh H, Cuddihy T, et al. Clinical implementation of routine whole-genome sequencing for hospital infection control of multi-drug resistant pathogens. Clin Infect Dis. 2023;76(3):e1277–e1284. doi:10.1093/cid/ciac726
   PubMed Web of Science ®Google Scholar
• Eyre DW, Fawley WN, Rajgopal A, et al. Comparison of control of Clostridium difficile infection in six English hospitals using whole-genome sequencing. Clin Infect Dis. 2017;65(3):433–441. doi:10.1093/cid/cix338
   PubMed Web of Science ®Google Scholar
• Wen X, Shen C, Xia J, et al. Whole-genome sequencing reveals the high nosocomial transmission and antimicrobial resistance of Clostridioides difficile in a Single Center in China, a four-year retrospective study. Microbiol Spectr. 2022;10(1):e0132221. doi:10.1128/spectrum.01322-21
   PubMed Web of Science ®Google Scholar
• Xu X, Luo Y, Chen H, et al. Genomic evolution and virulence association of Clostridioides difficile sequence type 37 (ribotype 017) in China. Emerg Microbes Infect. 2021;10(1):1331–1345. doi:10.1080/22221751.2021.1943538
   PubMed Web of Science ®Google Scholar
• van Prehn J, Reigadas E, Vogelzang EH, et al. European Society of Clinical Microbiology and Infectious Diseases: 2021 update on the treatment guidance document for Clostridioides difficile infection in adults. Clin Microbiol Infect. 2021;27 Suppl 2(Suppl 2):S1–S21. doi:10.1016/j.cmi.2021.09.038
   PubMedGoogle Scholar
• Bloomfield LE, Riley TV. Epidemiology and risk factors for community-associated Clostridium difficile Infection: a narrative review. Infect Dis Ther. 2016;5(3):231–251. doi:10.1007/s40121-016-0117-y
   PubMedGoogle Scholar
• 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(13):1195–1205. doi:10.1056/NEJMoa1216064
   PubMed Web of Science ®Google Scholar
• Kato H, Kato N, Watanabe K, et al. Identification of Toxin A-Negative, Toxin B-Positive Clostridium difficile by PCR. J Clin Microbiol. 1998;36(8):2178–2182. doi:10.1128/JCM.36.8.2178-2182.1998
   PubMed Web of Science ®Google Scholar
• Stubbs S, Rupnik M, Gibert M, et al. Production of actin-specific ADP-ribosyltransferase (binary toxin) by strains of Clostridium difficile. FEMS Microbiol Lett. 2000;186(2):307–312. doi:10.1111/j.1574-6968.2000.tb09122.x
   PubMed Web of Science ®Google Scholar
• Preston MD, Assefa SA, Ocholla H, et al. PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation. J Infect Dis. 2014;209(11):1808–1815. doi:10.1093/infdis/jit812
   PubMed Web of Science ®Google Scholar
• Griffiths D, Fawley W, Kachrimanidou M, et al. Multilocus sequence typing of Clostridium difficile. J Clin Microbiol. 2010;48(3):770–778. doi:10.1128/JCM.01796-09
   PubMed Web of Science ®Google Scholar
• Clinical and Laboratory Standards Institute. Performance Standards for Antimicrobial Susceptibility Testing. 32st ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2022.
   Google Scholar
• 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(3):e15. doi:10.1093/nar/gku1196
   PubMed Web of Science ®Google Scholar
• Silva M, Machado MP, Silva DN, et al. chewBBACA: a complete suite for gene-by-gene schema creation and strain identification. Microb Genom. 2018;4:3.
   Web of Science ®Google Scholar
• Tamura K, Stecher G, Kumar S, Battistuzzi FU. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38(7):3022–3027. doi:10.1093/molbev/msab120
   PubMed Web of Science ®Google Scholar
• Letunic I, Bork P. Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 2011;39(Web Server issue):W475–W478. doi:10.1093/nar/gkr201
   PubMed Web of Science ®Google Scholar
• 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(1):128–129. doi:10.1093/bioinformatics/btw582
   PubMed Web of Science ®Google Scholar
• Aliramezani A, Talebi M, Douraghi M. Polymorphisms in the genes encoding surface associated proteins of Clostridioides difficile isolates. Infect Genet Evol. 2020;86:104598. doi:10.1016/j.meegid.2020.104598
   PubMed Web of Science ®Google Scholar
• Azimirad M, Krutova M, Yadegar A, et al. Clostridioides difficile ribotypes 001 and 126 were predominant in Tehran healthcare settings from 2004 to 2018: a 14-year-long cross-sectional study. Emerg Microbes Infect. 2020;9(1):1432–1443. doi:10.1080/22221751.2020.1780949
   PubMed Web of Science ®Google Scholar
• Tateda K, Ishida J, Ito S, et al. Population-based incidence of hospitalized Clostridioides difficile infection among older adults in Ota-ku, Japan: a prospective surveillance study. Anaerobe. 2022;76:102607. doi:10.1016/j.anaerobe.2022.102607
   PubMed Web of Science ®Google Scholar
• Wen B-J, Dong N, Ouyang Z-R, et al. Prevalence and molecular characterization of Clostridioides difficile infection in China over the past 5 years: a systematic review and meta-analysis. Int J Infect Dis. 2023;130:86–93. doi:10.1016/j.ijid.2023.03.009
   PubMed Web of Science ®Google Scholar
• Peng Z, Jin D, Kim HB, et al. Update on antimicrobial resistance in Clostridium difficile: resistance mechanisms and antimicrobial susceptibility testing. J Clin Microbiol. 2017;55(7):1998–2008. doi:10.1128/JCM.02250-16
   PubMed Web of Science ®Google Scholar
• O’Connor JR, Johnson S, Gerding DN. Clostridium difficile infection caused by the epidemic BI/NAP1/027 strain. Gastroenterol. 2009;136(6):1913–1924. doi:10.1053/j.gastro.2009.02.073
   PubMed Web of Science ®Google Scholar
• Freeman J, Vernon J, Pilling S, et al. The ClosER study: results from a three-year pan-European longitudinal surveillance of antibiotic resistance among prevalent Clostridium difficile ribotypes, 2011–2014. Clin Microbiol Infect. 2018;24(7):724–731. doi:10.1016/j.cmi.2017.10.008
   PubMed Web of Science ®Google Scholar
• Sholeh M, Krutova M, Forouzesh M, et al. Antimicrobial resistance in Clostridioides (Clostridium) difficile derived from humans: a systematic review and meta-analysis. Antimicrob Resist Infect Control. 2020;9(1):158. doi:10.1186/s13756-020-00815-5
   PubMed Web of Science ®Google Scholar
• Li S, Chen F, Li Y, et al. Rhamnose-containing compounds: biosynthesis and applications. Molecules. 2022;27:16.
   Web of Science ®Google Scholar
• Bank NC, Singh V, Rodriguez-Palacios A. Classification of Parabacteroides distasonis and other Bacteroidetes using O- antigen virulence gene: RfbA-Typing and hypothesis for pathogenic vs. probiotic strain differentiation. Gut Microbes. 2022;14(1):1997293. doi:10.1080/19490976.2021.1997293
   PubMed Web of Science ®Google Scholar
• Murray SG, Yim JWL, Croci R, et al. Using spatial and temporal mapping to identify nosocomial disease transmission of Clostridium difficile. JAMA Intern Med. 2017;177(12):1863–1865. doi:10.1001/jamainternmed.2017.5506
   PubMed Web of Science ®Google Scholar
• Eyre DW, Davies KA, Davis G, et al. Two distinct patterns of Clostridium difficile diversity across Europe indicating contrasting routes of spread. Clin Infect Dis. 2018;67(7):1035–1044. doi:10.1093/cid/ciy252
   PubMed Web of Science ®Google Scholar
• Muto CA, Pokrywka M, Shutt K, et al. A large outbreak of Clostridium difficile –associated disease with an unexpected proportion of deaths and colectomies at a teaching hospital following increased fluoroquinolone use. Infect Control Hosp Epidemiol. 2005;26(3):273–280. doi:10.1086/502539
   PubMed Web of Science ®Google Scholar
• Deng L, Tay H, Peng G, et al. Prevalence and molecular subtyping of Blastocystis in patients with Clostridium difficile infection, Singapore. Parasit Vectors. 2021;14(1):277. doi:10.1186/s13071-021-04749-8
   PubMed Web of Science ®Google Scholar
• Chen YB, Gu S-L, 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(1):52–59. doi:10.1099/jmm.0.000646
   PubMed Web of Science ®Google Scholar
• 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(8):1094–1102. doi:10.1093/cid/cit475
   PubMed Web of Science ®Google Scholar
• Johnson S, Lavergne V, Skinner AM, et al. Clinical practice guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 focused update guidelines on management of Clostridioides difficile infection in adults. Clin Infect Dis. 2021;73(5):e1029–e1044. doi:10.1093/cid/ciab549
   PubMed Web of Science ®Google Scholar
• Wongkuna S, Janvilisri T, Phanchana M, et al. Temporal variations in patterns of Clostridioides difficile strain diversity and antibiotic resistance in Thailand. Antibiotics. 2021;10(6). doi:10.3390/antibiotics10060714
   Google Scholar