Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit

  • Guh, A. Y. et al. Trends in U.S. Burden of Clostridioides difficile infection and outcomes. N. Engl. J. Med. 382, 1320–1330 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Antibiotic Resistance Threats in the United States (Centers for Disease Control and Prevention, 2019); doi.org/10.15620/cdc:82532

  • Evans, C. T. & Safdar, N. Current trends in the epidemiology and outcomes of Clostridium difficile infection. Clin. Infect. Dis. 60, S66–S71 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Eyre, D. W. et al. Diverse sources of C. difficile infection identified on whole-genome sequencing. N. Engl. J. Med. 369, 1195–1205 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Walker, A. S. et al. Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing.PLoS Med. 9, e1001172 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Blixt, T. et al. Asymptomatic carriers contribute to nosocomial Clostridium difficile infection: a cohort study of 4508 patients. Gastroenterology 152, 1031–1041 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Galdys, A. L., Curry, S. R. & Harrison, L. H. Asymptomatic Clostridium difficile colonization as a reservoir for Clostridium difficile infection. Expert Rev. Anti Infect. Ther. 12, 967–980 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Furuya-Kanamori, L. et al. Asymptomatic Clostridium difficile colonization: epidemiology and clinical implications. BMC Infect. Dis. 15, 516 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sethi, A. K., Al-Nassir, W. N., Nerandzic, M. M., Bobulsky, G. S. & Donskey, C. J. Persistence of skin contamination and environmental shedding of Clostridium difficile during and after treatment of C. difficile infection. Infect. Control Hosp. Epidemiol. 31, 21–27 (2010).

    Article 
    PubMed 

    Google Scholar
     

  • McDonald, L. C. & Diekema, D. J. Point-counterpoint: active surveillance for carriers of toxigenic Clostridium difficile should be performed to guide prevention efforts. J. Clin. Microbiol. 56, e00782-18 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baron, S. W. et al. Screening of Clostridioides difficile carriers in an urban academic medical center: understanding implications of disease.Infect. Control Hosp. Epidemiol. 41, 149–153 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • McDonald, L. C. et al. Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin. Infect. Dis. 66, 987–994 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Didelot, X. et al. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol. 13, R118 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Surveillance for C. difficile, MRSA, and Other Drug-resistant Infections (Centers for Disease Control and Prevention, 2018); www.cdc.gov/nhsn/acute-care-hospital/cdiff-mrsa/index.html

  • Magill, S. S. et al. Multistate point-prevalence survey of health care–associated infections. N. Engl. J. Med. 370, 1198–1208 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ponnada, S. et al. Acquisition of Clostridium difficile colonization and infection after transfer from a Veterans Affairs hospital to an affiliated long-term care facility. Infect. Control Hosp. Epidemiol. 38, 1070–1076 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Curry, S. R. 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. 57, 1094–1102 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Riggs, M. M. 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. 45, 992–998 (2007).

    Article 
    PubMed 

    Google Scholar
     

  • Sheth, P. M. et al. Evidence of transmission of Clostridium difficile in asymptomatic patients following admission screening in a tertiary care hospital. PLoS ONE 14, e0207138 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kong, L. Y. et al. Clostridium difficile: investigating transmission patterns between infected and colonized patients using whole genome sequencing. Clin. Infect. Dis. 68, 204–209 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Zacharioudakis, I. M., Zervou, F. N., Pliakos, E. E., Ziakas, P. D. & Mylonakis, E. Colonization with toxinogenic C. difficile upon hospital admission, and risk of infection: a systematic review and meta-analysis. Am. J. Gastroenterol. 110, 381–390 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Eyre, D. W. et al. Asymptomatic Clostridium difficile colonisation and onward transmission. PLoS ONE 8, e78445 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Truong, C. et al. Clostridium difficile rates in asymptomatic and symptomatic hospitalized patients using nucleic acid testing. Diagn. Microbiol. Infect. Dis. 87, 365–370 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Clabots, C. R., Johnson, S., Olson, M. M., Peterson, L. R. & Gerding, D. N. Acquisition of Clostridium difficile by hospitalized patients: evidence for colonized new admissions as a source of infection. J. Infect. Dis. 166, 561–567 (1992).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Worley, J. et al. Genomic determination of relative risks for Clostridioides difficile infection from asymptomatic carriage in intensive care unit patients.Clin. Infect. Dis. 73, e1727–e1736 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Brazier, J. S. et al. Screening for carriage and nosocomial acquisition of Clostridium difficile by culture: a study of 284 admissions of elderly patients to six general hospitals in Wales. J. Hosp. Infect. 43, 317–319 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lanzas, C. & Dubberke, E. R. Effectiveness of screening hospital admissions to detect asymptomatic carriers of Clostridium difficile: a modeling evaluation. Infect. Control Hosp. Epidemiol. 35, 1043–1050 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Longtin, Y. et al. Effect of detecting and isolating Clostridium difficile carriers at hospital admission on the incidence of C. difficile infections: a quasi-experimental controlled study. JAMA Intern. Med. 176, 796–804 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Tickler, I. A. et al. Strain types and antimicrobial resistance patterns of Clostridium difficile isolates from the United States, 2011 to 2013. Antimicrob. Agents Chemother. 58, 4214–4218 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Keegan, J. et al. Toxigenic Clostridioides difficile colonization as a risk factor for development of C. difficile infection in solid-organ transplant patients. Infect. Control Hosp. Epidemiol. 42, 287–291 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Shim, J. K., Johnson, S., Samore, M. H., Bliss, D. Z. & Gerding, D. N. Primary symptomless colonisation by Clostridium difficile and decreased risk of subsequent diarrhoea. Lancet 351, 633–636 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Goldenberg, J. Z. et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children.Cochrane Database Syst. Rev. 12, CD006095 (2017).

    PubMed 

    Google Scholar
     

  • Mullane, K. M. et al. A randomized, placebo-controlled trial of fidaxomicin for prophylaxis of Clostridium difficile-associated diarrhea in adults undergoing hematopoietic stem cell transplantation. Clin. Infect. Dis. 68, 196–203 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Baunwall, S. M. D. et al. Faecal microbiota transplantation for recurrent Clostridioides difficile infection: an updated systematic review and meta-analysis. EClinicalMedicine 29–30, 100642 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tamma, P. D. et al. Association of a safety program for improving antibiotic use with antibiotic use and hospital-onset Clostridioides difficile infection rates among US hospitals. JAMA Netw. Open 4, e210235 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baur, D. et al. Effect of antibiotic stewardship on the incidence of infection and colonisation with antibiotic-resistant bacteria and Clostridium difficile infection: a systematic review and meta-analysis. Lancet Infect. Dis. 17, 990–1001 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Caroff, D. A., Yokoe, D. S. & Klompas, M. Evolving insights into the epidemiology and control of Clostridium difficile in hospitals. Clin. Infect. Dis. 65, 1232–1238 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Crobach, M. J. T. et al. Understanding Clostridium difficile colonization. Clin. Microbiol. Rev. 31, e00021-17 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Behroozian, A. A. et al. Detection of mixed populations of Clostridium difficile from symptomatic patients using capillary-based polymerase chain reaction ribotyping. Infect. Control Hosp. Epidemiol. 34, 961–966 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dayananda, P. & Wilcox, M. H. A review of mixed strain clostridium difficile colonization and infection. Front. Microbiol. 10, 692 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sun, J., Mc Millen, T., Babady, N. E. & Kamboj, M. Role of coinfecting strains in recurrent Clostridium difficile infection. Infect. Control Hosp. Epidemiol. 37, 1481–1484 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Seekatz, A. M. et al. Presence of multiple Clostridium difficile strains at primary infection is associated with development of recurrent disease. Anaerobe 53, 74–81 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gonzalez-Orta, M. et al. Are many patients diagnosed with healthcare-associated Clostridioides difficile infections colonized with the infecting strain on admission? Clin. Infect. Dis. 69, 1801–1804 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Lin, M. Y. et al. Impact of mandatory infectious disease specialist approval on hospital-onset Clostridioides difficile infection rates and testing appropriateness.Clin. Infect. Dis. 77, 346–350 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hunt, M. et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb. Genom. 3, e000131 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Crawford, R. D. & Snitkin, E. S. cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets. BMC Bioinformatics 22, 70 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Elliott, B., Androga, G. O., Knight, D. R. & Riley, T. V. Clostridium difficile infection: evolution, phylogeny and molecular epidemiology. Infect. Genet. Evol. 49, 1–11 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA–MEM. Preprint at doi.org/10.48550/arXiv.1303.3997 (2013).

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Koenigsknecht, M. J. et al. Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract. Infect. Immun. 83, 934–941 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schloss, P. D. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4, e8230 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Westcott, S. L. & Schloss, P. D. OptiClust, an improved method for assigning amplicon-based sequence data to operational taxonomic units. mSphere 2, e00073-17 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baggs, J. et al. Risk of subsequent sepsis within 90 days after a hospital stay by type of antibiotic exposure. Clin. Infect. Dis. 66, 1004–1012 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Read more here: Source link