Een tip: Wie advies wilt over hoe het microbioom te verbeteren zou contact op kunnen nemen met deze website: Www.microbiome-Center.nl Voor zowel artsen als individuele burgers staat een groep van artsen en wetenschappers klaar om u een persoonlijk advies te geven.

20 april 2024: Zie enkele artikelen op onze website met poeptransplantatie in de titel: https://kanker-actueel.nl/search.html?search_text=poeptransplantatie&search_in=title

20 april 2024: zie ook dit artikel: https://kanker-actueel.nl/gerichte-dieet-aanpak-met-uitsluiting-van-specifieke-voedingsstoffen-geeft-snel-resultaat-en-herstel-bij-kinderen-en-jongeren-met-een-actief-stadium-van-de-ziekte-van-crohn-na-1-maand-is-grootste-deel-van-de-klachten-al-weg.html

20 april 2024: Bron: LUMC

Een poeptransplantatie via een sonde met bewerkte ontlasting van gezonde donoren in de darmen van chronisch zieke mensen met de ziekte van Crohn (Clostridiodis difficile) onderdrukt de resistentie tegen bv antibiotica en nog beter doet de bacteriën die de resistentie veroorzaken verdwijnen. Ook blijkt uit een test na drie jaar bij de behandelde patiënten dat de resistentie nog steeds was opgeheven. Dat blijkt uit onderzoek van Liz Terveer, arts-microbioloog bij het LUMC en hoofd van de Nederlandse Donor Feces Bank (NDFB).

Extra interessant is dat Liz Terveer ook gaat onderzoeken wat het effect kan zijn van een poeptransplantatie bij patiënten met een melanoom die immuuntherapie krijgen: 

Een citaat uit een persbericht van het LUMC:

Terveer gaat verder met haar onderzoek door andere typen patiënten te betrekken bij poeptransplantatie. "We zijn nu een studie gestart met het Antoni van Leeuwenhoek Ziekenhuis om te kijken of dezelfde behandeling ook aanslaat bij patiënten met uitgezaaide melanomen om het effect van de immuuntherapie die zij krijgen te versterken. De gedachte daarachter is dat een poeptransplantatie zo'n sterke immuunrespons opwekt dat het eigen immuunsysteem van een patiënt de kankercellen veel adequater gaat opruimen."

Nog een citaat:

In het LUMC is drie jaar onderzoek verricht naar de mogelijkheid van poeptransplantatie bij chronisch zieke mensen. Terveer: "Dit hebben we gedaan bij alle patiënten die zich hadden aangemeld bij onze donorbank voor een fecestransplantatie. We hebben hun poep op kweek gezet en de persoonlijke gemeenschap van bacteriën in kaart gebracht. Zo kregen we een compleet beeld van de darmomgeving van iedere patiënt. Zo'n omgeving is te vergelijken met een ziek ecosysteem, waarin we de biodiversiteit willen herstellen door nieuwe soorten in te voeren. In dit geval brachten we gefilterde ontlasting van een donor via een sonde in bij de patiënt."

Het gevolg was dat patiënten na drie weken geen of een sterk verlaagde hoeveelheid resistente bacteriën bij zich droegen. Terveer: "Een mooi en snel resultaat. Een deel van de mensen hebben we drie jaar lang gevolgd en we weten nu dat het effect ook duurzaam is.">>>>>>lees het hele persbericht

Het originele studierapport is gratis in te zien met veel details en grafieken:

Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection

Genome Medicine volume 16, Article number: 37 (2024) Cite this article

Abstract

Background

Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases.

Methods

We study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1–3 years), combining culture methods and faecal metagenomics.

Results

Based on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients’ resistomes are still donor-like, suggesting the effect of FMT may last for years.

Conclusions

Taken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.

Conclusions

Our study points towards possibilities and limitations of the use of FMT for the eradication of MDR bacteria in the gut. Based on pre- and post-FMT resistome analysis (including a unique LTFU of 1–3 years), we find that FMT induces significant changes in the recipient resistome, that may be associated with a reduction in the abundance of Enterobacterales. However, we also find that specific recipient-ARGs persist. The clinical consequences of this persistence were not included in this study and require further analyses in large cohort of FMT-treated patients. To better assess the possible benefits in MDR eradication, we need larger (randomised controlled) trials and multi-omics studies combined with classical microbiological methods that can link ARGs to bacterial taxa, and to the host’s gut ecosystem. Additionally, the use of local, national and international registries for FMT can help collect long-term data to assess infection risks in different patient populations [81, 82]. Besides keeping track of MDR-related outcomes, these registries facilitate evaluation of other long-term microbiota-related risks, such as CDI recurrence or procarcinogenic bacteria [49, 83, 84]. Finally, studies with control patients and more diverse patients are needed to explain the resistome differences and obtain more generalisable results. This will pave the way for evaluating the feasibility of FMT to control antibiotic resistance in infection-susceptible patients.

Availability of data and materials

Sequencing reads generated for this study are available in the European Nucleotide Archive under project numbers PRJEB64622 (https://www.ebi.ac.uk/ena/browser/view/PRJEB64622) [48], PRJEB44737 (https://www.ebi.ac.uk/ena/browser/view/PRJEB44737) [50], and PRJEB64621 (https://www.ebi.ac.uk/ena/browser/view/PRJEB64621) [51]. Code to reproduce analyses and generate figures are available at Zenodo (https://doi.org/https://doi.org/10.5281/zenodo.10276220) [60].

Acknowledgements

We wish to express our gratitude to Eric K.L. Berssenbrugge and Ingrid M.G.J. Sanders from the Experimental Bacteriology group at the LUMC for culturing the MDR bacteria. We thank Prof. Dr. Hein W. Verspaget of the Netherlands Donor Feces Bank for continuous support and supervision. Also, our thanks go to GenomeScan B.V. for providing the DNA sequencing. Finally, we thank the Experimental Bacteriology group and the Center for Microbiome Analyses and Therapeutics of the LUMC for fruitful work discussions, and in particular Dr. Wiep Klaas Smits for feedback on the manuscript.

Funding

The Netherlands Donor Feces Bank have received an unrestricted research grant from Vedanta Biosciences.

Author information

Authors and Affiliations

  1. Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands

    Sam Nooij, Karuna E. W. Vendrik, Josbert J. Keller & Elisabeth M. Terveer

  2. Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands

    Sam Nooij, Karuna E. W. Vendrik, Romy D. Zwittink, Quinten R. Ducarmon, Ed J. Kuijper & Elisabeth M. Terveer

  3. Department of Gastroenterology, Haaglanden Medical Center, The Hague, Netherlands

    Josbert J. Keller

  4. Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands

    Karuna E. W. Vendrik & Romy D. Zwittink

Consortia

on behalf of the Netherlands Donor Feces Bank study group

Contributions

SN, KEWV, RDZ, EJK and EMT conceptualised and designed the study. QRD, EJK and EMT supervised the study. KEWV, JJK, EJK and EMT supervised treatment of patients. KEWV collected clinical and microbiological data and performed analyses. SN performed genomics, metagenomics and statistical analyses and drafted the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Sam Nooij.

Ethics declarations

Ethics approval and consent to participate

Written informed consent was obtained from all patients and donors for use of their faecal samples and follow-up data. Ethical approval was granted for the protocols and practice of the NDFB by the local medical ethics committee at the Leiden University Medical Center (reference P15.145, and long-term follow-up: B21.49). This study conforms to the principles of the Helsinki declaration.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.


References

  1. The new EU One Health action plan against antimicrobial resistance. https://ec.europa.eu/health/sites/health/files/antimicrobial_resistance/docs/amr_2017_summary-action-plan.pdf.

  2. Antimicrobial Resistance C. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629–55.

    Article Google Scholar 

  3. Blaser MJ. Antibiotic use and its consequences for the normal microbiome. Science. 2016;352(6285):544–5.

    Article ADS CAS PubMed PubMed Central Google Scholar 

  4. Goossens H, Ferech M, Vander Stichele R, Elseviers M, Group EP. Outpatient antibiotic use in Europe and association with resistance: a cross-national database study. Lancet. 2005;365(9459):579–87.

    Article PubMed Google Scholar 

  5. Karanika S, Karantanos T, Arvanitis M, Grigoras C, Mylonakis E. Fecal colonization with extended-spectrum beta-lactamase-producing Enterobacteriaceae and risk factors among healthy individuals: a systematic review and metaanalysis. Clin Infect Dis. 2016;63(3):310–8.

    Article PubMed Google Scholar 

  6. Smits WK, Lyras D, Lacy DB, Wilcox MH, Kuijper EJ. Clostridium difficile infection. Nat Rev Dis Primers. 2016;2:16020.

    Article PubMed PubMed Central Google Scholar 

  7. Quraishi MN, Widlak M, Bhala N, Moore D, Price M, Sharma N, Iqbal TH. Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Aliment Pharmacol Ther. 2017;46(5):479–93.

    Article CAS PubMed Google Scholar 

  8. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368(5):407–15.

    Article PubMed Google Scholar 

  9. Khoruts A, Sadowsky MJ. Understanding the mechanisms of faecal microbiota transplantation. Nat Rev Gastroenterol Hepatol. 2016;13(9):508–16.

    Article PubMed PubMed Central Google Scholar 

  10. McDonald LC, Gerding DN, Johnson S, Bakken JS, Carroll KC, Coffin SE, Dubberke ER, Garey KW, Gould CV, Kelly 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. 2018;66(7):987–94.

    Article CAS PubMed Google Scholar 

  11. Ooijevaar RE, van Beurden YH, Terveer EM, Goorhuis A, Bauer MP, Keller JJ, Mulder CJJ, Kuijper EJ. Update of treatment algorithms for Clostridium difficile infection. Clin Microbiol Infect. 2018;24(5):452–62.

    Article CAS PubMed Google Scholar 

  12. van Prehn J, Reigadas E, Vogelzang EH, Bouza E, Hristea A, Guery B, Krutova M, Noren T, Allerberger F, Coia JE, 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):S1–21.

    Article PubMed Google Scholar 

  13. Isles NS, Mu A, Kwong JC, Howden BP, Stinear TP. Gut microbiome signatures and host colonization with multidrug-resistant bacteria. Trends Microbiol. 2022;30(9):853–65.

    Article CAS PubMed Google Scholar 

  14. Dickstein Y, Edelman R, Dror T, Hussein K, Bar-Lavie Y, Paul M. Carbapenem-resistant Enterobacteriaceae colonization and infection in critically ill patients: a retrospective matched cohort comparison with non-carriers. J Hosp Infect. 2016;94(1):54–9.

    Article CAS PubMed Google Scholar 

  15. Carlet J. The gut is the epicentre of antibiotic resistance. Antimicrob Resist Infect Control. 2012;1(1):39.

    Article PubMed PubMed Central Google Scholar 

  16. Gorrie CL, Mirceta M, Wick RR, Judd LM, Wyres KL, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, et al. Antimicrobial-Resistant Klebsiella pneumoniae Carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital. Clin Infect Dis. 2018;67(2):161–70.

    Article CAS PubMed PubMed Central Google Scholar 

  17. Tillotson GS, Zinner SH. Burden of antimicrobial resistance in an era of decreasing susceptibility. Expert Rev Anti Infect Ther. 2017;15(7):663–76.

    Article CAS PubMed Google Scholar 

  18. Weterings V, van den Bijllaardt W, Bootsma M, Hendriks Y, Kilsdonk L, Mulders A, Kluytmans J. Duration of rectal colonization with extended-spectrum beta-lactamase-producing Escherichia coli: results of an open, dynamic cohort study in Dutch nursing home residents (2013–2019). Antimicrob Resist Infect Control. 2022;11(1):98.

    Article PubMed PubMed Central Google Scholar 

  19. van Weerlee C, van der Vorm ER, Nolles L, Meeuws-van den Ende S, van der Bij AK. Duration of carriage of multidrug resistant Enterobacterales in discharged hospital and general practice patients and factors associated with clearance. Infect Prev Pract. 2020;2(3):100066.

    Article PubMed PubMed Central Google Scholar 

  20. Tacconelli E, Mazzaferri F, de Smet AM, Bragantini D, Eggimann P, Huttner BD, Kuijper EJ, Lucet JC, Mutters NT, Sanguinetti M, et al. ESCMID-EUCIC clinical guidelines on decolonization of multidrug-resistant Gram-negative bacteria carriers. Clin Microbiol Infect. 2019;25(7):807–17.

    Article CAS PubMed Google Scholar 

  21. Millan B, Park H, Hotte N, Mathieu O, Burguiere P, Tompkins TA, Kao D, Madsen KL. Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile Infection. Clin Infect Dis. 2016;62(12):1479–86.

    Article CAS PubMed PubMed Central Google Scholar 

  22. Bilinski J, Grzesiowski P, Sorensen N, Madry K, Muszynski J, Robak K, Wroblewska M, Dzieciatkowski T, Dulny G, Dwilewicz-Trojaczek J, et al. Fecal microbiota transplantation in patients with blood disorders inhibits gut colonization with antibiotic-resistant bacteria: results of a prospective, single-center study. Clin Infect Dis. 2017;65(3):364–70.

    Article CAS PubMed Google Scholar 

  23. Crum-Cianflone NF, Sullivan E, Ballon-Landa G. Fecal microbiota transplantation and successful resolution of multidrug-resistant-organism colonization. J Clin Microbiol. 2015;53(6):1986–9.

    Article PubMed PubMed Central Google Scholar 

  24. Davido B, Batista R, Michelon H, Lepainteur M, Bouchand F, Lepeule R, Salomon J, Vittecoq D, Duran C, Escaut L, et al. Is faecal microbiota transplantation an option to eradicate highly drug-resistant enteric bacteria carriage? J Hosp Infect. 2017;95(4):433–7.

    Article CAS PubMed Google Scholar 

  25. Dinh A, Fessi H, Duran C, Batista R, Michelon H, Bouchand F, Lepeule R, Vittecoq D, Escaut L, Sobhani I, et al. Clearance of carbapenem-resistant Enterobacteriaceae vs vancomycin-resistant enterococci carriage after faecal microbiota transplant: a prospective comparative study. J Hosp Infect. 2018;99(4):481–6.

    Article CAS PubMed Google Scholar 

  26. Huttner BD, Galperine T, Kapel N, Harbarth S. ‘A five-day course of oral antibiotics followed by faecal transplantation to eradicate carriage of multidrug-resistant Enterobacteriaceae’ – Author’s reply. Clin Microbiol Infect. 2019;25(7):914–5.

    Article CAS PubMed Google Scholar 

  27. Lagier JC, Million M, Fournier PE, Brouqui P, Raoult D. Faecal microbiota transplantation for stool decolonization of OXA-48 carbapenemase-producing Klebsiella pneumoniae. J Hosp Infect. 2015;90(2):173–4.

    Article CAS PubMed Google Scholar 

  28. Manges AR, Steiner TS, Wright AJ. Fecal microbiota transplantation for the intestinal decolonization of extensively antimicrobial-resistant opportunistic pathogens: a review. Infect Dis (Lond). 2016;48(8):587–92.

    Article CAS PubMed Google Scholar 

  29. Singh R, Nieuwdorp M, ten Berge IJ, Bemelman FJ, Geerlings SE. The potential beneficial role of faecal microbiota transplantation in diseases other than Clostridium difficile infection. Clin Microbiol Infect. 2014;20(11):1119–25.

    Article CAS PubMed Google Scholar 

  30. Singh R, de Groot PF, Geerlings SE, Hodiamont CJ, Belzer C, Berge I, de Vos WM, Bemelman FJ, Nieuwdorp M. Fecal microbiota transplantation against intestinal colonization by extended spectrum beta-lactamase producing Enterobacteriaceae: a proof of principle study. BMC Res Notes. 2018;11(1):190.

    Article PubMed PubMed Central Google Scholar 

  31. Stalenhoef JE, Terveer EM, Knetsch CW, Van’t Hof PJ, Vlasveld IN, Keller JJ, Visser LG, Kuijper EJ. Fecal microbiota transfer for multidrug-resistant gram-negatives: a clinical success combined with microbiological failure. Open Forum Infect Dis. 2017;4(2):ofx047.

    Article PubMed PubMed Central Google Scholar 

  32. Huttner BD, de Lastours V, Wassenberg M, Maharshak N, Mauris A, Galperine T, Zanichelli V, Kapel N, Bellanger A, Olearo F, et al. A 5-day course of oral antibiotics followed by faecal transplantation to eradicate carriage of multidrug-resistant Enterobacteriaceae: a randomized clinical trial. Clin Microbiol Infect. 2019;25(7):830–8.

    Article CAS PubMed Google Scholar 

  33. Kuijper EJ, Vendrik KEW, Vehreschild M. Manipulation of the microbiota to eradicate multidrug-resistant Enterobacteriaceae from the human intestinal tract. Clin Microbiol Infect. 2019;25(7):786–9.

    Article CAS PubMed Google Scholar 

  34. Woodworth MH, Conrad RE, Haldopoulos M, Pouch SM, Babiker A, Mehta AK, Sitchenko KL, Wang CH, Strudwick A, Ingersoll JM, et al. Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement. Sci Transl Med. 2023;15(720):eabo2750.

    Article CAS PubMed Google Scholar 

  35. Terveer EM, van Beurden YH, Goorhuis A, Seegers J, Bauer MP, van Nood E, Dijkgraaf MGW, Mulder CJJ, Vandenbroucke-Grauls C, Verspaget HW, et al. How to: establish and run a stool bank. Clin Microbiol Infect. 2017;23(12):924–30.

    Article CAS PubMed Google Scholar 

  36. Terveer EM, Vendrik KE, Ooijevaar RE, Lingen EV, Boeije-Koppenol E, Nood EV, Goorhuis A, Bauer MP, van Beurden YH, Dijkgraaf MG, et al. Faecal microbiota transplantation for Clostridioides difficile infection: four years’ experience of the Netherlands Donor Feces Bank. United European Gastroenterol J. 2020;8(10):1236–47.

    Article CAS PubMed PubMed Central Google Scholar 

  37. Vendrik KEW, Terveer EM, Kuijper EJ, Nooij S, Boeije-Koppenol E, Sanders I, van Lingen E, Verspaget HW, Berssenbrugge EKL, Keller JJ, et al. Periodic screening of donor faeces with a quarantine period to prevent transmission of multidrug-resistant organisms during faecal microbiota transplantation: a retrospective cohort study. Lancet Infect Dis. 2021;21(5):711–21.

    Article CAS PubMed Google Scholar 

  38. Bijzonder resistente micro-organismen (BRMO) (in Dutch). https://www.rivm.nl/sites/default/files/2018-11/130424%20BRMO.pdf.

  39. Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. http://www.eucast.org.

  40. Genome assembly GRCh38. https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.26/.

  41. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.

    Article CAS PubMed PubMed Central Google Scholar 

  42. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.

    Article PubMed PubMed Central Google Scholar 

  43. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–90.

    Article PubMed PubMed Central Google Scholar 

  44. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinformatics. 2020;70(1):e102.

    Article CAS PubMed Google Scholar 

  45. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017;45(D1):D566–73.

    Article CAS PubMed Google Scholar 

  46. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–4.

    Article CAS PubMed PubMed Central Google Scholar 

  47. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics. 2022;38(23):5315–6.

    Article CAS PubMed PubMed Central Google Scholar 

  48. Netherlands Donor Feces Bank. Multidrug-resistant organisms cultured from pre- and post-faecal microbiota transplantation patient stools. European Nucleotide Archive; 2023. https://www.ebi.ac.uk/ena/browser/view/PRJEB64622.

  49. Nooij S, Ducarmon QR, Laros JFJ, Zwittink RD, Norman JM, Smits WK, Verspaget HW, Keller JJ, Terveer EM, Kuijper EJ, et al. Fecal microbiota transplantation influences Procarcinogenic Escherichia coli in recipient recurrent Clostridioides difficile patients. Gastroenterology. 2021;161(4):1218-1228 e1215.

    Article CAS PubMed Google Scholar 

  50. Netherlands Donor Feces Bank. Metagenomic shotgun sequencing of healthy stool bank donors and multiple recurrent Clostridioides infected recipients from the Netherlands Donor Feces Bank. European Nucleotide Archive; 2022. https://www.ebi.ac.uk/ena/browser/view/PRJEB44737.

  51. Netherlands Donor Feces Bank. Faecal shotgun metagenomes of healthy stool donors from the Netherlands Donor Feces Bank and multiple recurrent Clostridioides difficile infection patients with long-term follow-up. European Nucleotide Archive; 2023. https://www.ebi.ac.uk/ena/browser/view/PRJEB64621.

  52. Ducarmon QR, Hornung BVH, Geelen AR, Kuijper EJ, Zwittink RD. Toward standards in clinical microbiota studies: comparison of three DNA Extraction methods and two bioinformatic pipelines. mSystems. 2020;5(1):e00547.

    Article PubMed PubMed Central Google Scholar 

  53. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. In: arXiv: 13033997 [q-bioGN]. 2013. https://doi.org/10.48550/arXiv.1303.3997.

  54. Blanco-Miguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol. 2023;41:1633–44. https://doi.org/10.1038/s41587-023-01688-w.

    Article CAS PubMed PubMed Central Google Scholar 

  55. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.

    Article ADS CAS PubMed PubMed Central Google Scholar 

  56. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27(5):824–34.

    Article CAS PubMed PubMed Central Google Scholar 

  57. von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biol. 2019;20(1):217.

    Article Google Scholar 

  58. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.

    Article PubMed PubMed Central Google Scholar 

  59. Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021;18(4):366–8.

    Article CAS PubMed PubMed Central Google Scholar 

  60. Nooij S. Resistome and MDRO analyses of NDFB FMT cohort. Zenodo. 2023. https://zenodo.org/records/10276220.

  61. Fredriksen S, de Warle S, van Baarlen P, Boekhorst J, Wells JM. Resistome expansion in disease-associated human gut microbiomes. Microbiome. 2023;11(1):166.

    Article CAS PubMed PubMed Central Google Scholar 

  62. McCallum GE, Rossiter AE, Quraishi MN, Iqbal TH, Kuehne SA, Schaik WV. Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts. bioRxiv 2022:2022.2011.2005.514866. https://doi.org/10.1101/2022.11.05.514866.

  63. Langdon A, Schwartz DJ, Bulow C, Sun X, Hink T, Reske KA, Jones C, Burnham CD, Dubberke ER, Dantas G, et al. Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study. Genome Med. 2021;13(1):28.

    Article CAS PubMed PubMed Central Google Scholar 

  64. Ghani R, Mullish BH, Davies FJ, Marchesi JR. How to adapt an intestinal microbiota transplantation programme to reduce the risk of invasive multidrug-resistant infection. Clin Microbiol Infect. 2022;28(4):502–12.

    Article PubMed Google Scholar 

  65. Tariq R, Pardi DS, Tosh PK, Walker RC, Razonable RR, Khanna S. Fecal microbiota transplantation for recurrent Clostridium difficile infection reduces recurrent urinary tract infection frequency. Clin Infect Dis. 2017;65(10):1745–7.

    Article CAS PubMed Google Scholar 

  66. Bilsen MP, Lambregts MMC, van Prehn J, Kuijper EJ. Faecal microbiota replacement to eradicate antimicrobial resistant bacteria in the intestinal tract - a systematic review. Curr Opin Gastroenterol. 2022;38(1):15–25.

    Article PubMed Google Scholar 

  67. Momose Y, Hirayama K, Itoh K. Competition for proline between indigenous Escherichia coli and E. coli O157:H7 in gnotobiotic mice associated with infant intestinal microbiota and its contribution to the colonization resistance against E. coli O157:H7. Antonie Van Leeuwenhoek. 2008;94(2):165–71.

    Article CAS PubMed Google Scholar 

  68. Deriu E, Liu JZ, Pezeshki M, Edwards RA, Ochoa RJ, Contreras H, Libby SJ, Fang FC, Raffatellu M. Probiotic bacteria reduce salmonella typhimurium intestinal colonization by competing for iron. Cell Host Microbe. 2013;14(1):26–37.

    Article CAS PubMed PubMed Central Google Scholar 

  69. Litvak Y, Byndloss MX, Bäumler AJ. Colonocyte metabolism shapes the gut microbiota. Science. 2018;362(6418):eaat9076.

    Article ADS PubMed PubMed Central Google Scholar 

  70. Roe AJ, O’Byrne C, McLaggan D, Booth IR. Inhibition of Escherichia coli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity. Microbiology (Reading). 2002;148(Pt 7):2215–22.

    Article CAS PubMed Google Scholar 

  71. Cotter PD, Ross RP, Hill C. Bacteriocins - a viable alternative to antibiotics? Nat Rev Microbiol. 2013;11(2):95–105.

    Article CAS PubMed Google Scholar 

  72. Mason KL, Erb Downward JR, Falkowski NR, Young VB, Kao JY, Huffnagle GB. Interplay between the gastric bacterial microbiota and Candida albicans during postantibiotic recolonization and gastritis. Infect Immun. 2012;80(1):150–8.

    Article CAS PubMed PubMed Central Google Scholar 

  73. Seelbinder B, Chen J, Brunke S, Vazquez-Uribe R, Santhaman R, Meyer AC, de Oliveira Lino FS, Chan KF, Loos D, Imamovic L, et al. Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Microbiome. 2020;8(1):133.

    Article CAS PubMed PubMed Central Google Scholar 

  74. Tan CT, Xu X, Qiao Y, Wang Y. A peptidoglycan storm caused by beta-lactam antibiotic’s action on host microbiota drives Candida albicans infection. Nat Commun. 2021;12(1):2560.

    Article ADS CAS PubMed PubMed Central Google Scholar 

  75. Jannie GEH, Monique JTC, Elisabeth MT, WiepKlaas S, Ed JK, Romy DZ. Fungal and bacterial gut microbiota differ between Clostridioides difficile colonization and infection. Microbiome Res Rep. 2023;3(1):8.

    Google Scholar 

  76. Lin X, Hu T, Chen J, Liang H, Zhou J, Wu Z, Ye C, Jin X, Xu X, Zhang W, et al. The genomic landscape of reference genomes of cultivated human gut bacteria. Nat Commun. 2023;14(1):1663.

    Article ADS CAS PubMed PubMed Central Google Scholar 

  77. Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, et al. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nat Commun. 2023;14(1):7366.

    Article ADS CAS PubMed PubMed Central Google Scholar 

  78. Dolejska M, Papagiannitsis CC. Plasmid-mediated resistance is going wild. Plasmid. 2018;99:99–111.

    Article CAS PubMed Google Scholar 

  79. Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez J. Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. Gut Microbes. 2022;14(1):2055944.

    Article PubMed PubMed Central Google Scholar 

  80. Diebold PJ, New FN, Hovan M, Satlin MJ, Brito IL. Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR. Elife. 2021;10:e66834.

    Article CAS PubMed PubMed Central Google Scholar 

  81. Kelly CR, Yen EF, Grinspan AM, Kahn SA, Atreja A, Lewis JD, Moore TA, Rubin DT, Kim AM, Serra S, et al. Fecal microbiota transplantation is highly effective in real-world practice: initial results from the FMT National Registry. Gastroenterology. 2021;160(1):183-192 e183.

    Article PubMed Google Scholar 

  82. Hvas CL, Keller J, Baunwall SMD, Edwards LA, Ianiro G, Kupcinskas J, Link A, Mullish BH, Satokari R, Terveer E, Vehreshild MJG. European academic faecal microbiota transplantation (EURFMT) network: improving the safety and quality of microbiome therapies in Europe. Microb Health Dis. 2023;5:e954.

    Google Scholar 

  83. Khoruts A. Can FMT cause or prevent CRC? Maybe, but there is more to consider. Gastroenterology. 2021;161(4):1103–5.

    Article PubMed Google Scholar 

  84. Drewes JL, Chen J, Markham NO, Knippel RJ, Domingue JC, Tam AJ, Chan JL, Kim L, McMann M, Stevens C, et al. Human colon cancer-derived Clostridioides difficile strains drive colonic tumorigenesis in mice. Cancer Discov. 2022;12(8):1873–85.

    Article CAS PubMed PubMed Central Google Scholar 

Download references

chronisch zieke mensen, resistente bacterien, poeptransplantatie, Liz Terveer, arts-microbioloog bij het LUMC, darmbacterien


Plaats een reactie ...

Reageer op "Poeptransplantatie onderdrukt en laat resistente bacterien verdwijnen bij chronisch zieke mensen met ziekte van Crohn, blijkt uit Nederlandse studie"


Gerelateerde artikelen
 

Gerelateerde artikelen

Specifieke darmbacteriën >> De samenstelling van je poep >> Microbioom - darmflora van >> Darmbacterien beinvloeden >> Poeptransplantatie onderdrukt >> Specifieke bacterien in het >> Darmkanker: Oorspronkelijk >> Darmflora en hersenas: Verstoring >> Microbioom - Darmflora, een >>