{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T04:35:54Z","timestamp":1773722154664,"version":"3.50.1"},"reference-count":32,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2020,6,23]],"date-time":"2020-06-23T00:00:00Z","timestamp":1592870400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Commission under the Seventh Framework Programme (FP7\/2007) for Research and technology","award":["282512"],"award-info":[{"award-number":["282512"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Background: The R-GNOSIS (Resistance in Gram-Negative Organisms: Studying Intervention Strategies) WP3 study was the first multicenter randomized clinical trial systematically investigating fecal microbiota transplantation (FMT) for intestinal decolonization of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) or carbapenemase-producing Enterobacteriaceae (CPE). Here, we characterized the temporal dynamics of fecal microbiota changes in a sub-cohort of the R-GNOSIS WP3 participants before and after antibiotics\/FMT using whole metagenome shotgun sequencing. Methods: We sequenced fecal DNA obtained from 16 ESBL-E\/CPE carriers having received oral colistin\/neomycin followed by FMT and their corresponding seven donors. Ten treatment-na\u00efve controls from the same trial were included. Fecal samples were collected at baseline (V0), after antibiotics but before FMT (V2) and three times after FMT (V3, V4 and V5). Results: Antibiotic treatment transiently decreased species richness and diversity and increased the abundance of antibiotic resistance determinants (ARDs). Bifidobacterium species, together with butyrate- and propionate-producing species from Lachnospiraceae and Ruminococcaceae families were significantly enriched in post-FMT microbiota of treated carriers. After FMT, the proportion of Enterobacteriaceae was lower compared to baseline but without statistical significance. Conclusions: Combined antibiotic and FMT treatment resulted in enrichment of species that are likely to limit the gut colonization by ESBL-E\/CPE.<\/jats:p>","DOI":"10.3390\/microorganisms8060941","type":"journal-article","created":{"date-parts":[[2020,6,23]],"date-time":"2020-06-23T09:05:33Z","timestamp":1592903133000},"page":"941","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Metagenomic Characterization of Gut Microbiota of Carriers of Extended-Spectrum Beta-Lactamase or Carbapenemase-Producing Enterobacteriaceae Following Treatment with Oral Antibiotics and Fecal Microbiota Transplantation: Results from a Multicenter Randomized Trial"],"prefix":"10.3390","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5015-3051","authenticated-orcid":false,"given":"Stefano","family":"Leo","sequence":"first","affiliation":[{"name":"Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Rue Michel Servet 1, 1211 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6839-2536","authenticated-orcid":false,"given":"Vladimir","family":"Lazarevic","sequence":"additional","affiliation":[{"name":"Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Rue Michel Servet 1, 1211 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Myriam","family":"Girard","sequence":"additional","affiliation":[{"name":"Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Rue Michel Servet 1, 1211 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadia","family":"Ga\u00efa","sequence":"additional","affiliation":[{"name":"Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Rue Michel Servet 1, 1211 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacques","family":"Schrenzel","sequence":"additional","affiliation":[{"name":"Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Rue Michel Servet 1, 1211 Geneva, Switzerland"},{"name":"Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victoire","family":"de Lastours","sequence":"additional","affiliation":[{"name":"Division of Internal Medicine, Beaujon Hospital, APHP, Boulevard du G\u00e9n\u00e9ral Leclerc 100, 92110 Clichy, France"},{"name":"IAME Research Group, UMR 1137, INSERM and University of Paris, Rue Henri Huchard 16, 75870 Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruno","family":"Fantin","sequence":"additional","affiliation":[{"name":"Division of Internal Medicine, Beaujon Hospital, APHP, Boulevard du G\u00e9n\u00e9ral Leclerc 100, 92110 Clichy, France"},{"name":"IAME Research Group, UMR 1137, INSERM and University of Paris, Rue Henri Huchard 16, 75870 Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Bonten","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University Medical Centre, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands"},{"name":"Julius Center for Health Sciences and Primary Care, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yehuda","family":"Carmeli","sequence":"additional","affiliation":[{"name":"National Institute for Antibiotic Resistance and Infection Control, Tel Aviv Medical Center, and Sackler Faculty of Medicine, Tel Aviv University, Weizmann Street 6, Tel Aviv 6423906, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emilie","family":"Rondinaud","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, APHP, Bichat-Claude-Bernard Hospital, Rue Henri Huchard 46, 75018 Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephan","family":"Harbarth","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva, Switzerland"},{"name":"Infection Control Program and WHO Collaborating Center, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benedikt D.","family":"Huttner","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,6,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/S1473-3099(17)30753-3","article-title":"Discovery, research, and development of new antibiotics: The WHO priority list of antibiotic-resistant bacteria and tuberculosis","volume":"18","author":"Tacconelli","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/S1473-3099(18)30792-8","article-title":"Effect of carbapenem resistance on outcomes of bloodstream infection caused by Enterobacteriaceae in low-income and middle-income countries (PANORAMA): A multinational prospective cohort study","volume":"19","author":"Stewardson","year":"2019","journal-title":"Lancet Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1086\/669086","article-title":"Burden of bloodstream infection caused by extended-spectrum \u03b2-lactamase\u2013producing Enterobacteriaceae determined using multistate modeling at a Swiss University Hospital and a nationwide predictive model","volume":"34","author":"Stewardson","year":"2015","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"908","DOI":"10.3201\/eid1806.110139","article-title":"Pretransplant fecal carriage of extended-spectrum \u03b2-lactamase-producing Enterobacteriaceae and infection after liver transplant, France","volume":"18","author":"Bert","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Rieg, S., K\u00fcpper, M.F., de With, K., Serr, A., Bohnert, J.A., and Kern, W.V. (2015). Intestinal decolonization of Enterobacteriaceae producing extended-spectrum \u03b2-lactamases (ESBL): A retrospective observational study in patients at risk for infection and a brief review of the literature. BMC Infect. Dis., 15.","DOI":"10.1186\/s12879-015-1225-0"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1016\/j.cmi.2019.01.005","article-title":"ESCMID-EUCIC clinical guidelines on decolonization of multidrug-resistant Gram-negative bacteria carriers","volume":"25","author":"Tacconelli","year":"2019","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"630","DOI":"10.7326\/M14-2693","article-title":"Fecal microbiota transplantation for Clostridium difficile infection: A systematic review","volume":"162","author":"Drekonja","year":"2015","journal-title":"Ann. Intern. Med."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Caballero, S., Carter, R., Ke, X., Su\u0161ac, B., Leiner, I.M., Kim, G.J., Miller, L., Ling, L., Manova, K., and Pamer, E.G. (2015). Distinct but spatially overlapping intestinal niches for vancomycin-resistant Enterococcus faecium and carbapenem-resistant Klebsiella pneumoniae. PLoS Pathog., 11.","DOI":"10.1371\/journal.ppat.1005132"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.jhin.2019.03.010","article-title":"Faecal microbiota transplantation for the decolonization of antibiotic-resistant bacteria in the gut: A systematic review and meta-analysis","volume":"102","author":"Tavoukjian","year":"2019","journal-title":"J. Hosp. Infect."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1080\/14787210.2019.1645007","article-title":"Strategies for the eradication of extended-spectrum beta-lactamase or carbapenemase-producing Enterobacteriaceae intestinal carriage","volume":"17","author":"Catho","year":"2019","journal-title":"Expert Rev. Anti-Infect. Ther."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Huttner, B.D., de Lastours, V., Wassenberg, M., Maharshak, N., Mauris, A., Galperine, T., Zanichelli, V., Kapel, N., Bellanger, A., and Olearo, F. (2019). 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.","DOI":"10.1016\/j.cmi.2019.02.001"},{"key":"ref_12","doi-asserted-by":"crossref","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":"ref_13","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: Ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","article-title":"Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies","volume":"67","author":"Yoon","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_17","first-page":"e000197","article-title":"Extended-spectrum \u03b2-lactamase-producing and carbapenemase-producing Enterobacteriaceae","volume":"4","author":"Wilson","year":"2018","journal-title":"Microb. Genom."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Liakopoulos, A., Mevius, D., and Ceccarelli, D. (2016). A Review of SHV extended-spectrum \u03b2-lactamases: Neglected yet ubiquitous. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.01374"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1152\/physiolgenomics.00073.2018","article-title":"Disparate effects of antibiotics on hypertension","volume":"50","author":"Galla","year":"2018","journal-title":"Physiol. Genom."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1086\/429323","article-title":"Colistin: The revival of polymyxins for the management of multidrug-resistant Gram-negative bacterial infections","volume":"40","author":"Falagas","year":"2005","journal-title":"Clin. Infect. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2151","DOI":"10.1038\/ncomms3151","article-title":"Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota","volume":"4","author":"Hu","year":"2013","journal-title":"Nat. Commun."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1101\/gr.155465.113","article-title":"Country-specific antibiotic use practices impact the human gut resistome","volume":"23","author":"Forslund","year":"2013","journal-title":"Genome Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e00130-17","DOI":"10.1128\/mSystems.00130-17","article-title":"Colonic butyrate-producing communities in humans: An overview using omics data","volume":"2","author":"Vital","year":"2017","journal-title":"mSystems"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2826","DOI":"10.3748\/wjg.v13.i20.2826","article-title":"Anti-inflammatory properties of the short-chain fatty acids acetate and propionate: A study with relevance to inflammatory bowel disease","volume":"13","author":"Tedelind","year":"2007","journal-title":"World J. Gastroenterol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1111\/j.1348-0421.2011.00398.x","article-title":"Anti-inflammatory properties of intestinal Bifidobacterium strains isolated from healthy infants","volume":"56","author":"Khokhlova","year":"2012","journal-title":"Microbiol. Immunol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.anaerobe.2016.02.010","article-title":"Antagonistic activities of some Bifidobacterium sp. strains isolated from resident infant gastrointestinal microbiota on Gram-negative enteric pathogens","volume":"39","author":"Delcaru","year":"2016","journal-title":"Anaerobe"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Qin, P., Zou, Y., Dai, Y., Luo, G., Zhang, X., and Xiao, L. (2019). Characterization a novel butyric acid-producing bacterium Collinsella aerofaciens subsp. Shenzhenensis subsp. nov.. Microorganisms, 7.","DOI":"10.3390\/microorganisms7030078"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1093\/cid\/cix252","article-title":"Fecal microbiota transplantation in patients with blood disorders inhibits gut colonization with antibiotic-resistant bacteria: Results of a prospective, single-center study","volume":"65","author":"Bilinski","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1128\/IAI.01197-12","article-title":"Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization","volume":"81","author":"Ubeda","year":"2013","journal-title":"Infect. Immun."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1016\/j.resmic.2014.10.006","article-title":"Characterization of virus-like particles associated with the human faecal and caecal microbiota","volume":"165","author":"Hoyles","year":"2014","journal-title":"Res. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.chom.2019.09.009","article-title":"The human gut virome is highly diverse, stable, and individual specific","volume":"26","author":"Shkoporov","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.ijantimicag.2017.02.018","article-title":"Unexpected persistence of extended-spectrum \u03b2-lactamase-producing Enterobacteriaceae in the faecal microbiota of hospitalised patients treated with imipenem","volume":"50","author":"Grall","year":"2017","journal-title":"Int. J. Antimicrob. Agents"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/6\/941\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:41:46Z","timestamp":1760175706000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/6\/941"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,23]]},"references-count":32,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2020,6]]}},"alternative-id":["microorganisms8060941"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms8060941","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,23]]}}}