{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T20:58:06Z","timestamp":1788814686411,"version":"build-2803163510"},"reference-count":32,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T00:00:00Z","timestamp":1702339200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T00:00:00Z","timestamp":1702339200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2023,12,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            This study investigated the gut microbiome dynamics of index patients colonized with extended-spectrum beta-lactamase-producing\n            <jats:italic>Escherichia coli<\/jats:italic>\n            (ESBL-Ec) (\n            <jats:italic>n<\/jats:italic>\n            = 5) or extended-spectrum beta-lactamase-producing\n            <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n            (ESBL-Kp) (\n            <jats:italic>n<\/jats:italic>\n            = 3) and their household contacts (\n            <jats:italic>n<\/jats:italic>\n            = 9) up to 4 months after hospital discharge of the index patient using 16S rRNA amplicon gene sequencing. Samples were collected at the day of hospital discharge of the index patient, 1 week and 2 and 4 months after discharge. Compared to household contacts, we observed a significant lower alpha diversity (\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.001) among index patients and significant (\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.05) separation between the two groups for beta diversity. Principal component analysis of the samples from each household (i.e., index patient and respective household contact) showed a clear shift in microbiome composition, in 4\/8 index patients, from dissimilar to more similar to the household contact group. This suggests recovery of the microbiome to a healthier status, which was also reflected by\n            <jats:italic>de novo<\/jats:italic>\n            colonization of (health-associated) taxa. In contrast, the four time-point samples of the household contacts clustered together indicating a stable microbiome composition over time irrespective of low-level ESBL-Ec (\n            <jats:italic>n<\/jats:italic>\n            = 3) or ESBL-Kp (\n            <jats:italic>n<\/jats:italic>\n            = 2) colonization. In conclusion, here we show that, at the day of hospital discharge, the microbiome composition of index patients is dissimilar from that of household contacts. Over time, signals of microbiome recovery were observed in half of the index patients. The stable microbiome composition in household contacts irrespective of low-level ESBL-Ec or ESBL-Kp colonization suggests that the gut microbiome in these healthy people provided colonization resistance against ESBL-PE outgrowth.\n          <\/jats:p>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              Colonization with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) often precedes infections and is therefore considered as a great threat for public health. Here, we studied the gut microbiome dynamics in eight index patients colonized with ESBL-PE after hospital discharge and the impact of exposure to this index patient on the gut microbiome dynamics of their household contacts. We showed that the microbiome composition from index patients is different from their household contacts upon hospital discharge and that, in some of the index patients, their microbiome composition over time shifted toward the composition of their household contacts. In contrast, household contacts showed a stable microbiome composition over time irrespective of low-level extended-spectrum beta-lactamase-producing\n              <jats:italic>Escherichia coli<\/jats:italic>\n              (ESBL-Ec) or extended-spectrum beta-lactamase-producing\n              <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n              (ESBL-Kp) gut colonization, suggesting that, in healthy microbiomes, colonization resistance is able to prevent ESBL-PE expansion.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.01275-23","type":"journal-article","created":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T13:02:30Z","timestamp":1698411750000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":5,"title":["Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4620-8128","authenticated-orcid":false,"given":"Janetta","family":"Top","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology, University Medical Center Utrecht , Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tess D.","family":"Verschuuren","sequence":"additional","affiliation":[{"name":"Mahidol Oxford Tropical Medicine Research Unit (MORU) , Bangkok, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco C.","family":"Viveen","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University Medical Center Utrecht , Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Eugenia","family":"Riccio","sequence":"additional","affiliation":[{"name":"University of Geneva Hospitals and Faculty of Medicine, Infection Control Program, WHO Collaborating Center , Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Harbarth","sequence":"additional","affiliation":[{"name":"University of Geneva Hospitals and Faculty of Medicine, Infection Control Program, WHO Collaborating Center , Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan A. J. W.","family":"Kluytmans","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University Medical Center Utrecht , Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7370-0812","authenticated-orcid":false,"given":"Rob J. L.","family":"Willems","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University Medical Center Utrecht , Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9990-9203","authenticated-orcid":false,"given":"Fernanda L.","family":"Paganelli","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University Medical Center Utrecht , Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cix258"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks502"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2016.08.021"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01008-08"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis581"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1093\/jacamr\/dlac048"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1017\/ice.2019.336"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2020.12.024"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2022.2060676"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(22)00037-4"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00095-16"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-05817-4"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-6"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","unstructured":"Bolyen E Rideout JR Dillon MR Bokulich NA Abnet C Al-Ghalith GA Alexander H Alm EJ Arumugam M Asnicar F et al.\n. 2018. QIIME 2 : reproducible interactive scalable and extensible microbiome data science. Peerj Preprints. doi:10.7287\/peerj.preprints.27295v1","DOI":"10.7287\/peerj.preprints.27295v1"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1219"},{"key":"e_1_3_4_18_2","unstructured":"R Core Team\n. 2020. R: a language and environment for statistical computing. https:\/\/www.r-project.org."},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217"},{"key":"e_1_3_4_20_2","volume-title":"Package `ggplot2`: elegant graphics for data analysis","author":"Wickham H","year":"2016","unstructured":"Wickham H . 2016. Package `ggplot2`: elegant graphics for data analysis. Springer-Verlag New York, Cham."},{"key":"e_1_3_4_21_2","unstructured":"Oksanen J Blanchet FG Friendly M Kindt R Legendre P Mcglinn D Minchin PR O\u2019hara RB Simpson GL Solymos P Henry M Stevens H Szoecs E Maintainer HW\n. 2020. Package \u201cvegan\u201d. A community ecology package. Community ecology package"},{"key":"e_1_3_4_22_2","unstructured":"Lahti L Shetty S Blake T\n. 2017. Tools for microbiome analysis in R. Microbiome package version 099"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18476-8"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04567-7"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.1260"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad9358"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.572912"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0257-9"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2015.05.040"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2020-321747"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.38.3.409"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00007-19"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41385-018-0053-0"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01275-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01275-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T13:20:23Z","timestamp":1702387223000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01275-23"}},"subtitle":[],"editor":[{"given":"Se-Ran","family":"Jun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,12,12]]},"references-count":32,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,12,12]]}},"alternative-id":["10.1128\/spectrum.01275-23"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01275-23","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,12]]},"assertion":[{"value":"2023-03-31","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-10-05","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-10-27","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01275-23"}}