{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T03:46:23Z","timestamp":1791776783135,"version":"4.3.4"},"reference-count":68,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI165519"],"award-info":[{"award-number":["AI165519"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSphere"],"published-print":{"date-parts":[[2025,12,23]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Enterococcus faecium<\/jats:italic>\n                      is a member of the human gut microbiota that has evolved into a problematic nosocomial pathogen and a leading cause of infections in hospitalized patients. Treatment of\n                      <jats:italic toggle=\"yes\">E. faecium<\/jats:italic>\n                      infections is complicated by antibiotic resistance, making it important to understand resistance mechanisms and their broader consequences in this pathogen. Here, we explored the collateral effects of rifampin resistance-associated mutations in the\n                      <jats:italic toggle=\"yes\">E. faecium<\/jats:italic>\n                      RNA polymerase \u03b2-subunit (RpoB). Of 14,384 publicly available\n                      <jats:italic toggle=\"yes\">E. faecium<\/jats:italic>\n                      genomes, nearly one-third carried a mutation in the rifampin resistance-determining region (RRDR) of RpoB. In a local population of 710\n                      <jats:italic toggle=\"yes\">E. faecium<\/jats:italic>\n                      clinical isolates collected from patients at a single hospital, we found significant associations between the presence of RRDR mutations and prior exposure to rifamycin antibiotics, as well as associations between RRDR mutations and altered daptomycin susceptibility. To investigate the phenotypic impacts of RRDR mutations, we generated and studied four isogenic strains with distinct RRDR mutations (Q473K, G482D, H486Y, and S491L) that overlapped with clinical isolate variants. Transcriptomic and phenotypic analyses revealed allele-specific effects on\n                      <jats:italic toggle=\"yes\">E. faecium<\/jats:italic>\n                      gene expression, growth dynamics, antibiotic susceptibility, isopropanol tolerance, and cell wall physiology. One frequently observed mutation, H486Y, caused minimal transcriptional changes and enhanced bacterial fitness under antibiotic stress. In contrast, the S491L mutation induced extensive transcriptional changes and slowed bacterial growth but also conferred increased isopropanol tolerance, potentially enhancing bacterial survival on hospital surfaces. Overall, our findings highlight the multifaceted impacts of RRDR mutations in shaping\n                      <jats:italic toggle=\"yes\">E. faecium<\/jats:italic>\n                      physiology and antibiotic resistance, two important features of this hospital-associated pathogen.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Understanding how antimicrobial resistance affects bacterial physiology is critical for developing effective therapeutics against bacterial infections. In this study, we found that rifampin resistance-associated mutations in RpoB are widespread in\n                        <jats:italic toggle=\"yes\">Enterococcus faecium,<\/jats:italic>\n                        a leading multidrug-resistant pathogen. By studying isogenic wild-type and RpoB mutant strains, we discovered that RpoB mutations, although conferring resistance to rifampin, have distinct allele-specific effects on other bacterial phenotypes. Some of these collateral effects appear to promote\n                        <jats:italic toggle=\"yes\">E. faecium<\/jats:italic>\n                        resistance to antibiotics and survival in the hospital environment, raising questions about the selective pressures driving their emergence. Overall, our study underscores the importance of examining the collateral effects of resistance-associated mutations in multidrug-resistant pathogens, which could help mitigate their persistence and spread among vulnerable patients.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msphere.00506-25","type":"journal-article","created":{"date-parts":[[2025,12,4]],"date-time":"2025-12-04T14:00:19Z","timestamp":1764856819000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":4,"title":["Allele-specific effects of mutations in the rifampin resistance-determining region (RRDR) of RpoB on physiology and antibiotic resistance in\n                    <i>Enterococcus faecium<\/i>"],"prefix":"10.1128","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0310-3139","authenticated-orcid":false,"given":"Adeline","family":"Supandy","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases, University of Pittsburgh, School of Medicine","place":["Pittsburgh, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma G.","family":"Mills","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, University of Pittsburgh, School of Medicine","place":["Pittsburgh, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyong T.","family":"Fam","sequence":"additional","affiliation":[{"name":"Department of Immunology and Microbiology, Scripps Research","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9794-5665","authenticated-orcid":true,"given":"Ryan K.","family":"Shields","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, University of Pittsburgh, School of Medicine","place":["Pittsburgh, USA"]},{"id":[{"id":"https:\/\/ror.org\/01an3r305","id-type":"ROR","asserted-by":"publisher"}],"name":"Antibiotic Management Program, University of Pittsburgh Medical Center","place":["Pittsburgh, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3373-7140","authenticated-orcid":true,"given":"Howard C.","family":"Hang","sequence":"additional","affiliation":[{"name":"Department of Immunology and Microbiology, Scripps Research","place":["La Jolla, USA"]},{"id":[{"id":"https:\/\/ror.org\/02dxx6824","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Chemistry, Scripps Research","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7284-0103","authenticated-orcid":true,"given":"Daria","family":"Van Tyne","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, University of Pittsburgh, School of Medicine","place":["Pittsburgh, USA"]},{"id":[{"id":"https:\/\/ror.org\/01an3r305","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Evolutionary Biology and Medicine, University of Pittsburgh","place":["Pittsburgh, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(24)01867-1"},{"key":"e_1_3_5_3_2","unstructured":"O\u2019Neill J. 2016. Tackling drug-resistant infections globally: final report and recommendations. Government of the United Kingdom"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI43918"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1086\/533452"},{"key":"e_1_3_5_6_2","unstructured":"Arias CA Miller WR. 2023. Mechanisms of antibiotic resistance in enterococci. Available from: https:\/\/www.uptodate.com\/contents\/mechanisms-of-antibiotic-resistance-in-enterococci"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-micro-091213-113003"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2761"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.2147\/IDR.S270701"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2020.04.027"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2021.720647"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2013.01.006"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(21)02724-0"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.06077-11"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-08095-4"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2009.10.062"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-025-01958-0"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciab946"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.13606"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/ja.2014.107"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.000991"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.51407"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00398-11"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00901-07"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1917130117"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab293"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa1018"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tube.2011.05.002"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkh044"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/156.4.1471"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.46.11.3381-3385.2002"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01562-14"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00039-06"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00437-10"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aar6115"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(18)69397-4"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.1999.01430.x"},{"key":"e_1_3_5_38_2","first-page":"259","volume-title":"Methods in enzymology chemical microbiology part B","author":"Apostolos AJ","year":"2022","unstructured":"Apostolos AJ, Pires MM. 2022. Impact of crossbridge structure on peptidoglycan crosslinking: a synthetic stem peptide approach, p 259\u2013279. In Methods in enzymology chemical microbiology part B. Academic Press."},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-011-3486-x"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.44.9.2276-2285.2000"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.idh.2018.12.002"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02034-16"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2008.04.006"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.38.9.1899"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.02333-21"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02686-14"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00790-19"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.1111\/nyas.12948"},{"key":"e_1_3_5_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01317-20"},{"key":"e_1_3_5_50_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15257-1"},{"key":"e_1_3_5_51_2","doi-asserted-by":"publisher","DOI":"10.1086\/648473"},{"key":"e_1_3_5_52_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01073-15"},{"key":"e_1_3_5_53_2","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.173836"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01473-13"},{"key":"e_1_3_5_55_2","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03168-22"},{"key":"e_1_3_5_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"e_1_3_5_57_2","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"e_1_3_5_58_2","volume-title":"Performance standards for antimicrobial susceptibility testing","author":"CLSI","year":"2025","unstructured":"CLSI. 2025. Performance standards for antimicrobial susceptibility testing. 35th ed. Clinical and Laboratory Standards Institute.","edition":"35"},{"key":"e_1_3_5_59_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_5_60_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_5_61_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-0554-6_12"},{"key":"e_1_3_5_62_2","unstructured":"Krueger F. 2021. TrimGalore. Available from: https:\/\/github.com\/FelixKrueger\/TrimGalore"},{"key":"e_1_3_5_63_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"e_1_3_5_64_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt656"},{"key":"e_1_3_5_65_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"e_1_3_5_66_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.33"},{"key":"e_1_3_5_67_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.45343"},{"key":"e_1_3_5_68_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.95297"},{"key":"e_1_3_5_69_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiae173"}],"container-title":["mSphere"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msphere.00506-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msphere.00506-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T14:01:16Z","timestamp":1766498476000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msphere.00506-25"}},"subtitle":[],"editor":[{"given":"Paul D.","family":"Fey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,12,23]]},"references-count":68,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,12,23]]}},"alternative-id":["10.1128\/msphere.00506-25"],"URL":"https:\/\/doi.org\/10.1128\/msphere.00506-25","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.07.25.666922","asserted-by":"object"}]},"ISSN":["2379-5042"],"issn-type":[{"value":"2379-5042","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,23]]},"assertion":[{"value":"2025-07-25","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-11-11","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-12-04","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00506-25"}}