{"id":"https://openalex.org/W15363129","doi":null,"title":"Functional genomics of Enterococcus faecium: antibiotic resistance and niche adaptation","display_name":"Functional genomics of Enterococcus faecium: antibiotic resistance and niche adaptation","publication_year":2013,"publication_date":"2013-04-12","ids":{"openalex":"https://openalex.org/W15363129","mag":"15363129"},"language":"en","primary_location":{"id":"pmh:oai:dspace.library.uu.nl:1874/273379","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/273379","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://dspace.library.uu.nl/handle/1874/273379","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042948498","display_name":"Xueqiao Zhang","orcid":"https://orcid.org/0000-0002-6635-371X","observed_orcids":["https://orcid.org/0000-0002-6635-371X"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"X. Zhang","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-9186-4741","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5042948498"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.4528999924659729,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.4528999924659729,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10195","display_name":"Antimicrobial Resistance in Staphylococcus","score":0.4332999885082245,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.05139999836683273,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/enterococcus-faecium","display_name":"Enterococcus faecium","score":1.0},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"antibiotic resistance","score":0.949999988079071},{"id":"https://openalex.org/keywords/niche-adaptation","display_name":"niche adaptation","score":0.7760000228881836},{"id":"https://openalex.org/keywords/nosocomial-pathogens","display_name":"nosocomial pathogens","score":0.8389999866485596},{"id":"https://openalex.org/keywords/nosocomial-infections","display_name":"nosocomial infections","score":0.7369999885559082},{"id":"https://openalex.org/keywords/ampicillin-resistance","display_name":"ampicillin resistance","score":0.906000018119812},{"id":"https://openalex.org/keywords/bile-salt-tolerance","display_name":"bile salt tolerance","score":0.9890000224113464},{"id":"https://openalex.org/keywords/gastrointestinal-colonization","display_name":"intestinal colonization","score":0.9850000143051147},{"id":"https://openalex.org/keywords/commensal-strains","display_name":"commensal strains","score":0.7570000290870667},{"id":"https://openalex.org/keywords/megaplasmid","display_name":"megaplasmid","score":0.9120000004768372},{"id":"https://openalex.org/keywords/functional-genomics","display_name":"functional genomics","score":0.6729999780654907},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.6700000166893005},{"id":"https://openalex.org/keywords/molecular-epidemiology","display_name":"molecular epidemiology","score":0.6169999837875366},{"id":"https://openalex.org/keywords/population-structure","display_name":"population structure","score":0.5339999794960022},{"id":"https://openalex.org/keywords/gut-microbiota","display_name":"gut microbiota","score":0.41600000858306885}],"concepts":[{"id":"https://openalex.org/C2777677444","wikidata":"https://www.wikidata.org/wiki/Q140010","display_name":"Enterococcus faecium","level":3,"score":0.9250812530517578},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.761497974395752},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.6581656336784363},{"id":"https://openalex.org/C183641309","wikidata":"https://www.wikidata.org/wiki/Q306264","display_name":"Amp resistance","level":4,"score":0.5264236330986023},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.49910807609558105},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.46425965428352356},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.4417303800582886},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.4387117028236389},{"id":"https://openalex.org/C2776021129","wikidata":"https://www.wikidata.org/wiki/Q244150","display_name":"Ampicillin","level":3,"score":0.41964656114578247},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4086180329322815},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.40636035799980164},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.3682563900947571},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2967901825904846},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.26406562328338623},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.11260131001472473},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.05990821123123169},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:dspace.library.uu.nl:1874/273379","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/273379","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},{"id":"pmh:umcu:oai:dspace.library.uu.nl:1874/273379","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/273379","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralthesis"},{"id":"pmh:uu:oai:dspace.library.uu.nl:1874/273379","doi":null,"is_oa":true,"landing_page_url":"http://dspace.library.uu.nl/handle/1874/273379","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralthesis"},{"id":"mag:15363129","doi":null,"is_oa":false,"landing_page_url":"http://dspace.library.uu.nl/bitstream/1874/273379/3/Zhangverbeterdeversie.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:dspace.library.uu.nl:1874/273379","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/273379","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.8560000061988831,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W1497287772","https://openalex.org/W1508893821","https://openalex.org/W1591382601","https://openalex.org/W1932438771","https://openalex.org/W1965143457","https://openalex.org/W1965715358","https://openalex.org/W1970927928","https://openalex.org/W1971299795","https://openalex.org/W1976667730","https://openalex.org/W1980017270","https://openalex.org/W1980177626","https://openalex.org/W1993341437","https://openalex.org/W2030924818","https://openalex.org/W2031143719","https://openalex.org/W2045511565","https://openalex.org/W2053899751","https://openalex.org/W2057744551","https://openalex.org/W2060637207","https://openalex.org/W2065127848","https://openalex.org/W2066169311","https://openalex.org/W2067849157","https://openalex.org/W2069377402","https://openalex.org/W2083110628","https://openalex.org/W2084266616","https://openalex.org/W2087865186","https://openalex.org/W2090927759","https://openalex.org/W2098885132","https://openalex.org/W2100927178","https://openalex.org/W2101499441","https://openalex.org/W2104371716","https://openalex.org/W2104657177","https://openalex.org/W2108779461","https://openalex.org/W2108876055","https://openalex.org/W2111502970","https://openalex.org/W2115018455","https://openalex.org/W2117737102","https://openalex.org/W2123755502","https://openalex.org/W2128305261","https://openalex.org/W2129636433","https://openalex.org/W2135424953","https://openalex.org/W2137167776","https://openalex.org/W2137890456","https://openalex.org/W2139081288","https://openalex.org/W2139470960","https://openalex.org/W2145493018","https://openalex.org/W2148753657","https://openalex.org/W2161115481","https://openalex.org/W2167692246","https://openalex.org/W2169297879","https://openalex.org/W7075585795"],"related_works":["https://openalex.org/W2737284717","https://openalex.org/W2398608465","https://openalex.org/W1991603642","https://openalex.org/W7162126268","https://openalex.org/W2403130561","https://openalex.org/W2950991961","https://openalex.org/W7064152782","https://openalex.org/W134488039","https://openalex.org/W7097664380","https://openalex.org/W4308997879"],"abstract_inverted_index":{"The":[0,196,387,412],"Gram-positive":[1],"bacterium":[2,405],"Enterococcus":[3],"faecium":[4,75,110,236,273,284,295,318,340,399],"has":[5,24,95,167],"long":[6,132],"been":[7,46,96,133],"perceived":[8],"as":[9,27,116,240,401,407],"a":[10,118,122,223,263,312,369,402],"harmlessmember":[11],"of":[12,29,33,55,63,105,108,138,144,163,179,192,205,234,262,331,338,352,381,397,423],"the":[13,19,30,41,49,61,85,102,136,145,189,203,232,250,260,321,326,348,379,394],"mammalian":[14,251],"gut":[15,119,427],"microbiota.":[16],"However,":[17],"in":[18,99,127,148,202,218,270,281,292,301,335,363],"past":[20],"two":[21],"decades":[22],"it":[23],"rapidly":[25,98],"emerged":[26],"one":[28],"leading":[31],"causes":[32],"multidrug":[34],"resistant":[35],"hospital":[36],"acquired":[37],"infections":[38],"all":[39],"over":[40],"world.":[42],"Many":[43],"studies":[44,90,146,171,374,377],"have":[45,59,131,152],"performed":[47],"on":[48],"molecular":[50,155,197,354],"epidemiology":[51],"and":[52,91,121,130,157,175,182,275,328,350,359,375,406,429],"population":[53],"structure":[54],"E.":[56,74,109,164,219,235,272,283,294,317,339,364,398,432],"faecium.":[57,165,220,365,433],"These":[58,366],"revealed":[60],"existence":[62],"evolutionarily":[64],"separate":[65],"hospital-associated":[66],"lineages.":[67],"Comparative":[68,254],"genomic":[69],"analyses":[70,94,362],"showed":[71],"that":[72,111,185,199,213,229,266,297,310],"hospital-acquired":[73],"isolates":[76,274],"were":[77,200,208],"genetically":[78],"distinct":[79],"from":[80,88],"indigenous":[81],"intestinal":[82,252,279],"isolates.":[83,303],"Although":[84],"knowledge":[86,413],"generated":[87,414],"epidemiological":[89],"genome":[92,255],"sequence":[93,256],"increasing":[97],"recent":[100],"years,":[101],"functional":[103,169,372],"characterization":[104],"genetic":[106,140,161,177,264,313,332,361],"determinants":[107,178,333,389],"contribute":[112,214,230,391],"to":[113,172,210,215,226,231,237,248,259,278,319,393],"its":[114,128,246],"success":[115,191,396],"both":[117,357,400],"commensal":[120,293,404],"nosocomial":[123,194,385,410],"pathogen":[124],"is":[125,243,267,298,341],"still":[126],"infancy":[129],"hampered":[134],"by":[135,415,431],"lack":[137],"appropriate":[139],"tools.":[141],"As":[142],"part":[143],"described":[147],"this":[149,193,206,241,345,382,416],"thesis,":[150],"we":[151],"developed":[153,201],"powerful":[154],"tools":[156,198,355,367],"techniquesthat":[158],"allow":[159],"efficient":[160],"manipulation":[162],"This":[166],"facilitated":[168],"genomics-based":[170],"systemically":[173],"identify":[174,211,227],"characterize":[176],"antibiotic":[180],"resistance":[181,217,233],"niche":[183],"adaptation":[184,291],"are":[186],"responsible":[187],"for":[188,245,356,371,421],"ecological":[190,395],"pathogen.":[195,386,411],"course":[204],"research,":[207],"used":[209,222],"genes":[212,228],"ampicillin":[216],"We":[221,286],"similar":[224],"approach":[225],"bile":[238],"salts":[239],"trait":[242],"important":[244,290,384],"ability":[247],"colonize":[249],"tract.":[253],"analysis":[257,330],"led":[258],"identification":[261,327],"determinant":[265],"specifically":[268],"enriched":[269],"clinical":[271,282,302],"which":[276,315],"contributes":[277],"colonization":[280,428],"strains.":[285],"also":[287],"identified":[288,388],"an":[289,408],"strains":[296,305],"very":[299],"rare":[300],"Commensal":[304],"can":[306],"carry":[307],"transferable":[308],"megaplasmid":[309],"contains":[311],"element":[314],"allows":[316],"utilize":[320],"non-digestible":[322],"sugar":[323],"raffinose.":[324],"Finally,":[325],"transcriptional":[329],"involved":[334],"maltodextrin":[336],"utilization":[337],"described.":[342],"In":[343],"conclusion,":[344],"thesis":[346],"describes":[347],"development":[349,422],"implementation":[351],"new":[353],"genome-wide":[358],"targeted":[360],"provide":[368],"platform":[370],"genomic-based":[373],"allowed":[376],"into":[378],"biology":[380],"increasingly":[383],"may":[390,418],"importantly":[392],"human":[403],"emerging":[409],"study":[417],"be":[419],"applied":[420],"therapeutic":[424],"strategies":[425],"against":[426],"infection":[430]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
