{"id":"https://openalex.org/W7119201598","doi":"https://doi.org/10.1038/s44259-025-00171-7","title":"Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection","display_name":"Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection","publication_year":2026,"publication_date":"2026-01-08","ids":{"openalex":"https://openalex.org/W7119201598","doi":"https://doi.org/10.1038/s44259-025-00171-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/41507619"},"language":"en","primary_location":{"id":"doi:10.1038/s44259-025-00171-7","doi":"https://doi.org/10.1038/s44259-025-00171-7","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s44259-025-00171-7","pdf_url":"https://www.nature.com/articles/s44259-025-00171-7.pdf","source":{"id":"https://openalex.org/S4387289274","display_name":"npj Antimicrobials and Resistance","issn_l":"2731-8745","issn":["2731-8745"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"npj Antimicrobials and Resistance","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.nature.com/articles/s44259-025-00171-7.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045186199","display_name":"Merianne Mohamad","orcid":"https://orcid.org/0000-0001-7520-4911","observed_orcids":["https://orcid.org/0000-0001-7520-4911"]},"institutions":[{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]},{"id":"https://openalex.org/I335284955","display_name":"Foundation for Liver Research","ror":"https://ror.org/0143pk141","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I335284955"]},{"id":"https://openalex.org/I4210153400","display_name":"King's College Hospital","ror":"https://ror.org/044nptt90","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210111135","https://openalex.org/I4210153400"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Merianne Mohamad","raw_affiliation_strings":["Roger Williams Institute of Liver Studies, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, Foundation for Liver Research and King's College Hospital, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Roger Williams Institute of Liver Studies, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, Foundation for Liver Research and King's College Hospital, London, UK","institution_ids":["https://openalex.org/I183935753","https://openalex.org/I335284955","https://openalex.org/I4210153400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078006994","display_name":"Chrysi Sergaki","orcid":"https://orcid.org/0000-0003-0477-8680","observed_orcids":["https://orcid.org/0000-0003-0477-8680"]},"institutions":[{"id":"https://openalex.org/I4405282191","display_name":"Medicines and Healthcare products Regulatory Agency","ror":"https://ror.org/05fan1e59","country_code":"GB","type":"government","lineage":["https://openalex.org/I4405282191"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Chrysi Sergaki","raw_affiliation_strings":["Science and Research, Medicines and Healthcare products Regulatory Agency, South Mimms, Hertfordshire, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science and Research, Medicines and Healthcare products Regulatory Agency, South Mimms, Hertfordshire, UK","institution_ids":["https://openalex.org/I4405282191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080274937","display_name":"Vishal Patel","orcid":"https://orcid.org/0000-0001-6616-3628","observed_orcids":["https://orcid.org/0000-0001-6616-3628"]},"institutions":[{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]},{"id":"https://openalex.org/I335284955","display_name":"Foundation for Liver Research","ror":"https://ror.org/0143pk141","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I335284955"]},{"id":"https://openalex.org/I4210153400","display_name":"King's College Hospital","ror":"https://ror.org/044nptt90","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210111135","https://openalex.org/I4210153400"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Vishal C. Patel","raw_affiliation_strings":["Roger Williams Institute of Liver Studies, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, Foundation for Liver Research and King's College Hospital, London, UK. vish.patel@kcl.ac.uk"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Roger Williams Institute of Liver Studies, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, Foundation for Liver Research and King's College Hospital, London, UK. vish.patel@kcl.ac.uk","institution_ids":["https://openalex.org/I183935753","https://openalex.org/I335284955","https://openalex.org/I4210153400"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5080274937"],"corresponding_institution_ids":["https://openalex.org/I183935753","https://openalex.org/I335284955","https://openalex.org/I4210153400"],"apc_list":{"value":3190,"currency":"USD","value_usd":3190},"apc_paid":{"value":3190,"currency":"USD","value_usd":3190},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.01313025,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"4","issue":"1","first_page":"3","last_page":"3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.9785000085830688,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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"}},"topics":[{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.9785000085830688,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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"}},{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.004399999976158142,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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"}},{"id":"https://openalex.org/T10337","display_name":"Liver Disease and Transplantation","score":0.0034000000450760126,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/clinical-metagenomics","display_name":"clinical metagenomics","score":0.9570000171661377},{"id":"https://openalex.org/keywords/advanced-chronic-liver-disease","display_name":"advanced chronic liver disease","score":0.9409999847412109},{"id":"https://openalex.org/keywords/liver-cirrhosis","display_name":"liver cirrhosis","score":0.9359999895095825},{"id":"https://openalex.org/keywords/bacterial-infection","display_name":"bacterial infection","score":0.7900000214576721},{"id":"https://openalex.org/keywords/antimicrobial-resistance","display_name":"antimicrobial resistance","score":0.9129999876022339},{"id":"https://openalex.org/keywords/infection-diagnosis","display_name":"infection diagnosis","score":0.8119999766349792},{"id":"https://openalex.org/keywords/bioinformatics-pipeline","display_name":"bioinformatics pipeline","score":0.8460000157356262}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7127000093460083},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.6248000264167786},{"id":"https://openalex.org/C2777214474","wikidata":"https://www.wikidata.org/wiki/Q147778","display_name":"Cirrhosis","level":2,"score":0.5181000232696533},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.5163000226020813},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.4788999855518341},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.4772000014781952},{"id":"https://openalex.org/C4937899","wikidata":"https://www.wikidata.org/wiki/Q68541106","display_name":"Antimicrobial","level":2,"score":0.47279998660087585},{"id":"https://openalex.org/C40993552","wikidata":"https://www.wikidata.org/wiki/Q514654","display_name":"Gold standard (test)","level":2,"score":0.39329999685287476},{"id":"https://openalex.org/C114851261","wikidata":"https://www.wikidata.org/wiki/Q12147416","display_name":"Drug resistance","level":2,"score":0.38850000500679016},{"id":"https://openalex.org/C179786068","wikidata":"https://www.wikidata.org/wiki/Q16257937","display_name":"Molecular diagnostics","level":2,"score":0.3871000111103058},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.35269999504089355},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.34929999709129333},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.3319999873638153},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32600000500679016},{"id":"https://openalex.org/C177713679","wikidata":"https://www.wikidata.org/wiki/Q679690","display_name":"Intensive care medicine","level":1,"score":0.32190001010894775},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31630000472068787},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.31610000133514404},{"id":"https://openalex.org/C24527192","wikidata":"https://www.wikidata.org/wiki/Q17149729","display_name":"Human pathogen","level":3,"score":0.30309998989105225},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.30059999227523804},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2935999929904938},{"id":"https://openalex.org/C166888038","wikidata":"https://www.wikidata.org/wiki/Q4118322","display_name":"Infection control","level":2,"score":0.2935999929904938},{"id":"https://openalex.org/C2983449737","wikidata":"https://www.wikidata.org/wiki/Q177719","display_name":"Clinical diagnosis","level":2,"score":0.29159998893737793},{"id":"https://openalex.org/C2994294914","wikidata":"https://www.wikidata.org/wiki/Q1645075","display_name":"Acquired resistance","level":3,"score":0.287200003862381},{"id":"https://openalex.org/C2992965680","wikidata":"https://www.wikidata.org/wiki/Q598976","display_name":"Clinical microbiology","level":2,"score":0.2639000117778778},{"id":"https://openalex.org/C3019392825","wikidata":"https://www.wikidata.org/wiki/Q383126","display_name":"Chronic infection","level":3,"score":0.2632000148296356},{"id":"https://openalex.org/C2777075537","wikidata":"https://www.wikidata.org/wiki/Q929737","display_name":"Liver disease","level":2,"score":0.25540000200271606}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1038/s44259-025-00171-7","doi":"https://doi.org/10.1038/s44259-025-00171-7","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s44259-025-00171-7","pdf_url":"https://www.nature.com/articles/s44259-025-00171-7.pdf","source":{"id":"https://openalex.org/S4387289274","display_name":"npj Antimicrobials and Resistance","issn_l":"2731-8745","issn":["2731-8745"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"npj Antimicrobials and Resistance","raw_type":"journal-article"},{"id":"pmid:41507619","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41507619","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"npj antimicrobials and resistance","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:4e44f6b58e9a43929ff9da0a5e514d81","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/4e44f6b58e9a43929ff9da0a5e514d81","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"npj Antimicrobials and Resistance, Vol 4, Iss 1, Pp 1-5 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12783142","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12783142/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"NPJ Antimicrob Resist","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1038/s44259-025-00171-7","doi":"https://doi.org/10.1038/s44259-025-00171-7","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s44259-025-00171-7","pdf_url":"https://www.nature.com/articles/s44259-025-00171-7.pdf","source":{"id":"https://openalex.org/S4387289274","display_name":"npj Antimicrobials and Resistance","issn_l":"2731-8745","issn":["2731-8745"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"npj Antimicrobials and Resistance","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.98580002784729,"id":"https://metadata.un.org/sdg/3"}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320285","display_name":"King's College London","ror":"https://ror.org/0220mzb33"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7119201598.pdf","grobid_xml":"https://content.openalex.org/works/W7119201598.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1936183830","https://openalex.org/W1996282707","https://openalex.org/W2060849143","https://openalex.org/W2073316020","https://openalex.org/W2107013585","https://openalex.org/W2136919496","https://openalex.org/W2145889332","https://openalex.org/W2162940124","https://openalex.org/W2587322396","https://openalex.org/W2763934038","https://openalex.org/W2899103797","https://openalex.org/W2901655212","https://openalex.org/W2903823242","https://openalex.org/W2921501513","https://openalex.org/W2952926828","https://openalex.org/W2967125766","https://openalex.org/W2969234820","https://openalex.org/W2991689408","https://openalex.org/W2998927706","https://openalex.org/W3043625533","https://openalex.org/W3130614242","https://openalex.org/W3131565611","https://openalex.org/W3153947592","https://openalex.org/W3158060425","https://openalex.org/W3165543109","https://openalex.org/W3165837066","https://openalex.org/W3211050508","https://openalex.org/W3212458738","https://openalex.org/W4211037082","https://openalex.org/W4220990048","https://openalex.org/W4221041785","https://openalex.org/W4297907288","https://openalex.org/W4315436254","https://openalex.org/W4362474554","https://openalex.org/W4384664456","https://openalex.org/W4388489356","https://openalex.org/W4388661205","https://openalex.org/W4391656539","https://openalex.org/W4392472525","https://openalex.org/W4399745981","https://openalex.org/W4405268717","https://openalex.org/W4405894071","https://openalex.org/W4406115500","https://openalex.org/W4408207124","https://openalex.org/W4409170054","https://openalex.org/W4409285316"],"related_works":[],"abstract_inverted_index":{"Patients":[0],"with":[1,112],"advanced":[2],"chronic":[3],"liver":[4],"disease":[5],"who":[6],"have":[7],"underlying":[8],"cirrhosis":[9,113],"are":[10,51],"highly":[11],"susceptible":[12],"to":[13,57,116,139,150],"bacterial":[14],"infections,":[15],"which":[16],"significantly":[17],"increase":[18],"the":[19,83,107],"risk":[20],"of":[21,86,97,110,141,145],"complications":[22],"and":[23,37,54,60,94,99,125,148],"mortality,":[24],"compounded":[25],"by":[26],"escalating":[27],"antimicrobial":[28,38,65],"resistance.":[29],"The":[30],"current":[31],"gold":[32],"standard":[33],"for":[34],"infection":[35,79,133],"detection":[36],"resistance":[39,101],"(AMR)":[40],"profiling":[41],"remains":[42],"dependant":[43],"on":[44,122],"traditional":[45],"microbiological":[46],"methods.":[47],"These":[48],"conventional":[49],"approaches":[50],"slow,":[52],"labour-intensive,":[53],"often":[55],"fail":[56],"deliver":[58],"timely":[59],"accurate":[61],"results,":[62],"delaying":[63],"critical":[64],"treatment":[66],"decisions.":[67],"Clinical":[68],"metagenomics":[69],"(CMg)":[70],"is":[71],"emerging":[72],"as":[73],"a":[74],"transformative":[75],"molecular-based":[76],"tool":[77],"in":[78],"diagnostics.":[80],"By":[81],"enabling":[82],"direct":[84],"sequencing":[85],"pathogens":[87,98],"from":[88],"patient-derived":[89],"samples,":[90],"CMg":[91,131],"offers":[92],"rapid":[93],"comprehensive":[95],"identification":[96],"their":[100],"profiles.":[102],"Incorporating":[103],"this":[104],"technology":[105],"into":[106,132],"clinical":[108],"management":[109],"patients":[111],"has":[114],"potential":[115],"address":[117],"diagnostic":[118],"challenges,":[119],"reduce":[120],"reliance":[121],"broad-spectrum":[123],"antibiotics":[124],"improve":[126],"outcomes.":[127],"To":[128],"effectively":[129],"incorporate":[130],"diagnostics,":[134],"it":[135],"will":[136],"be":[137],"essential":[138],"embed":[140],"point-of-care":[142],"sequencing,":[143],"standardisation":[144],"AMR":[146],"databases,":[147],"accessibility":[149],"bioinformatics":[151],"workflows.":[152]},"counts_by_year":[],"updated_date":"2026-09-23T05:00:35.095934","created_date":"2026-01-08T00:00:00"}
