{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T17:23:09Z","timestamp":1791393789219,"version":"4.3.3"},"reference-count":50,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T00:00:00Z","timestamp":1759708800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000272","name":"National Institute for Health and Care Research","doi-asserted-by":"crossref","award":["16\/136\/111"],"award-info":[{"award-number":["16\/136\/111"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Medical Research Council","award":["MR\/L00464X\/1"],"award-info":[{"award-number":["MR\/L00464X\/1"]}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"crossref","award":["INV-036234"],"award-info":[{"award-number":["INV-036234"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,6]]},"abstract":"<jats:p>\n                  <jats:italic>Enterobacter<\/jats:italic> spp. are an important cause of healthcare-associated bloodstream infections that are uncommonly reported in Africa. This study utilized whole-genome sequencing to characterize <jats:italic>Enterobacter<\/jats:italic> spp. from hospitals in Nigeria\u2019s antimicrobial resistance surveillance system. Bloodstream <jats:italic>Enterobacter<\/jats:italic> spp. isolates from six sentinel tertiary-care hospitals recovered between 2014 and 2020 were re-identified and antimicrobial susceptibility-tested using VITEK 2 system. Illumina technology provided whole-genome sequences for genome nomenclature, antimicrobial resistance gene prediction, SNP phylogeny and multi-locus sequence typing via publicly available bioinformatics pipelines. Initial biochemical delineation often misclassifies <jats:italic>Enterobacter<\/jats:italic>, necessitating whole-genome sequencing for accurate classification. Among 98 <jats:italic>Enterobacter<\/jats:italic> received, <jats:italic>Enterobacter hormaechei<\/jats:italic> subspecies <jats:italic>xiangfangensis<\/jats:italic> predominated (43), followed by other <jats:italic>E. hormaechei<\/jats:italic> subspecies (18) and <jats:italic>Enterobacter<\/jats:italic> spp. such as <jats:italic>Enterobacter cloacae<\/jats:italic> (26), <jats:italic>Enterobacter roggenkampii<\/jats:italic> (4), <jats:italic>Enterobacter bugandensis<\/jats:italic> (3), <jats:italic>Enterobacter kobei<\/jats:italic> (2), <jats:italic>Enterobacter asburiae<\/jats:italic> (1) and <jats:italic>Enterobacter cancerogenus<\/jats:italic> (1). Resistance to extended-spectrum cephalosporins, aminoglycosides, phenicols, macrolides and carbapenems in <jats:italic>E. hormaechei<\/jats:italic> was attributed to known resistance genes. <jats:italic>E. hormaechei<\/jats:italic> isolates belonged to clusters III, IV and VIII based on <jats:italic>hsp60<\/jats:italic> typing and clades A, B, C and D according to Sutton and Co\u2019s nomenclature. This and other recent reports from Nigeria reveal the extensive diversity of <jats:italic>E. hormaechei<\/jats:italic>, as well as clusters representing potential outbreaks. <jats:italic>E. hormaechei<\/jats:italic>, often misidentified and rarely reported from Nigeria, is the most common <jats:italic>Enterobacter<\/jats:italic> spp. isolated from blood culture in this study. Uncovering underappreciated species as important bloodstream pathogens and retrospective detection of likely outbreaks emphasize the value of genomic surveillance in resource-limited settings.<\/jats:p>","DOI":"10.1099\/mgen.0.001508","type":"journal-article","created":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T17:16:12Z","timestamp":1759770972000},"source":"Crossref","is-referenced-by-count":2,"title":["Whole-genome sequencing reveals Enterobacter hormaechei as a key bloodstream pathogen in six tertiary care hospitals in southwestern Nigeria"],"prefix":"10.1099","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-9867-6503","authenticated-orcid":false,"given":"Faith I.","family":"Oni","sequence":"first","affiliation":[{"name":"Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1405-2365","authenticated-orcid":false,"given":"Ayorinde Oluwatobiloba","family":"Afolayan","sequence":"additional","affiliation":[{"name":"Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8803-5077","authenticated-orcid":false,"given":"Anderson O.","family":"Oaikhena","sequence":"additional","affiliation":[{"name":"Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4503-9403","authenticated-orcid":false,"given":"Erkison Ewomazino","family":"Odih","sequence":"additional","affiliation":[{"name":"Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Odion O.","family":"Ikhimiukor","sequence":"additional","affiliation":[{"name":"Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4439-4083","authenticated-orcid":false,"given":"Veronica O.","family":"Ogunleye","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4280-2218","authenticated-orcid":false,"given":"Aaron Oladipo","family":"Aboderin","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olatunde F.","family":"Olabisi","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5460-6732","authenticated-orcid":false,"given":"Adewale A.","family":"Amupitan","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0535-9296","authenticated-orcid":false,"given":"Abayomi","family":"Fadeyi","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-0262-5244","authenticated-orcid":false,"given":"Rasaki A.","family":"Raheem","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, University of Ilorin Teaching Hospital, Ilorin, Kwara state, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3433-831X","authenticated-orcid":false,"given":"Bashirat A.","family":"Olanipekun","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, University of Ilorin Teaching Hospital, Ilorin, Kwara state, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2721-2903","authenticated-orcid":false,"given":"Charles J.","family":"Elikwu","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Babcock University Teaching Hospital, Ilishan-Remo, Ogun State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0244-4209","authenticated-orcid":false,"given":"Oluwadamilola A.","family":"Sadare","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Babcock University Teaching Hospital, Ilishan-Remo, Ogun State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip O.","family":"Oshun","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2894-4367","authenticated-orcid":false,"given":"Oyinlola O.","family":"Oduyebo","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Folashade","family":"Ojo","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, UNIOSUN Teaching Hospital, Osogbo, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2257-2734","authenticated-orcid":false,"given":"Abolaji T.","family":"Adeyemo","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Parasitology, UNIOSUN Teaching Hospital, Osogbo, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4715-8019","authenticated-orcid":false,"given":"Ifeanyi E.","family":"Mba","sequence":"additional","affiliation":[{"name":"Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9369-4771","authenticated-orcid":false,"given":"Abiodun","family":"Egwuenu","sequence":"additional","affiliation":[{"name":"Nigeria Centre for Disease Control and Prevention, Jabi, Abuja, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2391-7770","authenticated-orcid":false,"given":"Tochi J.","family":"Okwor","sequence":"additional","affiliation":[{"name":"Nigeria Centre for Disease Control and Prevention, Jabi, Abuja, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8547-4277","authenticated-orcid":false,"given":"Anthony","family":"Underwood","sequence":"additional","affiliation":[{"name":"Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2884-3857","authenticated-orcid":false,"given":"Silvia","family":"Argimon","sequence":"additional","affiliation":[{"name":"Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0659-0833","authenticated-orcid":false,"given":"Chikwe","family":"Ihekweazu","sequence":"additional","affiliation":[{"name":"Nigeria Centre for Disease Control and Prevention, Jabi, Abuja, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6688-0854","authenticated-orcid":false,"given":"David M.","family":"Aanensen","sequence":"additional","affiliation":[{"name":"Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1694-7587","authenticated-orcid":false,"given":"Iruka N.","family":"Okeke","sequence":"additional","affiliation":[{"name":"Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00002-19"},{"key":"R2","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1016\/B978-0-12-384730-0.00095-1","volume-title":"Encyclopedia of Food Microbiology","author":"Iversen","year":"2014"},{"key":"R3","first-page":"424","article-title":"Nosocomial bacteremia caused by Enterobacter spp.: epidemiology and prognostic factors","volume":"11","author":"Pe\u00f1a","year":"1993","journal-title":"Enferm Infecc Microbiol Clin"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1086\/421946"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.2217\/fmb.12.61"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30093-8"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.003871"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-021-00870-7"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00527-20"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0230037"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciz516"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.4314\/tjpr.v10i6.13"},{"key":"R13","volume-title":"77_1511368219 National Action Plan for Antimicrobial Resistance 2017-2022"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.001208"},{"key":"R15","volume-title":"Performance Standards for Antimicrobial Susceptibility Testing","author":"Weinstein"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23091-2"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000131"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2011.03570.x"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-91456-0"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac920"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07641-9"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1038\/163688a0"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1111\/j.1654-1103.2003.tb02228.x"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1038\/srep24373"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad339"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgph.0001629"},{"key":"R28","volume-title":"Manual of Clinical Microbiology, 6th ed","author":"Murray","year":"1995"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciu182"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.05041-11"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01596-21"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02160-22"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02093-16"},{"key":"R34","volume-title":"StatPearls","author":"Ramirez D","year":"2024"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1017\/s0022172400069503"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciab785"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.9.5306-5318.2003"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv657"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.14566.1"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1186\/s13062-015-0085-2"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0074487"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9091928"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-023-03164-6"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-84870-7"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02154"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-021-00650-4"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00360-21"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.02054"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01889-16"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01127-22"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001508?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T17:16:14Z","timestamp":1759770974000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001508"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,6]]},"references-count":50,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2025,10,6]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001508","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,6]]}}}