{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T17:23:11Z","timestamp":1784568191879,"version":"3.55.0"},"reference-count":36,"publisher":"Microbiology Society","issue":"2","license":[{"start":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T00:00:00Z","timestamp":1771891200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"crossref","award":["KL2TR001448"],"award-info":[{"award-number":["KL2TR001448"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"crossref","award":["UL1TR001449"],"award-info":[{"award-number":["UL1TR001449"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,24]]},"abstract":"<jats:p>\n                    <jats:italic>Klebsiella aerogenes<\/jats:italic>\n                    is an opportunistic pathogen and a growing cause of healthcare-associated infections, characterized by multidrug resistance and the emergence of global high-risk clones. However, regional genomic surveillance data remain limited. Here, we sought to characterize the population structure, transmission dynamics and resistance mechanisms of clinical\n                    <jats:italic>K. aerogenes<\/jats:italic>\n                    in Albuquerque, New Mexico. We sequenced 177 clinical isolates collected between 2021 and 2023. We also developed a novel, species-specific PopPUNK database to facilitate rapid, high-resolution typing. The New Mexico\n                    <jats:italic>K. aerogenes<\/jats:italic>\n                    population was diverse but dominated by two global pandemic lineages, ST93 (47.5%) and ST4 (7.9%), which were significantly enriched for the virulence factors yersiniabactin and colibactin. Genomic evidence for recent local transmission was rare, with only four putative transmission pairs identified. The resistome was characterized by intrinsic and adaptive mutations. Nearly all isolates possessed\n                    <jats:italic>gyrA<\/jats:italic>\n                    mutations associated with decreased fluoroquinolone susceptibility. Mutations in the AmpC regulator AmpD and the outer membrane porin Omp36 were common, particularly within the dominant ST93 lineage. These mutations have been associated with increased AmpC-mediated carbapenem resistance. Our findings underscore the critical importance of genomic surveillance to monitor the transmission and evolution of adaptive resistance.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001650","type":"journal-article","created":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T16:16:45Z","timestamp":1771949805000},"source":"Crossref","is-referenced-by-count":1,"title":["Genomic analysis of Klebsiella aerogenes circulating in New Mexico"],"prefix":"10.1099","volume":"12","author":[{"given":"Leslie M.","family":"Huggins","sequence":"first","affiliation":[{"name":"Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Sidebottom","sequence":"additional","affiliation":[{"name":"Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kurt","family":"Schwalm","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karissa","family":"Culbreath","sequence":"additional","affiliation":[{"name":"TriCore Reference Laboratories, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesse","family":"Young","sequence":"additional","affiliation":[{"name":"TriCore Reference Laboratories, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6810-8067","authenticated-orcid":false,"given":"Meghan","family":"Brett","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Darrell L.","family":"Dinwiddie","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5389-9185","authenticated-orcid":false,"given":"Daryl","family":"Domman","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory, Los Alamos, USA"},{"name":"Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, USA"},{"name":"College of Population Health, University of New Mexico Health Sciences Center, Albuquerque, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00392"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00002-19"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.001572"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00582-20"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciz173"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciab1013"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-57245-1"},{"key":"R8","doi-asserted-by":"crossref","first-page":"2735","DOI":"10.2147\/IDR.S458182","article-title":"Genomic and phenotypic analysis of <em> bla <\/em> blakpc-2 associated carbapenem resistance in klebsiella aerogenes: insights into clonal spread and resistance mechanisms across hospital departments in Beijing","volume":"17","author":"Jin","journal-title":"IDR"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02577-18"},{"key":"R10","article-title":"Carbapenem-Resistant Organisms\/Carbapenemase-Producing Organisms - 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