{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T19:26:15Z","timestamp":1792092375487,"version":"4.4.0"},"reference-count":43,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"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":["R21AI190454"],"award-info":[{"award-number":["R21AI190454"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["U01AI187297"],"award-info":[{"award-number":["U01AI187297"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,8,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Klebsiella quasipneumoniae<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">similipneumoniae<\/jats:italic>\n                      is an important member of the\n                      <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                      species complex (KpSC) and is increasingly reported as multidrug-resistant (MDR) in healthcare- and community-associated infections. Since clinical laboratories do not routinely distinguish\n                      <jats:italic toggle=\"yes\">K. quasipneumoniae<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">similipneumoniae<\/jats:italic>\n                      from\n                      <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                      , national prevalence estimates, particularly for MDR, are lacking. In this study, a total of 2,006 community-associated MDR KpSC isolates were collected from 42 U.S. states, with 30\n                      <jats:italic toggle=\"yes\">K. quasipneumoniae<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">similipneumoniae<\/jats:italic>\n                      isolates originating from 12 states identified using whole genome sequencing. All isolates were resistant to ceftriaxone and exhibited high rates of resistance to other antimicrobial agents, including ampicillin-sulbactam (56.7%, 17\/30), levofloxacin (75.9%, 22\/29), and trimethoprim-sulfamethoxazole (53.3%, 16\/30). Notably, five isolates were also carbapenem-resistant. Genomic analysis resolved 10 sequence types (STs), with ST2059 (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 13) and ST414 (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 9) predominating. Ceftriaxone resistance in most isolates (90%, 27\/30) was conferred by an extended-spectrum \u03b2-lactamase gene, predominantly\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>CTX-M-15<\/jats:sub>\n                      (73.3%, 22\/30); the remaining isolates carried either a carbapenemase (\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>KPC-3<\/jats:sub>\n                      ) or an AmpC \u03b2-lactamase (\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>CMY-2<\/jats:sub>\n                      ). Nanopore sequencing identified\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>CTX-M-15<\/jats:sub>\n                      harbored on two types of IncFIB(Kpn3) antimicrobial resistance (AMR) plasmids, either with or without the conjugative\n                      <jats:italic toggle=\"yes\">tra<\/jats:italic>\n                      gene cluster. Interestingly, the KL1 locus, associated with canonical hypervirulent\n                      <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                      strains, was detected in all ST2059 isolates. Further analysis of public genomic data showed that the KL1 locus is widely distributed across KpSC. KL1 phylogenetic analyses indicated frequent intrasubspecies recombination but limited intersubspecies exchange of KL1. The identification of the dominant MDR\n                      <jats:italic toggle=\"yes\">K. quasipneumoniae<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">similipneumoniae<\/jats:italic>\n                      KL1-ST2059 clone in the U.S. underscores the importance of ongoing genomic surveillance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Klebsiella quasipneumoniae<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">similipneumoniae<\/jats:italic>\n                      is an underrecognized member of the\n                      <jats:italic toggle=\"yes\">Klebsiella pneumoniae<\/jats:italic>\n                      species complex that is frequently misidentified in clinical laboratories, leading to an incomplete understanding of its role in antimicrobial resistance. In this study, we used large-scale genomic surveillance of community-associated multidrug-resistant isolates across the U.S. to identify this subspecies as a reservoir of clinically relevant resistance plasmids. Notably, we detected a widely distributed ST2059 lineage carrying the K1 capsular locus, a feature traditionally associated with hypervirulent\n                      <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                      . These findings highlight the convergence of resistance and virulence-associated traits in an overlooked species and underscore the need for genomic surveillance to monitor emerging high-risk lineages in community settings.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01107-26","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T13:01:07Z","timestamp":1783688467000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Genomic analysis of community-associated multidrug-resistant\n                    <i>Klebsiella quasipneumoniae<\/i>\n                    subsp.\n                    <i>similipneumoniae<\/i>\n                    and the identification of the ST2059-KL1 clone in the U.S."],"prefix":"10.1128","volume":"14","author":[{"given":"Jianping","family":"Jiang","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p5zd128","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Discovery and Innovation, Hackensack Meridian Health","place":["Nutley, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8209-8922","authenticated-orcid":true,"given":"Austin J.","family":"Terlecky","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p5zd128","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Discovery and Innovation, Hackensack Meridian Health","place":["Nutley, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Shashkina","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p5zd128","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Discovery and Innovation, Hackensack Meridian Health","place":["Nutley, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-7648-2037","authenticated-orcid":true,"given":"Meghan W.","family":"Starolis","sequence":"additional","affiliation":[{"name":"Quest Diagnostics","place":["Secaucus, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5845-2235","authenticated-orcid":true,"given":"Liang","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Pharmacy and Pharmaceutical Sciences, University at Buffalo","place":["Buffalo, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0243-131X","authenticated-orcid":true,"given":"Barry N.","family":"Kreiswirth","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p5zd128","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Discovery and Innovation, Hackensack Meridian Health","place":["Nutley, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2018.04.004"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1501049112"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.001587"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00412-21"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000433"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(20)30061-6"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphereDirect.00290-17"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01150-06"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2018.06.008"},{"key":"e_1_3_5_11_2","unstructured":"WHO. 2024. Antimicrobial resistance hypervirulent Klebsiella pneumoniae - Global Situation. Available from: https:\/\/www.who.int\/emergencies\/disease-outbreak-news\/item\/2024-DON527"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2017.01.004"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2022.106628"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2011.03570.x"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(21)00399-6"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.102"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24448-3"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-91456-0"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000131"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000102"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-402"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr039"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02090-4"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-025-01428-6"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp077"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae268"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid3104.241396"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11020213"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000110"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0315-1"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.062737-0"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2024.107040"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02513-18"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02513-18"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx488"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1111\/nyas.14223"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00001-19"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evv062"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010693"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciae403"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01107-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01107-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T14:40:43Z","timestamp":1786027243000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01107-26"}},"subtitle":[],"editor":[{"given":"Ning","family":"Dong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,4]]},"references-count":43,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,4]]}},"alternative-id":["10.1128\/spectrum.01107-26"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01107-26","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,4]]},"assertion":[{"value":"2026-03-29","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-20","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-10","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01107-26"}}