{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T01:15:52Z","timestamp":1788225352340,"version":"build-2803163510"},"reference-count":43,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,7,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      The increasing prevalence of multidrug-resistant (MDR) gram-negative bacteria has reduced therapeutic options for bloodstream infections (BSIs) and complicates clinical management. In Lebanon, limited genomic surveillance has restricted insight into the molecular determinants underlying resistance and virulence in invasive pathogens. In this study, whole-genome sequencing was used to characterize antimicrobial resistance, mobilome composition, and virulence gene content among 24 gram-negative isolates recovered from BSIs. Six species were identified, including\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Klebsiella pneumoniae<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Citrobacter farmeri<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Citrobacter portucalensis<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Proteus mirabilis<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">Morganella morganii<\/jats:italic>\n                      . Phenotypic testing showed widespread resistance to \u03b2-lactam and non-\u03b2-lactam antimicrobial classes. Extended-spectrum \u03b2-lactamase production was detected in 62.5% of isolates, and 37.5% were classified as carbapenem-resistant Enterobacterales. Genomic analyses revealed that resistance in\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                      was largely driven by plasmid-mediated ESBL and carbapenemase genes associated with IncF replicons and insertion sequences, whereas chromosomal mechanisms predominated in\n                      <jats:italic toggle=\"yes\">Citrobacter<\/jats:italic>\n                      species. A chromosomally encoded\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>OXA-244<\/jats:sub>\n                      variant was identified in an\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      ST69 isolate, and a high-risk\n                      <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                      ST147 isolate carried multiple \u03b2-lactamase genes across distinct plasmids. Colistin resistance in one\n                      <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                      isolate was associated with a frameshift mutation in\n                      <jats:italic toggle=\"yes\">mgrB<\/jats:italic>\n                      in the absence of plasmid-mediated\n                      <jats:italic toggle=\"yes\">mcr<\/jats:italic>\n                      genes. Virulence profiling showed heterogeneous repertoires across species, with expanded adhesion, iron acquisition, and serum resistance determinants in\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      . This study provides the first genome-level characterization of\n                      <jats:italic toggle=\"yes\">C. farmeri<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">C. portucalensis<\/jats:italic>\n                      BSIs in Lebanon and supports the integration of genomic surveillance into routine monitoring of invasive infections.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>This study presents a pilot whole-genome sequencing analysis of 24 gram-negative bloodstream isolates from a tertiary care hospital in Lebanon. By integrating phenotypic susceptibility testing with genomic, mobilome, and virulence analyses, it reveals marked species- and isolate-level diversity. Resistance and virulence determinants were found within specific genetic contexts rather than being uniformly linked to species or sequence types, underscoring the value of genome-based surveillance to inform antimicrobial stewardship and infection control strategies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00503-26","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T13:01:07Z","timestamp":1781701267000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Genomic analysis of antimicrobial resistance and virulence among gram-negative bloodstream isolates from Lebanon"],"prefix":"10.1128","volume":"14","author":[{"given":"Carni","family":"Boujanian","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Lebanese American University, Byblos Campus","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0977-1242","authenticated-orcid":true,"given":"Charbel","family":"Al Khoury","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, Lebanese American University, Beirut Campus","place":["Beirut, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mira","family":"El Chaar","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01xvwxv41","id-type":"ROR","asserted-by":"publisher"}],"name":"Faculty of Health Sciences, University of Balamand","place":["Beirut, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rindala","family":"Saliba","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/044fxjq88","id-type":"ROR","asserted-by":"publisher"}],"name":"Faculty of Medicine, Saint Joseph University of Beirut","place":["Beirut, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lydia-Rossa","family":"Hanna","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/044fxjq88","id-type":"ROR","asserted-by":"publisher"}],"name":"Faculty of Medicine, Saint Joseph University of Beirut","place":["Beirut, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3653-8940","authenticated-orcid":true,"given":"Sima","family":"Tokajian","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Lebanese American University, Byblos Campus","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(19)32989-7"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00134-020-06151-x"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1373\/jalm.2018.026245"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00355-19"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2020.115016"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.799084"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics10081016"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mayocpiqo.2023.10.001"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2021.09.008"},{"key":"e_1_3_5_11_2","unstructured":"Clinical and Laboratory Standards Institute. 2020. 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