{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T20:58:02Z","timestamp":1781643482001,"version":"3.54.5"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T00:00:00Z","timestamp":1774224000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T00:00:00Z","timestamp":1777507200000},"content-version":"vor","delay-in-days":38,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      The global rise of multidrug-resistant Enterobacterales, particularly extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      and\n                      <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                      , poses a critical threat to intensive care unit (ICU) patients. Despite the clinical importance of these pathogens in sub-Saharan Africa, studies on their molecular characterization remains scarce.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We performed antibiotic susceptibility testing and whole-genome sequencing (WGS) on 22 multidrug-resistant isolates (\n                      <jats:italic>15 E. coli<\/jats:italic>\n                      and 7\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      ) recovered from ICU patients at Kenya\u2019s public referral hospital between January and June 2021. Isolates were obtained from blood, tracheal aspirates, urine, and pus swabs. We characterized antimicrobial resistance genes, virulence determinants, plasmid replicons, and genetic lineages, and assessed phenotype-genotype concordance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      All isolates exhibited resistance to third-generation cephalosporins, with resistance rates exceeding 80% for at least 10 antibiotics. The ESBL gene\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>CTX\u2212M\u221215<\/jats:sub>\n                      was detected in 93% of\n                      <jats:italic>E. coli<\/jats:italic>\n                      and 100% of\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      isolates. The concordance between phenotypic resistance and genotypic determinants was highest for \u03b2-lactams and lowest for aminoglycosides, trimethoprim-sulfamethoxazole and carbapenems. MLST revealed considerable genetic diversity among\n                      <jats:italic>E. coli<\/jats:italic>\n                      , including high-risk clones STc131 and ST648. Virulence genes (e.g.,\n                      <jats:italic>fimH<\/jats:italic>\n                      ,\n                      <jats:italic>chuA<\/jats:italic>\n                      ,\n                      <jats:italic>fyuA<\/jats:italic>\n                      ) were more prevalent in\n                      <jats:italic>E. coli<\/jats:italic>\n                      , particularly among isolates from urine and tracheal aspirate samples. Plasmid profiling revealed greater replicon diversity in\n                      <jats:italic>E. coli<\/jats:italic>\n                      , with frequent detection of IncFII and IncFIB plasmids, suggesting a stronger capacity for horizontal gene transfer.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>These findings underscore the complexity of multidrug-resistant pathogen dynamics in ICU environments. They emphasize the need for species-specific surveillance, rapid diagnostics, and context-informed stewardship strategies to guide infection control and therapeutic interventions. While limited in scale, this study adds to the genomic landscape of multidrug-resistant pathogens in African ICUs and highlights critical targets for infection control and therapeutic interventions.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12866-026-04880-5","type":"journal-article","created":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T00:23:58Z","timestamp":1774225438000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Phenotypic and genomic profiling of multidrug-resistant Escherichia coli and Klebsiella pneumoniae isolated from Intensive Care Unit patients in Kenya"],"prefix":"10.1186","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-9514-9843","authenticated-orcid":false,"given":"Beatrice","family":"Oduor","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Maina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Job","family":"Mwale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Ogoti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leon","family":"Otieno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moureen","family":"Jepleting","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charchil","family":"Ayodo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Mugoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa","family":"Ita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josiah","family":"Kuja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvia","family":"Omulo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,3,23]]},"reference":[{"key":"4880_CR1","unstructured":"Mestrovic T, Robles Aguilar G, Swetschinski LR, Ikuta KS, Gray AP, Davis Weaver N et al. 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Ethical approval was obtained from the Kenyatta National Hospital\u2013University of Nairobi Ethics and Research Committee (KNH-UoN ERC) under approval number P88\/02\/2023. In addition, a research license was granted by the National Commission for Science, Technology, and Innovation (NACOSTI) with license number NACOSTI\/P\/23\/28006. The study involved analysis of previously archived, de-identified bacterial isolates with no direct contact with patients or access to personal identifiers, therefore the requirement for informed consent was waived by the Kenyatta National Hospital\u2013University of Nairobi Ethics and Research Committee, approval number P88\/02\/2023.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"419"}}