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Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of <jats:italic>K. pneumoniae<\/jats:italic> infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>In the current study, one hundred extended spectrum \u03b2-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into <jats:italic>K. pneumoniae<\/jats:italic> WSF99 clinical isolate.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The isolate <jats:italic>K. pneumoniae<\/jats:italic> WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7\u00a0Mb with an estimated 5,718 protein-coding genes and a G\u2009+\u2009C content of 56.98\u00a0mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several \u03b2-lactamase genes, including <jats:italic>bla<\/jats:italic><jats:sub>CTX\u2212M\u221215<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>TEM\u22121<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>TEM\u221212<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>SHV\u221211<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>SHV\u221267<\/jats:sub>, and <jats:italic>bla<\/jats:italic><jats:sub>OXA\u22129<\/jats:sub>, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, <jats:italic>bla<\/jats:italic><jats:sub>NDM\u22125<\/jats:sub>, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, <jats:italic>aac<\/jats:italic>(6\u2019)-Ib, <jats:italic>aph<\/jats:italic>(3\u2019)-VI, <jats:italic>sul1<\/jats:italic>, <jats:italic>sul2<\/jats:italic>, <jats:italic>fosA<\/jats:italic>, <jats:italic>aadA<\/jats:italic>, <jats:italic>arr-2<\/jats:italic>, <jats:italic>qnrS1<\/jats:italic>, <jats:italic>tetA<\/jats:italic> and <jats:italic>tetC<\/jats:italic>. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-024-03389-z","type":"journal-article","created":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T06:02:41Z","timestamp":1720591361000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt"],"prefix":"10.1186","volume":"24","author":[{"given":"Fatma A.","family":"Elgayar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona K.","family":"Gouda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alaa Aboelnour","family":"Badran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy M.","family":"El Halfawy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,10]]},"reference":[{"key":"3389_CR1","doi-asserted-by":"publisher","first-page":"11387","DOI":"10.3389\/bjbs.2023.11387","volume":"80","author":"KWK Tang","year":"2023","unstructured":"Tang KWK, Millar BC, Moore JE. 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