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Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of <jats:italic>K. pneumoniae<\/jats:italic> to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in <jats:italic>Klebsiella<\/jats:italic> spp. The present study aimed to perform complete genome sequences of <jats:italic>Klebsiella<\/jats:italic> spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the <jats:italic>Klebsiella<\/jats:italic> spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of <jats:italic>rmpA<\/jats:italic> and <jats:italic>magA<\/jats:italic> genes. To the best of our knowledge, this is the first report on the presence of <jats:italic>ste, stf, stc<\/jats:italic> and <jats:italic>sti<\/jats:italic> major fimbrial operons of <jats:italic>Salmonella enterica<\/jats:italic> serotype Typhimurium in <jats:italic>K. pneumoniae<\/jats:italic> genome. The study identifies the discordance of virulome and virulence in <jats:italic>Klebsiella<\/jats:italic> spp. The complete genome analysis and phenotypic correlation identify uropathogenic <jats:italic>K. pneumoniae<\/jats:italic> kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of <jats:italic>K. pneumoniae<\/jats:italic> was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of <jats:italic>K. pneumoniae<\/jats:italic> high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk <jats:italic>K. pneumoniae<\/jats:italic> clones.<\/jats:p>","DOI":"10.1186\/s13568-024-01737-w","type":"journal-article","created":{"date-parts":[[2024,7,4]],"date-time":"2024-07-04T16:02:34Z","timestamp":1720108954000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Complete genome sequence, phenotypic correlation and pangenome analysis of uropathogenic Klebsiella spp"],"prefix":"10.1186","volume":"14","author":[{"given":"Abhirami Krishnamoorthy","family":"Sundaresan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaya","family":"Gangwar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aravind","family":"Murugavel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ganesh Babu","family":"Malli Mohan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayapradha","family":"Ramakrishnan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,4]]},"reference":[{"key":"1737_CR1","doi-asserted-by":"publisher","first-page":"103574","DOI":"10.1016\/j.micpath.2019.103574","volume":"134","author":"AM Algammal","year":"2019","unstructured":"Algammal AM, Wahdan A, Elhaig MM (2019) Potential efficiency of conventional and advanced approaches used to detect Mycobacterium bovis in cattle. 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