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Forty-two multidrug resistant (MDR)<jats:italic>K. pneumoniae<\/jats:italic>isolates were collected over a 4-month period. Antimicrobial susceptibility was determined using Microscan. The evolutionary epidemiology, resistome, virulome and mobilome of the isolates were characterised using whole-genome sequencing and bioinformatics analysis. All isolates contained the<jats:italic>bla<\/jats:italic><jats:sub>CTX-M<\/jats:sub>gene, whilst\u00a041\/42(97%) contained<jats:italic>bla<\/jats:italic><jats:sub>TEM<\/jats:sub>, 36\/42(86%) contained<jats:italic>bla<\/jats:italic><jats:sub>OXA<\/jats:sub>and 35\/42(83%) harboured<jats:italic>bla<\/jats:italic><jats:sub>SHV<\/jats:sub>genes. Other resistance genes found included<jats:italic>bla<\/jats:italic><jats:sub>LEN<\/jats:sub>,<jats:italic>aac(6<\/jats:italic>\u2032<jats:italic>)-lb-cr<\/jats:italic>,<jats:italic>qnr<\/jats:italic>A,<jats:italic>qnr<\/jats:italic>B,<jats:italic>qnr<\/jats:italic>S,<jats:italic>oqx<\/jats:italic>AB,<jats:italic>aad<\/jats:italic>,<jats:italic>aph<\/jats:italic>,<jats:italic>dfr<\/jats:italic>,<jats:italic>sul<\/jats:italic>1,<jats:italic>sul<\/jats:italic>2,<jats:italic>fos<\/jats:italic>A, and<jats:italic>cat<\/jats:italic>genes. Fluoroquinolone and colistin resistance-conferring mutations in<jats:italic>par<\/jats:italic>C,<jats:italic>gyr<\/jats:italic>AB,<jats:italic>pmr<\/jats:italic>AB,<jats:italic>pho<\/jats:italic>PQ and<jats:italic>kpn<\/jats:italic>EF were identified. The<jats:italic>bla<\/jats:italic><jats:sub>LEN<\/jats:sub>gene, rarely described worldwide, was identified in four isolates. The isolates comprised diverse sequence types, the most common being ST152 in 7\/42(17%)\u00a0isolates; clone-specific O and K capsule types were identified. Diverse virulence genes that were not clone-specific were identified in all but one isolate. IncF, IncH and IncI plasmid replicons and two novel integrons were present. The<jats:italic>bla<\/jats:italic><jats:sub>CTX-M-15<\/jats:sub>and<jats:italic>bla<\/jats:italic><jats:sub>TEM-1<\/jats:sub>genes were bracketed by Tn3 transposons, IS<jats:italic>Ec9<\/jats:italic>, a resolvase and IS91 insertion sequence. There were 20 gene cassettes in 14 different cassette arrays, with the<jats:italic>dfrA<\/jats:italic>and<jats:italic>aadA<\/jats:italic>gene cassettes being the most frequent. Phylogenetic analysis demonstrated that the isolates were evolutionarily associated with strains from both South Africa and abroad. These findings depict the rich resistome, mobilome and virulome repertoire in clinical<jats:italic>K. pneumoniae<\/jats:italic>strains, which are mainly transmitted by clonal, multiclonal and horizontal means in South Africa.<\/jats:p>","DOI":"10.1038\/s41598-020-58012-8","type":"journal-article","created":{"date-parts":[[2020,1,27]],"date-time":"2020-01-27T11:02:44Z","timestamp":1580122964000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":61,"title":["Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa"],"prefix":"10.1038","volume":"10","author":[{"given":"Nontombi Marylucy","family":"Mbelle","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Feldman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9508-984X","authenticated-orcid":false,"given":"John Osei","family":"Sekyere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nontuthuko Excellent","family":"Maningi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lesedi","family":"Modipane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabiha Yusuf","family":"Essack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,1,27]]},"reference":[{"key":"58012_CR1","unstructured":"World Health Organization. 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