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This study sought to establish the resistance phenotype, and strains of 32 non-duplicate clinical MRSA and MSSA<jats:italic>S. aureus<\/jats:italic>isolates from four Kenyan hospitals<jats:italic>,<\/jats:italic>identify their resistance and virulence genes and determine the genetic relationships of MRSA with global strains.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Antimicrobial susceptibility profiles were determined on a Vitek 2, genomic DNA sequenced on an Illumina Miseq and isolates typed in-silico. Resistance and virulence genes were identified using ARIBA and phylogenies generated using RAxML.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The MRSA isolates were 100% susceptible to vancomycin, teicoplanin, linezolid, and tigecycline. Nine distinct CC, 12 ST and 15 spa types including the novel t17826 and STs (4705, 4707) were identified with CC8 and CC152 predominating. MRSA isolates distributed across 3 CCs; CC5-ST39 (1), CC8 \u2013 ST241 (4), a novel CC8-ST4705 (1), ST8 (1) and CC152 (1). There was &gt;\u200990% phenotype-genotype concordance with key resistance genes identified only among MRSA isolates:<jats:italic>gyrA<\/jats:italic>,<jats:italic>rpoB<\/jats:italic>, and<jats:italic>parC<\/jats:italic>mutations,<jats:italic>mecA<\/jats:italic>,<jats:italic>ant (4\u2032)-lb, aph (3\u2032)-IIIa, ermA, sat-4, fusA, mphC<\/jats:italic>and<jats:italic>msrA<\/jats:italic>. Kenyan MRSA isolates were genetically diverse and most closely related to Tanzanian and UK isolates. There was a significant correlation between<jats:italic>map<\/jats:italic>,<jats:italic>hlgA<\/jats:italic>,<jats:italic>selk<\/jats:italic>,<jats:italic>selq<\/jats:italic>and<jats:italic>cap8d<\/jats:italic>virulence genes and severe infections.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The findings showed a heterogeneous<jats:italic>S. aureus<\/jats:italic>population with novel strain types. Though limited by the low number of isolates, this study begins to fill gaps and expand our knowledge of<jats:italic>S. aureus<\/jats:italic>epidemiology while uncovering interesting patterns of distribution of strain types which should be further explored. Although last-line treatments are still effective<jats:italic>,<\/jats:italic>the potential for outbreaks of both virulent and resistant strains remain, requiring sustained surveillance of<jats:italic>S. aureus<\/jats:italic>populations.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12866-019-1597-1","type":"journal-article","created":{"date-parts":[[2019,11,6]],"date-time":"2019-11-06T14:03:27Z","timestamp":1573049007000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya"],"prefix":"10.1186","volume":"19","author":[{"given":"Cecilia","family":"Kyany\u2019a","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin","family":"Nyasinga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Matano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerie","family":"Oundo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Wacira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Willie","family":"Sang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1418-6523","authenticated-orcid":false,"given":"Lillian","family":"Musila","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,11,6]]},"reference":[{"issue":"9","key":"1597_CR1","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1038\/nrmicro2200","volume":"7","author":"HF Chambers","year":"2009","unstructured":"Chambers HF, Deleo FR. 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