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Although quinolones have historically been effective against both MRSA and methicillin-susceptible\n                      <jats:italic>S. aureus<\/jats:italic>\n                      (MSSA) strains, the rising resistance to quinolones among\n                      <jats:italic>S. aureus<\/jats:italic>\n                      isolates, particularly in MRSA, has severely curtailed their potency and further narrowed down the therapeutic options. This study aimed to determine the burden of MRSA among isolates, as well as their resistance profile, genotypic characterization, and molecular relatedness through the construction of a phylogenetic tree.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and methods<\/jats:title>\n                    <jats:p>\n                      Archived clinical\n                      <jats:italic>S. aureus<\/jats:italic>\n                      isolates from a descriptive, cross-sectional study involving six regional referral hospitals in Dodoma, Songea, Kigoma, Kitete, and Morogoro in the mainland Tanzania and Mnazi Mmoja in Zanzibar were analyzed. Bacterial identification was performed using both classical microbiology and whole genome sequencing on Illumina Nextseq 550 Sequencer. Species identification was done using KmerFinder 3.2, Multilocus Sequence Typing using MLST 2.0, SCC\n                      <jats:italic>mec<\/jats:italic>\n                      typing using SCCmecFinder 1.2, resistance genes using ResFinder 4.1, and phylogenetic relatedness using CSI Phylogeny 1.4.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Out of the 140 isolates analyzed, 69 (49.3%) were identified as MRSA, with 57 (82.6%) exhibiting quinolone resistance. Conversely, 71 isolates were identified as MSSA, and none of them exhibited resistance to quinolones.\n                      <jats:italic>Spa<\/jats:italic>\n                      -typing revealed six spa types, with t355, t1476, and t498 being the most common. Moreover, all (69) MRSA were found to carry SCC\n                      <jats:italic>mec<\/jats:italic>\n                      type IV. The isolates exhibited 14 different sequence types (STs). Notably, ST152 was prevalent among MSSA (50 isolates, 70%), while ST8 was the predominant sequence type among MRSA (58 isolates, 84%). The antimicrobial resistance profile revealed at least three horizontally acquired resistance genes, with\n                      <jats:italic>blaZ<\/jats:italic>\n                      ,\n                      <jats:italic>dfrG<\/jats:italic>\n                      ,\n                      <jats:italic>tet(K)<\/jats:italic>\n                      , and\n                      <jats:italic>aac (6\u2019)-aph (2\u2019\u2019)<\/jats:italic>\n                      genes being highly prevalent.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      There is a high genetic diversity among the\n                      <jats:italic>S. aureus<\/jats:italic>\n                      isolates existing in Tanzania regional hospitals, with a concerning burden of quinolone resistance among MRSA isolates. The diversity in resistance genes among MRSA lineages emphasizes the necessity for the development of sustainable antimicrobial stewardship and surveillance to support evidence-based guidelines for managing and controlling MRSA infections in both community and hospital settings.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-024-11045-z","type":"journal-article","created":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T05:32:32Z","timestamp":1732253552000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Whole genome sequencing-based characterization and determination of quinolone resistance among methicillin-resistant and methicillin-susceptible S. 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Permission to access the Biotech laboratory and the archived samples was granted by the KCRI administration. The parent study secured its ethical clearance from NIMR Tanzania with reference number NIMR\/HQ\/R.8a\/Vol.IX\/3273. Informed consent was obtained from all participants or their legal guardians before the use of their samples for research purposes.","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":"1130"}}