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From 1600 clinical specimens, only 100 <jats:italic>A. baumannii<\/jats:italic> isolates could be recovered. A high prevalence of\u2009\u2265\u200978% resistant isolates was recorded for the recovered isolates against a total of 19 tested antimicrobial agents. These isolates could be divided into 12 profiles according to the number of antimicrobial agents to which they were resistant. The isolates were assorted as XDR (68; 68%), Multi-Drug Resistant (MDR: 30; 30%), and PDR (2; 2%). Genotypically, the isolates showed three major clusters with similarities ranging from 10.5 to 97.8% as revealed by ERIC-PCR technique. As a resistance mechanism to fluoroquinolones (FQs), target site mutation analyses in <jats:italic>gyrA <\/jats:italic>and <jats:italic>parC<\/jats:italic> genes amplified from twelve selected <jats:italic>A. baumannii<\/jats:italic> isolates and subjected to sequencing showed 12 profiles. The selected isolates included two CIP-susceptible ones, these showed the wild-type profile of being have no mutations. For the ten selected CIP-resistant isolates, 9 of them (9\/10; 90%) had 1 <jats:italic>gyrA<\/jats:italic>\/1 <jats:italic>parC<\/jats:italic>\u00a0mutations (Ser 81\u2009\u2192\u2009Leu mutation for <jats:italic>gyrA <\/jats:italic>gene and Ser 84\u2009\u2192\u2009Leu mutation for <jats:italic>parC <\/jats:italic>gene). The remaining CIP-resistant isolate (1\/10; 10%) had 0 <jats:italic>gyrA<\/jats:italic>\/1 <jats:italic>parC<\/jats:italic> mutation (Ser 84\u2009\u2192\u2009Leu mutation for <jats:italic>parC<\/jats:italic>\u00a0gene). Detection of plasmid-associated resistance genes revealed that the 86 ciprofloxacin-resistant isolates carry <jats:italic>qnrA<\/jats:italic> (66.27%; 57\/86), <jats:italic>qnrS<\/jats:italic> (70.93%; 61\/86), <jats:italic>aac (6')-Ib-cr<\/jats:italic> (52.32%; 45\/86), <jats:italic>oqxA<\/jats:italic> (73.25%; 63\/86) and <jats:italic>oqxB<\/jats:italic> (39.53%; 34\/86), while <jats:italic>qepA<\/jats:italic> and <jats:italic>qnrB<\/jats:italic> were undetected in these isolates. Different isolates were selected from profiles 1, 2, and 3 and <jats:italic>qnrS, acc(6,)-ib-cr, oqxA,<\/jats:italic> and <jats:italic>oqxB<\/jats:italic> genes harbored by these isolates were amplified and sequenced. The BLAST results revealed that the <jats:italic>oqxA<\/jats:italic> and <jats:italic>oqxB<\/jats:italic> sequences were not identified previously in <jats:italic>A. baumannii<\/jats:italic> but they were identified in <jats:italic>Klebsiella aerogenes<\/jats:italic> strain NCTC9793 and <jats:italic>Klebsiella pneumoniae<\/jats:italic>, respectively. On the other hand, the sequence of <jats:italic>qnrS,<\/jats:italic> and <jats:italic>acc(6,)-ib-cr<\/jats:italic> showed homology to those of <jats:italic>A. baumannii<\/jats:italic>. MDR, XDR, and PDR <jats:italic>A. baumannii<\/jats:italic> isolates are becoming prevalent in certain hospitals. Chromosomal mutations in the sequences of GyrA and ParC encoding genes and acquisition of PAFQR encoding genes (up to five genes per isolate) are demonstrated to be resistance mechanisms exhibited by fluoroquinolones resistant <jats:italic>A. baumannii<\/jats:italic> isolates. It is advisable to monitor the antimicrobial resistance profiles of pathogens causing nosocomial infections and properly apply and update antibiotic stewardship in hospitals and outpatients to control infectious diseases and prevent development of the microbial resistance to antimicrobial agents.<\/jats:p>","DOI":"10.1038\/s41598-021-99230-y","type":"journal-article","created":{"date-parts":[[2021,10,11]],"date-time":"2021-10-11T10:18:43Z","timestamp":1633947523000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":31,"title":["Impact of target site mutations and plasmid associated resistance genes acquisition on resistance of Acinetobacter baumannii to fluoroquinolones"],"prefix":"10.1038","volume":"11","author":[{"given":"Mostafa Ahmed","family":"Mohammed","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed T. 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