Citaton: Badawi H, Reda A, El-Said M, et al. Phenotypic and Molecular Detecton of Antseptc Resistance Genes among Clinical Staphylococcus aureus Isolates During COVID-19 Pandemic. J Pure Appl Microbiol . 2022;16(4):2619-2630. doi: 10.22207/JPAM.16.4.29 © The Author(s) 2022. Open Access. This artcle is distributed under the terms of the Creatve Commons Atributon 4.0 Internatonal License which permits unrestricted use, sharing, distributon, and reproducton in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creatve Commons license, and indicate if changes were made. Badawi et al. | Artcle 7764 J Pure Appl Microbiol. 2022;16(4):2619-2630. doi: 10.22207/JPAM.16.4.29 Received: 14 April 2022 | Accepted: 27 September 2022 Published Online: 01 November 2022 ReSeARCH ARtiCle OPeN ACCeSS www.microbiologyjournal.org 2619 Journal of Pure and Applied Microbiology P-ISSN: 0973-7510; E-ISSN: 2581-690X *Correspondence: manalmicrobiology@gmail.com Phenotypic and Molecular Detecton of Antseptc Resistance Genes among Clinical Staphylococcus aureus isolates During COViD-19 Pandemic Hala Badawi 1 , Alaa Reda 2 , Manal el Said 1,3 *, Amira el-Far 4 , Reham Magdy 1 , Ahmed el-Shenawy 4  and Noha Yousry 4 1 Department of Microbiology & Infecton Preventon & Control Unit, Theodor Bilharz Research Insttute (TBRI), Giza 12411, Egypt. 2 Department of Microbiology & Immunology, Faculty of Medicine, Cairo University, Egypt. 3 Department of Microbiology, Medicine Program, Baterjee Medical College, Jeddah 21442, Saudi Arabia. 4 Department of Microbiology, Theodor Bilharz Research Insttute, (TBRI), Egypt. Abstract the coronavirus disease (COViD-19) pandemic has expanded the use of chlorhexidine digluconate, a biocide frequently used in hospitals, to inhibit the spread of infecton. Genes responsible for resistance against the quaternary ammonium compound qac in Staphylococcus aureus isolates have been shown to confer tolerance to a number of biocidal chemicals, including chlorhexidine. the aim of this study was to determine the occurrence of antseptc resistance genes (qacA/B and qacC) in clinical isolates of methicillin-susceptble (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA). the study also aimed to investgate the associaton between the presence of the mecA, qacA/B, and qacC genes in MRSA isolates and the susceptbility of the isolates to chlorhexidine to evaluate its future use in the theodor Bilharz Research insttute (tBRi) hospital, following the Centers for Disease Control and Preventon recommendatons for patents with MRSA. S. aureus isolates (n = 100) were collected from inpatents and outpatents at tBRi. A minimal inhibitory concentraton of chlorhexidine was also detected. Polymerase chain reacton was used to detect the mecA, qacA/B, and qacC genes. the results revealed that 84% of S. aureus isolates were MRSA. MRSA (61.9%) and MSSA (68.8%) isolates were susceptble to chlorhexidine. the qacA/B gene was more dominant, being detected in 34%, while qacC was detected in only 5% of S. aureus isolates. All S. aureus isolates with reduced susceptbility to chlorhexidine harbored either the qacA/B or qacC genes. the clinical use of chlorhexidine may contnue to increase, emphasizing the signifcance of contnuous cauton underlining the emergence of new clones with reduced susceptbility and avoiding antseptc misuse. Keywords: Staphylococcus aureus, MRSA, MSSA, Chlorhexidine, qacA/B ,qacC Genes, Antseptc Resistance