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Deforet F, Carrière R, Dufour PL'A, Prat R, Desbiolles C, Cottin N, Reuzeau A, Dauwalder O, Dupieux-Chabert C, Tristan A, Cecchini T, Lemoine J, Vandenesch F. Proteomic assay for rapid characterisation of Staphylococcus aureus antimicrobial resistance mechanisms directly from blood cultures. Eur J Clin Microbiol Infect Dis 2024; 43:1329-1342. [PMID: 38750334 DOI: 10.1007/s10096-024-04811-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/11/2024] [Indexed: 07/20/2024]
Abstract
PURPOSE Staphylococcus aureus is one of the most common pathogens causing bloodstream infection. A rapid characterisation of resistance to methicillin and, occasionally, to aminoglycosides for particular indications, is therefore crucial to quickly adapt the treatment and improve the clinical outcomes of septic patients. Among analytical technologies, targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a promising tool to detect resistance mechanisms in clinical samples. METHODS A rapid proteomic method was developed to detect and quantify the most clinically relevant antimicrobial resistance effectors in S. aureus in the context of sepsis: PBP2a, PBP2c, APH(3')-III, ANT(4')-I, and AAC(6')-APH(2''), directly from positive blood cultures and in less than 70 min including a 30-min cefoxitin-induction step. The method was tested on spiked blood culture bottles inoculated with 124 S.aureus, accounting for the known genomic diversity of SCCmec types and the genetic background of the strains. RESULTS This method provided 99% agreement for PBP2a (n = 98/99 strains) detection. Agreement was 100% for PBP2c (n = 5/5), APH(3')-III (n = 16/16), and ANT(4')-I (n = 20/20), and 94% for AAC(6')-APH(2'') (n = 16/17). Across the entire strain collection, 100% negative agreement was reported for each of the 5 resistance proteins. Additionally, relative quantification of ANT(4')-I expression allowed to discriminate kanamycin-susceptible and -resistant strains, in all strains harbouring the ant(4')-Ia gene. CONCLUSION The LC-MS/MS method presented herein demonstrates its ability to provide a reliable determination of S. aureus resistance mechanisms, directly from positive blood cultures and in a short turnaround time, as required in clinical laboratories.
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Affiliation(s)
- Francis Deforet
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - Romain Carrière
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - Pierre L 'Aour Dufour
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Lyon, France
| | - Roxane Prat
- Hospices Civils de Lyon, Institut des Agents Infectieux, Lyon, France
| | - Chloé Desbiolles
- Hospices Civils de Lyon, Institut des Agents Infectieux, Lyon, France
| | - Noémie Cottin
- Hospices Civils de Lyon, Institut des Agents Infectieux, Lyon, France
| | - Alicia Reuzeau
- Hospices Civils de Lyon, Institut des Agents Infectieux, Lyon, France
| | - Olivier Dauwalder
- Hospices Civils de Lyon, Institut des Agents Infectieux, Lyon, France
| | - Céline Dupieux-Chabert
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| | - Anne Tristan
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Tiphaine Cecchini
- Hospices Civils de Lyon, Institut des Agents Infectieux, Lyon, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - François Vandenesch
- Hospices Civils de Lyon, Institut des Agents Infectieux, Lyon, France.
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France.
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France.
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Cao H, Zhang G, Ma H, Xue Z, Huo R, Wang K, Liu Z. Sensitive and Extraction-Free Detection of Methicillin-Resistant Staphylococcus aureus through Ag + Aptamer-Based Color Reaction. J Microbiol Biotechnol 2024; 34:192-197. [PMID: 37957116 PMCID: PMC10840478 DOI: 10.4014/jmb.2308.08044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 11/15/2023]
Abstract
Refractory infections, such as hospital-acquired pneumonia, can be better diagnosed with the assistance of precise methicillin-resistant Staphylococcus aureus (MRSA) testing. However, traditional methods necessitate high-tech tools, rigorous temperature cycling, and the extraction of genetic material from MRSA cells. Herein, we propose a sensitive, specific, and extraction-free strategy for MRSA detection by integrating allosteric probe-based target recognition and exonuclease-III (Exo-III)-enhanced color reaction. The penicillin-binding protein 2a (PBP2a) aptamer in the allosteric probe binds with MRSA to convert protein signals to nucleic acid signals. This is followed by the DNA polymerase-assisted target recycle and the production of numerous single-strand DNA (ssDNA) chains which bind with silver ion (Ag+) aptamer to form a blunt terminus that can be identified by Exo-III. As a result, the Ag+ aptamer pre-coupled to magnetic nanoparticles is digested. After magnetic separation, the Ag+ in liquid supernatant catalyzes 3,3',5,5'-tetramethylbenzidine (TMB) for a color reaction. In addition, a concentration of 54 cfu/mL is predicted to be the lowest detectable value. Based on this, our assay has a wide linear detection range, covering 5 orders of magnitude and demonstrating a high specificity, which allows it to accurately distinguish the target MRSA from other microorganisms.
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Affiliation(s)
- Hongli Cao
- Emergency Department, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Guosheng Zhang
- Emergency Department, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Hui Ma
- Emergency Department, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Zhongwen Xue
- Emergency Department, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Ran Huo
- Emergency Department, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Kun Wang
- Emergency Department, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Zijin Liu
- Orthopedic Rehabilitation Department, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
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Gant MS, Chamot-Rooke J. Present and future perspectives on mass spectrometry for clinical microbiology. Microbes Infect 2024:105296. [PMID: 38199266 DOI: 10.1016/j.micinf.2024.105296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/01/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
In the last decade, MALDI-TOF Mass Spectrometry (MALDI-TOF MS) has been introduced and broadly accepted by clinical laboratory laboratories throughout the world as a powerful and efficient tool for rapid microbial identification. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. Whilst MALDI-TOF MS is currently the gold-standard, it suffers from several shortcomings such as lack of direct information on antibiotic resistance, poor depth of analysis and insufficient discriminatory power for the distinction of closely related bacterial species or for reliably sub-differentiating isolates to the level of clones or strains. Thus, new approaches targeting proteins and allowing a better characterization of bacterial strains are strongly needed, if possible, on a very short time scale after sample collection in the hospital. Bottom-up proteomics (BUP) is a nice alternative to MALDI-TOF MS, offering the possibility for in-depth proteome analysis. Top-down proteomics (TDP) provides the highest molecular precision in proteomics, allowing the characterization of proteins at the proteoform level. A number of studies have already demonstrated the potential of these techniques in clinical microbiology. In this review, we will discuss the current state-of-the-art of MALDI-TOF MS for the rapid microbial identification and detection of resistance to antibiotics and describe emerging approaches, including bottom-up and top-down proteomics as well as ambient MS technologies.
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Affiliation(s)
- Megan S Gant
- Institut Pasteur, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology 75015 Paris, France
| | - Julia Chamot-Rooke
- Institut Pasteur, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology 75015 Paris, France.
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Yamin D, Uskoković V, Wakil AM, Goni MD, Shamsuddin SH, Mustafa FH, Alfouzan WA, Alissa M, Alshengeti A, Almaghrabi RH, Fares MAA, Garout M, Al Kaabi NA, Alshehri AA, Ali HM, Rabaan AA, Aldubisi FA, Yean CY, Yusof NY. Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria. Diagnostics (Basel) 2023; 13:3246. [PMID: 37892067 PMCID: PMC10606640 DOI: 10.3390/diagnostics13203246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.
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Affiliation(s)
- Dina Yamin
- Al-Karak Public Hospital, Karak 61210, Jordan;
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
| | - Vuk Uskoković
- TardigradeNano LLC., Irvine, CA 92604, USA;
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Abubakar Muhammad Wakil
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Maiduguri, Maiduguri 600104, Borno, Nigeria
| | - Mohammed Dauda Goni
- Public Health and Zoonoses Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia;
| | - Shazana Hilda Shamsuddin
- Department of Pathology, School of Medical Sciences, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fatin Hamimi Mustafa
- Department of Electronic & Computer Engineering, Faculty of Electrical Engineering, University Teknologi Malaysia, Johor Bharu 81310, Johor, Malaysia;
| | - Wadha A. Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait;
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia;
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Rana H. Almaghrabi
- Pediatric Department, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia;
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Hamza M. Ali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia;
| | - Ali A. Rabaan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | | | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, University Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
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Hu XL, Gan HQ, Qin ZY, Liu Q, Li M, Chen D, Sessler JL, Tian H, He XP. Phenotyping of Methicillin-Resistant Staphylococcus aureus Using a Ratiometric Sensor Array. J Am Chem Soc 2023; 145:8917-8926. [PMID: 37040584 DOI: 10.1021/jacs.2c12798] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Chemical tools capable of classifying multidrug-resistant bacteria (superbugs) can facilitate early-stage disease diagnosis and help guide precision therapy. Here, we report a sensor array that permits the facile phenotyping of methicillin-resistant Staphylococcus aureus (MRSA), a clinically common superbug. The array consists of a panel of eight separate ratiometric fluorescent probes that provide characteristic vibration-induced emission (VIE) profiles. These probes bear a pair of quaternary ammonium salts in different substitution positions around a known VIEgen core. The differences in the substituents result in varying interactions with the negatively charged cell walls of bacteria. This, in turn, dictates the molecular conformation of the probes and affects their blue-to-red fluorescence intensity ratios (ratiometric changes). Within the sensor array, the differences in the ratiometric changes for the probes result in "fingerprints" for MRSA of different genotypes. This allows them to be identified using principal component analysis (PCA) without the need for cell lysis and nucleic acid isolation. The results obtained with the present sensor array agree well with those obtained using polymerase chain reaction (PCR) analysis.
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Affiliation(s)
- Xi-Le Hu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
| | - Hui-Qi Gan
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
| | - Zhao-Yang Qin
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
| | - Qian Liu
- Department of Laboratory Medicine, Ren Ji Hospital (Eastern), 160 Pujian Rd, Shanghai 200127, China
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital (Eastern), 160 Pujian Rd, Shanghai 200127, China
| | - Daijie Chen
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Rd, Minhang District, Shanghai 200240, China
| | - Jonathan L Sessler
- Department of Chemistry, The University of Texas at Austin, 105 East 24th Street-A5300, Austin, Texas 78712-1224, United States
| | - He Tian
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
- The International Cooperation Laboratory on Signal Transduction, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
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Kalpana S, Lin WY, Wang YC, Fu Y, Lakshmi A, Wang HY. Antibiotic Resistance Diagnosis in ESKAPE Pathogens-A Review on Proteomic Perspective. Diagnostics (Basel) 2023; 13:1014. [PMID: 36980322 PMCID: PMC10047325 DOI: 10.3390/diagnostics13061014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Antibiotic resistance has emerged as an imminent pandemic. Rapid diagnostic assays distinguish bacterial infections from other diseases and aid antimicrobial stewardship, therapy optimization, and epidemiological surveillance. Traditional methods typically have longer turn-around times for definitive results. On the other hand, proteomic studies have progressed constantly and improved both in qualitative and quantitative analysis. With a wide range of data sets made available in the public domain, the ability to interpret the data has considerably reduced the error rates. This review gives an insight on state-of-the-art proteomic techniques in diagnosing antibiotic resistance in ESKAPE pathogens with a future outlook for evading the "imminent pandemic".
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | | | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA
| | - Amrutha Lakshmi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
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Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection in Staphylococcus aureus: A Narrative Review. Diagnostics (Basel) 2022; 12:diagnostics12010208. [PMID: 35054375 PMCID: PMC8774325 DOI: 10.3390/diagnostics12010208] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of infections in humans, such as skin and soft tissue infections, pneumonia, food poisoning or sepsis. Historically, S. aureus was able to rapidly adapt to anti-staphylococcal antibiotics and become resistant to several classes of antibiotics. Today, methicillin-resistant S. aureus (MRSA) is a multidrug-resistant pathogen and is one of the most common bacteria responsible for hospital-acquired infections and outbreaks, in community settings as well. The rapid and accurate diagnosis of antimicrobial resistance in S. aureus is crucial to the early initiation of directed antibiotic therapy and to improve clinical outcomes for patients. In this narrative review, I provide an overview of recent phenotypic and molecular diagnostic methods for antimicrobial resistance detection in S. aureus, with a particular focus on MRSA detection. I consider methods for resistance detection in both clinical samples and isolated S. aureus cultures, along with a brief discussion of the advantages and the challenges of implementing such methods in routine diagnostics.
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