Discrepancies between phenotypic and genotypic identification methods of antibiotic resistant genes harboring Staphylococcusaureus.
Abstract: Antimicrobial resistance is a global issue that limits therapeutic options for infections. S. aureus being a member of the ESKAPE group is capable of "escaping" the biocidal action of antimicrobial agents. There are phenotypic and genotypic methods used for the identification of antibiotic resistant genes harboring S. aureus but these methods do not always show concordant results. To address these discrepancies, a total of 335 equine nasal swab samples from four districts of Punjab were collected using a convenient sampling technique. These samples were first subjected to common microbial techniques to identify S. aureus. The disc diffusion assay was performed for the phenotypic identification of antibiotic resistant S. aureus by using discs of oxacillin, penicillin, vancomycin, gentamycin, and tetracycline. After this, PCR was performed by targeting mecA, blaZ, vanB, aaca-aphd, and tetK genes for genotypic identification of respective antibiotic-resistant S. aureus. Phenotypic discrepancies (number of antibiotic resistant isolates found from disc diffusion who appeared to be negative for the resistant gene), and genotypic discrepancies (number of antibiotic sensitive isolates found from disc diffusion who appeared to be positive for the resistant gene) were calculated. The discrepancy ratio for mecA, blaZ, vanB, aaca-aphd, and tetK genes were 3.09, 1.96, 2.67, 1.93, and 1.67 respectively. These discrepant results indicate that the absence or presence of only one gene is not a true marker of resistant or sensitive isolates. There are multiple resistance determinants and resistance mechanisms. This study also highlighted the phenomenon of silencing of antibiotic resistance determinants.
Copyright © 2023 Elsevier Ltd. All rights reserved.
Publication Date: 2023-09-11 PubMed ID: 37704062DOI: 10.1016/j.micpath.2023.106342Google Scholar: Lookup
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- Journal Article
Summary
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This research investigated the differences between two methods of identifying antibiotic-resistant Staphylococcus aureus, a bacteria that can “escape” the killing effects of antibiotics. Using samples from horse nostrils in four districts of Punjab, the authors found that the results of the two methods do not always match up, and argue that multiple factors and mechanisms contribute to antibiotic resistance.
Sampling and Testing Methods
- The researchers collected 335 nasal swab samples from horses in Punjab, using a common microbial technique to identify the presence of S. aureus, a bacteria known for its ability to resist antimicrobial agents.
- The team used a test called the disc diffusion assay for the phenotypic identification of antibiotic-resistant S. aureus, applying discs of five different antibiotics to detect resistance on a physical, observable level.
Genotypic Identification
- Genotypic tests were performed after the assays, using a technique called polymerase chain reaction (PCR) which amplifies the DNA of the bacteria to be analyzed. These tests targeted five genes that are known markers of antibiotic resistance.
- The authors noted instances where the physical (phenotypic) tests indicated the bacteria was antibiotic-resistant, but the genetic (genotypic) tests did not find the expected resistance genes (phenotypic discrepancies).
- They also found cases where the phenotypic tests did not indicate resistance, yet the genotypic tests detected the resistance genes (genotypic discrepancies).
Discrepancies and Implications
- Through these tests, the researchers found that results showing antibiotic resistance or sensitivity can be misleading if they only take one gene into account. As there are multiple factors contributing to antibiotic resistance, it is not reliable to consider only the presence or absence of one gene.
- This study also sheds light on the phenomenon of gene “silencing”, where genes associated with antibiotic resistance are present but not activated, leading to discrepancies between phenotypic and genotypic results.
- By highlighting these discrepancies, this research invites further study into how S. aureus can develop and show antibiotic resistance, with potential implications for treatment strategies and drug design.
Cite This Article
APA
Rasheed H, Ijaz M, Ahmed A, Javed MU, Shah SFA, Anwaar F.
(2023).
Discrepancies between phenotypic and genotypic identification methods of antibiotic resistant genes harboring Staphylococcusaureus.
Microb Pathog, 184, 106342.
https://doi.org/10.1016/j.micpath.2023.106342 Publication
Researcher Affiliations
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, 54000, Lahore, Pakistan.
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, 54000, Lahore, Pakistan. Electronic address: mijaz@uvas.edu.pk.
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, 54000, Lahore, Pakistan.
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, 54000, Lahore, Pakistan.
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, 54000, Lahore, Pakistan.
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, 54000, Lahore, Pakistan.
MeSH Terms
- Animals
- Horses
- Anti-Bacterial Agents / pharmacology
- Staphylococcus aureus / genetics
- Methicillin-Resistant Staphylococcus aureus / genetics
- Microbial Sensitivity Tests
- Oxacillin
- Staphylococcal Infections / veterinary
Conflict of Interest Statement
Declaration of competing interest All authors have read and approved the final version of manuscript and have no conflict of interest.
Citations
This article has been cited 9 times.- Zhao Y, Yang S, He M, Chai P, Sun Z, Zhu Q, Li Z, Guo Q, Liu H. Phenotypic Characterization and Genomic Mining of Uric Acid Catabolism Genes in Lactiplantibacillus plantarum YC. Foods 2025 Dec 17;14(24).
- Kumari H, Singh M, Chakrawarti MK, Mukhopadhyay K. Distribution and antibiotic resistance patterns of airborne staphylococci in urban environments of Delhi, India. Sci Rep 2025 Dec 3;15(1):43026.
- Bowie K, Luhung I, Burke T, Roberts S, Martinello R, Gerstein M, Peccia J, Healy H. Disinfection of Hospital Sink Drains Enriches Pseudomonadota and Efflux Pump-Mediated Antibiotic Resistance in Reestablished Biofilms. Res Sq 2025 Oct 27;.
- Lan Anh NT, Hong Loan NVT, Y Vi NT, Tran DH, Thanh Hang LT, Steele S, Nguyen LT. Prevalence, species identification, and antibiotic resistance of Staphylococci in dogs visiting veterinary clinics in Vietnam. PLoS One 2025;20(7):e0328472.
- You X, Song S, Li B, Wang H, Zhang L, Li X, Chen J, Zhu Z, Zhao G. A Comprehensive Safety Assessment of Ralstonia eutropha H16 for Food Applications: Integrating Genomic, Phenotypic, and Toxicological Analyzes. Microorganisms 2025 Jun 6;13(6).
- Rasheed H, Ijaz M, Ahmed A, Ali MM. Antimicrobial resistance, virulence profiling, and drug repurposing analysis of Staphylococcus aureus from camel mastitis. Vet Res Commun 2024 Dec 28;49(1):59.
- Farrar A, Feehily C, Turner P, Zagajewski A, Chatzimichail S, Crook D, Andersson M, Oakley S, Barrett L, El Sayyed H, Fowler PW, Nellåker C, Kapanidis AN, Stoesser N. Infection Inspection: using the power of citizen science for image-based prediction of antibiotic resistance in Escherichia coli treated with ciprofloxacin. Sci Rep 2024 Aug 22;14(1):19543.
- Yaikhan T, Chukamnerd A, Singkhamanan K, Nokchan N, Chintakovid N, Chusri S, Pomwised R, Wonglapsuwan M, Surachat K. Genomic Characterization of Mobile Genetic Elements Associated with Multidrug-Resistant Acinetobacter Non-baumannii Species from Southern Thailand. Antibiotics (Basel) 2024 Feb 2;13(2).
- Ijaz M, Javed MU, Ahmed A, Rasheed H, Shah SFA, Ali M. Evidence-based identification and characterization of methicillin-resistant Staphylococcusaureus isolated from subclinical mastitis in dairy buffaloes of Pakistan. Iran J Vet Res 2023;24(3):215-226.
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