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Pirolo M, Menezes M, Poulsen M, Søndergaard V, Damborg P, Poirier AC, La Ragione R, Schjærff M, Guardabassi L. A LAMP point-of-care test to guide antimicrobial choice for treatment of Staphylococcus pseudintermedius pyoderma in dogs. Vet J 2024; 304:106105. [PMID: 38547963 DOI: 10.1016/j.tvjl.2024.106105] [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: 01/10/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/16/2024]
Abstract
Staphylococcus pseudintermedius is the most common cause of pyoderma in dogs. We validated a point-of-care (PoC) test based on colorimetric loop-mediated isothermal amplification (LAMP) for rapid S. pseudintermedius identification and susceptibility testing for first line antimicrobials for systemic treatment of canine pyoderma, i.e., lincosamides, first generation cephalosporins and amoxicillin clavulanate. Newly designed LAMP primers targeting clinically relevant resistance genes were combined with a previously validated set of primers targeting spsL for species identification. After laboratory validation on 110 clinical isolates, we assessed the performance of the test on 101 clinical specimens using routine culture and susceptibility testing as a reference standard. The average hands-on and turnaround times for the PoC test were 30 and 90 min, respectively. The assay showed sensitivity and specificity near 100% for both species identification and susceptibility testing when performed on bacterial cultures or clinical specimens in the laboratory. However, the PoC test yielded less accurate results when performed on-site by clinical staff (92% sensitivity and 64% specificity for species identification, 67% sensitivity and 96% specificity for β-lactam susceptibility, and 83% sensitivity and 71% specificity for lincosamide susceptibility). These results indicate that the PoC test should be adapted to a user-friendly technology to facilitate performance and interpretation of results by clinical staff. If properly developed, the test would allow veterinarians to gain rapid information on antimicrobial choice, limiting the risk of treatment failure and facilitating adherence to antimicrobial use guidelines in small animal veterinary dermatology.
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Affiliation(s)
- M Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - M Menezes
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - M Poulsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - V Søndergaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - P Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - A C Poirier
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK
| | - R La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK; Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford GU2 7XH, UK
| | - M Schjærff
- Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - L Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark.
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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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Liao X, Deng R, Warriner K, Ding T. Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers. Compr Rev Food Sci Food Saf 2023; 22:3212-3253. [PMID: 37222539 DOI: 10.1111/1541-4337.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/22/2023] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.
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Affiliation(s)
- Xinyu Liao
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- School of Mechanical and Energy Engineering, NingboTech University, Ningbo, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, China
| | - Keith Warriner
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
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4
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Pereira HS, Tagliaferri TL, Mendes TADO. Enlarging the Toolbox Against Antimicrobial Resistance: Aptamers and CRISPR-Cas. Front Microbiol 2021; 12:606360. [PMID: 33679633 PMCID: PMC7932999 DOI: 10.3389/fmicb.2021.606360] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
In the post-genomic era, molecular treatments and diagnostics have been envisioned as powerful techniques to tackle the antimicrobial resistance (AMR) crisis. Among the molecular approaches, aptamers and CRISPR-Cas have gained support due to their practicality, sensibility, and flexibility to interact with a variety of extra- and intracellular targets. Those characteristics enabled the development of quick and onsite diagnostic tools as well as alternative treatments for pan-resistant bacterial infections. Even with such potential, more studies are necessary to pave the way for their successful use against AMR. In this review, we highlight those two robust techniques and encourage researchers to refine them toward AMR. Also, we describe how aptamers and CRISPR-Cas can work together with the current diagnostic and treatment toolbox.
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Affiliation(s)
| | | | - Tiago Antônio de Oliveira Mendes
- Laboratory of Synthetic Biology and Modelling of Biological Systems, Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Brazil
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Schoepp NG, Liaw EJ, Winnett A, Savela ES, Garner OB, Ismagilov RF. Differential DNA accessibility to polymerase enables 30-minute phenotypic β-lactam antibiotic susceptibility testing of carbapenem-resistant Enterobacteriaceae. PLoS Biol 2020; 18:e3000652. [PMID: 32191697 PMCID: PMC7081982 DOI: 10.1371/journal.pbio.3000652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/14/2020] [Indexed: 12/22/2022] Open
Abstract
The rise in carbapenem-resistant Enterobacteriaceae (CRE) infections has created a global health emergency, underlining the critical need to develop faster diagnostics to treat swiftly and correctly. Although rapid pathogen-identification (ID) tests are being developed, gold-standard antibiotic susceptibility testing (AST) remains unacceptably slow (1-2 d), and innovative approaches for rapid phenotypic ASTs for CREs are urgently needed. Motivated by this need, in this manuscript we tested the hypothesis that upon treatment with β-lactam antibiotics, susceptible Enterobacteriaceae isolates would become sufficiently permeabilized, making some of their DNA accessible to added polymerase and primers. Further, we hypothesized that this accessible DNA would be detectable directly by isothermal amplification methods that do not fully lyse bacterial cells. We build on these results to develop the polymerase-accessibility AST (pol-aAST), a new phenotypic approach for β-lactams, the major antibiotic class for gram-negative infections. We test isolates of the 3 causative pathogens of CRE infections using ceftriaxone (CRO), ertapenem (ETP), and meropenem (MEM) and demonstrate agreement with gold-standard AST. Importantly, pol-aAST correctly categorized resistant isolates that are undetectable by current genotypic methods (negative for β-lactamase genes or lacking predictive genotypes). We also test contrived and clinical urine samples. We show that the pol-aAST can be performed in 30 min sample-to-answer using contrived urine samples and has the potential to be performed directly on clinical urine specimens.
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Affiliation(s)
- Nathan G. Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Eric J. Liaw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Alexander Winnett
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Emily S. Savela
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Omai B. Garner
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, United States of America
| | - Rustem F. Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
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Singha M, Kumar G, Jain D, Kumar N G, Ray D, Ghosh AS, Basak A. Rapid Fluorescent-Based Detection of New Delhi Metallo-β-Lactamases by Photo-Cross-Linking Using Conjugates of Azidonaphthalimide and Zinc(II)-Chelating Motifs. ACS OMEGA 2019; 4:10891-10898. [PMID: 31460186 PMCID: PMC6648899 DOI: 10.1021/acsomega.9b01145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A method for rapid detection of metallo-β-lactamases NDM-5 and NDM-7 using conjugates of azidonaphthalimide and Zn(II) chelating motifs (like sulfonamides, hydroxamate, and terpyridine) is described. Incubation and irradiation, followed by gel electrophoresis, clearly show the presence of NDMs. The o-sulfonamide-based probe has the highest efficiency of detection for both the NDMs. The proteins are detectable at nM concentrations, and the method is also selective, works both in vitro and in vivo, as revealed by cellular imaging and also with clinical isolates.
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Affiliation(s)
- Monisha Singha
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Gaurav Kumar
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Diamond Jain
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Ganesh Kumar N
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Debashis Ray
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Anindya S. Ghosh
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Amit Basak
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
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