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Huang J, Zhai L, Wang J, Sun X, Wang B, Wei Z. An Evaluation of the Sensitivity and Applicability of a Droplet Digital Polymerase Chain Reaction Assay to Simultaneously Detect Pseudomonas aeruginosa and Pseudomonas fragi in Foods. Foods 2024; 13:1453. [PMID: 38790753 PMCID: PMC11120221 DOI: 10.3390/foods13101453] [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: 03/31/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Achieving effective control over microbial contamination necessitates the precise and concurrent identification of numerous pathogens. As a common bacterium in the environment, Pseudomonas is rich in variety. It not only has pathogenic strains, but also spoilage bacteria that cause food spoilage. In this research, we devised a remarkably sensitive duplex droplet digital PCR (dddPCR) reaction system to simultaneously detect pathogenic Pseudomonas aeruginosa (P. aeruginosa) and spoilage Pseudomonas fragi (P. fragi). By employing comparative genomics, we identified four genes of P. fragi. Through a specific analysis, the RS22680 gene was selected as the detection target for P. fragi, and the lasR gene was chosen for P. aeruginosa, which were applied to construct a dddPCR reaction. In terms of specificity, sensitivity and anti-interference ability, the constructed dddPCR detection system was verified and analyzed. The assay showed excellent sensitivity and applicability, as evidenced by a limit of detection of 100 cfu/mL. When the concentration of natural background bacteria in milk or fresh meat was 100 times that of the target detection bacteria, the method was still capable of completing the absolute quantification. In the simulation of actual sample contamination, P. aeruginosa could be detected after 3 h of enrichment culture, and P. fragi could be detected after 6 h. The established dddPCR detection system exhibits exceptional performance, serving as a foundation for the simultaneous detection of various pathogenic bacteria in food products.
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Affiliation(s)
| | - Ligong Zhai
- Department of Food Engineering College, Anhui Science and Technology University, Chuzhou 233100, China; (J.H.); (J.W.); (X.S.); (B.W.); (Z.W.)
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2
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Ali M, Nair P, Capretta A, Brennan JD. In-vitro Clinical Diagnostics using RNA-Cleaving DNAzymes. Chembiochem 2024:e202400085. [PMID: 38574237 DOI: 10.1002/cbic.202400085] [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: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.
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Affiliation(s)
- Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Parameswaran Nair
- Division of Respirology, McMaster University, and, Firestone Institute of Respiratory Health at St. Joseph's Health Care, Hamilton, ON, L8N 4A6, Canada
| | - Alfredo Capretta
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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3
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Gutiérrez-Santana JC, Coria-Jiménez VR. Diagnosis and Therapeutic Strategies Based on Nucleic Acid Aptamers Selected against Pseudomonas aeruginosa: The Challenge of Cystic Fibrosis. ChemMedChem 2024; 19:e202300544. [PMID: 38016927 DOI: 10.1002/cmdc.202300544] [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: 10/09/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Antimicrobial resistance (AMR) is a rapidly spreading global health problem, and approximately five million deaths associated with AMR pathogens were identified prior to the COVID-19 pandemic. Pseudomonas aeruginosa has developed increasing AMR, and in patients with cystic fibrosis (CF) colonized by this bacterium, rare phenotypes have emerged that complicate the diagnosis and treatment of the hosts, in addition to multiple associated "epidemic strains" with high morbidities and mortalities. The conjugation of aptamers with fluorochromes or nanostructures has allowed the design of new identification strategies for Pseudomonas aeruginosa with detection limits of up to 1 cell ⋅ mL-1 , and the synergy of aptamers with antibiotics, antimicrobial peptides and nanostructures has exhibited promising therapeutic qualities. Some selected aptamers against this bacterium have shown intrinsic antimicrobial activity. However, these aptamers have been poorly evaluated in clinical isolates and have shown decreased interactions for CF isolates, demonstrating, in these cases, uncommon phenotypes resulting from the selective qualities of this disease as well as the great adaptive capacity of the pathogen. Therefore, finding an aptamer or set of aptamers that have the ability to recognize strange phenotypes of this bacillus is crucial in the battle against AMR.
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Affiliation(s)
- Juan Carlos Gutiérrez-Santana
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco Coyoacán, 04530, Ciudad de México, México
| | - Victor Rafael Coria-Jiménez
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco Coyoacán, 04530, Ciudad de México, México
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Khan S, Monteiro JK, Prasad A, Filipe CDM, Li Y, Didar TF. Material Breakthroughs in Smart Food Monitoring: Intelligent Packaging and On-Site Testing Technologies for Spoilage and Contamination Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2300875. [PMID: 37085965 DOI: 10.1002/adma.202300875] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/26/2023] [Indexed: 05/03/2023]
Abstract
Despite extensive commercial and regulatory interventions, food spoilage and contamination continue to impose massive ramifications on human health and the global economy. Recognizing that such issues will be significantly eliminated by the accurate and timely monitoring of food quality markers, smart food sensors have garnered significant interest as platforms for both real-time, in-package food monitoring and on-site commercial testing. In both cases, the sensitivity, stability, and efficiency of the developed sensors are largely informed by underlying material design, driving focus toward the creation of advanced materials optimized for such applications. Herein, a comprehensive review of emerging intelligent materials and sensors developed in this space is provided, through the lens of three key food quality markers - biogenic amines, pH, and pathogenic microbes. Each sensing platform is presented with targeted consideration toward the contributions of the underlying metallic or polymeric substrate to the sensing mechanism and detection performance. Further, the real-world applicability of presented works is considered with respect to their capabilities, regulatory adherence, and commercial potential. Finally, a situational assessment of the current state of intelligent food monitoring technologies is provided, discussing material-centric strategies to address their existing limitations, regulatory concerns, and commercial considerations.
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Affiliation(s)
- Shadman Khan
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Jonathan K Monteiro
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8N 3Z5, Canada
| | - Akansha Prasad
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L7, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Mechanical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
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5
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Miao Q, Ding W, Bao X, Wang S, Lin Q, Xu Y, Lu J, Lyu M, Wang S. An efficient
DNAzyme
for the fluorescence detection of
Vibrio cholerae. Food Sci Nutr 2023. [DOI: 10.1002/fsn3.3304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Affiliation(s)
- Qingzhen Miao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Wen Ding
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Xiuli Bao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Siyuan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Qianru Lin
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Yingying Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Jing Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
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Mohammadi-Arani R, Javadi-Zarnaghi F, Boccaletto P, Bujnicki JM, Ponce-Salvatierra A. DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes. Nucleic Acids Res 2022; 50:W261-W265. [PMID: 35446426 PMCID: PMC9252740 DOI: 10.1093/nar/gkac269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/13/2022] [Accepted: 04/05/2022] [Indexed: 01/05/2023] Open
Abstract
Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize. In spite of their attractiveness, the choice of which DNAzyme should be used to cleave a given substrate is far from obvious, and requires expert knowledge as well as in-depth literature scrutiny. DNAzymeBuilder enables fast and automatic assembly of DNAzymes for the first time, superseding the manual design of DNAzymes. DNAzymeBuilder relies on an internal database with information on RNA and DNA cleaving DNAzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNAzyme. Based on this information and the input sequence provided by the user, DNAzymeBuilder provides a list of DNAzymes to carry out the cleavage reaction and detailed information for each of them, including the expected yield, reaction products and optimal reaction conditions. DNAzymeBuilder is a resource to help researchers introduce DNAzymes in their day-to-day research, and is publicly available at https://iimcb.genesilico.pl/DNAzymeBuilder.
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Affiliation(s)
- Razieh Mohammadi-Arani
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Azadi Square, Hezar Jerib Avenue, 8174673441, Isfahan, Iran
| | - Fatemeh Javadi-Zarnaghi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Azadi Square, Hezar Jerib Avenue, 8174673441, Isfahan, Iran
| | - Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
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DEOXYRIBOZYMES IN DETECTION OF PATHOGENIC BACTERIA. BIOTECHNOLOGIA ACTA 2021. [DOI: 10.15407/biotech14.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim. The purpose of the review was to analyze the use of DNAzyme biosensors for the detection of pathogens. In the recent years, deoxyribozymes (DNAzymes) have a significant impact as biosensors in diverse fields, from detection of metal ions in the environment to theranostic applications and detection of microorganisms. Although routinely used sophisticated instrumental methods are available to detect pathogenic bacterial contamination, they involve time-consuming, complicated sample pre-treatment and expensive instruments. As an alternative, pathogen-specific DNAzymes have demonstrated a series of advantages: a non-destructive rapid analysis technique with in situ and real-time detection of bacteria with high sensitivity and selectivity. A wide range of pathogen-specific DNAzymes has been developed using colorimetric and fluorescence-based detections for pathogenic bacterial contamination in various samples. The current review summarizes the in vitro selection of pathogen-specific DNAzymes, various strategies utilized in the sensor designs, and their potential use in theranostic applications.
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