1
|
Wu S, Yuan J, Xu A, Wang L, Li Y, Lin J, Yue X, Xi X. A Lab-on-a-Tube Biosensor Combining Recombinase-Aided Amplification and CRISPR-Cas12a with Rotated Magnetic Extraction for Salmonella Detection. MICROMACHINES 2023; 14:830. [PMID: 37421063 DOI: 10.3390/mi14040830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Foodborne pathogenic bacteria threaten worldwide public health, and simple bacterial detection methods are in urgent need. Here, we established a lab-on-a-tube biosensor for simple, rapid, sensitive, and specific detection of foodborne bacteria. METHODS A rotatable Halbach cylinder magnet and an iron wire netting with magnetic silica beads (MSBs) were used for simple and effective extraction and purification of DNA from the target bacteria, and recombinase-aided amplification (RAA) was combined with clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins12a(CRISPR-Cas12a) to amplify DNA and generate fluorescent signal. First, 15 mL of the bacterial sample was centrifuged, and the bacterial pellet was lysed by protease to release target DNA. Then, DNA-MSB complexes were formed as the tube was intermittently rotated and distributed uniformly onto the iron wire netting inside the Halbach cylinder magnet. Finally, the purified DNA was amplified using RAA and quantitatively detected by the CRISPR-Cas12a assay. RESULTS This biosensor could quantitatively detect Salmonella in spiked milk samples in 75 min, with a lower detection limit of 6 CFU/mL. The fluorescent signal of 102 CFU/mL Salmonella Typhimurium was over 2000 RFU, while 104 CFU/mL Listeria monocytogenes, Bacillus cereus, and E. coli O157:H7 were selected as non-target bacteria and had signals less than 500 RFU (same as the negative control). CONCLUSIONS This lab-on-a-tube biosensor integrates cell lysis, DNA extraction, and RAA amplification in one 15 mL tube to simplify the operation and avoid contamination, making it suitable for low-concentration Salmonella detection.
Collapse
Affiliation(s)
- Shangyi Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Jing Yuan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Ai Xu
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Lei Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinge Xi
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| |
Collapse
|
2
|
Linke RB, Zeki S, Mayer R, Keiblinger K, Savio D, Kirschner AKT, Reischer GH, Mach RL, Sommer R, Farnleitner AH. Identifying Inorganic Turbidity in Water Samples as Potential Loss Factor During Nucleic Acid Extraction: Implications for Molecular Fecal Pollution Diagnostics and Source Tracking. Front Microbiol 2021; 12:660566. [PMID: 34745021 PMCID: PMC8565874 DOI: 10.3389/fmicb.2021.660566] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular diagnostic methods are increasingly applied for food and environmental analysis. Since several steps are involved in sample processing which can affect the outcome (e.g., adhesion of DNA to the sample matrix, inefficient precipitation of DNA, pipetting errors and (partial) loss of the DNA pellet during DNA isolation), quality control is essential at all processing levels. In soil microbiology, particular attention has been paid to the inorganic component of the sample matrix affecting DNA extractability. In water quality testing, however, this aspect has mostly been neglected so far, although it is conceivable that these mechanisms have a similar impact. The present study was therefore dedicated to investigate possible matrix effects on results of water quality analysis. Field testing in an aquatic environment with pronounced chemo-physical gradients [total suspended solids (TSS), inorganic turbidity, total organic carbon (TOC), and conductivity] indicated a negative association between DNA extractability (using a standard phenol/chloroform extraction procedure) and turbidity (spearman ρ = −0.72, p < 0.001, n = 21). Further detailed laboratory experiments on sediment suspensions confirmed the hypothesis of inorganic turbidity being the main driver for reduced DNA extractability. The observed effects, as known from soil samples, were also indicated to result from competitive effects for free charges on clay minerals, leading to adsorption of DNA to these inorganic particles. A protocol modification by supplementing the extraction buffer with salmon sperm DNA, to coat charged surfaces prior to cell lysis, was then applied on environmental water samples and compared to the standard protocol. At sites characterized by high inorganic turbidity, DNA extractability was significantly improved or made possible in the first place by applying the adapted protocol. This became apparent from intestinal enterococci and microbial source tracking (MST)-marker levels measured by quantitative polymerase chain reaction (qPCR) (100 to 10,000-fold median increase in target concentrations). The present study emphasizes the need to consider inorganic turbidity as a potential loss factor in DNA extraction from water-matrices. Negligence of these effects can lead to a massive bias, by up to several orders of magnitude, in the results of molecular MST and fecal pollution diagnostics.
Collapse
Affiliation(s)
- Rita B Linke
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Sibel Zeki
- Department of Marine Environment, Institute of Marine Sciences and Management, Istanbul University, Istanbul, Turkey
| | - René Mayer
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Katharina Keiblinger
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Domenico Savio
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Alexander K T Kirschner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Georg H Reischer
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Research Area Molecular Diagnostics, Department IFA-Tulln, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Tulln, Austria
| | - Robert L Mach
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Regina Sommer
- Unit of Water Microbiology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Andreas H Farnleitner
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| |
Collapse
|