1
|
Liu J, Shan S, Lai W, Chen Q, Jing X, Li R, Tan Y, Liu D, Peng J. Phage based magnetic capture method as an aid for real time RPA detection of Salmonella spp. in milk. J Dairy Sci 2024:S0022-0302(24)00778-1. [PMID: 38754822 DOI: 10.3168/jds.2023-24237] [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: 09/25/2023] [Accepted: 02/28/2024] [Indexed: 05/18/2024]
Abstract
Salmonella is a major cause of foodborne diseases worldwide. Conventional rapid assays for detecting Salmonella in real samples often encounter severe matrix interference or detect the limited number of species of a genus, resulting the inaccuracy of detection. In this study, we developed a method that combined phage-based magnetic capture with real time recombinase polymerase amplification (RPA) for the rapid, highly sensitive, and specific detection of Salmonella in milk with an ultra-low detection limit. The Felix O-1 phage-conjugated magnetic beads (O-1 pMBs) synthesized in this method showed excellent capture ability for Salmonella spp. and ideal specificity for non-Salmonella strains. After O-1 pMBs-based magnetic separation, the limit of detection (LOD) of the real time RPA assay was 50 cfu/mL in milk samples, which was significantly increased by a magnitude of 3-4 orders. The method exhibited a high sensitivity (compatibility) of 100% (14/14) for all tested Salmonella serotype strains and an ideal specificity (exclusivity) of 100% (7/7) for the tested non-Salmonella strains. The entire detection process including Salmonella capture, DNA extraction, and real time RPA detection was completed within 1.5 h. Furthermore, milk samples spiked with 10 cfu/25 mL of Salmonella were detected positive after cultured in buffered peptone water for only 3 h. Therefore, the proposed method could be an alternative for the rapid and accurate detection of Salmonella.
Collapse
Affiliation(s)
- Jie Liu
- State Key Laboratory of Food Science and Resources, Nanchang University, 235 East Nanjing Road, Nanchang 330047, China
| | - Shan Shan
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Centre for Disease Control and Prevention, 555 East Beijing Road, Nanchang 330029, China.; College of Life Science, National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China
| | - Weihua Lai
- State Key Laboratory of Food Science and Resources, Nanchang University, 235 East Nanjing Road, Nanchang 330047, China
| | - Qi Chen
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Xudong Jing
- State Key Laboratory of Food Science and Resources, Nanchang University, 235 East Nanjing Road, Nanchang 330047, China
| | - Rui Li
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Centre for Disease Control and Prevention, 555 East Beijing Road, Nanchang 330029, China.; Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang 330019, China
| | - Yucheng Tan
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Centre for Disease Control and Prevention, 555 East Beijing Road, Nanchang 330029, China.; Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang 330019, China
| | - Daofeng Liu
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Centre for Disease Control and Prevention, 555 East Beijing Road, Nanchang 330029, China..
| | - Juan Peng
- School of Food Science, Nanchang University, Nanchang 330047, China..
| |
Collapse
|
2
|
Forghani F, Li S, Zhang S, Mann DA, Deng X, den Bakker HC, Diez-Gonzalez F. Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing. Appl Environ Microbiol 2020; 86:e00097-20. [PMID: 32358002 PMCID: PMC7301854 DOI: 10.1128/aem.00097-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/14/2020] [Indexed: 11/20/2022] Open
Abstract
Food safety is a new area for novel applications of metagenomics analysis, which not only can detect and subtype foodborne pathogens in a single workflow but may also produce additional information with in-depth analysis capabilities. In this study, we applied a quasimetagenomic approach by combining short-term enrichment, immunomagnetic separation (IMS), multiple-displacement amplification (MDA), and nanopore sequencing real-time analysis for simultaneous detection of Salmonella and Escherichia coli in wheat flour. Tryptic soy broth was selected for the 12-h enrichment of samples at 42°C. Enrichments were subjected to IMS using beads capable of capturing both Salmonella and E. coli MDA was performed on harvested beads, and amplified DNA fragments were subjected to DNA library preparation for sequencing. Sequencing was performed on a portable device with real-time basecalling adaptability, and resulting sequences were subjected to two parallel pipelines for further analysis. After 1 h of sequencing, the quasimetagenomic approach could detect all targets inoculated at approximately 1 CFU/g flour to the species level. Discriminatory power was determined by simultaneous detection of dual inoculums of Salmonella and E. coli, absence of detection in control samples, and consistency in microbial flora composition of the same flour samples over several rounds of experiments. The total turnaround time for detection was approximately 20 h. Longer sequencing for up to 15 h enabled serotyping for many of the samples with more than 99% genome coverage, which could be subjected to other appropriate genetic analysis pipelines in less than a total of 36 h.IMPORTANCE Enterohemorrhagic Escherichia coli (EHEC) and Salmonella are of serious concern in low-moisture foods, including wheat flour and its related products, causing illnesses, outbreaks, and recalls. The development of advanced detection methods based on molecular principles of analysis is essential to incorporate into interventions intended to reduce the risk from these pathogens. In this work, a quasimetagenomic method based on real-time sequencing analysis and assisted by magnetic capture and DNA amplification was developed. This protocol is capable of detecting multiple Salmonella and/or E. coli organisms in the sample within less than a day, and it can also generate sufficient whole-genome sequences of the target organisms suitable for subsequent bioinformatics analysis. Multiplex detection and identification were accomplished in less than 20 h and additional whole-genome analyses of different nature were attained within 36 h, in contrast to the several days required in previous sequencing pipelines.
Collapse
Affiliation(s)
- Fereidoun Forghani
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Shaoting Li
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Shaokang Zhang
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - David A Mann
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Xiangyu Deng
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Henk C den Bakker
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Francisco Diez-Gonzalez
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| |
Collapse
|