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Yi J, Wisuthiphaet N, Raja P, Nitin N, Earles JM. AI-enabled biosensing for rapid pathogen detection: From liquid food to agricultural water. WATER RESEARCH 2023; 242:120258. [PMID: 37390659 DOI: 10.1016/j.watres.2023.120258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023]
Abstract
Rapid pathogen detection in food and agricultural water is essential for ensuring food safety and public health. However, complex and noisy environmental background matrices delay the identification of pathogens and require highly trained personnel. Here, we present an AI-biosensing framework for accelerated and automated pathogen detection in various water samples, from liquid food to agricultural water. A deep learning model was used to identify and quantify target bacteria based on their microscopic patterns generated by specific interactions with bacteriophages. The model was trained on augmented datasets to maximize data efficiency, using input images of selected bacterial species, and then fine-tuned on a mixed culture. Model inference was performed on real-world water samples containing environmental noises unseen during model training. Overall, our AI model trained solely on lab-cultured bacteria achieved rapid (< 5.5 h) prediction with 80-100% accuracy on the real-world water samples, demonstrating its ability to generalize to unseen data. Our study highlights the potential applications in microbial water quality monitoring during food and agricultural processes.
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Affiliation(s)
- Jiyoon Yi
- Department of Biological & Agricultural Engineering, University of California, Davis, CA 95616, United States of America; Department of Biosystems & Agricultural Engineering, Michigan State University, East Lansing, MI 48824, United States of America
| | - Nicharee Wisuthiphaet
- Department of Food Science & Technology, University of California, Davis, CA 95616, United States of America; Department of Biotechnology, Faculty of Applied Science, King Mongkut's University of Technology North Bangkok, Bangkok, 10800, Thailand
| | - Pranav Raja
- Department of Biological & Agricultural Engineering, University of California, Davis, CA 95616, United States of America
| | - Nitin Nitin
- Department of Biological & Agricultural Engineering, University of California, Davis, CA 95616, United States of America; Department of Food Science & Technology, University of California, Davis, CA 95616, United States of America
| | - J Mason Earles
- Department of Biological & Agricultural Engineering, University of California, Davis, CA 95616, United States of America; Department of Viticulture & Enology, University of California, Davis, CA 95616, United States of America.
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2
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Yang SM, Kim E, Kim D, Kim HB, Baek J, Ko S, Kim D, Yoon H, Kim HY. Rapid Real-Time Polymerase Chain Reaction for Salmonella Serotyping Based on Novel Unique Gene Markers by Pangenome Analysis. Front Microbiol 2021; 12:750379. [PMID: 34621261 PMCID: PMC8491608 DOI: 10.3389/fmicb.2021.750379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
An accurate diagnostic method for Salmonella serovars is fundamental to preventing the spread of associated diseases. A diagnostic polymerase chain reaction (PCR)-based method has proven to be an effective tool for detecting pathogenic bacteria. However, the gene markers currently used in real-time PCR to detect Salmonella serovars have low specificity and are developed for only a few serovars. Therefore, in this study, we explored the novel unique gene markers for 60 serovars that share similar antigenic formulas and show high prevalence using pangenome analysis and developed a real-time PCR to detect them. Before exploring gene markers, the 535 Salmonella genomes were evaluated, and some genomes had serovars different from the designated serovar information. Based on these analyses, serovar-specific gene markers were explored. These markers were identified as genes present in all strains of target serovar genomes but absent in strains of other serovar genomes. Serovar-specific primer pairs were designed from the gene markers, and a real-time PCR method that can distinguish between 60 of the most common Salmonella serovars in a single 96-well plate assay was developed. As a result, real-time PCR showed 100% specificity for 199 Salmonella and 29 non-Salmonella strains. Subsequently, the method developed was applied successfully to both strains with identified serovars and an unknown strain, demonstrating that real-time PCR can accurately detect serovars of strains compared with traditional serotyping methods, such as antisera agglutination. Therefore, our method enables rapid and economical Salmonella serotyping compared with the traditional serotyping method.
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Affiliation(s)
- Seung-Min Yang
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Eiseul Kim
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Dayoung Kim
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Hyeon-Be Kim
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Jiwon Baek
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Seyoung Ko
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
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3
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Nucleic acid lateral flow assay for simultaneous detection of hygiene indicator bacteria. Anal Bioanal Chem 2021; 413:5003-5011. [PMID: 34132819 DOI: 10.1007/s00216-021-03462-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/29/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023]
Abstract
A simple and rapid polymerase chain reaction (PCR)-based lateral flow assay (LFA) was developed for multiplex detection of hygiene indicator bacteria. Specifically, new PCR primers were designed for accurately detecting Escherichia coli, coliform bacteria, and total bacteria, and the results obtained as a colorimetric signal (generated by the accumulation of gold nanoparticles at distinct test zones on flow strips) could be identified by the naked eye in <10 min after the completion of PCR. The proposed LFA system did not exhibit any cross-reactivities with 8 distinct bacterial strains and can detect down to 1 colony forming unit (CFU)/mL. Furthermore, three species of cultured bacteria (Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) inoculated onto sterilized ham were successfully analyzed using the LFA system, which demonstrated that this system shows sufficient sensitivity and specificity for food hygiene monitoring. The speed and simplicity of this LFA make it suitable for use in the food industry as part of routine screening analysis.
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Murray LP, Mace CR. Usability as a guiding principle for the design of paper-based, point-of-care devices - A review. Anal Chim Acta 2020; 1140:236-249. [PMID: 33218486 DOI: 10.1016/j.aca.2020.09.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]
Abstract
Due to their portability, versatility for supporting multiple assay formats, and potential for resulting in low-cost assays, paper-based analytical devices (PADs) are an increasingly popular format as a platform for the development of point-of-care tests. However, very few PADs have been translated successfully to their intended environments outside of academic settings. Often overlooked as a factor that inhibits translation, usability is a vital characteristic of any successful point-of-care test. Recent advancements in PAD design have demonstrated improved usability by simplifying various aspects of user operation, including sample collection, sample processing, device operation, detection, and readout/interpretation. Field testing at various stages of device design can offer critical feedback about device usability, especially when it involves the proposed end-user or other stakeholders. By highlighting advances in usability, we aim to encourage thoughtful and rigorous design at the academic prototyping stage to address one outstanding hurdle that limits the number of PADs that make it from the benchtop to the point-of-care.
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Affiliation(s)
- Lara P Murray
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Charles R Mace
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA.
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A Multicenter Proposal for a Fast Tool To Screen Biosecure Chicken Flocks for the Foodborne Pathogen Campylobacter. Appl Environ Microbiol 2020; 86:AEM.01051-20. [PMID: 32769183 DOI: 10.1128/aem.01051-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/02/2020] [Indexed: 11/20/2022] Open
Abstract
The present multicenter study aimed at assessing the performance of air sampling as a novel method for monitoring Campylobacter in biosecure poultry farms. We compared, using a harmonized procedure, the bacteriological isolation protocol (ISO 10272-1:2017) and a real-time PCR method used on air filter samples. Air samples and boot swabs were collected from 62 biosecure flocks from five European countries during the summer of 2019. For air filters, the frequency of PCR-positive findings was significantly higher (n = 36; 58%) than that obtained with the cultivation methods (P < 0.01; standardized residuals). The cultivation protocols (one with Bolton enrichment and one with Preston enrichment) were comparable to each other but returned fewer positive samples (0 to 8%). The association between type of sample and frequency of PCR-positive findings was statistically confirmed (P < 0.01; Fisher´s exact test), although no culture-positive air filters were detected using direct plating. For the boot swabs, the highest number of positive samples were detected after enrichment in Preston broth (n = 23; 37%), followed by direct plating after homogenization in Preston (n = 21; 34%) or Bolton broth (n = 20; 32%). It is noteworthy that the flocks in Norway, a country known to have low Campylobacter prevalence in biosecure chicken flocks, tested negative for Campylobacter by the new sensitive approach. In conclusion, air sampling combined with real-time PCR is proposed as a multipurpose, low-cost, and convenient screening method that can be up to four times faster and four times more sensitive than the current boot-swab testing scheme used for screening biosecure chicken production.IMPORTANCE Campylobacter bacteria are the cause of the vast majority of registered cases of foodborne illness in the industrialized world. In fact, the bacteria caused 246,571 registered cases of foodborne illness in 2018, which equates to 70% of all registered cases in Europe that year. An important tool to prevent campylobacters from making people sick is good data on where in the food chain the bacterium is present. The present study reports a new test method that quadruples the likelihood of identifying campylobacter-positive chicken flocks. It is important to identify campylobacter-positive flocks before they arrive at the slaughterhouse, because negative flocks can be slaughtered first in order to avoid cross-contamination along the production line.
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Zhou YY, Kang XL, Meng C, Xiong D, Xu Y, Geng SZ, Pan ZM, Jiao XA. Multiple PCR assay based on the cigR gene for detection of Salmonella spp. and Salmonella Pullorum/Gallinarum identification. Poult Sci 2020; 99:5991-5998. [PMID: 33142517 PMCID: PMC7647733 DOI: 10.1016/j.psj.2020.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 11/24/2022] Open
Abstract
Salmonella spp. are important zoonotic pathogens that are responsible for severe diseases in both animals and humans. Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum (S. Gallinarum) and biovar Pullorum (S. Pullorum) are typical infectious pathogens detected in the chicken industry that have caused great economic losses. To facilitate their detection and prevent contamination, we developed a rapid multiple PCR method, which can simultaneously detect Salmonella spp. and further identify the biovars S. Pullorum/Gallinarum. This PCR detection method is based on the cigR gene, which is conserved among Salmonella spp. but has a 42-bp deletion in S. Pullorum/Gallinarum. The specificity and sensitivity of the PCR assay was evaluated with 41 different strains: 34 Salmonella strains, including 5 S. Pullorum/Gallinarum strains, and 7 non-Salmonella strains. The lower limit of detection was 8.15 pg of S. Pullorum (S06004) genomic DNA and 20 cfu in PCR, which shows a great sensitivity. In addition, this method was applied to detect or identify Salmonella from processing chicken liver and egg samples, and the results corresponded to those obtained from serotype analysis using the conventional slide agglutination test. Overall, the new cigR-based PCR assay is efficient and practical for Salmonella detection and S. Pullorum/Gallinarum identification and will greatly reduce the workload of epidemiologic investigation.
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Affiliation(s)
- Ying-Ying Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xi-Long Kang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Chuang Meng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Dan Xiong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ying Xu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shi-Zhong Geng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhi-Ming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Xin-An Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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7
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Salimi G, Mousavi ZE, Kiani H. Efficiency of fluorescence in situ hybridization (FISH) method for the rapid detection of Salmonella in minced lamb meat: Method analysis and optimization. J Microbiol Methods 2020; 175:105989. [DOI: 10.1016/j.mimet.2020.105989] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 11/27/2022]
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8
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Chai C, Oh SW. Electrochemical impedimetric biosensors for food safety. Food Sci Biotechnol 2020; 29:879-887. [PMID: 32582450 PMCID: PMC7297935 DOI: 10.1007/s10068-020-00776-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/12/2020] [Accepted: 05/17/2020] [Indexed: 12/20/2022] Open
Abstract
Electrochemical impedimetric biosensors (EIBs) have a simple structure and can be used to rapidly and sensitively detect and measure hazards in food. EIBs detect and measure target molecules by transducing biochemical reactions on their surface to electrical signal outputs responding to a sinusoidal electrical signal input. Due to their structural simplicity and analytical sensitivity, EIBs are regarded as the most potent method of food hazard monitoring that can be implemented in the food supply chain. This paper discusses the theoretical background, structure, and construction of EIB and its applications in food safety.
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Affiliation(s)
- Changhoon Chai
- Department of Applied Animal Science, Kangwon National University, Chuncheon, 24341 Republic of Korea
| | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul, 02707 Republic of Korea
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Wang Y, Ke Y, Liu W, Sun Y, Ding X. A One-Pot Toolbox Based on Cas12a/crRNA Enables Rapid Foodborne Pathogen Detection at Attomolar Level. ACS Sens 2020; 5:1427-1435. [PMID: 32337966 DOI: 10.1021/acssensors.0c00320] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacterial contamination accounts for more than half of food poisoning cases. Conventional methods such as colony-counting and general polymerase chain reaction are time-consuming, instrument-dependent, and sometimes not accurate. Herein, we developed a novel one-pot toolbox with precision and ultra sensitivity (OCTOPUS) platform for foodborne pathogen detection based on the mechanism in which Cas12a nontarget binding unleashes its collateral DNase activity. We demonstrated its application on two widespread foodborne bacteria, namely, E. coli O157:H7 and Streptococcus aureus, using specific crRNA targeting rfbE and nuc gene, respectively. For better sensitivity, recombinase polymerase amplification (RPA) was integrated without product purification. This one-pot detection, that is, RPA reagent, crRNA, and ssDNA-FQ reporter are all in one tube with the subsequent addition of Cas12a enzyme, was able to detect genomic DNA at the attomolar level. It omits an extra cap-opening process to avoid practical inconvenience and possible cross-sample contamination. Moreover, we demonstrated this platform for a real food matrix. A simple water boiling method for genome extraction together with one-pot assay achieved a limit of detection value of 1 CFU/mL in less than 50 min. This OCTOPUS technique integrates bacterial genome extraction, preamplification based on RPA, and Cas12a/crRNA cleavage assay.
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Affiliation(s)
- Yunqing Wang
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yuqing Ke
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Wenjia Liu
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yiqing Sun
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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10
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Evaluation of DNA Extraction Methods for Culture-Independent Real-Time PCR-Based Detection of Listeria monocytogenes in Cheese. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01686-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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High-Throughput 16S rRNA Sequencing to Assess Potentially Active Bacteria and Foodborne Pathogens: A Case Example in Ready-to-Eat Food. Foods 2019; 8:foods8100480. [PMID: 31614586 PMCID: PMC6836182 DOI: 10.3390/foods8100480] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 09/20/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
Technologies to detect the entire bacterial diversity spectra and foodborne pathogens in food represent a fundamental advantage in the control of foodborne illness. Here, we applied high-throughput 16S rRNA sequencing of amplicons obtained by PCR and RT-PCR from extracted DNA and RNA targeting the entire bacterial community and the active bacterial fraction present in some of the most consumed and distributed ready-to-eat (RTE) salad brands in Europe. Customer demands for RTE food are increasing worldwide along with the number of associated foodborne illness and outbreaks. The total aerobic bacterial count in the analyzed samples was in the range of 2-4 × 106 CFU/g (SD ± 1.54 × 106). Culture validated methods did not detect Salmonella spp., Escherichia coli, and other fecal coliforms. 16S rRNA gene Illumina next-generation sequencing (NGS) data were congruent with these culture-based results and confirmed that these and other well-known foodborne bacterial pathogens, such as Listeria, were not detected. However, the fine-resolution of the NGS method unveiled the presence of the opportunistic pathogens Aeromonas hydrophyla and Rahnella aquatilis (relative frequency of 1.33-7.33%) that were metabolically active in addition to non-pathogenic, active members of Yersinia spp. (relative frequency of 0.0015-0.003%). The common ail and foxA marker genes of Yersinia enterocolitica were not detected by qPCR. Finally, our NGS data identified to non-pathogenic Pseudomonas spp. as the most abundant and metabolically active bacteria in the analyzed RTE salads (53-75% of bacterial abundance). Our data demonstrate the power of sequencing, in parallel, both 16S rRNA and rDNA to identify and discriminate those potentially and metabolically active bacteria and pathogens to provide a more complete view that facilitates the control of foodborne diseases, although further work should be conducted to determine the sensitivity of this method for targeting bacteria.
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12
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Metagenomics of Meat and Poultry. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Sabike II, Yamazaki W. Improving the Detection Accuracy and Time for Campylobacter jejuni and Campylobacter coli in Naturally Infected Live and Slaughtered Chicken Broilers Using a Real-Time Fluorescent Loop-Mediated Isothermal Amplification Approach. J Food Prot 2019; 82:189-193. [PMID: 30702350 DOI: 10.4315/0362-028x.jfp-18-179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rapid and accurate identification of Campylobacter-positive broiler flocks and carcasses expedites separation and control interventions before release into the food supply chain and directly facilitates a reduction in the prevalence of human campylobacteriosis. In this study, the diagnostic performance of fluorescent loop-mediated isothermal amplification (LAMP) assays for the direct detection of Campylobacter jejuni and Campylobacter coli in broiler cloacal and cecal samples were evaluated and compared with that of turbidimetric LAMP approaches investigated previously. The duplex fluorescent LAMP assay had significantly higher ( P < 0.05) diagnostic sensitivity (93.1%, 54 of 58 samples) than did the turbidimetric LAMP assay (82.8%, 48 of 58 samples) for detecting C. jejuni and C. coli in broiler cloacal samples, whereas the singleplex fluorescent LAMP assay had equivalent diagnostic sensitivity. For cecal samples, the diagnostic sensitivity of the fluorescent LAMP assay (100%, 38 of 38 samples) was the same as that of the turbidimetric LAMP. Fluorescent LAMP significantly reduced ( P < 0.05) the maximum detection time for Campylobacter-positive cloacal and cecal samples to 28 and 11 min, respectively, and reduced the influence of amplification inhibitors responsible for most false-negative results obtained for cloacal samples with the turbidimetric LAMP assay. The diagnostic accuracy of the fluorescent LAMP assay for the direct detection of C. jejuni and C. coli in cloacal and cecal samples was 97.7 and 100%, respectively. These findings indicate that fluorescent LAMP assays are robust, highly accurate, and field-applicable methods for the identification of C. jejuni and C. coli, which will allow more accurate monitoring of food safety at various stages of the food supply chain at farms and slaughter facilities.
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Affiliation(s)
- Islam Ibrahim Sabike
- 1 Department of Veterinary Sciences, Faculty of Agriculture (ORCID: http://orcid.org/0000-0002-7874-8014 [W.Y.]), University of Miyazaki, Miyazaki, Japan.,2 Department of Food Control, Faculty of Veterinary Medicine, Benha University, Egypt
| | - Wataru Yamazaki
- 1 Department of Veterinary Sciences, Faculty of Agriculture (ORCID: http://orcid.org/0000-0002-7874-8014 [W.Y.]), University of Miyazaki, Miyazaki, Japan.,3 Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
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Jones SL, Ricke SC, Keith Roper D, Gibson KE. Swabbing the surface: critical factors in environmental monitoring and a path towards standardization and improvement. Crit Rev Food Sci Nutr 2018; 60:225-243. [DOI: 10.1080/10408398.2018.1521369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sarah L. Jones
- Department of Food Science, Center for Food Safety, Division of Agriculture, University of Arkansas, Fayetteville, Arkansas, USA
| | - Steven C. Ricke
- Department of Food Science, Center for Food Safety, Division of Agriculture, University of Arkansas, Fayetteville, Arkansas, USA
| | - D. Keith Roper
- Department of Chemical Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Kristen E. Gibson
- Department of Food Science, Center for Food Safety, Division of Agriculture, University of Arkansas, Fayetteville, Arkansas, USA
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15
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Xiong D, Song L, Pan Z, Jiao X. Identification and Discrimination of Salmonella enterica Serovar Gallinarum Biovars Pullorum and Gallinarum Based on a One-Step Multiplex PCR Assay. Front Microbiol 2018; 9:1718. [PMID: 30108571 PMCID: PMC6079294 DOI: 10.3389/fmicb.2018.01718] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/10/2018] [Indexed: 01/27/2023] Open
Abstract
Salmonella enterica serovar Gallinarum biovars Pullorum (S. Pullorum) and Gallinarum (S. Gallinarum) can result in pullorum disease and fowl typhoid in avian species, respectively, and cause considerable economic losses in poultry in many developing countries. Conventional Salmonella serotyping is a time-consuming, labor-intensive and expensive process, and the two biovars cannot be distinguished using the traditional serological method. In this study, we developed a rapid and reliable one-step multiplex polymerase chain reaction (PCR) assay to simultaneously identify and discriminate the biovars Pullorum and Gallinarum. The multiplex PCR method focused on three specific genes, stn, I137_08605 and ratA. Based on bioinformatics analysis, we found that gene I137_08605 was present only in S. Pullorum and S. Gallinarum, and a region of difference in ratA was deleted only in S. Pullorum after comparison with that of S. Gallinarum and other Salmonella serovars. Three pairs of primers specific for the three genes were designed for the multiplex PCR system and their selectivity and sensitivity were determined. The multiplex PCR results showed that S. Pullorum and S. Gallinarum could be identified and discriminated accurately from all tested strains including 124 strains of various Salmonella serovars and 42 strains of different non-Salmonella pathogens. In addition, this multiplex PCR assay could detect a minimum genomic DNA concentration of 67.4 pg/μL, and 100 colony forming units. The efficiency of the multiplex PCR was evaluated by detecting natural-occurring Salmonella isolates from a chicken farm. The results demonstrated that the established multiplex PCR was able to identify S. Gallinarum and S. Pullorum individually, with results being consistent with traditional serotyping and biochemical testing. These results demonstrated that a highly accurate and simple biovar-specific multiplex PCR assay could be performed for the rapid identification and discrimination of Salmonella biovars Gallinarum and Pullorum, which will be useful, particularly under massive screening situations.
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Affiliation(s)
- Dan Xiong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Li Song
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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16
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Ricke SC, Kim SA, Shi Z, Park SH. Molecular-based identification and detection of Salmonella in food production systems: current perspectives. J Appl Microbiol 2018; 125:313-327. [PMID: 29675864 DOI: 10.1111/jam.13888] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/25/2022]
Abstract
Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies have greatly improved the resolution for differentiating strains within a particular serovar. This, in turn, has led to the continued improvement in Salmonella detection technologies for utilization in food production systems. In this review, the focus will be on recent advancements in these technologies, as well as potential issues associated with the application of these tools in food production. In addition, the recent and emerging research developments on Salmonella detection and identification methodologies and their potential application in food production systems will be discussed.
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Affiliation(s)
- S C Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S A Kim
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Z Shi
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S H Park
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
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17
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Xu L, Liu Z, Li Y, Yin C, Hu Y, Xie X, Li Q, Jiao X. A rapid method to identify Salmonella enterica serovar Gallinarum biovar Pullorum using a specific target gene ipaJ. Avian Pathol 2018; 47:238-244. [PMID: 29231761 DOI: 10.1080/03079457.2017.1412084] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Salmonella enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is the pathogen of pullorum disease, which leads to severe economic losses in many developing countries. Traditional methods to identify S. enterica have relied on biochemical reactions and serotyping, which are time-consuming with accurate identification if properly carried out. In this study, we developed a rapid polymerase chain reaction (PCR) method targeting the specific gene ipaJ to detect S. Pullorum. Among the 650 S. Pullorum strains isolated from 1962 to 2016 all over China, 644 strains were identified to harbour ipaJ gene in the plasmid pSPI12, accounting for a detection rate of 99.08%. Six strains were ipaJ negative because pSPI12 was not found in these strains according to whole genome sequencing results. There was no cross-reaction with other Salmonella serotypes, including Salmonella enterica serovar Gallinarum biovar Gallinarum (S. Gallinarum), which show a close genetic relationship with S. Pullorum. This shows that the PCR method could distinguish S. Gallinarum from S. Pullorum in one-step PCR without complicated biochemical identification. The limit of detection of this PCR method was as low as 90 fg/μl or 102 CFU, which shows a high sensitivity. Moreover, this method was applied to identify Salmonella isolated from the chicken farm and the results were consistent with what we obtained from biochemical reactions and serotyping. Together, all the results demonstrated that this one-step PCR method is simple and feasible to efficiently identify S. Pullorum.
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Affiliation(s)
- Lijuan Xu
- a Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China , Yangzhou University , Yangzhou , People's Republic of China.,b Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , People's Republic of China
| | - Zijian Liu
- a Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China , Yangzhou University , Yangzhou , People's Republic of China.,b Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , People's Republic of China
| | - Yang Li
- a Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China , Yangzhou University , Yangzhou , People's Republic of China.,b Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , People's Republic of China
| | - Chao Yin
- a Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China , Yangzhou University , Yangzhou , People's Republic of China.,c Joint International Research Laboratory of Agriculture and Agri-Product Safety , Yangzhou University , Yangzhou , People's Republic of China
| | - Yachen Hu
- a Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China , Yangzhou University , Yangzhou , People's Republic of China.,b Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , People's Republic of China
| | - Xiaolei Xie
- a Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China , Yangzhou University , Yangzhou , People's Republic of China.,b Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , People's Republic of China
| | - Qiuchun Li
- a Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China , Yangzhou University , Yangzhou , People's Republic of China.,b Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , People's Republic of China
| | - Xinan Jiao
- a Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China , Yangzhou University , Yangzhou , People's Republic of China.,b Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , People's Republic of China.,c Joint International Research Laboratory of Agriculture and Agri-Product Safety , Yangzhou University , Yangzhou , People's Republic of China
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Suo Y, Gao S, Xie Y, Liu Y, Qu Y, Lin T, Zhou C. A multipathogen selective enrichment broth for simultaneous growth of
Salmonella enteria
,
Escherichia coli
O157:H7, and
Shigella flexneri. J Food Saf 2017. [DOI: 10.1111/jfs.12388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yujuan Suo
- Institute of Agro‐Food Standard and Testing Technology, Shanghai Academy of Agricultural Science, No. 1000 Jinqi RoadShanghai201403 People's Republic of China
| | - Shigang Gao
- Eco‐Environmental Protection Research Institute, Shanghai Academy of Agricultural Science, No. 1000 Jinqi RoadShanghai201403 People's Republic of China
| | - Yanping Xie
- Molecular Characterization of Foodborne Pathogens Research UnitEastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid LaneWyndmoor Pennsylvania
| | - Yanhong Liu
- Molecular Characterization of Foodborne Pathogens Research UnitEastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid LaneWyndmoor Pennsylvania
| | - Yang Qu
- Institute of Agro‐Food Standard and Testing Technology, Shanghai Academy of Agricultural Science, No. 1000 Jinqi RoadShanghai201403 People's Republic of China
| | - Ting Lin
- Institute of Agro‐Food Standard and Testing Technology, Shanghai Academy of Agricultural Science, No. 1000 Jinqi RoadShanghai201403 People's Republic of China
| | - Changyan Zhou
- Institute of Agro‐Food Standard and Testing Technology, Shanghai Academy of Agricultural Science, No. 1000 Jinqi RoadShanghai201403 People's Republic of China
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Hernández Porras EE, Rosero Torres LE, Parra Barrera EL, Guerrero Montilla JA, Gómez Rubio AL, Moreno Castañeda JE. Brotes de enfermedades transmitidas por los alimentos estudiados mediante técnicas moleculares. Rev Salud Publica (Bogota) 2017; 19:671-678. [DOI: 10.15446/rsap.v19n5.52317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/28/2017] [Indexed: 11/09/2022] Open
Abstract
Objetivo Aplicar una técnica de reacción en cadena de la polimerasa (PCR) múltiple en tiempo real para la detección de Salmonella spp., Listeria monocytogenes y Yersinia enterocolitica, como herramienta de apoyo diagnóstico en la vigilancia de brotes de enfermedad transmitida por alimentos.Materiales y Métodos Se aplicó la metodología molecular en muestras clínicas provenientes de individuos que estaban asociados a brotes de enfermedad transmitida por alimentos de dos departamentos de Colombia. Los resultados se compararon con los datos arrojados por la metodología convencional de cultivo. Adicionalmente a los aislamientos obtenidos se les evaluó relación clonal mediante la técnica de electroforesis de campo pulsado (PFGE).Resultados Se determinó un total de 123 casos de enfermedad transmitida por alimentos de los cuales 45 muestras biológicas fueron confirmadas por laboratorio y 88 mediante nexo epidemiológico. La metodología molecular detectó 35/45 muestras positivas frente a 17/45 muestras positivas detectadas mediante la metodología convencional. La PFGE demostró relación clonal en cada brote.Conclusión Los resultados del estudio demuestran la aplicabilidad de la técnica molecular como herramienta útil de apoyo diagnóstico en la caracterización de brotes de enfermedad transmitida por alimentos, permitiendo una respuesta oportuna y confiable.
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20
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Andjelković U, Šrajer Gajdošik M, Gašo-Sokač D, Martinović T, Josić D. Foodomics and Food Safety: Where We Are. Food Technol Biotechnol 2017; 55:290-307. [PMID: 29089845 PMCID: PMC5654429 DOI: 10.17113/ftb.55.03.17.5044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.
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Affiliation(s)
- Uroš Andjelković
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, RS-11000 Belgrade, Serbia
| | - Martina Šrajer Gajdošik
- Department of Chemistry, J. J. Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Dajana Gašo-Sokač
- Faculty of Food Technology, J. J. Strossmayer University of Osijek, Franje Kuhača 20, HR-31000 Osijek, Croatia
| | - Tamara Martinović
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Warren Alpert Medical School, Brown University, 222 Richmond St, Providence, RI 02903, USA
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21
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Andersen SC, Kiil K, Harder CB, Josefsen MH, Persson S, Nielsen EM, Hoorfar J. Towards diagnostic metagenomics of Campylobacter in fecal samples. BMC Microbiol 2017; 17:133. [PMID: 28595575 PMCID: PMC5465461 DOI: 10.1186/s12866-017-1041-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/01/2017] [Indexed: 11/28/2022] Open
Abstract
Background The development of diagnostic metagenomics is driven by the need for universal, culture-independent methods for detection and characterization of pathogens to substitute the time-consuming, organism-specific, and often culture-based laboratory procedures for epidemiological source-tracing. Some of the challenges in diagnostic metagenomics are, that it requires a great next-generation sequencing depth and unautomated data analysis. Results DNA from human fecal samples spiked with 7.75 × 101−7.75 × 107 colony forming unit (CFU)/ml Campylobacter jejuni and chicken fecal samples spiked with 1 × 102–1 × 106 CFU/g Campylobacter jejuni was sequenced and data analysis was done by the metagenomic tools Kraken and CLARK. More hits were obtained at higher spiking levels, however with no significant linear correlations (human samples p = 0.12, chicken samples p = 0.10). Therefore, no definite detection limit could be determined, but the lowest spiking levels found positive were 7.75 × 104 CFU/ml in human feces and 103 CFU/g in chicken feces. Eight human clinical fecal samples with estimated Campylobacter infection loads from 9.2 × 104–1.0 × 109 CFU/ml were analyzed using the same methods. It was possible to detect Campylobacter in all the clinical samples. Conclusions Sensitivity in diagnostic metagenomics is improving and has reached a clinically relevant level. There are still challenges to overcome before real-time diagnostic metagenomics can replace quantitative polymerase chain reaction (qPCR) or culture-based surveillance and diagnostics, but it is a promising new technology.
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Affiliation(s)
- Sandra Christine Andersen
- National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860, Søborg, Denmark.
| | - Kristoffer Kiil
- Statens Serum Institut, Artillerivej 5, DK-2300, København S, Denmark
| | | | | | - Søren Persson
- Statens Serum Institut, Artillerivej 5, DK-2300, København S, Denmark
| | | | - Jeffrey Hoorfar
- National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860, Søborg, Denmark
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22
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Ferrario C, Lugli GA, Ossiprandi MC, Turroni F, Milani C, Duranti S, Mancabelli L, Mangifesta M, Alessandri G, van Sinderen D, Ventura M. Next generation sequencing-based multigene panel for high throughput detection of food-borne pathogens. Int J Food Microbiol 2017; 256:20-29. [PMID: 28578266 DOI: 10.1016/j.ijfoodmicro.2017.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 01/20/2023]
Abstract
Contamination of food by chemicals or pathogenic bacteria may cause particular illnesses that are linked to food consumption, commonly referred to as foodborne diseases. Bacteria are present in/on various foods products, such as fruits, vegetables and ready-to-eat products. Bacteria that cause foodborne diseases are known as foodborne pathogens (FBPs). Accurate detection methods that are able to reveal the presence of FBPs in food matrices are in constant demand, in order to ensure safe foods with a minimal risk of causing foodborne diseases. Here, a multiplex PCR-based Illumina sequencing method for FBP detection in food matrices was developed. Starting from 25 bacterial targets and 49 selected PCR primer pairs, a primer collection called foodborne pathogen - panel (FPP) consisting of 12 oligonucleotide pairs was developed. The FPP allows a more rapid and reliable identification of FBPs compared to classical cultivation methods. Furthermore, FPP permits sensitive and specific FBP detection in about two days from food sample acquisition to bioinformatics-based identification. The FPP is able to simultaneously identify eight different bacterial pathogens, i.e. Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Salmonella enterica subsp. enterica serovar enteritidis, Escherichia coli, Shigella sonnei, Staphylococcus aureus and Yersinia enterocolitica, in a given food matrix at a threshold contamination level of 101cell/g. Moreover, this novel detection method may represent an alternative and/or a complementary approach to PCR-based techniques, which are routinely used for FBP detection, and could be implemented in (parts of) the food chain as a quality check.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute, School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
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23
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Wang Y, Duncan TV. Nanoscale sensors for assuring the safety of food products. Curr Opin Biotechnol 2017; 44:74-86. [DOI: 10.1016/j.copbio.2016.10.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/22/2016] [Indexed: 12/16/2022]
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24
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Rohde A, Hammerl JA, Boone I, Jansen W, Fohler S, Klein G, Dieckmann R, Al Dahouk S. Overview of validated alternative methods for the detection of foodborne bacterial pathogens. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.02.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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25
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Evaluation of the performance of quantitative detection of the Listeria monocytogenes prfA locus with droplet digital PCR. Anal Bioanal Chem 2016; 408:7583-7593. [PMID: 27558101 PMCID: PMC5061835 DOI: 10.1007/s00216-016-9861-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/03/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023]
Abstract
Fast and reliable pathogen detection is an important issue for human health. Since conventional microbiological methods are rather slow, there is growing interest in detection and quantification using molecular methods. The droplet digital polymerase chain reaction (ddPCR) is a relatively new PCR method for absolute and accurate quantification without external standards. Using the Listeria monocytogenes specific prfA assay, we focused on the questions of whether the assay was directly transferable to ddPCR and whether ddPCR was suitable for samples derived from heterogeneous matrices, such as foodstuffs that often included inhibitors and a non-target bacterial background flora. Although the prfA assay showed suboptimal cluster formation, use of ddPCR for quantification of L. monocytogenes from pure bacterial cultures, artificially contaminated cheese, and naturally contaminated foodstuff was satisfactory over a relatively broad dynamic range. Moreover, results demonstrated the outstanding detection limit of one copy. However, while poorer DNA quality, such as resulting from longer storage, can impair ddPCR, internal amplification control (IAC) of prfA by ddPCR, that is integrated in the genome of L. monocytogenes ΔprfA, showed even slightly better quantification over a broader dynamic range. Evaluating the absolute quantification potential of ddPCR targeting Listeria monocytogenes prfA ![]()
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26
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Souii A, M’hadheb-Gharbi MB, Gharbi J. Nucleic acid-based biotechnologies for food-borne pathogen detection using routine time-intensive culture-based methods and fast molecular diagnostics. Food Sci Biotechnol 2016; 25:11-20. [PMID: 30263230 PMCID: PMC6049363 DOI: 10.1007/s10068-016-0002-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/23/2023] Open
Abstract
Diseases caused by food-borne pathogens constitute a major burden to consumers, food business operators, and national governments. Bacterial and viral pathogens are the major biotic factors influencing food safety. A vast array of culture dependent analytical methods and protocols have been developed. Recently, nucleic acid-based methods have begun to replace or complement culture-based methods for routine use in food control laboratories. Basic advantages provided by nucleic acid-based technologies are faster speed and more information, such as sub-species identification, antibiotic resistance, and food microbiology. In particular, PCR and alternative methods have been developed to a stage that provides good speed, sensitivity, specificity, and reproducibility with minimized risk of carryover contamination. This review briefly summarizes currently available and developing molecular technologies that may be candidates for involvement in microbiological molecular diagnostic methods in the next decade.
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Affiliation(s)
- Amira Souii
- The Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El manar-Tunis, Rommana, 1068 Tunisia
- The Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, 5000 Tunisia
| | | | - Jawhar Gharbi
- The Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, 5000 Tunisia
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27
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Skerniškytė J, Armalytė J, Kvietkauskaitė R, Šeputienė V, Povilonis J, Sužiedėlienė E. Detection ofSalmonellaspp.,Yersinia enterocolitica,Listeria monocytogenesandCampylobacterspp. by real-time multiplex PCR using amplicon DNA melting analysis and probe-based assay. Int J Food Sci Technol 2015. [DOI: 10.1111/ijfs.12990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jūratė Skerniškytė
- Department of Biochemistry and Molecular Biology; Faculty of Natural Sciences; Vilnius University; M. K. Čiurlionio 21 Vilnius LT-03101 Lithuania
| | - Julija Armalytė
- Department of Biochemistry and Molecular Biology; Faculty of Natural Sciences; Vilnius University; M. K. Čiurlionio 21 Vilnius LT-03101 Lithuania
| | - Raimonda Kvietkauskaitė
- Department of Biochemistry and Molecular Biology; Faculty of Natural Sciences; Vilnius University; M. K. Čiurlionio 21 Vilnius LT-03101 Lithuania
| | - Vaida Šeputienė
- Department of Biochemistry and Molecular Biology; Faculty of Natural Sciences; Vilnius University; M. K. Čiurlionio 21 Vilnius LT-03101 Lithuania
| | - Justas Povilonis
- Department of Biochemistry and Molecular Biology; Faculty of Natural Sciences; Vilnius University; M. K. Čiurlionio 21 Vilnius LT-03101 Lithuania
| | - Edita Sužiedėlienė
- Department of Biochemistry and Molecular Biology; Faculty of Natural Sciences; Vilnius University; M. K. Čiurlionio 21 Vilnius LT-03101 Lithuania
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Fachmann M, Josefsen M, Hoorfar J, Nielsen M, Löfström C. Cost-effective optimization of real-time PCR-based detection of Campylobacter
and Salmonella
with inhibitor tolerant DNA polymerases. J Appl Microbiol 2015; 119:1391-402. [DOI: 10.1111/jam.12937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/03/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022]
Affiliation(s)
- M.S.R. Fachmann
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
| | - M.H. Josefsen
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
| | - J. Hoorfar
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
| | - M.T. Nielsen
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
| | - C. Löfström
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
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29
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Factors affecting cell population density during enrichment and subsequent molecular detection of Salmonella enterica and Escherichia coli O157:H7 on lettuce contaminated during field production. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.01.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Baker CA, Rubinelli PM, Park SH, Ricke SC. Immuno-based detection of Shiga toxin-producing pathogenic Escherichia coli in food – A review on current approaches and potential strategies for optimization. Crit Rev Microbiol 2015; 42:656-75. [DOI: 10.3109/1040841x.2015.1009824] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Christopher A. Baker
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Peter M. Rubinelli
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Si Hong Park
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Steven C. Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
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31
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Rohde A, Hammerl JA, Appel B, Dieckmann R, Al Dahouk S. FISHing for bacteria in food – A promising tool for the reliable detection of pathogenic bacteria? Food Microbiol 2015; 46:395-407. [DOI: 10.1016/j.fm.2014.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/15/2014] [Accepted: 09/05/2014] [Indexed: 12/28/2022]
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32
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Lee YJ, Kim D, Lee K, Chun JY. Single-channel multiplexing without melting curve analysis in real-time PCR. Sci Rep 2014; 4:7439. [PMID: 25501038 PMCID: PMC4262828 DOI: 10.1038/srep07439] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/21/2014] [Indexed: 01/08/2023] Open
Abstract
Multiplex real-time PCR with quantification of targets in a single fluorescence channel has been the demand in biotechnology industry. Here, we develop a novel analytical real-time PCR technique to detect multiple targets in a single fluorescence channel without melting curve analysis. In this technique, we show the intensity of the fluorescence signals of two discrete Tm targets is different at certain temperatures called detection temperatures, by which a high Tm target can be detected regardless of a low Tm target. We then identify the low Tm target by utilizing a change of the fluorescence signals between two different detection temperatures. Furthermore, it enables us to determine quantification of each target in a single channel, possibly facilitating convenient patient care for drug treatment in clinics.
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Affiliation(s)
- Young-Jo Lee
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Daeyoung Kim
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Kihoon Lee
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Jong-Yoon Chun
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
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33
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Rapid detection of Staphylococcus aureus by loop-mediated isothermal amplification. Appl Biochem Biotechnol 2014; 175:882-91. [PMID: 25349088 DOI: 10.1007/s12010-014-1328-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 10/15/2014] [Indexed: 01/15/2023]
Abstract
Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), is a major bacterial pathogen associated with nosocomial and community-acquired S. aureus infections all over the world. A rapid detection assay for staphylococcal gene of nuc and mecA is needed. In this study, a rapid identification assay based on the loop-mediated isothermal amplification (LAMP) method was established. PCR and LAMP assays were used to detect Staphylococcus aureus and other related species for nuc and mecA. With optimization of the primers and reaction temperature, the LAMP successfully amplified the genes under isothermal conditions at 62 °C within 60 min, of which the results were identical with those of the conventional PCR methods. The detection limits of the LAMP for nuc and mecA were 1.47 and 14.7 pg/μl DNA per tube, respectively, by naked eye inspections, while the detection limits of the PCR for nuc and mecA were 14.7 pg/μl and 147 pg/μl DNA, respectively. Finally, The LAMP method was then applied to clinical blood plaque samples. The LAMP and PCR demonstrated identical results for the plaque samples with the culture assay. Together, the LAMP offers an alternative detection assay for nuc and mecA with a great advantage of the sensitivity and rapidity.
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34
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Cremonesi P, Pisani LF, Lecchi C, Ceciliani F, Martino P, Bonastre AS, Karus A, Balzaretti C, Castiglioni B. Development of 23 individual TaqMan® real-time PCR assays for identifying common foodborne pathogens using a single set of amplification conditions. Food Microbiol 2014; 43:35-40. [DOI: 10.1016/j.fm.2014.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 04/07/2014] [Accepted: 04/18/2014] [Indexed: 11/28/2022]
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35
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Rapid Methods for Quality Assurance of Foods: the Next Decade with Polymerase Chain Reaction (PCR)-Based Food Monitoring. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9915-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Kuchta T, Knutsson R, Fiore A, Kudirkiene E, Höhl A, Horvatek Tomic D, Gotcheva V, Pöpping B, Scaramagli S, To Kim A, Wagner M, De Medici D. A decade with nucleic acid-based microbiological methods in safety control of foods. Lett Appl Microbiol 2014; 59:263-71. [PMID: 24820436 DOI: 10.1111/lam.12283] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/19/2014] [Accepted: 05/07/2014] [Indexed: 12/11/2022]
Abstract
In the last decade, nucleic acid-based methods gradually started to replace or complement the culture-based methods and immunochemical assays in routine laboratories involved in food control. In particular, real-time polymerase chain reaction (PCR) was technically developed to the stage of good speed, sensitivity and reproducibility, at minimized risk of carry-over contamination. Basic advantages provided by nucleic acid-based methods are higher speed and added information, such as subspecies identification, information on the presence of genes important for virulence or antibiotic resistance. Nucleic acid-based methods are attractive also to detect important foodborne pathogens for which no classical counterparts are available, namely foodborne pathogenic viruses. This review briefly summarizes currently available or developing molecular technologies that may be candidates for involvement in microbiological molecular methods in the next decade. Potential of nonamplification as well as amplification methods is discussed, including fluorescent in situ hybridization, alternative PCR chemistries, alternative amplification technologies, digital PCR and nanotechnologies.
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Affiliation(s)
- T Kuchta
- Department of Microbiology and Molecular Biology, Food Research Institute, Bratislava 26, Slovakia
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37
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Rapid detection of Shigella and enteroinvasive Escherichia coli in produce enrichments by a conventional multiplex PCR assay. Food Microbiol 2014; 40:48-54. [DOI: 10.1016/j.fm.2013.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 12/03/2013] [Accepted: 12/10/2013] [Indexed: 11/21/2022]
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38
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Park SH, Aydin M, Khatiwara A, Dolan MC, Gilmore DF, Bouldin JL, Ahn S, Ricke SC. Current and emerging technologies for rapid detection and characterization of Salmonella in poultry and poultry products. Food Microbiol 2014; 38:250-62. [DOI: 10.1016/j.fm.2013.10.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 07/28/2013] [Accepted: 10/04/2013] [Indexed: 12/19/2022]
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39
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Deiss F, Funes-Huacca ME, Bal J, Tjhung KF, Derda R. Antimicrobial susceptibility assays in paper-based portable culture devices. LAB ON A CHIP 2014; 14:167-71. [PMID: 24185315 DOI: 10.1039/c3lc50887k] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To detect antibiotic-resistant bacteria in areas remote from microbiology laboratories, we designed portable culture devices performing an analogue of the Kirby-Bauer disk diffusion test inside patterned papers embedded in tape. We quantified the antibiotic susceptibility of several strains of Escherichia coli and Salmonella typhimurium by measuring blue-colored zones of inhibited growth.
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Affiliation(s)
- Frédérique Deiss
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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40
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Abstract
The objectives of this chapter are to provide a brief understanding of the following:Clinical evaluation of infectious diseases and altered immune disorders, including physical examination and laboratory studies Various infectious disease processes, including etiology, pathogenesis, clinical presentation, and management Commonly encountered altered immune disorders, including etiology, clinical presentation, and management Precautions and guidelines that a physical therapist should implement when treating a patient with an infectious disease process or altered immunity
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41
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Mano J, Hatano S, Futo S, Minegishi Y, Ninomiya K, Nakamura K, Kondo K, Teshima R, Takabatake R, Kitta K. Development of direct real-time PCR system applicable to a wide range of foods and agricultural products. SHOKUHIN EISEIGAKU ZASSHI. JOURNAL OF THE FOOD HYGIENIC SOCIETY OF JAPAN 2014; 55:25-33. [PMID: 24598224 DOI: 10.3358/shokueishi.55.25] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To improve the efficiency of DNA analysis of foods and agricultural products, we investigated a direct real-time PCR based on the real-time monitoring of DNA amplification directly from crude cell lysates of analytical samples. We established a direct real-time PCR system comprising sample pretreatment with a specified lysis buffer and real-time PCR using the developed master mix reagent. No PCR inhibition was observed in the analysis of crude cell lysates from 50 types of samples, indicating that the direct real-time PCR system is applicable to a wide range of materials. The specificity of the direct real-time PCR was evaluated by means of a model assay system for single nucleotide discrimination. Even when crude cell lysates coexisted in the reaction mixtures, the primer selectivity was not affected, suggesting that the sequence specificity of the direct real-time PCR was equivalent to that of PCR from purified DNA templates. We evaluated the sensitivity and quantitative performance of the direct real-time PCR using soybean flour samples including various amounts of genetically modified organisms. The results clearly showed that the direct real-time PCR system provides sensitive detection and precise quantitation.
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Affiliation(s)
- Junichi Mano
- National Food Research Institute, National Agriculture and Food Research Organization
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42
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Extraction of Bacillus endospores from water, apple juice concentrate, raw milk and lettuce rinse solutions using tangential flow filtration. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.01.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Riyaz-Ul-Hassan S, Verma V, Qazi GN. Real-time PCR-based rapid and culture-independent detection of Salmonella in dairy milk--addressing some core issues. Lett Appl Microbiol 2013; 56:275-82. [PMID: 23347051 DOI: 10.1111/lam.12046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/12/2013] [Accepted: 01/16/2013] [Indexed: 11/29/2022]
Abstract
In this study, methodologies were developed for cost-effective, rapid and user-friendly culture-independent detection of Salmonella in milk by real-time PCR. The SYBR Green-based real-time PCR assay was standardized with primers targeting the Salmonella enterotoxin gene (stn) that have been earlier used for its detection by conventional PCR. Inclusivity tests generated the specific amplifications with a Tm corresponding to 81 ± 0·5°C. The specificity of the reaction was evaluated with a panel of 36 non-Salmonella strains. Standard curves generated, with different number of cells of this organism in milk, depicted the detection of five cells with a CT value of 37·17 (SD 0·43). To make the assays user-friendly and suitable for field applications, protocols were also established for the immobilization of the SYBR Green reaction mixes in the reaction tubes. The immobilized master mixes were stable at 25°C for 4 months and at 8°C for over 6 months. Total DNA was prepared from 150 samples of full-fat dairy milk and subjected to real-time PCR detection wherein 31 samples tested positive for Salmonella. The time of analysis was <5 h.
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Affiliation(s)
- S Riyaz-Ul-Hassan
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu Tawi, India.
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44
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Validation of a 1-Day Analytical Diagnostic Real-Time PCR for the Detection of Salmonella in Different Food Meat Categories. FOOD ANAL METHOD 2013. [DOI: 10.1007/s12161-013-9570-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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45
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Pinior B, Konschake M, Platz U, Thiele HD, Petersen B, Conraths FJ, Selhorst T. The trade network in the dairy industry and its implication for the spread of contamination. J Dairy Sci 2012; 95:6351-61. [PMID: 22999280 DOI: 10.3168/jds.2012-5809] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 07/11/2012] [Indexed: 11/19/2022]
Abstract
In case of an outbreak of a foodborne disease, administrative decisions in the context of crisis management are only efficient if they follow standard practices and are specifically adapted to the outbreak situation in a timely manner. These goals are hard to achieve. The complexity of national and global trade structures obscures a clear view of trade flows and, consequently, it is often impossible to unravel complex trade links quickly. Furthermore, increasing public concerns about possible health hazards caused by global trade put additional pressure on decision makers. The aim of this paper was to unveil the specific trade structures of the German milk supply chain, to highlight how these structures could affect the spatial spread of a hypothetical contaminant, and to quantify the risk of the contaminant reaching the consumer. To achieve this goal, the vertical and horizontal trade links between milk producers, dairies, and consumers were taken into account. The horizontal flow of milk between dairies (inter-dairy trade), which is intended to compensate a temporary over- or undersupply of milk, is of special importance in this respect. We hypothesized that the extent of inter-dairy trade would significantly influence the spatial spread of contaminated milk and the contamination risk. This hypothesis was tested using a computer simulation model that predicts the hypothetical spread of a contaminant via trade of milk. The model parameters were estimated using trade data collected in 2004 and 2010. The results of our study indicate that inter-dairy trade significantly influenced the contamination risk. Compared with a scenario with no inter-dairy trade, the risk that contaminated milk will reach the consumer was up to 4 times higher, even with moderate inter-dairy trade. The contamination risk depended on the extent of inter-dairy trade in a nonlinear way and reached its maximum asymptotically when inter-dairy trade increased. The contamination risk exhibited considerable spatial variation, which could be utilized to implement more accurate food control interventions in times of crisis caused by a foodborne disease.
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Affiliation(s)
- B Pinior
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Seestr. 55, 16868 Wusterhausen, Germany
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Elliott GN, Thomas N, Macrae M, Campbell CD, Ogden ID, Singh BK. Multiplex T-RFLP allows for increased target number and specificity: detection of Salmonella enterica and six species of Listeria in a single test. PLoS One 2012; 7:e43672. [PMID: 22937073 PMCID: PMC3427147 DOI: 10.1371/journal.pone.0043672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/24/2012] [Indexed: 01/14/2023] Open
Abstract
A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs) following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required.
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