1
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Fernandez-Tejero N, Sanchez AN, Ghemrawi M, Bilodeau C, Etim S, Duncan G, Cochran M, McCord B. A study of the potential application of digital PCR in the detection of fecal contamination of strawberries using Bacteroides markers. J Microbiol Methods 2023; 212:106811. [PMID: 37611849 DOI: 10.1016/j.mimet.2023.106811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Food-borne illnesses can result from contamination of agricultural products. In this study, we examined nanoplate digital PCR (dPCR) to test for fecal contamination of agricultural products. In nanoplate technique, the PCR mastermix is divided into 8.526,000 partitions, providing direct detection of individual DNA molecules, with correction by Poisson distribution. In this project, strawberries were inoculated with fecal material from animals, and the result detected by nanoplate digital PCR. A detection limit of 250 fg/uL was determined. Overall, dPCR offers a quick and sensitive method to detect contaminated produce.
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Affiliation(s)
- Nicole Fernandez-Tejero
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Alyssa N Sanchez
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Mirna Ghemrawi
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Catherine Bilodeau
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Dania Beach, FL 33004, United States of America
| | - Sylvia Etim
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - George Duncan
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Dania Beach, FL 33004, United States of America
| | - Matt Cochran
- Cross-Border Threat Screening and Supply Chain Defense, Texas A&M University System, Brazos, TX 77843, United States of America
| | - Bruce McCord
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, United States of America.
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2
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Wang B, Wang H, Lu X, Zheng X, Yang Z. Recent Advances in Electrochemical Biosensors for the Detection of Foodborne Pathogens: Current Perspective and Challenges. Foods 2023; 12:2795. [PMID: 37509887 PMCID: PMC10379338 DOI: 10.3390/foods12142795] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023] Open
Abstract
Foodborne pathogens cause many diseases and significantly impact human health and the economy. Foodborne pathogens mainly include Salmonella spp., Escherichia coli, Staphylococcus aureus, Shigella spp., Campylobacter spp. and Listeria monocytogenes, which are present in agricultural products, dairy products, animal-derived foods and the environment. Various pathogens in many different types of food and water can cause potentially life-threatening diseases and develop resistance to various types of antibiotics. The harm of foodborne pathogens is increasing, necessitating effective and efficient methods for early monitoring and detection. Traditional methods, such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA) and culture plate, are time-consuming, labour-intensive and expensive and cannot satisfy the demands of rapid food testing. Therefore, new fast detection methods are urgently needed. Electrochemical biosensors provide consumer-friendly methods to quickly detect foodborne pathogens in food and the environment and achieve extensive accuracy and reproducible results. In this paper, by focusing on various mechanisms of electrochemical transducers, we present a comprehensive overview of electrochemical biosensors for the detection of foodborne pathogens. Furthermore, the review introduces the hazards of foodborne pathogens, risk analysis methods and measures of control. Finally, the review also emphasizes the recent research progress and solutions regarding the use of electrochemical biosensors to detect foodborne pathogens in food and the environment, evaluates limitations and challenges experienced during the development of biosensors to detect foodborne pathogens and discusses future possibilities.
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Affiliation(s)
- Bo Wang
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China
| | - Hang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiangfeng Zheng
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China
| | - Zhenquan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China
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3
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Vishnuraj MR, Ajay G, Aravind Kumar N, Renuka J, Pollumahanti N, Anusha Chauhan H, Vaithiyanathan S, Rawool DB, Barbuddhe SB. Duplex real-time PCR assay with high-resolution melt analysis for the detection and quantification of Listeria species and Listeria monocytogenes in meat products. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:1541-1550. [PMID: 37033312 PMCID: PMC10076466 DOI: 10.1007/s13197-023-05695-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 01/30/2023] [Accepted: 02/12/2023] [Indexed: 03/05/2023]
Abstract
Listeria contamination in foods of animal origin is one of the most concerning food safety issues. A duplex, SYBR green-based, real-time PCR assay was developed with high-resolution melting analysis-based differentiation of the genus Listeria and Listeria monocytogenes. The primers were designed and tested against other related foodborne pathogens. The assay was optimized for standard parameters in a non-orthogonal fashion and validated following international standards. The LODabs and LOQ of the assay were calculated to be 0.78 and 1.56 ng of the target DNA. The LODrel of the assay was found to be 1% Listeria DNA in background DNA. The assay was evaluated for applicability in artificially spiked samples, providing a 120 CFU/ml detection. The assay was validated with proficiency test samples and also with samples collected for surveillance analysis. This well-established and validated assay can be utilized as a qualitative and quantitative tool for addressing the Listeria contamination in the food safety contexts. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05695-2.
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Affiliation(s)
- M. R. Vishnuraj
- ICAR - National Meat Research Institute, Chengicherla, Hyderabad, 500092 India
| | - G. Ajay
- ICAR - National Meat Research Institute, Chengicherla, Hyderabad, 500092 India
| | - N. Aravind Kumar
- ICAR - National Meat Research Institute, Chengicherla, Hyderabad, 500092 India
| | - J. Renuka
- ICAR - National Meat Research Institute, Chengicherla, Hyderabad, 500092 India
| | | | - H. Anusha Chauhan
- ICAR - National Meat Research Institute, Chengicherla, Hyderabad, 500092 India
| | - S. Vaithiyanathan
- ICAR - National Meat Research Institute, Chengicherla, Hyderabad, 500092 India
| | - Deepak B. Rawool
- ICAR - National Meat Research Institute, Chengicherla, Hyderabad, 500092 India
| | - S. B. Barbuddhe
- ICAR - National Meat Research Institute, Chengicherla, Hyderabad, 500092 India
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4
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Soto-Beltrá N M, Lee BG, Amézquita-López BA, Quiñones B. Overview of methodologies for the culturing, recovery and detection of Campylobacter. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023; 33:307-323. [PMID: 35168460 DOI: 10.1080/09603123.2022.2029366] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Campylobacter species are responsible for human gastroenteritis with diverse clinical spectra, ranging from acute watery or bloody diarrhea to life-threatening autoimmune disorders. Given the importance of Campylobacter in causing human illness, this article has reviewed the transmission and attribution sources as well as methodologies for the detection and virulence characterization of campylobacteria. The recovery and detection of Campylobacter from clinical, food and environmental samples has been achieved by the combinatorial use of selective enrichment and culturing methods. Biochemical, immunological, and nucleic acid-based methodologies have enabled the detection and differentiation of closely related Campylobacter isolates in foodborne outbreak investigations and have assessed the diversity and phylogenetic relationships of these bacterial pathogens. Analyses of motility, adherence, and invasiveness in host cells have assessed the pathogenic potential of campylobacteria. Further examination of determinants conferring antimicrobial resistance in Campylobacter have supported the growing need to closely monitor antimicrobials use in clinical and agricultural sectors.
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Affiliation(s)
- Marcela Soto-Beltrá N
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, México
| | - Bertram G Lee
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture/Agricultural Research Service,Western Regional Research Center, Albany, CA, USA
| | | | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture/Agricultural Research Service,Western Regional Research Center, Albany, CA, USA
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5
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Paramithiotis S. Molecular Targets for Foodborne Pathogenic Bacteria Detection. Pathogens 2023; 12:pathogens12010104. [PMID: 36678453 PMCID: PMC9865778 DOI: 10.3390/pathogens12010104] [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: 11/30/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The detection of foodborne pathogenic bacteria currently relies on their ability to grow on chemically defined liquid and solid media, which is the essence of the classical microbiological approach. Such procedures are time-consuming and the quality of the result is affected by the selectivity of the media employed. Several alternative strategies based on the detection of molecular markers have been proposed. These markers may be cell constituents, may reside on the cell envelope or may be specific metabolites. Each marker provides specific advantages and, at the same time, suffers from specific limitations. The food matrix and chemical composition, as well as the accompanying microbiota, may also severely compromise detection. The aim of the present review article is to present and critically discuss all available information regarding the molecular targets that have been employed as markers for the detection of foodborne pathogens. Their strengths and limitations, as well as the proposed alleviation strategies, are presented, with particular emphasis on their applicability in real food systems and the challenges that are yet to be effectively addressed.
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Affiliation(s)
- Spiros Paramithiotis
- Laboratory of Food Process Engineering, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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6
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Rapid identification and absolute quantitation of zero tolerance-Salmonella enterica subsp. enterica serovar Thompson using droplet digital polymerase chain reaction. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2022.114333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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Pang L, Pi X, Yang X, Song D, Qin X, Wang L, Man C, Zhang Y, Jiang Y. Nucleic acid amplification-based strategy to detect foodborne pathogens in milk: a review. Crit Rev Food Sci Nutr 2022; 64:5398-5413. [PMID: 36476145 DOI: 10.1080/10408398.2022.2154073] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Milk contaminated with trace amounts of foodborne pathogens can considerably threaten food safety and public health. Therefore, rapid and accurate detection techniques for foodborne pathogens in milk are essential. Nucleic acid amplification (NAA)-based strategies are widely used to detect foodborne pathogens in milk. This review article covers the mechanisms of the NAA-based detection of foodborne pathogens in milk, including polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), rolling circle amplification (RCA), and enzyme-free amplification, among others. Key factors affecting detection efficiency and the advantages and disadvantages of the above techniques are analyzed. Potential on-site detection tools based on NAA are outlined. We found that NAA-based strategies were effective in detecting foodborne pathogens in milk. Among them, PCR was the most reliable. LAMP showed high specificity, whereas RPA and RCA were most suitable for on-site and in-situ detection, respectively, and enzyme-free amplification was more economical. However, factors such as sample separation, nucleic acid target conversion, and signal transduction affected efficiency of NAA-based strategies. The lack of simple and effective sample separation methods to reduce the effect of milk matrices on detection efficiency was noteworthy. Further research should focus on simplifying, integrating, and miniaturizing microfluidic on-site detection platforms.
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Affiliation(s)
- Lidong Pang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xiaowen Pi
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Danliangmin Song
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xue Qin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Lihan Wang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yu Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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8
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Fang Z, Zhou X, Wang X, Shi X. Development of a 3-plex droplet digital PCR for identification and absolute quantification of Salmonella and its two important serovars in various food samples. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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9
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Daddy Gaoh S, Kweon O, Lee YJ, Hussong D, Marasa B, Ahn Y. A Propidium Monoazide (PMAxx)-Droplet Digital PCR (ddPCR) for the Detection of Viable Burkholderia cepacia Complex in Nuclease-Free Water and Antiseptics. Microorganisms 2022; 10:943. [PMID: 35630385 PMCID: PMC9147393 DOI: 10.3390/microorganisms10050943] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Pharmaceutical products contaminated with Burkholderia cepacia complex (BCC) strains constitute a serious health issue for susceptible individuals. New detection methods to distinguish DNA from viable cells are required to ensure pharmaceutical product quality and safety. In this study, we have assessed a droplet digital PCR (ddPCR) with a variant propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in autoclaved nuclease-free water after 365 days, in 0.001% chlorhexidine gluconate (CHX), and in 0.005% benzalkonium chloride (BZK) solutions after 184 days. Using 10 μM PMAxx and 5 min light exposure, a proportion of dead BCC was quantified by ddPCR. The detection limit of culture-based method was 104 CFU/mL, equivalent to 9.7 pg/μL for B. cenocepacia J2315, while that of ddPCR was 9.7 fg/μL. The true positive rate from nuclease-free water and CHX using PMAxx-ddPCR assay was 60.0% and 38.3%, respectively, compared to 85.0% and 74.6% without PMAxx (p < 0.05), respectively. However, in BZK-treated cells, no difference in the detection rate was observed between the ddPCR assay on samples treated with PMAxx (67.1%) and without PMAxx (63.3%). This study shows that the PMAxx-ddPCR assay provides a better tool for selective detection of live BCC cells in non-sterile pharmaceutical products.
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Affiliation(s)
- Soumana Daddy Gaoh
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| | - Yong-Jin Lee
- Department of Natural Sciences, Albany State University, Albany, GA 31705, USA;
| | - David Hussong
- Office of Pharmaceutical Science, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Beltsville, MD 20993, USA;
| | - Bernard Marasa
- Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA;
| | - Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
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10
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Effects of Lacidophilin Tablets, Yogurt, and Bifid Triple Viable Capsules on the Gut Microbiota of Mice with Antibiotic-Associated Diarrhea. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:6521793. [PMID: 35360462 PMCID: PMC8964159 DOI: 10.1155/2022/6521793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 02/08/2022] [Accepted: 02/23/2022] [Indexed: 12/14/2022]
Abstract
Antibiotic-associated diarrhea (AAD) is a common morbidity caused by antibiotic use and is characterized by the dysbiosis of the gut microbiota. Several clinical trials have shown that probiotics can prevent AAD. This study aimed at investigating the effects of Lacidophilin tablets (LB), yogurt (YG), and bifid triple viable capsules (BT) on the gut microbiota of mice with AAD. Mice with diarrhea were randomly allocated to treatment groups or the control group and were treated with either LB, YG, BT, or vehicle control. The body weight, diarrhea scores, cecum index, and cecal length were determined. Fecal samples of all mice were analyzed using 16S rRNA high-throughput sequencing. The results showed that LB, YG, and BT significantly decreased the diarrhea scores and inhibited increases in the cecum index and cecal length induced by AAD. In addition, they significantly changed the composition and richness of the gut microbiota. Specifically, they increased the abundance of the phylum Firmicutes and decreased the abundance of the phyla Bacteroidetes and the family Bacteroidaceae. Treatment with LB and YG also decreased the abundance of the phylum Proteobacteria and only LB could mediate the reduced levels of Lactobacillaceae in AAD mice. At the genus level, YG and BT treatment decreased the abundance of Bacteroides or Parasutterella. To our surprise, only LB treatment dramatically increased the abundance of Lactobacillus and decreased that of potential pathogens, such as Bacteroides, Parabacteroides, and Parasutterella, to almost normal values. Our findings indicate that LB, YG, and BT ameliorated diarrhea by regulating the composition and structure of the gut microbiota and that LB plays an important role in regulating the gut microbiota.
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11
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Basanisi MG, La Bella G, Nobili G, Raele DA, Cafiero MA, Coppola R, Damato AM, Fraccalvieri R, Sottili R, La Salandra G. Detection of Coxiella burnetii DNA in sheep and goat milk and dairy products by droplet digital PCR in south Italy. Int J Food Microbiol 2022; 366:109583. [PMID: 35182931 DOI: 10.1016/j.ijfoodmicro.2022.109583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
Abstract
Coxiella burnetii is a Gram-negative obligate intracellular bacterium that is responsible for Q fever, a common zoonosis which is present virtually worldwide. This microorganism infects a wide range of wild and domestic mammals, but the main reservoirs are cattle, goats and sheep, which also represent sources of human infection. A potential route of transmission of this pathogen to humans is the consumption of C. burnetii-contaminated raw milk or dairy products derived from contaminated raw milk, although the role of these foods as possible infection sources is controversial. The aims of this study were (i) to apply two ddPCR based assays targeting the C. burnetii IS1111 and icd genes for the detection and quantification of C. burnetii DNA, and (ii) to evaluate the occurrence of C. burnetii DNA in raw milk and raw milk products from sheep and goats in Apulia and Basilicata regions of Southern Italy. Of 413 milk and cheese samples tested, 78 were positive for the presence of C. burnetii DNA (18.9%), specifically, 68 of 285 milk samples (23.9%) and 10 of 128 cheese samples (7.8%) The presence of both IS1111 and icd genes was detected in only 2 (2.6%) of the 78 positive samples, while the remaining 76 (97.4%) were positive only for IS1111. C. burnetii DNA was specifically detected by the ddPCR method, whereas no cross-amplification was observed with the DNA of other foodborne bacterial pathogens. The sensitivity of the ddPCR method was determined as 0.35 and 0.56 copies/μL for IS1111 and icd genes, respectively. The findings of this study demonstrate the presence of C. burnetii DNA in a significant proportion of raw milk and dairy products. Although there is no conclusive epidemiological evidence that C. burnetii infection occurs via food, the presence of this organism in raw milk and dairy products made of raw milk should be considered a potential hazard. ddPCR is a useful tool to investigate the quality and safety of food products due to its sensitivity and precision, and could be applied to routine testing.
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Affiliation(s)
- Maria Grazia Basanisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy.
| | - Gianfranco La Bella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Gaia Nobili
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Donato Antonio Raele
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Maria Assunta Cafiero
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Rosa Coppola
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Annita Maria Damato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Rosa Fraccalvieri
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Roldano Sottili
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Giovanna La Salandra
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
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12
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Advances in improvement strategies of digital nucleic acid amplification for pathogen detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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13
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Chon JW, Jung JY, Ahn Y, Bae D, Khan S, Seo KH, Kim H, Sung K. Detection of Campylobacter jejuni from Fresh Produce: Comparison of Culture- and PCR-based Techniques, and Metagenomic Approach for Analyses of the Microbiome before and after Enrichment. J Food Prot 2021; 84:1704-1712. [PMID: 33878155 DOI: 10.4315/jfp-20-408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/14/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT In this study, we compared the efficiency of culture-based methods with or without membrane filtration, real-time PCR, and digital droplet PCR (ddPCR) for the detection of Campylobacter in fresh produce. Alfalfa sprouts, clover sprouts, coleslaw, and lettuce salad spiked with Campylobacter jejuni were enriched in Bolton broth for 48 h, and enrichment cultures were either directly inoculated onto modified charcoal-cefoperazone-deoxycholate agar or applied on membrane filters placed on the surface of plating media. In parallel, 2-mL Bolton broth cultures were taken to extract DNA for real-time PCR and ddPCR assays and bacterial community analysis. A developed primer set for ddPCR and real-time PCR was evaluated for its inclusivity and exclusivity using pure culture of C. jejuni and non-C. jejuni strains, respectively. In pure culture, the primer set reacted only with C. jejuni strains and showed negative reaction to non-C. jejuni strains. There was no significant difference (P > 0.05) in the detection efficiency of positive Campylobacter isolates from coleslaw and lettuce salad using four detection methods. However, for sprout samples, the detection efficiency of the culture method was significantly (P < 0.05) lower than those of the two PCR assays and the filtration method. The analysis also revealed the presence of Pseudomonas and Acinetobacter as the most prevalent competing microbiota in enriched culture and only Acinetobacter on agar plates in the selective culture step. HIGHLIGHTS
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Affiliation(s)
- Jung-Whan Chon
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Ji Young Jung
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Dongryeoul Bae
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Saeed Khan
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Kun-Ho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hyunsook Kim
- Department of Food & Nutrition, College of Human Ecology, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Kidon Sung
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
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14
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Cremonesi P, Garofalo C, Picozzi C, Castiglioni B, Mangieri N, Milanović V, Osimani A, Aquilanti L. Development of quantitative real-time PCR and digital droplet-PCR assays for rapid and early detection of the spoilage yeasts Saccharomycopsis fibuligera and Wickerhamomyces anomalus in bread. Food Microbiol 2021; 101:103894. [PMID: 34579854 DOI: 10.1016/j.fm.2021.103894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 11/26/2022]
Abstract
In the present study, for the first time, high sensitive quantitative polymerase chain reaction (qPCR) and digital droplet polymerase chain reaction (ddPCR) assays were developed to detect and quantify total eumycetes with potential application in several food matrices and to specifically determine the level of contamination by Saccharomycopsis fibuligera and Wickerhamomyces anomalus cells directly in bread. Among the candidate target genes used to develop the assays, car1 gene was chosen to detect the two spoilage yeasts S. fibuligera and W. anomalus. The specificity of the PCR assays was tested using purified genomic DNA from 36 bacterial and fungal strains. The sensitivity of the assays was defined by using tenfold serial dilutions of genomic DNA starting from 106 cfu/mL to 1 cfu/mL of S. fibuligera and W. anomalus. Validation of the assays was achieved by enumeration of S. fibuligera and W. anomalus DNA copies from samples of artificially contaminated bread homogenates detecting up to 10 cfu/mL (0.06 ± 0.01 copies/μL) of W. anomalus by using ddPCR. In conclusion, the developed qPCR and ddPCR assays demonstrate strong performance in the early detection of S. fibuligera and W. anomalus in bread, representing promising tools for applying high-throughput approaches to regularly monitor bread quality.
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Affiliation(s)
- Paola Cremonesi
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Consiglio Nazionale delle Ricerche, Via Einstein S/n, 26900, Lodi, Italy
| | - Cristiana Garofalo
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Claudia Picozzi
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Sezione di Microbiologia degli Alimenti e Bioprocessi, Via Celoria 2, 20133, Milano, Italy.
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Consiglio Nazionale delle Ricerche, Via Einstein S/n, 26900, Lodi, Italy
| | - Nicola Mangieri
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Sezione di Microbiologia degli Alimenti e Bioprocessi, Via Celoria 2, 20133, Milano, Italy
| | - Vesna Milanović
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Lucia Aquilanti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
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15
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Cui X, Abd El-Aty AM, Zhang C, Xu L, Liu H, Jia H, Wang Y, Cao Z, Salvador JP, She Y, Jin F, Wang J, Jin M, Hammock BD. Enhanced Bio-Barcode Immunoassay Using Droplet Digital PCR for Multiplex Detection of Organophosphate Pesticides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11131-11141. [PMID: 34494438 DOI: 10.1021/acs.jafc.1c03216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A bio-barcode immunoassay based on droplet digital polymerase chain reaction (ddPCR) was developed to simultaneously quantify triazophos, parathion, and chlorpyrifos in apple, cucumber, cabbage, and pear. Three gold nanoparticle (AuNP) probes and magnetic nanoparticle (MNP) probes were prepared, binding through their antibodies with the three pesticides in the same tube. Three groups of primers, probes, templates, and three antibodies were designed to ensure the specificity of the method. Under the optimal conditions, the detection limits (expressed as IC10) of triazophos, parathion, and chlorpyrifos were 0.22, 0.45, and 4.49 ng mL-1, respectively. The linear ranges were 0.01-20, 0.1-100, and 0.1-500 ng mL-1, and the correlation coefficients (R2) were 0.9661, 0.9834, and 0.9612, respectively. The recoveries and relative standard deviations (RSDs) were in the ranges of 75.5-98.9 and 8.3-16.7%. This study provides the first insights into the ddPCR for the determination of organophosphate pesticides. It also laid the foundation for high-throughput detection of other small molecules.
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Affiliation(s)
- Xueyan Cui
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - A M Abd El-Aty
- State Key Laboratory of Biobased Material and Green Papermaking, College of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, P. R. China
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum 25240, Turkey
| | - Chan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Lingyuan Xu
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Haijin Liu
- Inspection and Testing Center of Agricultural and Livestock Products of Tibet, Lhasa 850000, P. R. China
| | - Huiyan Jia
- Ningbo Academy of Agricultural Sciences, Ningbo 315040, Zhengjiang, P. R. China
| | - Yuanshang Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Zhen Cao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - J-Pablo Salvador
- Nanobiotechnology for Diagnostics Group, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, C/ Jordi Girona, 18-26, 08034 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Avenida Monforte de Lemos, 3-5, Pavillion 11, Floor 0, 28029 Madrid, Spain
| | - Yongxin She
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Fen Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Maojun Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Bruce D Hammock
- Department of Entomology & Nematology and the UC Davis Comprehensive Cancer Center, University of California, Davis, Davis, California 95616, United States
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16
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Development and validation of a method for quantification of common wheat, durum wheat, rye and barley by droplet digital PCR. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03786-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractFood fraud is becoming a prominent topic in the food industry. Thus, valid methods for detecting potential adulterations are necessary to identify instances of food fraud in cereal products, a significant component of human diet. In this work, primer–probe systems for real-time PCR and droplet digital PCR (ddPCR) for the detection of these cereal species: bread wheat (together with spelt), durum wheat, rye and barley for real-time PCR and ddPCR were established, optimized and validated. In addition, it was projected to validate a molecular system for differentiation of bread wheat and spelt; however, attempts for molecular differentiation between common wheat and spelt based on the gene GAG56D failed because of the genetic variability of the molecular target. Primer–probe systems were further developed and optimized on the basis of alignments of DNA sequences, as well as already developed PCR systems. The specificity of each system was demonstrated on 10 (spelt), 11 (durum wheat and rye) and 12 (bread wheat) reference samples. Specificity of the barley system was already proved in previous work. The calculated limits of detection (LOD95%) were between 2.43 and 4.07 single genome copies in real-time PCR. Based on the “three droplet rule”, the LOD95% in ddPCR was calculated to be 9.07–13.26 single genome copies. The systems were tested in mixtures of flours (rye and common wheat) and of semolina (durum and common wheat). The methods proved to be robust with regard to the tested conditions in the ddPCR. The developed primer–probe systems for ddPCR proved to be effective in quantitatively detecting the investigated cereal species rye and common wheat in mixtures by taking into account the haploid genome weight and the degree of milling of a flour. This method can correctly detect proportions of 50%, 60% and 90% wholemeal rye flour in a mixture of wholemeal common wheat flour. Quantitative results depend on the DNA content, on ploidy of cereal species and are also influenced by comminution. Hence, the proportion of less processed rye is overestimated in higher processed bread wheat and adulteration of durum wheat by common wheat by 1–5% resulted in underestimation of common wheat.
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17
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Ma T, Shen L, Wen Q, Lv R, Hou Q, Kwok LY, Sun Z, Zhang H. PacBio sequencing revealed variation in the microbiota diversity, species richness and composition between milk collected from healthy and mastitis cows. MICROBIOLOGY-SGM 2021; 167. [PMID: 34292863 DOI: 10.1099/mic.0.000968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mastitis is the economically most important disease of dairy cows. This study used PacBio single-molecule real-time sequencing technology to sequence the full-length 16S rRNAs from 27 milk samples (18 from mastitis and nine from healthy cows; the cows were at different stages of lactation). We observed that healthy or late stage milk microbiota had significantly higher microbial diversity and richness. The community composition of the microbiota of different groups also varied greatly. The healthy cow milk microbiota was predominantly comprised of Lactococcus lactis, Acinetobacter johnsonii, and Bacteroides dorei, while the milk from mastitis cows was predominantly comprised of Bacillus cereus. The prevalence of L. lactis and B. cereus in the milk samples was confirmed by digital droplets PCR. Differences in the milk microbiota diversity and composition could suggest an important role for some these microbes in protecting the host from mastitis while others associated with mastitis. The results of our research serve as useful references for designing strategies to prevent and treat mastitis.
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Affiliation(s)
- Teng Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Lingling Shen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Qiannan Wen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Ruirui Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Lai Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
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18
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Cristiano D, Peruzy MF, Aponte M, Mancusi A, Proroga YTR, Capuano F, Murru N. Comparison of droplet digital PCR vs real-time PCR for Yersinia enterocolitica detection in vegetables. Int J Food Microbiol 2021; 354:109321. [PMID: 34225034 DOI: 10.1016/j.ijfoodmicro.2021.109321] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
Yersiniosis - the 4th most commonly reported zoonosis in the European Union - is caused by the consumption of food contaminated with the bacterium Yersinia enterocolitica. The number of human cases and contaminated food samples is probably underestimated since conventional molecular methods currently proposed for Yersinia enterocolitica detection proved to have several limitations. Critical issues associated with the detection of Yersinia enterocolitica in meat and/or meat product has already been investigated, whereas data on the possible limits of the molecular methods for Yersinia enterocolitica detection in vegetables are still lacking. According to ISO method (ISO 18867:2015), real-time polymerase chain reaction (rtPCR) should be adopted for Yersinia enterocolitica detection, even if it proved to be affected by some biases. Recently, Droplet Digital PCR (ddPCR) has been introduced as a useful tool to detect and quantify different pathogenic bacteria in complex food matrices. However, its potential application for Yersinia enterocolitica detection in vegetables has never been investigated before. In the present study two molecular platforms (rtPCR and ddPCR) were used to evaluate the pathogen's behaviour in experimentally contaminated leafy greens (Lactuca sativa L.) and to assess the rate of detection achievable after the incubation for eleven days at different temperatures. By comparing, noticeable differences emerged between the two technical approaches: only ddPCR allowed the detection of the pathogen in leafy greens when contaminated at low levels. Moreover, results of the present work highlighted the importance of length and temperature of incubation on the survival and/or the growth of Yersinia enterocolitica in vegetables: at 18 and 25 °C the concentration of the pathogen considerably decreases along incubation. Based on data, the use of rtPCR leads to an underestimation of the true prevalence of pathogenic Y. enterocolitica in vegetables, while temperature and time currently proposed for Y. enterocolitica (25 °C for 24 h), allow optimizing detection. To conclude, ddPCR may be undoubtedly proposed as a reliable alternative strategy for the quick detection of the pathogen in food samples.
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Affiliation(s)
- D Cristiano
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 8055 Portici, NA, Italy
| | - M F Peruzy
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Via Delpino 1, 80137 Napoli, Italy.
| | - M Aponte
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, Portici, NA, Italy
| | - A Mancusi
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 8055 Portici, NA, Italy
| | - Y T R Proroga
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 8055 Portici, NA, Italy
| | - F Capuano
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 8055 Portici, NA, Italy
| | - N Murru
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Via Delpino 1, 80137 Napoli, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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19
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Rapid and absolute quantification of VBNC Cronobacter sakazakii by PMAxx combined with single intact cell droplet digital PCR in infant foods. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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20
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Moniente M, García‐Gonzalo D, Ontañón I, Pagán R, Botello‐Morte L. Histamine accumulation in dairy products: Microbial causes, techniques for the detection of histamine‐producing microbiota, and potential solutions. Compr Rev Food Sci Food Saf 2021; 20:1481-1523. [DOI: 10.1111/1541-4337.12704] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Marta Moniente
- Departamento de Producción Animal y Ciencia de los Alimentos Facultad de Veterinaria, Instituto Agroalimentario de Aragón‐IA2 (Universidad de Zaragoza‐CITA) Zaragoza Spain
| | - Diego García‐Gonzalo
- Departamento de Producción Animal y Ciencia de los Alimentos Facultad de Veterinaria, Instituto Agroalimentario de Aragón‐IA2 (Universidad de Zaragoza‐CITA) Zaragoza Spain
| | - Ignacio Ontañón
- Laboratorio de Análisis del Aroma y Enología, Química Analítica Facultad de Ciencias, Instituto Agroalimentario de Aragón‐IA2 (Universidad de Zaragoza‐CITA) Zaragoza Spain
| | - Rafael Pagán
- Departamento de Producción Animal y Ciencia de los Alimentos Facultad de Veterinaria, Instituto Agroalimentario de Aragón‐IA2 (Universidad de Zaragoza‐CITA) Zaragoza Spain
| | - Laura Botello‐Morte
- Departamento de Producción Animal y Ciencia de los Alimentos Facultad de Veterinaria, Instituto Agroalimentario de Aragón‐IA2 (Universidad de Zaragoza‐CITA) Zaragoza Spain
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21
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Lei S, Gu X, Zhong Q, Duan L, Zhou A. Absolute quantification of Vibrio parahaemolyticus by multiplex droplet digital PCR for simultaneous detection of tlh, tdh and ureR based on single intact cell. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107207] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Rapid and sensitive detection of Salmonella spp. in raw minced meat samples using droplet digital PCR. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03531-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Iacumin L, Cecchini F, Vendrame M, Comi G. Emulsion PCR (ePCR) as a Tool to Improve the Power of DGGE Analysis for Microbial Population Studies. Microorganisms 2020; 8:microorganisms8081099. [PMID: 32717823 PMCID: PMC7465085 DOI: 10.3390/microorganisms8081099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/26/2022] Open
Abstract
To the authors’ knowledge, this is the first report of the use of emulsion-Polymerase chain reaction (e-PCR) coupled with denaturing gradient gel electrophoresis (DGGE) analysis. In the present work the effectiveness of ePCR in improving the power of the DGGE technique for microbial population studies was tested. Our results indicated that ePCR results in uniform amplification of several DNA molecules, overcoming the major limitations of conventional PCR, such as preferential amplification and DNA concentration dependence. Moreover, ePCR-DGGE resulted in higher sensitivity when compared to conventional PCR-DGGE methods used for studying microbial populations in a complex matrix. In fact, compared to conventional PCR, the DGGE profiles of ePCR products permitted the detection of a higher number of the species that were present in the tested sample.
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24
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Quantitative detection of viable but nonculturable state Escherichia coli O157:H7 by ddPCR combined with propidium monoazide. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107140] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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25
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Grudlewska-Buda K, Skowron K, Gospodarek-Komkowska E. Comparison of the intensity of biofilm formation by Listeria monocytogenes using classical culture-based method and digital droplet PCR. AMB Express 2020; 10:75. [PMID: 32303851 PMCID: PMC7165217 DOI: 10.1186/s13568-020-01007-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/07/2020] [Indexed: 12/27/2022] Open
Abstract
Listeria monocytogenes is a Gram-positive bacterium, commonly found in food, water or sewage. This microorganism is capable of forming biofilm on different surfaces such as steel, glass, polypropylene etc. Recently an increase in cases of listeriosis has been noted, making L. monocytogenes the important health threat. Therefore, there is a need for rapid and sensitive detection of this pathogen. This study aimed to compare the number of L. monocytogenes cells recovered from the biofilm (prepared on steel and polypropylene) using the detection and amplification of the hlyA gene (droplet digital PCR, ddPCR) and the classical culture method. The research material consisted of 96 L. monocytogenes strains. A total of 58 isolates were obtained from clinical samples and 38 isolates derived from the municipal sewage treatment plant. Additionally, the reference strain ATCC®19111™ (WDCM00020) was used. The Pearson correlation coefficient for the results obtained by the classical culture-based method and ddPCR was 0.864 and 0.725, for biofilms produced on AISI 304 stainless steel surface and the polypropylene surface, respectively. Correlations were statistically significant (p ≤ 0.001), indicating that the ddPCR technique is an effective tool for the assessment of bacteria number in the biofilm.
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Affiliation(s)
- Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, Bydgoszcz, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, Bydgoszcz, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, Bydgoszcz, Poland
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26
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Salipante SJ, Jerome KR. Digital PCR—An Emerging Technology with Broad Applications in Microbiology. Clin Chem 2019; 66:117-123. [DOI: 10.1373/clinchem.2019.304048] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Abstract
BACKGROUND
The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.
CONTENT
Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.
SUMMARY
dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.
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Affiliation(s)
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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27
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Kitamura R, Miura N, Okada K, Motone K, Takagi T, Ueda M, Kataoka M. Design of novel primer sets for easy detection of Ruegeria species from seawater. Biosci Biotechnol Biochem 2019; 84:854-864. [PMID: 31814534 DOI: 10.1080/09168451.2019.1700776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Some coral-associated bacteria show protective roles for corals against pathogens. However, the distribution of coral-protecting bacteria in seawater is not well known. In addition, compared with the methods for investigating coral pathogens, few methods have been developed to detect coral-protecting bacteria. Here we prepared a simple method for detecting Ruegeria spp., some strains of which inhibit growth of the coral pathogen Vibrio coralliilyticus. We successfully obtained two Ruegeria-targeting primer sets through in silico and in vitro screening. The primer sets r38F-r30R and r445F-r446R, in addition to the newly designed universal primer set U357'F-U515'R, were evaluated in vitro using environmental DNA extracted from seawater collected in Osaka. These methods and primers should contribute to revealing the distribution of Ruegeria spp. in marine environments.
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Affiliation(s)
- Ruriko Kitamura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Natsuko Miura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Keiko Okada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Keisuke Motone
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.,Japan Society for the Promotion of Science, Kyoto, Japan
| | - Toshiyuki Takagi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Mitsuyoshi Ueda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Michihiko Kataoka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
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28
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Barone V, Bertoldo G, Magro F, Broccanello C, Puglisi I, Baglieri A, Cagnin M, Concheri G, Squartini A, Pizzeghello D, Nardi S, Stevanato P. Molecular and Morphological Changes Induced by Leonardite-based Biostimulant in Beta vulgaris L. PLANTS 2019; 8:plants8060181. [PMID: 31216763 PMCID: PMC6630732 DOI: 10.3390/plants8060181] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 11/16/2022]
Abstract
Humic substances extracted from leonardite are widely considered to be bioactive compounds, influencing the whole-plant physiology and the crop yield. The aim of this work was to evaluate the effect of a new formulate based on leonardite in the early stage of growth of sugar beet (Beta vulgaris L.). A commercial preparation of leonardite (BLACKJAK) was characterized by ionomic analysis, solid-state 13C MAS NMR spectroscopy. Seedlings of sugar beet were grown in Hoagland's solution under controlled conditions. After five days of growth, an aliquot of the concentrated BLACKJAK was added to the solution to obtain a final dilution of 1:1000 (0.5 mg C L-1). The sugar beet response in the early stage of growth was determined by evaluating root morphological traits as well as the changes in the expression of 53 genes related to key morphophysiological processes. Root morphological traits, such as total root length, fine root length (average diameter < 0.5 mm), and number of root tips, were significantly (p < 0.001) increased in plants treated with BLACKJAK, compared to the untreated plants at all sampling times. At the molecular level, BLACKJAK treatment upregulated many of the evaluated genes. Moreover, both Real Time PCR and digital PCR showed that genes involved in hormonal response, such as PIN, ARF3, LOGL 10, GID1, and BRI1, were significantly (p < 0.05) upregulated by treatment with BLACKJAK. Our study provides essential information to understand the effect of a leonardite-based formulate on plant growth hormone metabolism, although the molecular and physiological basis for these complicated regulatory mechanisms deserve further investigations.
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Affiliation(s)
- Valeria Barone
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Giovanni Bertoldo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | | | - Chiara Broccanello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Ivana Puglisi
- Department of Agriculture, Food and Environment, University of Catania, Via S. Sofia 98, 95123 Catania, Italy.
| | - Andrea Baglieri
- Department of Agriculture, Food and Environment, University of Catania, Via S. Sofia 98, 95123 Catania, Italy.
| | - Massimo Cagnin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Diego Pizzeghello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Serenella Nardi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
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Shin DJ, Andini N, Hsieh K, Yang S, Wang TH. Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:41-67. [PMID: 30939033 PMCID: PMC7369001 DOI: 10.1146/annurev-anchem-061318-115529] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.
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Affiliation(s)
- Dong Jin Shin
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Nadya Andini
- Department of Emergency Medicine, Stanford University, Stanford, California 94305, USA;
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, California 94305, USA;
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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Ramírez JD, Herrera G, Hernández C, Cruz-Saavedra L, Muñoz M, Flórez C, Butcher R. Evaluation of the analytical and diagnostic performance of a digital droplet polymerase chain reaction (ddPCR) assay to detect Trypanosoma cruzi DNA in blood samples. PLoS Negl Trop Dis 2018; 12:e0007063. [PMID: 30586355 PMCID: PMC6324824 DOI: 10.1371/journal.pntd.0007063] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/08/2019] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The recent development of novel Polymerase Chain Reaction (PCR) technologies that confer theoretical advantages over quantitative PCR has considerable potential in the diagnosis of low load infections, such as Trypanosoma cruzi in the chronic phase of Chagas disease. We evaluated the utility of the digital droplet (dd)PCR platform in the detection of T. cruzi infection. METHODOLOGY/PRINCIPAL FINDINGS We imported a validated qPCR assay targeting the T. cruzi satellite tandem repeat (TcSTR) region to the ddPCR platform. Following optimization, we tested and repeated a standard curve of TcI epimastigotes to characterise the analytical performance of the assay on the ddPCR platform. We compared this to published qPCR performance data, and the performance of the qPCR assay in our own testing. We subsequently tested a panel of 192 previously characterized DNA specimens, extracted from the blood of individuals with and without T. cruzi infection. The assay performed well on the ddPCR platform, showing a limit of detection of 5 copies/μL or 1 parasite/mL. This was higher than the published limit of detection for qPCR, which was 0.46 parasites/mL. The ddPCR platform was not significantly more accurate than qPCR at any concentration tested. However, the clinical sensitivity and specificity of the assay were both 100% with perfect agreement between qPCR and ddPCR positive and negative result calling in clinical specimens. An average of 9,286 copies of TcSTR were detected per parasite. CONCLUSIONS/SIGNIFICANCE The use of the ddPCR platform to run this assay was comparable, but not superior in terms of performance, to the qPCR platform.
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Affiliation(s)
- Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Giovanny Herrera
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Hernández
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Flórez
- Grupo de Parasitología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Robert Butcher
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Agrimonti C, Bottari B, Sardaro MLS, Marmiroli N. Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products. Crit Rev Food Sci Nutr 2017; 59:423-442. [DOI: 10.1080/10408398.2017.1375893] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Caterina Agrimonti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Benedetta Bottari
- Department of Food and Drug Science, University of Parma, Parma, Italy
| | - Maria Luisa Savo Sardaro
- Department of Food and Drug Science, University of Parma, Parma, Italy; Department of Nutrition and Gastronomy, University San Raffaele Roma Srl, Rome, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Papić B, Pate M, Henigman U, Zajc U, Gruntar I, Biasizzo M, Ocepek M, Kušar D. New Approaches on Quantification of Campylobacter jejuni in Poultry Samples: The Use of Digital PCR and Real-time PCR against the ISO Standard Plate Count Method. Front Microbiol 2017; 8:331. [PMID: 28303130 PMCID: PMC5332403 DOI: 10.3389/fmicb.2017.00331] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/17/2017] [Indexed: 11/13/2022] Open
Abstract
Campylobacteriosis is the most frequently reported bacterial food-borne illness in the European Union and contaminated broiler meat is considered the most important source of infection in humans. The aim of the present study was to evaluate real-time PCR (qPCR) and digital PCR (dPCR) for quantification of Campylobacter jejuni in 75 broiler neck-skin samples collected from a poultry slaughterhouse, and to compare them with the ISO 10272-2 standard plate count method. For qPCR standard curve, C. jejuni-negative neck-skin samples were spiked with C. jejuni suspension with a known number of bacterial cells. The observed CFU/g values by qPCR correlated greatly with the expected values and qPCR showed good performance with the reliable limit of detection (rLOD) and limit of quantification (LOQ) of three and 31 target copies per reaction, respectively. However, both rLOD (1219 CFU/g) and LOQ (12,523 CFU/g) were beyond the EFSA-proposed critical limit of 500-1,000 CFU/g of neck skin. Although C. jejuni cell counts were ≤1,000 CFU/g in only 7/75 samples by plate counting, they were ≤LOQ in 60/75 and ≤rLOD in 26/75 (≤1,000 CFU/g in 24/75) samples by qPCR. A strong and statistically significant correlation was observed between qPCR and dPCR. Both PCR-based methods correlated significantly with the plate count method; however, the correlation was moderate. Using the Bland-Altman analysis, an average agreement was noted between all three methods, although with a large standard deviation. A significant bias toward overestimation in dPCR was observed, probably due to the relatively high number of false positive calls. The linear dynamic range was comparable in both PCR-based methods; however, qPCR proved to be more suitable for routine use. In the future, the establishment of a reliable molecular quantification of C. jejuni in poultry samples showing a wide range of contamination levels down to the proposed critical limit is needed to enable time- and cost-effective surveillance throughout all stages in the food production chain. As both rLOD and LOQ were beyond this limit, a modification of the procedure is suggested to include less sample dilution prior to DNA extraction to enable PCR-based quantification of C. jejuni at the proposed microbiological criteria.
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Affiliation(s)
- Bojan Papić
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Mateja Pate
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Urška Henigman
- Veterinary Faculty, Institute of Food Safety, Feed and Environment, University of LjubljanaLjubljana, Slovenia
| | - Urška Zajc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Igor Gruntar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Majda Biasizzo
- Veterinary Faculty, Institute of Food Safety, Feed and Environment, University of LjubljanaLjubljana, Slovenia
| | - Matjaž Ocepek
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Darja Kušar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
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