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Patnaik A, Rai SK, Dhaked RK. CRISPR-Cas12a assisted recombinase based strand invading isothermal amplification platform designed for targeted detection of Bacillus anthracis Sterne. Int J Biol Macromol 2024; 263:130216. [PMID: 38378112 DOI: 10.1016/j.ijbiomac.2024.130216] [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: 12/29/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Detection of a pathogen is crucial prior to all prophylaxis and post exposure treatment, as it can prevent further disease manifestation. In this study, we have developed a nucleic acid pre-amplification based CRISPR diagnostic for detection and surveillance of Bacillus anthracis Sterne. Strand Invasion Based isothermal Amplification (SIBA) platform and Cas12a (CRISPR endo-nuclease) was used to develop CRISPR-SIBA, a multifaceted diagnostic platform. SIBA was employed as the isothermal pre-amplification platform. CRISPR-Cas12a based collateral trans-cleavage reaction was used to ensure and enhance the specificity of the system. Efficiency of the detection system was evaluated by detecting Bacillus anthracis Sterne in complex wastewater sample backgrounds. Previously reported, Prophage 3, Cya and Pag genes of Bacillus anthracis were used as targets for this assay. The amplification system provided reliable and specific detection readout, with a sensitivity limit of 100 colony forming units in 40 min. The endpoint fluorescence from CRISPR collateral cleavage reactions gave a detection limit of 105 to 106 CFUs. The experiments conducted in this study provide the evidence for SIBA's applicability and compatibility with CRISPR-Cas system and its efficiency to specifically detect Bacillus anthracis Sterne. CRISPR-SIBA can be translated into developing cost-effective diagnostics for pathogens in resource constrained settings.
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Affiliation(s)
- Abhinandan Patnaik
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Sharad Kumar Rai
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Ram Kumar Dhaked
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India.
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Bhardwaj N, Bhardwaj SK, Bhatt D, Lim DK, Kim KH, Deep A. Optical detection of waterborne pathogens using nanomaterials. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.02.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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3
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Vidic J, Vizzini P, Manzano M, Kavanaugh D, Ramarao N, Zivkovic M, Radonic V, Knezevic N, Giouroudi I, Gadjanski I. Point-of-Need DNA Testing for Detection of Foodborne Pathogenic Bacteria. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1100. [PMID: 30836707 PMCID: PMC6427207 DOI: 10.3390/s19051100] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/18/2022]
Abstract
Foodborne pathogenic bacteria present a crucial food safety issue. Conventional diagnostic methods are time-consuming and can be only performed on previously produced food. The advancing field of point-of-need diagnostic devices integrating molecular methods, biosensors, microfluidics, and nanomaterials offers new avenues for swift, low-cost detection of pathogens with high sensitivity and specificity. These analyses and screening of food items can be performed during all phases of production. This review presents major developments achieved in recent years in point-of-need diagnostics in land-based sector and sheds light on current challenges in achieving wider acceptance of portable devices in the food industry. Particular emphasis is placed on methods for testing nucleic acids, protocols for portable nucleic acid extraction and amplification, as well as on the means for low-cost detection and read-out signal amplification.
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Affiliation(s)
- Jasmina Vidic
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Priya Vizzini
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Devon Kavanaugh
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nalini Ramarao
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Milica Zivkovic
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, 11000 Belgrade, Serbia.
| | - Vasa Radonic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Nikola Knezevic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ioanna Giouroudi
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ivana Gadjanski
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Comparative analysis of the sensitivity of metagenomic sequencing and PCR to detect a biowarfare simulant (Bacillus atrophaeus) in soil samples. PLoS One 2017; 12:e0177112. [PMID: 28472119 PMCID: PMC5417559 DOI: 10.1371/journal.pone.0177112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 04/21/2017] [Indexed: 11/19/2022] Open
Abstract
To evaluate the sensitivity of high-throughput DNA sequencing for monitoring biowarfare agents in the environment, we analysed soil samples inoculated with different amounts of Bacillus atrophaeus, a surrogate organism for Bacillus anthracis. The soil samples considered were a poorly carbonated soil of the silty sand class, and a highly carbonated soil of the silt class. Control soil samples and soil samples inoculated with 10, 103, or 105 cfu were processed for DNA extraction. About 1% of the DNA extracts was analysed through the sequencing of more than 108 reads. Similar amounts of extracts were also studied for Bacillus atrophaeus DNA content by real-time PCR. We demonstrate that, for both soils, high-throughput sequencing is at least equally sensitive than real-time PCR to detect Bacillus atrophaeus DNA. We conclude that metagenomics allows the detection of less than 10 ppm of DNA from a biowarfare simulant in complex environmental samples.
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Amoako KK, Thomas MC, Janzen TW, Goji N. Rapid SNP Detection and Genotyping of Bacterial Pathogens by Pyrosequencing. Methods Mol Biol 2017; 1492:203-220. [PMID: 27822867 DOI: 10.1007/978-1-4939-6442-0_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bacterial identification and typing are fixtures of microbiology laboratories and are vital aspects of our response mechanisms in the event of foodborne outbreaks and bioterrorist events. Whole genome sequencing (WGS) is leading the way in terms of expanding our ability to identify and characterize bacteria through the identification of subtle differences between genomes (e.g. single nucleotide polymorphisms (SNPs) and insertions/deletions). Modern high-throughput technologies such as pyrosequencing can facilitate the typing of bacteria by generating short-read sequence data of informative regions identified by WGS analyses, at a fraction of the cost of WGS. Thus, pyrosequencing systems remain a valuable asset in the laboratory today. Presented in this chapter are two methods developed in the Amoako laboratory that detail the identification and genotyping of bacterial pathogens. The first targets canonical single nucleotide polymorphisms (canSNPs) of evolutionary importance in Bacillus anthracis, the causative agent of Anthrax. The second assay detects Shiga-toxin (stx) genes, which are associated with virulence in Escherichia coli and Shigella spp., and differentiates the subtypes of stx-1 and stx-2 based on SNP loci. These rapid methods provide end users with important information regarding virulence traits as well as the evolutionary and biogeographic origin of isolates.
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Affiliation(s)
- Kingsley K Amoako
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, 640, Township Road 9-1, Lethbridge, AB, Canada, T1J 3Z4.
| | - Matthew C Thomas
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, 640, Township Road 9-1, Lethbridge, AB, Canada, T1J 3Z4
| | - Timothy W Janzen
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, 640, Township Road 9-1, Lethbridge, AB, Canada, T1J 3Z4
| | - Noriko Goji
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, 640, Township Road 9-1, Lethbridge, AB, Canada, T1J 3Z4
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7
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Waller DF, Hew BE, Holdaway C, Jen M, Peckham GD. Rapid Detection of Bacillus anthracis Spores Using Immunomagnetic Separation and Amperometry. BIOSENSORS-BASEL 2016; 6:bios6040061. [PMID: 27999382 PMCID: PMC5192381 DOI: 10.3390/bios6040061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/09/2016] [Accepted: 12/14/2016] [Indexed: 01/04/2023]
Abstract
Portable detection and quantitation methods for Bacillus anthracis (anthrax) spores in pure culture or in environmental samples are lacking. Here, an amperometric immunoassay has been developed utilizing immunomagnetic separation to capture the spores and remove potential interferents from test samples followed by amperometric measurement on a field-portable instrument. Antibody-conjugated magnetic beads and antibody-conjugated glucose oxidase were used in a sandwich format for the capture and detection of target spores. Glucose oxidase activity of spore pellets was measured indirectly via amperometry by applying a bias voltage after incubation with glucose, horseradish peroxidase, and the electron mediator 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid). Target capture was mediated by polyclonal antisera, whereas monoclonal antibodies were used for signal generation. This strategy maximized sensitivity (500 target spores, 5000 cfu/mL), while also providing a good specificity for Bacillus anthracis spores. Minimal signal deviation occurs in the presence of environmental interferents including soil and modified pH conditions, demonstrating the strengths of immunomagnetic separation. The simultaneous incubation of capture and detection antibodies and rapid substrate development (5 min) result in short sample-to-signal times (less than an hour). With attributes comparable or exceeding that of ELISA and LFDs, amperometry is a low-cost, low-weight, and practical method for detecting anthrax spores in the field.
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Affiliation(s)
- David F Waller
- Black Ivory Biotech, Inc., P.O. Box 893128, Mililani, HI 96789, USA.
| | - Brian E Hew
- Black Ivory Biotech, Inc., P.O. Box 893128, Mililani, HI 96789, USA.
| | - Charlie Holdaway
- Holatron Systems, LLC., 833 Ilaniwai Street, Suite 2, Honolulu, HI 96813, USA.
| | - Michael Jen
- Mike Jen Software Services, 1035 Aster Ave #2103, Sunnyvale, CA 94086, USA.
| | - Gabriel D Peckham
- Black Ivory Biotech, Inc., P.O. Box 893128, Mililani, HI 96789, USA.
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Deshmukh RA, Joshi K, Bhand S, Roy U. Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview. Microbiologyopen 2016; 5:901-922. [PMID: 27397728 PMCID: PMC5221461 DOI: 10.1002/mbo3.383] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/20/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022] Open
Abstract
Waterborne diseases have emerged as global health problems and their rapid and sensitive detection in environmental water samples is of great importance. Bacterial identification and enumeration in water samples is significant as it helps to maintain safe drinking water for public consumption. Culture‐based methods are laborious, time‐consuming, and yield false‐positive results, whereas viable but nonculturable (VBNCs) microorganisms cannot be recovered. Hence, numerous methods have been developed for rapid detection and quantification of waterborne pathogenic bacteria in water. These rapid methods can be classified into nucleic acid‐based, immunology‐based, and biosensor‐based detection methods. This review summarizes the principle and current state of rapid methods for the monitoring and detection of waterborne bacterial pathogens. Rapid methods outlined are polymerase chain reaction (PCR), digital droplet PCR, real‐time PCR, multiplex PCR, DNA microarray, Next‐generation sequencing (pyrosequencing, Illumina technology and genomics), and fluorescence in situ hybridization that are categorized as nucleic acid‐based methods. Enzyme‐linked immunosorbent assay (ELISA) and immunofluorescence are classified into immunology‐based methods. Optical, electrochemical, and mass‐based biosensors are grouped into biosensor‐based methods. Overall, these methods are sensitive, specific, time‐effective, and important in prevention and diagnosis of waterborne bacterial diseases.
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Affiliation(s)
- Rehan A Deshmukh
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Kopal Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Sunil Bhand
- Biosensor Lab, Department of Chemistry, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Utpal Roy
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
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Ramírez-Castillo FY, Loera-Muro A, Jacques M, Garneau P, Avelar-González FJ, Harel J, Guerrero-Barrera AL. Waterborne pathogens: detection methods and challenges. Pathogens 2015; 4:307-34. [PMID: 26011827 PMCID: PMC4493476 DOI: 10.3390/pathogens4020307] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/08/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022] Open
Abstract
Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.
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Affiliation(s)
- Flor Yazmín Ramírez-Castillo
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Abraham Loera-Muro
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Mario Jacques
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Philippe Garneau
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Francisco Javier Avelar-González
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Josée Harel
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Alma Lilián Guerrero-Barrera
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
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Pyrosequencing analysis of microbial community and food-borne bacteria on restaurant cutting boards collected in Seri Kembangan, Malaysia, and their correlation with grades of food premises. Int J Food Microbiol 2015; 200:57-65. [PMID: 25679309 DOI: 10.1016/j.ijfoodmicro.2015.01.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 01/10/2023]
Abstract
This study adopts the pyrosequencing technique to identify bacteria present on 26 kitchen cutting boards collected from different grades of food premises around Seri Kembangan, a city in Malaysia. Pyrosequencing generated 452,401 of total reads of OTUs with an average of 1.4×10(7) bacterial cells/cm(2). Proteobacteria, Firmicutes and Bacteroides were identified as the most abundant phyla in the samples. Taxonomic richness was generally high with >1000 operational taxonomic units (OTUs) observed across all samples. The highest appearance frequencies (100%) were OTUs closely related to Enterobacter sp., Enterobacter aerogenes, Pseudomonas sp. and Pseudomonas putida. Several OTUs were identified most closely related to known food-borne pathogens, including Bacillus cereus, Cronobacter sakazaki, Cronobacter turisensis, Escherichia coli, E. coli O157:H7, Hafnia alvei, Kurthia gibsonii, Salmonella bongori, Salmonella enterica, Salmonella paratyphi, Salmonella tyhpi, Salmonella typhimurium and Yersinia enterocolitica ranging from 0.005% to 0.68% relative abundance. The condition and grade of the food premises on a three point cleanliness scale did not correlate with the bacterial abundance and type. Regardless of the status and grades, all food premises have the same likelihood to introduce food-borne bacteria from cutting boards to their foods and must always prioritize the correct food handling procedure in order to avoid unwanted outbreak of food-borne illnesses.
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A new pyrosequencing assay for rapid detection and genotyping of Shiga toxin, intimin and O157-specific rfbE genes of Escherichia coli. J Microbiol Methods 2015; 109:167-79. [DOI: 10.1016/j.mimet.2014.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/03/2014] [Accepted: 12/04/2014] [Indexed: 01/02/2023]
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12
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Janzen TW, Thomas MC, Goji N, Shields MJ, Hahn KR, Amoako KK. Rapid detection method for Bacillus anthracis using a combination of multiplexed real-time PCR and pyrosequencing and its application for food biodefense. J Food Prot 2015; 78:355-61. [PMID: 25710151 DOI: 10.4315/0362-028x.jfp-14-216] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Bacillus anthracis, the causative agent of anthrax, has the capacity to form highly resilient spores as part of its life cycle. The potential for the dissemination of these spores using food as a vehicle is a huge public health concern and, hence, requires the development of a foodborne bioterrorism response approach. In this work, we address a critical gap in food biodefense by presenting a novel, combined, sequential method involving the use of real-time PCR and pyrosequencing for the rapid, specific detection of B. anthracis spores in three food matrices: milk, apple juice, and bottled water. The food samples were experimentally inoculated with 40 CFU ml(-1), and DNA was extracted from the spores and analyzed after immunomagnetic separation. Applying the combination of multiplex real-time PCR and pyrosequencing, we successfully detected the presence of targets on both of the virulence plasmids and the chromosome. The results showed that DNA amplicons generated from a five-target multiplexed real-time PCR detection using biotin-labeled primers can be used for single-plex pyrosequencing detection. The combined use of multiplexed real-time PCR and pyrosequencing is a novel, rapid detection method for B. anthracis from food and provides a tool for accurate, quantitative identification with potential biodefense applications.
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Affiliation(s)
- Timothy W Janzen
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Matthew C Thomas
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Noriko Goji
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Michael J Shields
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Kristen R Hahn
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Kingsley K Amoako
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4.
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13
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Amoako KK. Application of Pyrosequencing® in Food Biodefense. Methods Mol Biol 2015; 1315:363-375. [PMID: 26103911 DOI: 10.1007/978-1-4939-2715-9_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The perpetration of a bioterrorism attack poses a significant risk for public health with potential socioeconomic consequences. It is imperative that we possess reliable assays for the rapid and accurate identification of biothreat agents to make rapid risk-informed decisions on emergency response. The development of advanced methodologies for the detection of biothreat agents has been evolving rapidly since the release of the anthrax spores in the mail in 2001, and recent advances in detection and identification techniques could prove to be an essential component in the defense against biological attacks. Sequence-based approaches such as Pyrosequencing(®), which has the capability to determine short DNA stretches in real time using biotinylated PCR amplicons, have potential biodefense applications. Using markers from the virulence plasmids and chromosomal regions, my laboratory has demonstrated the power of this technology in the rapid, specific, and sensitive detection of B. anthracis spores and Yersinia pestis in food. These are the first applications for the detection of the two organisms in food. Furthermore, my lab has developed a rapid assay to characterize the antimicrobial resistance (AMR) gene profiles for Y. pestis using Pyrosequencing. Pyrosequencing is completed in about 60 min (following PCR amplification) and yields accurate and reliable results with an added layer of confidence, thus enabling rapid risk-informed decisions to be made. A typical run yields 40-84 bp reads with 94-100 % identity to the expected sequence. It also provides a rapid method for determining the AMR profile as compared to the conventional plate method which takes several days. The method described is proposed as a novel detection system for potential application in food biodefense.
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Affiliation(s)
- Kingsley Kwaku Amoako
- National Centers for Animal Disease, Lethbridge Laboratory, Canadian Food Inspection Agency, P.O. Box 640, Township Road 9-1, Lethbridge, AB, Canada, T1J 3Z4,
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