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Weller SA, Armstrong SR, Bailey S, Burnell HT, Burt EL, Cant NE, Cawthorne KR, Chester M, Choules JE, Coe NA, Coward L, Cox VL, Emery ER, Evans CP, Finn A, Halford CM, Hamblin KA, Harrison GV, Hartley MG, Hudson C, James B, Jones HE, Keyser E, Lonsdale CL, Marshall LE, Maule CE, Miles JA, Newstead SL, Nicholls M, Osborne C, Pearcy AS, Penny LD, Perrot R, Rachwal P, Robinson V, Rushton D, Stahl FM, Staplehurst SV, Stapleton HL, Steeds K, Stephenson K, Thompson IJ, Thwaite JE, Ulaeto DO, Waters N, Wills DJ, Wills ZS, Rees C, Hutley EJ. Development and operation of the defence COVID-19 lab as a SARS-CoV-2 diagnostic screening capability for UK military personnel. BMJ Mil Health 2022; 170:e002134. [PMID: 35878971 PMCID: PMC10958320 DOI: 10.1136/military-2022-002134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/03/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND In the face of the COVID-19 pandemic, the Defence Science and Technology Laboratory (Dstl) and Defence Pathology combined to form the Defence Clinical Lab (DCL), an accredited (ISO/IEC 17025:2017) high-throughput SARS-CoV-2 PCR screening capability for military personnel. LABORATORY STRUCTURE AND RESOURCE The DCL was modular in organisation, with laboratory modules and supporting functions combining to provide the accredited SARS-CoV-2 (envelope (E)-gene) PCR assay. The DCL was resourced by Dstl scientists and military clinicians and biomedical scientists. LABORATORY RESULTS Over 12 months of operation, the DCL was open on 289 days and tested over 72 000 samples. Six hundred military SARS-CoV-2-positive results were reported with a median E-gene quantitation cycle (Cq) value of 30.44. The lowest Cq value for a positive result observed was 11.20. Only 64 samples (0.09%) were voided due to assay inhibition after processing started. CONCLUSIONS Through a sustained effort and despite various operational issues, the collaboration between Dstl scientific expertise and Defence Pathology clinical expertise provided the UK military with an accredited high-throughput SARS-CoV-2 PCR test capability at the height of the COVID-19 pandemic. The DCL helped facilitate military training and operational deployments contributing to the maintenance of UK military capability. In offering a bespoke capability, including features such as testing samples in unit batches and oversight by military consultant microbiologists, the DCL provided additional benefits to the UK Ministry of Defence that were potentially not available from other SARS-CoV-2 PCR laboratories. The links between Dstl and Defence Pathology have also been strengthened, benefitting future research activities and operational responses.
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Affiliation(s)
- Simon A Weller
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - S R Armstrong
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - S Bailey
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - H T Burnell
- Operations Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
| | - E L Burt
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - N E Cant
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - K R Cawthorne
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - M Chester
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - J E Choules
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - N A Coe
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - L Coward
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - V L Cox
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - E R Emery
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - C P Evans
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - A Finn
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - C M Halford
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - K A Hamblin
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - G V Harrison
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - M G Hartley
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - C Hudson
- Defence Pathology, Royal Centre for Defence Medicine, Birmingham, UK
| | - B James
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - H E Jones
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - E Keyser
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - C L Lonsdale
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - L E Marshall
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - C E Maule
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - J A Miles
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - S L Newstead
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - M Nicholls
- Defence Pathology, Royal Centre for Defence Medicine, Birmingham, UK
| | - C Osborne
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - A S Pearcy
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - L D Penny
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - R Perrot
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - P Rachwal
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - V Robinson
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - D Rushton
- Platform Systems Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
| | - F M Stahl
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - S V Staplehurst
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - H L Stapleton
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - K Steeds
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - K Stephenson
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - I J Thompson
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - J E Thwaite
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - D O Ulaeto
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - N Waters
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - D J Wills
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - Z S Wills
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - C Rees
- CBR Division, Defence Science and Technology Laboratory Porton Down, Salisbury, UK
| | - E J Hutley
- Defence Pathology, Royal Centre for Defence Medicine, Birmingham, UK
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2
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Geiger K, Zach C, Leiherer A, Fraunberger P, Drexel H, Muendlein A. Real-time PCR based HLA-B*27 screening directly in whole blood. HLA 2019; 95:189-195. [PMID: 31749313 DOI: 10.1111/tan.13767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/09/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022]
Abstract
The linkage between the occurrence of human leucocyte antigen B*27 (HLA-B*27) and ankylosing spondylitis or other related spondyloarthritides is well documented. PCR based methods are widely used for HLA-B*27 screening. To refine HLA-B*27 testing we aimed at establishing a real-time PCR protocol to detect the HLA-B*27 allele directly in blood samples, without DNA extraction. HLA-B*27 analysis was performed by two real-time PCRs using TaqMan primer-probe assays for B*27 specific amplification of exon 2 or exon 3 of the HLA-B gene together with a mutant of Taq polymerase for direct blood PCR. Conditions for direct blood PCR were optimized and the reliability of the direct blood PCR protocol was evaluated by re-genotyping over 200 blood samples from patients who previously underwent routine DNA-based HLA-B*27 testing. Heating blood samples at 95°C for 10 minutes significantly improved PCR performance. Results from real-time PCR based HLA-B*27 testing directly in blood of over 200 patients were in 100% concordance with results obtained by routine DNA-based HLA-B*27 genotyping. In summary, we present a reliable real-time PCR protocol for HLA-B*27 screening directly in whole blood supporting fast clarification of the presence of ankylosing spondylitis or other spondyloarthritides in suspected cases.
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Affiliation(s)
- Kathrin Geiger
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria
| | - Christina Zach
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria.,Medical Central Laboratories, Feldkirch, Austria
| | - Andreas Leiherer
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria.,Medical Central Laboratories, Feldkirch, Austria.,Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
| | | | - Heinz Drexel
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria.,Private University of the Principality of Liechtenstein, Triesen, Liechtenstein.,Division of Angiology, Swiss Cardiovascular Center, University Hospital of Berne, Berne, Switzerland.,Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Axel Muendlein
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria
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3
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Advances in Directly Amplifying Nucleic Acids from Complex Samples. BIOSENSORS-BASEL 2019; 9:bios9040117. [PMID: 31574959 PMCID: PMC6955841 DOI: 10.3390/bios9040117] [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: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.
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4
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Pohanka M. Current Trends in the Biosensors for Biological Warfare Agents Assay. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2303. [PMID: 31323857 PMCID: PMC6678440 DOI: 10.3390/ma12142303] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
Abstract
Biosensors are analytical devices combining a physical sensor with a part of biological origin providing sensitivity and selectivity toward analyte. Biological warfare agents are infectious microorganisms or toxins with the capability to harm or kill humans. They can be produced and spread by a military or misused by a terrorist group. For example, Bacillus anthracis, Francisella tularensis, Brucella sp., Yersinia pestis, staphylococcal enterotoxin B, botulinum toxin and orthopoxviruses are typical biological warfare agents. Biosensors for biological warfare agents serve as simple but reliable analytical tools for the both field and laboratory assay. There are examples of commercially available biosensors, but research and development of new types continue and their application in praxis can be expected in the future. This review summarizes the facts and role of biosensors in the biological warfare agents' assay, and shows current commercially available devices and trends in research of the news. Survey of actual literature is provided.
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Affiliation(s)
- Miroslav Pohanka
- Faculty of Military Health Sciences, University of Defense, Trebesska 1575, CZ-50001 Hradec Kralove, Czech Republic.
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5
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Papaiakovou M, Gasser RB, Littlewood DTJ. Quantitative PCR-Based Diagnosis of Soil-Transmitted Helminth Infections: Faecal or Fickle? Trends Parasitol 2019; 35:491-500. [PMID: 31126720 DOI: 10.1016/j.pt.2019.04.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/19/2022]
Abstract
Treatment and control programmes tackling soil-transmitted helminth (STH) infections require sensitive, reliable, and accurate diagnostic tools. There is a growing need for measures of infection intensity as programmes approach STH control. Quantitative real-time PCR (qPCR) is well suited to the detection of DNA targets present in stool, even in low-prevalence settings. Detecting low levels of infection becomes increasingly important when the breakpoint of transmission is approached, and is vital when monitoring for recrudescence once control, or possibly 'elimination', is achieved. We address key challenges and questions that remain as barriers to incorporating qPCR as a cornerstone diagnostic tool for STH infections.
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Affiliation(s)
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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6
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Geiger K, Leiherer A, Brandtner EM, Fraunberger P, Drexel H, Muendlein A. Direct blood PCR: TaqMan-probe based detection of the venous thromboembolism associated mutations factor V Leiden and prothrombin c.20210G>A without DNA extraction. Clin Chim Acta 2018; 488:221-225. [PMID: 30439355 DOI: 10.1016/j.cca.2018.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 10/27/2022]
Abstract
BACKGROUND Practically, the initial step of genetic analysis is the extraction of DNA from blood or other cells, which is often time consuming and cost-intensive. We aimed at establishing a real-time PCR protocol for the detection of the venous thromboembolism associated mutations factor V Leiden (F5 c.1691G>A; p.R506Q) and prothrombin (F2) c.20210G>A from whole blood, without DNA extraction. METHODS F5 c.1691G>A (p.R506Q) and F2 c.20210G>A mutations were determined in 205 EDTA anti-coagulated whole blood samples from patients who underwent routine clinical genotyping using the DirectBlood Genotyping PCR Kit (myPOLS Biotec, Konstanz, Germany) together with in-house developed TaqMan primer-probe assays. RESULTS Validity score values of genotype calls using whole blood were similar and did not significantly differ compared to those using genomic DNA as substrate in PCR. Mutation analysis of 205 whole blood samples showed a negligible PCR dropout rate (one in 410 reactions) and were in 100% concordance with results obtained by conventional genotyping. CONCLUSION We successfully established a robust and valid real-time PCR protocol for the detection of the venous thromboembolism associated mutations F5 c.1691G>A (p.R506Q) and F2 c.20210G>A directly from whole blood.
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Affiliation(s)
- Kathrin Geiger
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria
| | - Andreas Leiherer
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria; Medical Central Laboratories, Feldkirch, Austria; Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Eva-Maria Brandtner
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria
| | | | - Heinz Drexel
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria; Private University of the Principality of Liechtenstein, Triesen, Liechtenstein; Division of Angiology, Swiss Cardiovascular Center, University Hospital of Berne, Berne, Switzerland; Drexel University College of Medicine, Philadelphia, PA, USA
| | - Axel Muendlein
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria.
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7
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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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8
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Julich S, Hotzel H, Gärtner C, Trouchet D, Fawzy El Metwaly Ahmed M, Kemper N, Tomaso H. Evaluation of a microfluidic chip system for preparation of bacterial DNA from swabs, air, and surface water samples. Biologicals 2016; 44:574-580. [PMID: 27520284 PMCID: PMC5119575 DOI: 10.1016/j.biologicals.2016.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 12/17/2015] [Accepted: 06/29/2016] [Indexed: 11/18/2022] Open
Abstract
The detection of bacterial pathogens from complex sample matrices by PCR requires efficient DNA extraction. In this study, a protocol for extraction and purification of DNA from swabs, air, and water samples using a microfluidic chip system was established. The optimized protocol includes a combination of thermal, chemical and enzymatic lysis followed by chip-based DNA purification using magnetic particles. The procedure was tested using Gram-positive Bacillus thuringiensis Berliner var. kurstaki as a model organism for Bacillus anthracis and the attenuated live vaccine strain of Francisella tularensis subsp. holarctica as Gram-negative bacterium. The detection limits corresponded to 103 genome equivalents per milliliter (GE/ml) for surface water samples spiked with F. tularensis and 102 GE/ml for B. thuringiensis. In air, 10 GE of F. tularensis per 10 L and 1 GE of B. thuringiensis per 10 L were detectable. For swab samples obtained from artificially contaminated surfaces the detection limits were 4 × 103 GE/cm2 for F. tularensis and 4 × 102 GE/cm2 for B. thuringiensis. Suitability of the chip-assisted procedure for DNA preparation of real samples was demonstrated using livestock samples. The presence of thermophilic Campylobacter spp. DNA could be confirmed in air samples collected on pig and broiler farms. A microfluidic chip system for magnetic bead-based DNA preparation was evaluated. Bacterial DNA was recovered from swabs, air, and surface water. A universal protocol was used for Gram-positive and Gram-negative bacteria. 10 GE of F. tularensis and 1 GE of B. thuringiensis per 10 l air were detectable. Thermophilic Campylobacter DNA was detected in air samples of pig and broiler farms.
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Affiliation(s)
- Sandra Julich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Naumburger Straße 96a, 07743 Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Naumburger Straße 96a, 07743 Jena, Germany
| | - Claudia Gärtner
- microfluidic ChipShop, Stockholmer Straße 20, 07747 Jena, Germany
| | - Daniel Trouchet
- Bertin Technologies, 10 Avenue André Marie Ampére, 78180 Montigny-le-Bretonneux, France
| | - Marwa Fawzy El Metwaly Ahmed
- Mansoura University, Faculty of Veterinary Medicine, Department of Animal Hygiene and Zoonoses, 60 El Gomhoria Street, 35516 Mansoura, Egypt
| | - Nicole Kemper
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Hygiene, Animal Welfare and Farm Animal Behaviour, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Naumburger Straße 96a, 07743 Jena, Germany.
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9
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Mahaffee WF, Stoll R. The Ebb and Flow of Airborne Pathogens: Monitoring and Use in Disease Management Decisions. PHYTOPATHOLOGY 2016; 106:420-431. [PMID: 27003505 DOI: 10.1094/phyto-02-16-0060-rvw] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Perhaps the earliest form of monitoring the regional spread of plant disease was a group of growers gathering together at the market and discussing what they see in their crops. This type of reporting continues to this day through regional extension blogs, by crop consultants and more formal scouting of sentential plots in the IPM PIPE network (http://www.ipmpipe.org/). As our knowledge of plant disease epidemiology has increased, we have also increased our ability to detect and monitor the presence of pathogens and use this information to make management decisions in commercial production systems. The advent of phylogenetics, next-generation sequencing, and nucleic acid amplification technologies has allowed for development of sensitive and accurate assays for pathogen inoculum detection and quantification. The application of these tools is beginning to change how we manage diseases with airborne inoculum by allowing for the detection of pathogen movement instead of assuming it and by targeting management strategies to the early phases of the epidemic development when there is the greatest opportunity to reduce the rate of disease development. While there are numerous advantages to using data on inoculum presence to aid management decisions, there are limitations in what the data represent that are often unrecognized. In addition, our understanding of where and how to effectively monitor airborne inoculum is limited. There is a strong need to improve our knowledge of the mechanisms that influence inoculum dispersion across scales as particles move from leaf to leaf, and everything in between.
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Affiliation(s)
- Walter F Mahaffee
- First author: U.S. Department of Agriculture-Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR 97330; and second author: Department of Mechanical Engineering, University of Utah, Salt Lake City 84112
| | - Rob Stoll
- First author: U.S. Department of Agriculture-Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR 97330; and second author: Department of Mechanical Engineering, University of Utah, Salt Lake City 84112
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10
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Evaluation of the Biofire FilmArray BioThreat-E Test (v2.5) for Rapid Identification of Ebola Virus Disease in Heat-Treated Blood Samples Obtained in Sierra Leone and the United Kingdom. J Clin Microbiol 2015; 54:114-9. [PMID: 26537445 DOI: 10.1128/jcm.02287-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023] Open
Abstract
Rapid Ebola virus (EBOV) detection is crucial for appropriate patient management and care. The performance of the FilmArray BioThreat-E test (v2.5) using whole-blood samples was evaluated in Sierra Leone and the United Kingdom and was compared with results generated by a real-time Ebola Zaire PCR reference method. Samples were tested in diagnostic laboratories upon availability, included successive samples from individual patients, and were heat treated to facilitate EBOV inactivation prior to PCR. The BioThreat-E test had a sensitivity of 84% (confidence interval [CI], 64% to 95%) and a specificity of 89% (CI, 73% to 97%) in Sierra Leone (n = 60; 44 patients) and a sensitivity of 75% (CI, 19% to 99%) and a specificity of 100% (CI, 97% to 100%) in the United Kingdom (n = 108; 70 patients) compared to the reference real-time PCR. Statistical analysis (Fisher's exact test) indicated there was no significant difference between the methods at the 99% confidence level in either country. In 9 discrepant results (5 real-time PCR positives and BioThreat-E test negatives and 4 real-time PCR negatives and BioThreat-E test positives), the majority (n = 8) were obtained from samples with an observed or probable low viral load. The FilmArray BioThreat-E test (v2.5) therefore provides an attractive option for laboratories (either in austere field settings or in countries with an advanced technological infrastructure) which do not routinely offer an EBOV diagnostic capability.
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Buffer AVL Alone Does Not Inactivate Ebola Virus in a Representative Clinical Sample Type. J Clin Microbiol 2015; 53:3148-54. [PMID: 26179307 DOI: 10.1128/jcm.01449-15] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/14/2015] [Indexed: 11/20/2022] Open
Abstract
Rapid inactivation of Ebola virus (EBOV) is crucial for high-throughput testing of clinical samples in low-resource, outbreak scenarios. The EBOV inactivation efficacy of Buffer AVL (Qiagen) was tested against marmoset serum (EBOV concentration of 1 × 10(8) 50% tissue culture infective dose per milliliter [TCID50 · ml(-1)]) and murine blood (EBOV concentration of 1 × 10(7) TCID50 · ml(-1)) at 4:1 vol/vol buffer/sample ratios. Posttreatment cell culture and enzyme-linked immunosorbent assay (ELISA) analysis indicated that treatment with Buffer AVL did not inactivate EBOV in 67% of samples, indicating that Buffer AVL, which is designed for RNA extraction and not virus inactivation, cannot be guaranteed to inactivate EBOV in diagnostic samples. Murine blood samples treated with ethanol (4:1 [vol/vol] ethanol/sample) or heat (60°C for 15 min) also showed no viral inactivation in 67% or 100% of samples, respectively. However, combined Buffer AVL and ethanol or Buffer AVL and heat treatments showed total viral inactivation in 100% of samples tested. The Buffer AVL plus ethanol and Buffer AVL plus heat treatments were also shown not to affect the extraction of PCR quality RNA from EBOV-spiked murine blood samples.
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12
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Papadopoulou E, Goodchild SA, Cleary DW, Weller SA, Gale N, Stubberfield MR, Brown T, Bartlett PN. Using surface-enhanced Raman spectroscopy and electrochemically driven melting to discriminate Yersinia pestis from Y. pseudotuberculosis based on single nucleotide polymorphisms within unpurified polymerase chain reaction amplicons. Anal Chem 2015; 87:1605-12. [PMID: 25551670 DOI: 10.1021/ac503063c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of sensors for the detection of pathogen-specific DNA, including relevant species/strain level discrimination, is critical in molecular diagnostics with major impacts in areas such as bioterrorism and food safety. Herein, we use electrochemically driven denaturation assays monitored by surface-enhanced Raman spectroscopy (SERS) to target single nucleotide polymorphisms (SNPs) that distinguish DNA amplicons generated from Yersinia pestis, the causative agent of plague, from the closely related species Y. pseudotuberculosis. Two assays targeting SNPs within the groEL and metH genes of these two species have been successfully designed. Polymerase chain reaction (PCR) was used to produce Texas Red labeled single-stranded DNA (ssDNA) amplicons of 262 and 251 bases for the groEL and metH targets, respectively. These amplicons were used in an unpurified form to hybridize to immobilized probes then subjected to electrochemically driven melting. In all cases electrochemically driven melting was able to discriminate between fully homologous DNA and that containing SNPs. The metH assay was particularly challenging due to the presence of only a single base mismatch in the middle of the 251 base long PCR amplicon. However, manipulation of assay conditions (conducting the electrochemical experiments at 10 °C) resulted in greater discrimination between the complementary and mismatched DNA. Replicate data were collected and analyzed for each duplex on different days, using different batches of PCR product and different sphere segment void (SSV) substrates. Despite the variability introduced by these differences, the assays are shown to be reliable and robust providing a new platform for strain discrimination using unpurified PCR samples.
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Affiliation(s)
- Evanthia Papadopoulou
- Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
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Smartphones for Cell and Biomolecular Detection. Ann Biomed Eng 2014; 42:2205-17. [DOI: 10.1007/s10439-014-1055-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/04/2014] [Indexed: 10/25/2022]
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