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Talamantes-Becerra B, Carling J, Kennedy K, Gahan ME, Georges A. Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping. J Microbiol Methods 2019; 160:11-19. [PMID: 30894330 DOI: 10.1016/j.mimet.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/16/2019] [Accepted: 03/17/2019] [Indexed: 11/25/2022]
Abstract
Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Complexity-reduced bacterial genome sequencing provides an alternative. We evaluate genomic complexity-reduction using restriction enzymes and sequencing to identify bacterial isolates. A total of 165 bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015 were used in this study. They were identified and typed by the Microbiology Department of Canberra Public Hospital, and represented 14 bacterial species. DNA extractions from these samples were processed using a combination of the restriction enzymes PstI with MseI, PstI with HpaII and MseI with HpaII. The resulting sequences (length 30-69 bp) were aligned against publicly available bacterial genome and plasmid sequences. Results of the alignment were processed using a bioinformatics pipeline developed for this project, Currito3.1 DNA Fragment Analysis Software. All 165 samples were correctly identified to genus and species by each of the three combinations of restriction enzymes. A further 35 samples typed to the level of strain identified and compared for consistency with MLST typing data and in silico MLST data derived from the nearest sequenced candidate reference. The high level of agreement between bacterial identification using complexity-reduced genome sequencing and standard hospital identifications indicating that this new approach is a viable alternative for identification of bacterial isolates derived from pathology specimens. The effectiveness of species identification and in particular, strain typing, depends on access to a comprehensive and taxonomically accurate bacterial genome sequence database containing relevant bacterial species and strains.
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Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT 2617, Australia
| | - Karina Kennedy
- Canberra Health Services, Departments of Microbiology and Infectious Diseases, Canberra Hospital, Yamba Drive, Garran 2605, Australia
| | - Michelle E Gahan
- National Centre for Forensic Studies, University of Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, ACT 2601, Australia
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Mölsä M, Kalin-Mänttäri L, Tonteri E, Hemmilä H, Nikkari S. Comparison of four commercial DNA extraction kits for the recovery of Bacillus spp. spore DNA from spiked powder samples. J Microbiol Methods 2016; 128:69-73. [PMID: 27435532 DOI: 10.1016/j.mimet.2016.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 11/28/2022]
Abstract
Bacillus spp. include human pathogens such as Bacillus anthracis, the causative agent of anthrax and a biothreat agent. Bacillus spp. form spores that are physically highly resistant and may remain active over sample handling. We tested four commercial DNA extraction kits (QIAamp DNA Mini Kit, RTP Pathogen Kit, ZR Fungal/Bacterial DNA MiniPrep, and genesig Easy DNA/RNA Extraction kit) for sample inactivation and DNA recovery from two powders (icing sugar and potato flour) spiked with Bacillus thuringiensis spores. The DNA was analysed using a B. thuringiensis-specific real-time PCR assay. The detection limit was 3×10(1)CFU of spiked B. thuringiensis spores with the QIAamp DNA Mini, RTP Pathogen, and genesig Easy DNA/RNA Extraction kits, and 3×10(3)CFU with the ZR Fungal/Bacterial DNA MiniPrep kit. The results showed that manual extraction kits are effective and safe for fast and easy DNA extraction from powder samples even in field conditions. Adding a DNA filtration step to the extraction protocol ensures the removal of Bacillus spp. spores from DNA samples without affecting sensitivity.
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Affiliation(s)
- Markos Mölsä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland.
| | | | - Elina Tonteri
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Heidi Hemmilä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Simo Nikkari
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
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3
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Recent literature review of soil processing methods for recovery of Bacillus anthracis spores. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0932-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Abstract
In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.
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Affiliation(s)
- Max Maurin
- Laboratoire de Bactériologie, Département des Agents Infectieux, Institut de Biologie et Pathologie, CHU de Grenoble, Université Joseph Fourier Grenoble 1, France.
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Adams NM, Creecy AE, Majors CE, Wariso BA, Short PA, Wright DW, Haselton FR. Design criteria for developing low-resource magnetic bead assays using surface tension valves. BIOMICROFLUIDICS 2013; 7:14104. [PMID: 24403996 PMCID: PMC3562276 DOI: 10.1063/1.4788922] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 01/08/2013] [Indexed: 05/12/2023]
Abstract
Many assays for biological sample processing and diagnostics are not suitable for use in settings that lack laboratory resources. We have recently described a simple, self-contained format based on magnetic beads for extracting infectious disease biomarkers from complex biological samples, which significantly reduces the time, expertise, and infrastructure required. This self-contained format has the potential to facilitate the application of other laboratory-based sample processing assays in low-resource settings. The technology is enabled by immiscible fluid barriers, or surface tension valves, which stably separate adjacent processing solutions within millimeter-diameter tubing and simultaneously permit the transit of magnetic beads across the interfaces. In this report, we identify the physical parameters of the materials that maximize fluid stability and bead transport and minimize solution carryover. We found that fluid stability is maximized with ≤0.8 mm i.d. tubing, valve fluids of similar density to the adjacent solutions, and tubing with ≤20 dyn/cm surface energy. Maximizing bead transport was achieved using ≥2.4 mm i.d. tubing, mineral oil valve fluid, and a mass of 1-3 mg beads. The amount of solution carryover across a surface tension valve was minimized using ≤0.2 mg of beads, tubing with ≤20 dyn/cm surface energy, and air separators. The most favorable parameter space for valve stability and bead transport was identified by combining our experimental results into a single plot using two dimensionless numbers. A strategy is presented for developing additional self-contained assays based on magnetic beads and surface tension valves for low-resource diagnostic applications.
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Affiliation(s)
- Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA ; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Amy E Creecy
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Catherine E Majors
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Bathsheba A Wariso
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Philip A Short
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - David W Wright
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
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Matero P, Hemmilä H, Tomaso H, Piiparinen H, Rantakokko-Jalava K, Nuotio L, Nikkari S. Rapid field detection assays for Bacillus anthracis, Brucella spp., Francisella tularensis and Yersinia pestis. Clin Microbiol Infect 2011; 17:34-43. [PMID: 20132255 DOI: 10.1111/j.1469-0691.2010.03178.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid detection is essential for timely initiation of medical post-exposure prophylactic measures in the event of intentional release of biological threat agents. We compared real-time PCR assay performance between the Applied Biosystems 7300/7500 and the RAZOR instruments for specific detection of the causative agents of anthrax, brucellosis, tularemia and plague. Furthermore, an assay detecting Bacillus thuringiensis, a Bacillus anthracis surrogate, was developed for field-training purposes. Assay sensitivities for B. anthracis, Brucella spp., Francisella tularensis and Yersinia pestis were 10-100 fg of target DNA per reaction, and no significant difference in assay performance was observed between the instrument platforms. Specificity testing of the diagnostic panels with both instrument platforms did not reveal any cross-reactivity with other closely related bacteria. The duration of thermocycling with the RAZOR instrument was shorter, i.e. 40 min as compared with 100 min for the Applied Biosystems 7300/7500 instruments. These assays provide rapid tools for the specific detection of four biological threat agents. The detection assays, as well as the training assay for B. thuringiensis powder preparation analysis, may be utilized under field conditions and for field training, respectively.
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Affiliation(s)
- P Matero
- CB Defence and Environmental Health Centre, Centres for Biothreat Preparedness and Military Medicine, Helsinki, Finland
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Kramme S, Nissen N, Soblik H, Erttmann K, Tannich E, Fleischer B, Panning M, Brattig N. Novel real-time PCR for the universal detection of Strongyloides species. J Med Microbiol 2010; 60:454-458. [PMID: 21163829 DOI: 10.1099/jmm.0.025338-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strongyloidiasis is a neglected disease that is prevalent mainly in tropical and subtropical regions. It is caused by intestinal nematodes of the genus Strongyloides. Due to the rise in worldwide travel, infections are increasingly encountered in non-endemic regions. Diagnosis is hampered by insensitive and laborious detection methods. A universal Strongyloides species real-time PCR was developed with an internal competitive control system. The 95% limit of detection as determined by probit analysis was one larva per PCR equivalent to 100 larvae per 200 mg stool. The assay proved to be 100% specific as assessed using a panel of parasites and bacteria and thus might be useful in the diagnostic setting as well as for Strongyloides research.
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Affiliation(s)
- Stefanie Kramme
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Nicole Nissen
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hanns Soblik
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Klaus Erttmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Egbert Tannich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Marcus Panning
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Norbert Brattig
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Janse I, Hamidjaja RA, Bok JM, van Rotterdam BJ. Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification. BMC Microbiol 2010; 10:314. [PMID: 21143837 PMCID: PMC3016324 DOI: 10.1186/1471-2180-10-314] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 12/08/2010] [Indexed: 11/20/2022] Open
Abstract
Background Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Results Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. Conclusions The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum
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Affiliation(s)
- Ingmar Janse
- National Institute for Public Health and the Environment, Laboratory for Zoonoses and Environmental Microbiology, Bilthoven, The Netherlands.
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Detection and quantitation of HBV DNA in miniaturized samples: multi centre study to evaluate the performance of the COBAS ® AmpliPrep/COBAS ® TaqMan ® hepatitis B virus (HBV) test v2.0 by the use of plasma or serum specimens. J Virol Methods 2010; 169:404-8. [PMID: 20728470 DOI: 10.1016/j.jviromet.2010.07.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 07/20/2010] [Accepted: 07/26/2010] [Indexed: 02/06/2023]
Abstract
Laboratory analysis of blood specimens is an increasingly important tool for rapid diagnosis and control of therapy. So, miniaturization of test systems is needed, but reduced specimens might impair test quality. For rapid detection and quantitation of HBV DNA, the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV test has proved a robust instrument in routine diagnostic services. The test system has been modified recently for application of reduced samples of blood plasma and for blood serum, too. The performance of this modified COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV v2.0 (HBV v2.0 (this test is currently not available in the USA)) test was evaluated by comparison with the former COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV v1.0 (HBV v1.0) test. In this study a platform correlation of both assay versions was done including 275 HBV DNA positive EDTA plasma samples. Comparable results were obtained (R(2)=0.97, mean difference -0.03 log(10)IU/ml). The verification of equivalency of the sample matrix (plasma vs. serum samples tested in HBV v2.0 in the same run) showed comparable results for all 278 samples with a R(2)=0.99 and a mean difference of 0.06 log(10)IU/ml. In conclusion, the new test version HBV v2.0 is highly specific and reproducible and quantifies accurately HBV DNA in EDTA plasma and serum samples from patients with chronic HBV infection.
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Providenti MA, Begin M, Hynes S, Lamarche C, Chitty D, Hahn J, Beaudette LA, Scroggins R, Smith ML. Identification and application of AFLP-derived genetic markers for quantitative PCR-based tracking of Bacillus and Paenibacillus spp. released in soil. Can J Microbiol 2010; 55:1166-75. [PMID: 19935889 DOI: 10.1139/w09-071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we show that noncoding sequences from amplified fragment length polymorphisms (AFLPs) can provide robust and sensitive genetic markers suitable for PCR-based discrimination of closely related strains of Bacillus and Paenibacillus, and quantitative PCR (qPCR)-based tracking of the strains in complex natural systems like soil. Quantitative PCR was accurate in the approximately 1 x 10(9) to approximately 1 x 10(4) colony forming units (CFU)/g soil range. The detection limit was improved to approximately 1 x 10(2) CFU/g when amplicons were analyzed by gel electrophoresis. Studies with laboratory-contained intact soil-core microcosms indicated that environmental persistence trends vary among different strains. For example, Bacillus circulans ATCC 9500, Bacillus amyloliquefaciens DSL 13563-0, Bacillus licheniformis ATCC 12713, Paenibacillus polymyxa NRRL B-4317, and 3 Bacillus subtilisstrains (ATCC 6051A, ATCC 55405, and NRRL B-941) died down to below the 1 x 10(2) CFU/g detection limit by days 28-105. In contrast, over a 105-day period, B. licheniformis ATCC 55406, Bacillus megaterium NRRL B-14308, and P. polymyxa strains ATCC 55407 and DSL 13540-4 died down but persisted at levels just above the detection limit, whereas Bacillus thuringiensis ATCC 13367 experienced a less than 10-fold decrease in cell numbers.
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Dauphin LA, Moser BD, Bowen MD. Evaluation of five commercial nucleic acid extraction kits for their ability to inactivate Bacillus anthracis spores and comparison of DNA yields from spores and spiked environmental samples. J Microbiol Methods 2009; 76:30-7. [DOI: 10.1016/j.mimet.2008.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 09/05/2008] [Accepted: 09/05/2008] [Indexed: 10/21/2022]
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Dauphin LA, Bowen MD. A simple method for the rapid removal of Bacillus anthracis spores from DNA preparations. J Microbiol Methods 2008; 76:212-4. [PMID: 18996156 DOI: 10.1016/j.mimet.2008.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 10/09/2008] [Indexed: 10/21/2022]
Abstract
This study establishes a filtration method for the safe removal of Bacillus anthracis spores which may contaminate DNA preparations. Centrifugal filtration with 0.1-microm filter units can be used following extraction of DNA from B. anthracis spores to render samples safe without compromising the sensitivity of diagnostic real-time PCR assays for B. anthracis.
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Affiliation(s)
- Leslie A Dauphin
- Division of Bioterrorism Preparedness and Response (DBPR), National Center for Preparedness, Detection, and Control of Infectious Diseases (NCPDCID), CDC, Atlanta, Georgia, USA.
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Panning M, Kilwinski J, Greiner-Fischer S, Peters M, Kramme S, Frangoulidis D, Meyer H, Henning K, Drosten C. High throughput detection of Coxiella burnetii by real-time PCR with internal control system and automated DNA preparation. BMC Microbiol 2008; 8:77. [PMID: 18489780 PMCID: PMC2397412 DOI: 10.1186/1471-2180-8-77] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 05/19/2008] [Indexed: 11/25/2022] Open
Abstract
Background Coxiella burnetii is the causative agent of Q-fever, a widespread zoonosis. Due to its high environmental stability and infectivity it is regarded as a category B biological weapon agent. In domestic animals infection remains either asymptomatic or presents as infertility or abortion. Clinical presentation in humans can range from mild flu-like illness to acute pneumonia and hepatitis. Endocarditis represents the most common form of chronic Q-fever. In humans serology is the gold standard for diagnosis but is inadequate for early case detection. In order to serve as a diagnostic tool in an eventual biological weapon attack or in local epidemics we developed a real-time 5'nuclease based PCR assay with an internal control system. To facilitate high-throughput an automated extraction procedure was evaluated. Results To determine the minimum number of copies that are detectable at 95% chance probit analysis was used. Limit of detection in blood was 2,881 copies/ml [95%CI, 2,188–4,745 copies/ml] with a manual extraction procedure and 4,235 copies/ml [95%CI, 3,143–7,428 copies/ml] with a fully automated extraction procedure, respectively. To demonstrate clinical application a total of 72 specimens of animal origin were compared with respect to manual and automated extraction. A strong correlation between both methods was observed rendering both methods suitable. Testing of 247 follow up specimens of animal origin from a local Q-fever epidemic rendered real-time PCR more sensitive than conventional PCR. Conclusion A sensitive and thoroughly evaluated real-time PCR was established. Its high-throughput mode may show a useful approach to rapidly screen samples in local outbreaks for other organisms relevant for humans or animals. Compared to a conventional PCR assay sensitivity of real-time PCR was higher after testing samples from a local Q-fever outbreak.
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Affiliation(s)
- Marcus Panning
- Clinical Virology, Bernhard-Nocht Institute for Tropical Medicine, Bernhard Nocht Str, 74, 20359 Hamburg, Germany.
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Orthopoxvirus detection in environmental specimens during suspected bioterror attacks: inhibitory influences of common household products. Appl Environ Microbiol 2007; 74:32-7. [PMID: 17965204 DOI: 10.1128/aem.01501-07] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After terrorists attacked the United States in 2001, the appearance of letters and other objects containing powdery substances with unknown potentials for biological threat focused attention on the speed, sensitivity, and reliability of diagnostic methods. This study summarizes the abilities and limitations of real-time PCR, electron microscopy (EM), and virus isolation when used to detect potential bioweapons. In particular, we investigated the inhibitory influences of different common household products present in environmental specimens on PCR yield, EM detection, and virus isolation. We used vaccinia virus as a model for orthopoxviruses by spiking it into specimens. In the second part of the study, we describe modifications of diagnostic methods to overcome inhibitory effects. A variety of PCR amplification enhancers, DNA extraction protocols, and applications of internal controls were evaluated to improve diagnostic simplicity, speed, and reliability. As a result, we strongly recommend using at least two different frontline techniques in parallel, e.g., EM and PCR. A positive result obtained by any one of these techniques should be followed by a biological method to confirm the putative diagnosis. Confirmatory methods include virus isolation followed by an agent-specific immunofluorescence assay to confirm the presence of replication-competent particles.
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