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Maddock KJ, Rickey CV, Pecoraro HL. Wild lagomorphs as potential sources of Francisella tularensis in an urban zoo: a case study. J Vet Diagn Invest 2024:10406387241248608. [PMID: 38653738 DOI: 10.1177/10406387241248608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
A 9-y-old captive male Pallas' cat (Otocolobus manul) had a 1-mo history of worsening lameness and was euthanized. The animal was submitted to the North Dakota State University-Veterinary Diagnostic Laboratory for autopsy with differential diagnoses of suspected degenerative joint disease or neoplasia. Autopsy revealed icteric tissues and pinpoint foci in the liver, spleen, and all lung lobes. PCR testing was positive for Francisella tularensis, the causative agent of tularemia. Additional cases of tularemia were later identified in wild eastern cottontail rabbits found dead at the same urban zoo. Tularemia has been reported in captive non-human primates and rodent populations with one case linked to wild lagomorph exposure, which was likely the route of exposure in our Pallas' cat case. Tularemia is an occupational risk for zoo staff and laboratorians. Pest management and disease surveillance of wild lagomorph populations in zoos are important preventive measures.
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Affiliation(s)
- Kelli J Maddock
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND, USA
| | | | - Heidi L Pecoraro
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND, USA
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2
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Lind K, Mölsä M, Kalin-Mänttäri L, Hemmilä H, Voutilainen L, Nikkari S. Vacuum Oven Drying: A Cost-Effective Way of Producing Field-Deployable Reagents for In-house Real-Time PCR Methods. Mol Biotechnol 2023:10.1007/s12033-023-00999-2. [PMID: 38135831 DOI: 10.1007/s12033-023-00999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023]
Abstract
The polymerase chain reaction (PCR), is a widely used, sensitive and reliable method for detecting pathogens. However, technical limitations may restrict its use outside sophisticated laboratories, e.g. for detecting pathogens at the site of a disease outbreak. In this study, real-time PCR reagents specific to four bacteria (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella spp.) and to the Influenza A virus were dried using a vacuum oven drying method. The performance of the dried reagents stored at different temperatures, was monitored using both a standard-size and a portable real-time PCR instrument. The vacuum oven dried real-time PCR reagents were stable and retained the sensitivity for at least 14 months when stored in a refrigerator (+ 4 °C). When stored at room temperature, DNA assays remained stable for at least 10 weeks and Influenza A RNA assay for 3 weeks. These results demonstrate the feasibility of vacuum oven dried real-time PCR reagents and a portable thermocycler for the rapid and reliable detection of pathogens. The drying protocol presented here is cost-effective and easy to use, and could be applied to real-time PCR methods specific to other pathogens as well. In addition, this in-house drying protocol reduces reliance on commercial PCR tests during a time of shortage, such as that experienced during the Corovirus disease (COVID-19) crisis.
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Affiliation(s)
- Katja Lind
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland.
- Finnish Institute for Health and Welfare, P.O. Box 30, 00271, Helsinki, Finland.
| | - Markos Mölsä
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
| | | | - Heidi Hemmilä
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
| | - Liina Voutilainen
- Finnish Institute for Health and Welfare, P.O. Box 30, 00271, Helsinki, Finland
| | - Simo Nikkari
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
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3
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Mäki-Koivisto V, Korkala M, Simola L, Suutari-Kontio S, Koivunen S, Puhto T, Junttila IS. Positive Francisella tularensis meningitis outcome despite delayed identification: a case report. Ann Clin Microbiol Antimicrob 2023; 22:92. [PMID: 37875923 PMCID: PMC10598999 DOI: 10.1186/s12941-023-00642-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
Francisella tularensis is a Gram-negative bacteria, that may cause a zoonotic disease, tularemia. Here, we describe a patient case, where a previously healthy young woman in Northern Finland contacted health care because of fever and headache. Due to the symptoms and lack of further diagnostic tools in primary health care, she was transferred to University Hospital (UH) where ampicillin and ceftriaxone was given empirically. A cerebrospinal fluid sample (CSF) was drawn showing small Gram-negative rods that grew on chocolate agar after 2 days of incubation. Matrix-assisted laser-desorption-ionization time of-flight (Maldi-tof) did not provide identification, but the bacteria was interpreted as sensitive to ciprofloxacin and the treatment was changed to ciprofloxacin. During the time the patient was infected, there were several positive tularemia samples found in the area. Therefore, an in house tularemia nucleic acid method (PCR) was used on the bacterial culture. Additionally, 16S rDNA sequencing was performed and these methods identified the bacteria as F. tularensis. Fortunately, the patient recovered completely with ciprofloxacin and was discharged without any complications. Our case underlines the need to understand the limits of specific diagnostic methods, such as Maldi-tof, used in clinical laboratory settings. It also highlights the need of both clinicians and laboratory staff to be aware of the many clinical presentations of tularemia when working in an endemic area.
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Affiliation(s)
| | | | | | | | | | | | - Ilkka S Junttila
- NordLab, Oulu, Finland.
- University of Oulu, Oulu, Finland.
- Tampere University, Tampere, Finland.
- Fimlab Laboratories, Tampere, Finland.
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4
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Zhang Y, Wang Z, Wang W, Yu H, Jin M. Applications of polymerase chain reaction‑based methods for the diagnosis of plague (Review). Exp Ther Med 2022; 24:511. [DOI: 10.3892/etm.2022.11438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Yanan Zhang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Zhanli Wang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Wenrui Wang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, Inner Mongolia 010031, P.R. China
| | - Hui Yu
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Min Jin
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
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Yersinia pestis Plasminogen Activator. Biomolecules 2020; 10:biom10111554. [PMID: 33202679 PMCID: PMC7696990 DOI: 10.3390/biom10111554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 12/18/2022] Open
Abstract
The Gram-negative bacterium Yersinia pestis causes plague, a fatal flea-borne anthropozoonosis, which can progress to aerosol-transmitted pneumonia. Y. pestis overcomes the innate immunity of its host thanks to many pathogenicity factors, including plasminogen activator, Pla. This factor is a broad-spectrum outer membrane protease also acting as adhesin and invasin. Y. pestis uses Pla adhesion and proteolytic capacity to manipulate the fibrinolytic cascade and immune system to produce bacteremia necessary for pathogen transmission via fleabite or aerosols. Because of microevolution, Y. pestis invasiveness has increased significantly after a single amino-acid substitution (I259T) in Pla of one of the oldest Y. pestis phylogenetic groups. This mutation caused a better ability to activate plasminogen. In paradox with its fibrinolytic activity, Pla cleaves and inactivates the tissue factor pathway inhibitor (TFPI), a key inhibitor of the coagulation cascade. This function in the plague remains enigmatic. Pla (or pla) had been used as a specific marker of Y. pestis, but its solitary detection is no longer valid as this gene is present in other species of Enterobacteriaceae. Though recovering hosts generate anti-Pla antibodies, Pla is not a good subunit vaccine. However, its deletion increases the safety of attenuated Y. pestis strains, providing a means to generate a safe live plague vaccine.
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Sormunen JJ, Kulha N, Klemola T, Mäkelä S, Vesilahti EM, Vesterinen EJ. Enhanced threat of tick-borne infections within cities? Assessing public health risks due to ticks in urban green spaces in Helsinki, Finland. Zoonoses Public Health 2020; 67:823-839. [PMID: 32969182 PMCID: PMC7702030 DOI: 10.1111/zph.12767] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 01/23/2023]
Abstract
Most tick‐related studies in Europe have been conducted in nonurban areas, but ticks and tick‐borne pathogens also occur in urban green spaces. From a public health perspective, risks regarding tick‐borne infections should be studied in these urban areas, where contacts between infected ticks and humans may be more frequent than elsewhere, due to high human activity. We examined the risk of encountering an infected tick in urban green spaces in Helsinki, Finland. We collected ticks at nine sites throughout Helsinki, recorded the prevalence of several pathogens and identified areas with a high potential for contacts between infected ticks and humans. Moreover, we explored the relationship between the density of Borrelia burgdorferi sensu lato‐infected ticks and locally diagnosed cases of borreliosis and compared the potential for human‐tick encounters in Helsinki to those in nonurban areas in south‐western Finland. During 34.8 km of cloth dragging, 2,417 Ixodes ricinus were caught (402 adults, 1,399 nymphs and 616 larvae). From analysed nymphs, we found 11 distinct tick‐borne pathogens, with 31.5% of nymphs carrying at least one pathogen. Tick activity was highest in August and September, leading to the density of nymphs infected with B. burgdorferi s.l., and concurrently infection risk, to also be highest during this time. Nymph densities varied between the sampling sites, with obvious implications to spatial variation in infection risk. While ticks and tick‐borne pathogens were found in both Helsinki and nonurban areas in south‐western Finland, the estimates of human activity were generally higher in urban green spaces, leading to a higher potential for human‐tick contacts therein. The presence of ticks and tick‐borne pathogens and high local human activity in urban green spaces suggest that they form potential foci regarding the acquisition of tick‐borne infections. Risk areas within cities should be identified and knowledge regarding urban ticks increased.
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Affiliation(s)
| | - Niko Kulha
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland.,Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
| | - Tero Klemola
- Department of Biology, University of Turku, Turku, Finland
| | - Satu Mäkelä
- Department of Biology, University of Turku, Turku, Finland
| | | | - Eero Juhani Vesterinen
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Magriñá I, Jauset-Rubio M, Ortiz M, Tomaso H, Simonova A, Hocek M, O’Sullivan CK. Duplex Electrochemical DNA Sensor to Detect Bacillus anthracis CAP and PAG DNA Targets Based on the Incorporation of Tailed Primers and Ferrocene-Labeled dATP. ACS OMEGA 2019; 4:21900-21908. [PMID: 31891068 PMCID: PMC6933787 DOI: 10.1021/acsomega.9b02890] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/21/2019] [Indexed: 05/08/2023]
Abstract
We report the duplex amplification of two plasmid DNA markers involved in the virulence of Bacillus anthracis, CAP and PAG, and the direct electrochemical detection of these amplicons. The method consists of the simultaneous amplification of the two targets in a single-pot reaction via polymerase chain reaction (PCR) using tailed primers and ferrocene-labeled dATP. Following amplification, the PCR products hybridize to probes immobilized on electrodes in a microfabricated electrode array chip. The incorporated ferrocene labeled dATP is then detected using square wave voltammetry. We evaluated the effect of electrolyte cations, anions, and concentration to condense, bend, and shrink double-stranded DNA and their effect on the intensity of the ferrocene signal. We obtained detection limits of 0.8 and 3.4 fM for CAP and PAG targets, respectively. We successfully developed a method to detect the presence of both targets in genomic DNA extracted from real samples.
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Affiliation(s)
- Ivan Magriñá
- INTERFIBIO
Consolidated Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
| | - Miriam Jauset-Rubio
- INTERFIBIO
Consolidated Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
| | - Mayreli Ortiz
- INTERFIBIO
Consolidated Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany
| | - Anna Simonova
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
- E-mail: (M.H.)
| | - Ciara K. O’Sullivan
- INTERFIBIO
Consolidated Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
- Institució
Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
- E-mail: (C.K.O.)
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8
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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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Tick-borne pathogens in Finland: comparison of Ixodes ricinus and I. persulcatus in sympatric and parapatric areas. Parasit Vectors 2018; 11:556. [PMID: 30355331 PMCID: PMC6201636 DOI: 10.1186/s13071-018-3131-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/02/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Almost 3500 tick samples, originally collected via a nationwide citizen science campaign in 2015, were screened to reveal the prevalence and distribution of a wide spectrum of established and putative tick-borne pathogens vectored by Ixodes ricinus and I. persulcatus in Finland. The unique geographical distribution of these two tick species in Finland allowed us to compare pathogen occurrence between an I. ricinus-dominated area (southern Finland), an I. persulcatus-dominated area (northern Finland), and a sympatric area (central Finland). RESULTS Of the analysed ticks, almost 30% carried at least one pathogen and 2% carried more than one pathogen. A higher overall prevalence of tick-borne pathogens was observed in I. ricinus than in I. persulcatus: 30.0% (604/2014) versus 24.0% (348/1451), respectively. In addition, I. ricinus were more frequently co-infected than I. persulcatus: 2.4% (49/2014) versus 0.8% (12/1451), respectively. Causative agents of Lyme borreliosis, i.e. bacterial genospecies in Borrelia burgdorferi (sensu lato) group, were the most prevalent pathogens (overall 17%). "Candidatus Rickettsia tarasevichiae" was found for the first time in I. ricinus ticks and in Finnish ticks in general. Moreover, Babesia divergens, B. venatorum and "Candidatus Neoehrlichia mikurensis" were reported for the first time from the Finnish mainland. CONCLUSIONS The present study provides valuable information on the prevalence and geographical distribution of various tick-borne pathogens in I. ricinus and I. persulcatus ticks in Finland. Moreover, this comprehensive subset of ticks revealed the presence of rare and potentially dangerous pathogens. The highest prevalence of infected ticks was in the I. ricinus-dominated area in southern Finland, while the prevalence was essentially equal in sympatric and I. persulcatus-dominated areas. However, the highest infection rates for both species were in areas of their dominance, either in south or north Finland.
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Feng N, Zhou Y, Fan Y, Bi Y, Yang R, Zhou Y, Wang X. Yersinia pestis detection by loop-mediated isothermal amplification combined with magnetic bead capture of DNA. Braz J Microbiol 2018; 49:128-137. [PMID: 28887007 PMCID: PMC5790586 DOI: 10.1016/j.bjm.2017.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/30/2016] [Accepted: 03/17/2017] [Indexed: 12/25/2022] Open
Abstract
We developed a loop-mediated isothermal amplification (LAMP) assay for the detection of Y. pestis by targeting the 3a sequence on chromosome. All 11 species of the genus Yersinia were used to evaluate the specificity of LAMP and PCR, demonstrating that the primers had a high level of specificity. The sensitivity of LAMP or PCR was 2.3 or 23CFU for pure culture, whereas 2.3×104 or 2.3×106CFU for simulated spleen and lung samples. For simulated liver samples, the sensitivity of LAMP was 2.3×106CFU, but PCR was negative at the level of 2.3×107CFU. After simulated spleen and lung samples were treated with magnetic beads, the sensitivity of LAMP or PCR was 2.3×103 or 2.3×106CFU, whereas 2.3×105 or 2.3×107CFU for magnetic bead-treated liver samples. These results indicated that some components in the tissues could inhibit LAMP and PCR, and liver tissue samples had a stronger inhibition to LAMP and PCR than spleen and lung tissue samples. LAMP has a higher sensitivity than PCR, and magnetic bead capture of DNAs could remarkably increase the sensitivity of LAMP. LAMP is a simple, rapid and sensitive assay suitable for application in the field or poverty areas.
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Affiliation(s)
- Na Feng
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yazhou Zhou
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yanxiao Fan
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yujing Bi
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yusen Zhou
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China.
| | - Xiaoyi Wang
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China.
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11
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Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System. J Clin Microbiol 2016; 55:291-301. [PMID: 27847371 DOI: 10.1128/jcm.01126-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/02/2016] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a potential bioterrorism agent that is highly infectious at very low doses. Diagnosis of tularemia by blood culture and nucleic acid-based diagnostic tests is insufficiently sensitive. Here, we demonstrate a highly sensitive F. tularensis assay that incorporates sample processing and detection into a single cartridge suitable for point-of-care detection. The assay limit of detection (LOD) and dynamic range were determined in a filter-based cartridge run on the GeneXpert system. F. tularensis DNA in buffer or CFU of F. tularensis was spiked into human or macaque blood. To simulate detection in human disease, the assay was tested on blood drawn from macaques infected with F. tularensis Schu S4 at daily intervals. Assay detection was compared to that with a conventional quantitative PCR (qPCR) assay and blood culture. The assay LOD was 0.1 genome equivalents (GE) per reaction and 10 CFU/ml F. tularensis in both human and macaque blood. In infected macaques, the assay detected F. tularensis on days 1 to 4 postinfection in 21%, 17%, 60%, and 83% of macaques, respectively, compared to conventional qPCR positivity rates of 0%, 0%, 30%, and 100% and CFU detection of blood culture at 0%, 0%, 0%, and 10% positive, respectively. Assay specificity was 100%. The new cartridge-based assay can rapidly detect F. tularensis in bloodstream infections directly in whole blood at the early stages of infection with a sensitivity that is superior to that of other methods. The simplicity of the automated testing procedures may make this test suitable for rapid point-of-care detection.
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12
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Seo Y, Kim JE, Jeong Y, Lee KH, Hwang J, Hong J, Park H, Choi J. Engineered nanoconstructs for the multiplexed and sensitive detection of high-risk pathogens. NANOSCALE 2016; 8:1944-1951. [PMID: 26462853 DOI: 10.1039/c5nr06230f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Many countries categorize the causative agents of severe infectious diseases as high-risk pathogens. Given their extreme infectivity and potential to be used as biological weapons, a rapid and sensitive method for detection of high-risk pathogens (e.g., Bacillus anthracis, Francisella tularensis, Yersinia pestis, and Vaccinia virus) is highly desirable. Here, we report the construction of a novel detection platform comprising two units: (1) magnetic beads separately conjugated with multiple capturing antibodies against four different high-risk pathogens for simple and rapid isolation, and (2) genetically engineered apoferritin nanoparticles conjugated with multiple quantum dots and detection antibodies against four different high-risk pathogens for signal amplification. For each high-risk pathogen, we demonstrated at least 10-fold increase in sensitivity compared to traditional lateral flow devices that utilize enzyme-based detection methods. Multiplexed detection of high-risk pathogens in a sample was also successful by using the nanoconstructs harboring the dye molecules with fluorescence at different wavelengths. We ultimately envision the use of this novel nanoprobe detection platform in future applications that require highly sensitive on-site detection of high-risk pathogens.
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Affiliation(s)
- Youngmin Seo
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea.
| | - Ji-eun Kim
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea.
| | - Yoon Jeong
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea.
| | - Kwan Hong Lee
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea. and Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, Korea
| | - Jangsun Hwang
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea.
| | - Jongwook Hong
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea. and Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, Korea
| | - Hansoo Park
- School of Integrative Engineering, Chung-Ang University, Seoul 156-756, Korea.
| | - Jonghoon Choi
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea. and Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, Korea
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13
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Mölsä M, Hemmilä H, Katz A, Niemimaa J, Forbes KM, Huitu O, Stuart P, Henttonen H, Nikkari S. Monitoring biothreat agents (Francisella tularensis, Bacillus anthracis and Yersinia pestis) with a portable real-time PCR instrument. J Microbiol Methods 2015; 115:89-93. [PMID: 26043838 DOI: 10.1016/j.mimet.2015.05.026] [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: 03/19/2015] [Revised: 05/29/2015] [Accepted: 05/29/2015] [Indexed: 11/17/2022]
Abstract
In the event of suspected releases or natural outbreaks of contagious pathogens, rapid identification of the infectious agent is essential for appropriate medical intervention and disease containment. The purpose of this study was to compare the performance of a novel portable real-time PCR thermocycler, PikoReal™, to the standard real-time PCR thermocycler, Applied Biosystems® 7300 (ABI 7300), for the detection of three high-risk biothreat bacterial pathogens: Francisella tularensis, Bacillus anthracis and Yersinia pestis. In addition, a novel confirmatory real-time PCR assay for the detection of F. tularensis is presented and validated. The results show that sensitivity of the assays, based on a dilution series, for the three infectious agents ranged from 1 to 100 fg of target DNA with both instruments. No cross-reactivity was revealed in specificity testing. Duration of the assays with the PikoReal and ABI 7300 systems were 50 and 100 min, respectively. In field testing for F. tularensis, results were obtained with the PikoReal system in 95 min, as the pre-PCR preparation, including DNA extraction, required an additional 45 min. We conclude that the PikoReal system enables highly sensitive and rapid on-site detection of biothreat agents under field conditions, and may be a more efficient alternative to conventional diagnostic methods.
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Affiliation(s)
- Markos Mölsä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland.
| | - Heidi Hemmilä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland.
| | - Anna Katz
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland.
| | | | | | - Otso Huitu
- Natural Resources Institute Finland, Suonenjoki, Finland.
| | - Peter Stuart
- Natural Resources Institute Finland, Suonenjoki, Finland.
| | | | - Simo Nikkari
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland.
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14
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Rossow H, Forbes KM, Tarkka E, Kinnunen PM, Hemmilä H, Huitu O, Nikkari S, Henttonen H, Kipar A, Vapalahti O. Experimental Infection of voles with Francisella tularensis indicates their amplification role in tularemia outbreaks. PLoS One 2014; 9:e108864. [PMID: 25271640 PMCID: PMC4182746 DOI: 10.1371/journal.pone.0108864] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/26/2014] [Indexed: 11/21/2022] Open
Abstract
Tularemia outbreaks in humans have been linked to fluctuations in rodent population density, but the mode of bacterial maintenance in nature is unclear. Here we report on an experiment to investigate the pathogenesis of Francisella tularensis infection in wild rodents, and thereby assess their potential to spread the bacterium. We infected 20 field voles (Microtus agrestis) and 12 bank voles (Myodes glareolus) with a strain of F. tularensis ssp. holarctica isolated from a human patient. Upon euthanasia or death, voles were necropsied and specimens collected for histological assessment and identification of bacteria by immunohistology and PCR. Bacterial excretion and a rapid lethal clinical course with pathological changes consistent with bacteremia and tissue necrosis were observed in infected animals. The results support a role for voles as an amplification host of F. tularensis, as excreta and, in particular, carcasses with high bacterial burden could serve as a source for environmental contamination.
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Affiliation(s)
- Heidi Rossow
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Kristian M. Forbes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Finnish Forest Research Institute, Vantaa, Finland
| | - Eveliina Tarkka
- Division of Clinical Microbiology, Helsinki University Hospital Laboratory (HUSLAB), Helsinki, Finland
| | - Paula M. Kinnunen
- Centre for Biothreat Preparedness, Centre for Military Medicine, Finnish Defence Forces, Helsinki, Finland
| | - Heidi Hemmilä
- Centre for Biothreat Preparedness, Centre for Military Medicine, Finnish Defence Forces, Helsinki, Finland
| | - Otso Huitu
- Finnish Forest Research Institute, Vantaa, Finland
| | - Simo Nikkari
- Centre for Biothreat Preparedness, Centre for Military Medicine, Finnish Defence Forces, Helsinki, Finland
| | | | - Anja Kipar
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Centre for Laboratory Animal Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- School of Veterinary Science and Department of Infection Biology, Institute of Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Olli Vapalahti
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, Helsinki University Hospital Laboratory (HUSLAB), Helsinki, Finland
- Department of Virology, Haartman Institute, University of Helsinki, Helsinki, Finland
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15
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Balakrishna K, Tuteja U, Murali H, Batra HV. Application of r-PFE hyperimmune sera for concurrent detection of Bacillus anthracis, Yersinia pestis
and staphylococcal enterotoxin B. J Appl Microbiol 2014; 116:1465-73. [DOI: 10.1111/jam.12465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 11/30/2022]
Affiliation(s)
- K. Balakrishna
- Division of Microbiology; Defence Food Research Laboratory; Mysore India
| | - U. Tuteja
- Division of Microbiology; Defence Research and Development Establishment; Gwalior India
| | - H.S. Murali
- Division of Microbiology; Defence Food Research Laboratory; Mysore India
| | - H. V. Batra
- Division of Microbiology; Defence Food Research Laboratory; Mysore India
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16
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Rossow H, Sissonen S, Koskela KA, Kinnunen PM, Hemmilä H, Niemimaa J, Huitu O, Kuusi M, Vapalahti O, Henttonen H, Nikkari S. Detection of Francisella tularensis in voles in Finland. Vector Borne Zoonotic Dis 2014; 14:193-8. [PMID: 24575824 DOI: 10.1089/vbz.2012.1255] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Francisella tularensis is a highly virulent intracellular bacterium causing the zoonotic disease tularemia. It recurrently causes human and animal outbreaks in northern Europe, including Finland. Although F. tularensis infects several mammal species, only rodents and lagomorphs seem to have importance in its ecology. Peak densities of rodent populations may trigger tularemia outbreaks in humans; however, it is still unclear to which extent rodents or other small mammals maintain F. tularensis in nature. The main objective of this study was to obtain information about the occurrence of F. tularensis in small mammals in Finland. We snap-trapped 547 wild small mammals representing 11 species at 14 locations around Finland during 6 years and screened them for the presence of F. tularensis DNA using PCR analysis. High copy number of F. tularensis-specific DNA was detected in tissue samples of five field voles (Microtus agrestis) originating from one location and 2 years. According to DNA sequences of the bacterial 23S ribosomal RNA gene amplified from F. tularensis-infected voles, the infecting agent belongs to the subspecies holarctica. To find out the optimal tissue for tularemia screening in voles, we compared the amounts of F. tularensis DNA in lungs, liver, spleen, and kidney of the infected animals. F. tularensis DNA was detectable in high levels in all four organs except for one animal, whose kidney was F. tularensis DNA-negative. Thus, at least liver, lung, and spleen seem suitable for F. tularensis screening in voles. Thus, liver, lung, and spleen all seem suitable for F. tularensis screening in voles. In conclusion, field voles can be heavily infected with F. tularensis subsp. holarctica and thus potentially serve as the source of infection in humans and other mammals.
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Affiliation(s)
- Heidi Rossow
- 1 Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki , Helsinki, Finland
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17
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Cross-institute evaluations of inhibitor-resistant PCR reagents for direct testing of aerosol and blood samples containing biological warfare agent DNA. Appl Environ Microbiol 2013; 80:1322-9. [PMID: 24334660 DOI: 10.1128/aem.03478-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid pathogen detection is crucial for the timely introduction of therapeutics. Two groups (one in the United Kingdom and one in the United States) independently evaluated inhibitor-resistant PCR reagents for the direct testing of substrates. In the United Kingdom, a multiplexed Bacillus anthracis (target) and Bacillus subtilis (internal-control) PCR was used to evaluate 4 reagents against 5 PCR inhibitors and down-selected the TaqMan Fast Virus 1-Step master mix (Life Technologies Inc.). In the United States, four real-time PCR assays (targeting B. anthracis, Brucella melitensis, Venezuelan equine encephalitis virus [VEEV], and Orthopoxvirus spp.) were used to evaluate 5 reagents (plus the Fast Virus master mix) against buffer, blood, and soil samples and down-selected the KAPA Blood Direct master mix (KAPA Biosystems Inc.) with added Platinum Taq (Life Technologies). The down-selected reagents underwent further testing. In the United Kingdom experiments, both reagents were tested against seven contrived aerosol collector samples containing B. anthracis Ames DNA and B. subtilis spores from a commercial formulation (BioBall). In PCR assays with reaction mixtures containing 40% crude sample, an airfield-collected sample induced inhibition of the B. subtilis PCR with the KAPA reagent and complete failure of both PCRs with the Fast Virus reagent. However, both reagents allowed successful PCR for all other samples-which inhibited PCRs with a non-inhibitor-resistant reagent. In the United States, a cross-assay limit-of-detection (LoD) study in blood was conducted. The KAPA Blood Direct reagent allowed the detection of agent DNA (by four PCRs) at higher concentrations of blood in the reaction mixture (2.5%) than the Fast Virus reagent (0.5%), although LoDs differed between assays and reagent combinations. Across both groups, the KAPA Blood Direct reagent was determined to be the optimal reagent for inhibition relief in PCR.
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18
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Safari Foroshani N, Karami A, Pourali F. Simultaneous and Rapid Detection of Salmonella typhi, Bacillus anthracis, and Yersinia pestis by Using Multiplex Polymerase Chain Reaction (PCR). IRANIAN RED CRESCENT MEDICAL JOURNAL 2013; 15:e9208. [PMID: 24719692 PMCID: PMC3971784 DOI: 10.5812/ircmj.9208] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 06/02/2013] [Accepted: 07/14/2013] [Indexed: 11/16/2022]
Abstract
BACKGROUND Salmonella typhi, Bacillus anthracis, and Yersinia pestis are some serious human pathogens, which their early diagnosis is of great importance. Salmonella typhi, Bacillus anthracis, and Yersinia pestis cause typhoid fever, anthrax, and plague respectively. These bacteria can be used to make biologic weapons. OBJECTIVES In this study, we designed a new and rapid diagnostic method based on Uniplex and Multiplex PCR method. MATERIALS AND METHODS Uniplex and multiplex Polymerase Chain Reaction (PCR) were conducted on virulent genes of hp and invA of Salmonella typhimurium, Pa and chr of Bacillus anthracis, and pla of Yersinia pestis. A genome from other bacteria was used to study the specificity of the primer and the PCR test. RESULTS Standard strains used in this study showed that primers were specific. As for sensitivity, it was shown that this method can diagnose 1-10 copies of the genome, or 1-10 Colony Forming Units (CFU) for each of the bacteria. All pieces except anthrax were sequenced in PCR to validate the product. DNA fragment resulted from Bacillus anthracis was confirmed by restriction enzyme digestions. CONCLUSION The designed methods are accurate, rapid, and inexpensive to find and differentiate these bacteria from similar bacteria. They can be applied for rapid diagnosis of these agents in different specimens, and bioterrorism cases.
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Affiliation(s)
| | - Ali Karami
- Research Center of Molecular Biology, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Corresponding Author: Ali Karami, Ali Karami, Research Center of Molecular Biology, Baqiyatallah University of Medical Sciences, P.O. Box: 19945-581, Tehran, IR Iran. Tel: +98-2188039883, Fax: +98-2188057023., E-mail:
| | - Fatemeh Pourali
- Research Center of Molecular Biology, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
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19
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Evaluation of inhibitor-resistant real-time PCR methods for diagnostics in clinical and environmental samples. PLoS One 2013; 8:e73845. [PMID: 24040090 PMCID: PMC3767612 DOI: 10.1371/journal.pone.0073845] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/24/2013] [Indexed: 11/25/2022] Open
Abstract
Polymerase chain reaction (PCR) is commonly used for pathogen detection in clinical and environmental samples. These sample matrices often contain inhibitors of PCR, which is a primary reason for sample processing; however, the purification process is highly inefficient, becoming unacceptable at lower signature concentrations. One potential solution is direct PCR assessment without sample processing. Here, we evaluated nine inhibitor-resistant PCR reagents for direct detection of Francisella tularensis in seven different clinical and environmental samples using an established real-time PCR assay to assess ability to overcome PCR inhibition. While several of these reagents were designed for standard PCR, the described inhibitor resistant properties (ex. Omni Klentaq can amplify target DNA samples of up to 20% whole blood or soil) led to our evaluation with real-time PCR. A preliminary limit of detection (LOD) was determined for each chemistry in whole blood and buffer, and LODs (20 replicates) were determined for the top five chemistries in each matrix (buffer, whole blood, sputum, stool, swab, soil, and sand). Not surprisingly, no single chemistry performed the best across all of the different matrices evaluated. For instance, Phusion Blood Direct PCR Kit, Phire Hot Start DNA polymerase, and Phire Hot Start DNA polymerase with STR Boost performed best for direct detection in whole blood while Phire Hot Start DNA polymerase with STR Boost were the only reagents to yield an LOD in the femtogram range for soil. Although not the best performer across all matrices, KAPA Blood PCR kit produced the most consistent results among the various conditions assessed. Overall, while these inhibitor resistant reagents show promise for direct amplification of complex samples by real-time PCR, the amount of template required for detection would not be in a clinically relevant range for most matrices.
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20
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Janse I, Hamidjaja RA, Reusken C. Yersinia pestis plasminogen activator gene homolog in rat tissues. Emerg Infect Dis 2013; 19:342-4. [PMID: 23347636 PMCID: PMC3559043 DOI: 10.3201/eid1902.120659] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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21
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Hsu HL, Huang HH, Liang CC, Lin HC, Liu WT, Lin FP, Kau JH, Sun KH. Suspension Bead Array of the Single-Stranded Multiplex Polymerase Chain Reaction Amplicons for Enhanced Identification and Quantification of Multiple Pathogens. Anal Chem 2013; 85:5562-8. [DOI: 10.1021/ac400778b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hui-Ling Hsu
- Department of Biotechnology
and Laboratory Science in Medicine, Infection and Immunity Center, National Yang-Ming University, Taipei, Taiwan, Republic
of China
| | | | | | | | | | | | | | - Kuang-Hui Sun
- Department of Biotechnology
and Laboratory Science in Medicine, Infection and Immunity Center, National Yang-Ming University, Taipei, Taiwan, Republic
of China
- Department of
Education and
Research, Taipei City Hospital, Taipei,
Taiwan, Republic of China
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22
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Wang DB, Tian B, Zhang ZP, Deng JY, Cui ZQ, Yang RF, Wang XY, Wei HP, Zhang XE. Rapid detection of Bacillus anthracis spores using a super-paramagnetic lateral-flow immunological detectionsystem. Biosens Bioelectron 2013. [DOI: 10.1016/j.bios.2012.10.088] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Thavachelvam K, Tuteja U, Sarika K, Nagendra S, Kumar S. Reverse line blot macroarray for simultaneous detection and characterization of four biological warfare agents. Indian J Microbiol 2012; 53:41-7. [PMID: 24426077 DOI: 10.1007/s12088-012-0330-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/29/2012] [Indexed: 11/26/2022] Open
Abstract
The need for a rapid detection and characterization of biowarfare (BW) agents cannot be over emphasized. With diverse array of potential BW pathogen available presently, rapid identification of the pathogen is crucial, so that specific therapy and control measures can be initiated. We have developed a multiplex polymerase chain reaction based reverse line blot macroarray to simultaneously detect four pathogens of BW importance viz. Bacillus anthracis, Yersinia pestis, Brucella melitensis and Burkholderia pseudomallei. The multiplex PCR utilizes 14 pairs of primers targeting 18 specific markers. These markers include genes which are genus specific, species-specific chromosomal sequences and virulence markers of plasmid origin. The assay was evaluated on various human, environment and animal isolates. The assay w successful in simultaneous detection and characterization of isolates of the four pathogens on as a single platform with sensitivity ranging from 0.3 pg to 0.3 ng of genomic DNA. The assay was able to detect 5 × 10(2) cfu/ml for B. anthracis, 8 × 10(2) cfu/ml for Yersinia sp., 1.4 × 10(2) cfu/ml for B. melitensis and 4 × 10(2) cfu/ml for B. pseudomallei.
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Affiliation(s)
- Kulanthaivel Thavachelvam
- Division of Microbiology, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
| | - Urmil Tuteja
- Division of Microbiology, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
| | - Kumari Sarika
- Division of Microbiology, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
| | - Suryanarayana Nagendra
- Division of Microbiology, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
| | - Subodh Kumar
- Division of Microbiology, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
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Comparison of nucleic acid extraction platforms for detection of select biothreat agents for use in clinical resource limited settings. J Microbiol Methods 2012; 91:179-83. [PMID: 22750394 DOI: 10.1016/j.mimet.2012.06.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/14/2012] [Accepted: 06/14/2012] [Indexed: 10/28/2022]
Abstract
High-quality nucleic acids are critical for optimal PCR-based diagnostics and pathogen detection. Rapid sample processing time is important for the earliest administration of therapeutic and containment measures, especially in the case of biothreat agents. In this context, we compared the Fujifilm QuickGene-Mini80 to Qiagen's QIAamp Mini Purification kits for extraction of DNA and RNA for potential use in austere settings. Qiagen (QIAamp) column-based extraction is the currently recommended purification platform by United States Army Medical Research Institute for Infectious Diseases for both DNA and RNA extraction. However, this sample processing system requires dedicated laboratory equipment including a centrifuge. In this study, we investigated the QuickGene-Mini80, which does not require centrifugation, as a suitable platform for nucleic acid extraction for use in resource-limited locations. Quality of the sample extraction was evaluated using pathogen-specific, real-time PCR assays for nucleic acids extracted from viable and γ-irradiated Bacillus anthracis, Yersinia pestis, vaccinia virus, Venezuelan equine encephalitis virus, or B. anthracis spores in buffer or human whole blood. QuickGene-Mini80 and QIAamp performed similarly for DNA extraction regardless of organism viability. It was noteworthy that γ-irradiation did not have a significant impact on real-time PCR for organism detection. Comparison with QIAamp showed a less than adequate performance of the Fujifilm instrument for RNA extraction. However, QuickGene-Mini80 remains a viable alternative to QIAamp for DNA extraction for use in remote settings due to extraction quality, time efficiency, reduced instrument requirements, and ease of use.
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Scasciamacchia S, Serrecchia L, Giangrossi L, Garofolo G, Balestrucci A, Sammartino G, Fasanella A. Plague epidemic in the Kingdom of Naples, 1656-1658. Emerg Infect Dis 2012; 18:186-8. [PMID: 22260781 PMCID: PMC3310102 DOI: 10.3201/eid1801.110597] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Woubit A, Yehualaeshet T, Habtemariam T, Samuel T. Novel genomic tools for specific and real-time detection of biothreat and frequently encountered foodborne pathogens. J Food Prot 2012; 75:660-70. [PMID: 22488053 PMCID: PMC3524339 DOI: 10.4315/0362-028x.jfp-11-480] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The bacterial genera Escherichia, Salmonella, Shigella, Vibrio, Yersinia, and Francisella include important food safety and biothreat agents. By extensive mining of the whole genome and protein databases of diverse, closely and distantly related bacterial species and strains, we have identified novel genome regions, which we utilized to develop a rapid detection platform for these pathogens. The specific genomic targets we have identified to design the primers in Francisella tularensis subsp. tularensis, F. tularensis subsp. novicida, Shigella dysenteriae, Salmonella enterica serovar Typhimurium, Vibrio cholerae, Yersinia pestis, and Yersinia pseudotuberculosis contained either known genes or putative proteins. Primer sets were designed from the target regions for use in real-time PCR assays to detect specific biothreat pathogens at species or strain levels. The primer sets were first tested by in silico PCR against whole-genome sequences of different species, subspecies, or strains and then by in vitro PCR against genomic DNA preparations from 23 strains representing six biothreat agents (Escherichia coli O157:H7 strain EDL 933, Shigella dysenteriae, S. enterica serovar Typhi, F. tularensis subsp. tularensis, V. cholerae, and Y. pestis) and six foodborne pathogens (Salmonella Typhimurium, Salmonella Saintpaul, Shigella sonnei, F. tularensis subsp. novicida, Vibrio parahaemolyticus, and Y. pseudotuberculosis). Each pathogen was specifically identifiable at the genus and species levels. Sensitivity assays performed with purified DNA showed the lowest detection limit of 128 fg of DNA/μl for F. tularensis subsp. tularensis. A preliminary test to detect Shigella organisms in a milk matrix also enabled the detection of 6 to 60 CFU/ml. These new tools could ultimately be used to develop platforms to simultaneously detect these pathogens.
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Affiliation(s)
- Abdela Woubit
- Department of Pathobiology, College of Veterinary Medicine, Nursing and Allied Health, Tuskegee University, Tuskegee, AL 36088, USA
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27
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Wielinga PR, de Heer L, de Groot A, Hamidjaja RA, Bruggeman G, Jordan K, van Rotterdam BJ. Evaluation of DNA extraction methods for Bacillus anthracis spores spiked to food and feed matrices at biosafety level 3 conditions. Int J Food Microbiol 2011; 150:122-7. [DOI: 10.1016/j.ijfoodmicro.2011.07.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 05/25/2011] [Accepted: 07/21/2011] [Indexed: 11/30/2022]
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28
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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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29
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Riehm JM, Rahalison L, Scholz HC, Thoma B, Pfeffer M, Razanakoto LM, Al Dahouk S, Neubauer H, Tomaso H. Detection of Yersinia pestis using real-time PCR in patients with suspected bubonic plague. Mol Cell Probes 2011; 25:8-12. [DOI: 10.1016/j.mcp.2010.09.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 09/28/2010] [Accepted: 09/29/2010] [Indexed: 10/19/2022]
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30
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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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Irenge LM, Durant JF, Tomaso H, Pilo P, Olsen JS, Ramisse V, Mahillon J, Gala JL. Development and validation of a real-time quantitative PCR assay for rapid identification of Bacillus anthracis in environmental samples. Appl Microbiol Biotechnol 2010; 88:1179-92. [PMID: 20827474 DOI: 10.1007/s00253-010-2848-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 08/13/2010] [Accepted: 08/14/2010] [Indexed: 11/28/2022]
Abstract
A real-time polymerase chain reaction (PCR) assay was developed for rapid identification of Bacillus anthracis in environmental samples. These samples often harbor Bacillus cereus bacteria closely related to B. anthracis, which may hinder its specific identification by resulting in false positive signals. The assay consists of two duplex real-time PCR: the first PCR allows amplification of a sequence specific of the B. cereus group (B. anthracis, B. cereus, Bacillus thuringiensis, Bacillus weihenstephanensis, Bacillus pseudomycoides, and Bacillus mycoides) within the phosphoenolpyruvate/sugar phosphotransferase system I gene and a B. anthracis specific single nucleotide polymorphism within the adenylosuccinate synthetase gene. The second real-time PCR assay targets the lethal factor gene from virulence plasmid pXO1 and the capsule synthesis gene from virulence plasmid pXO2. Specificity of the assay is enhanced by the use of minor groove binding probes and/or locked nucleic acids probes. The assay was validated on 304 bacterial strains including 37 B. anthracis, 67 B. cereus group, 54 strains of non-cereus group Bacillus, and 146 Gram-positive and Gram-negative bacteria strains. The assay was performed on various environmental samples spiked with B. anthracis or B. cereus spores. The assay allowed an accurate identification of B. anthracis in environmental samples. This study provides a rapid and reliable method for improving rapid identification of B. anthracis in field operational conditions.
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Affiliation(s)
- Léonid M Irenge
- Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium
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Pelletier N, La Scola B. Détection moléculaire et immunologique des bactéries dans le cadre du bioterrorisme. Med Mal Infect 2010; 40:506-16. [DOI: 10.1016/j.medmal.2010.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 02/04/2010] [Accepted: 03/08/2010] [Indexed: 12/18/2022]
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Wielinga PR, Hamidjaja RA, Agren J, Knutsson R, Segerman B, Fricker M, Ehling-Schulz M, de Groot A, Burton J, Brooks T, Janse I, van Rotterdam B. A multiplex real-time PCR for identifying and differentiating B. anthracis virulent types. Int J Food Microbiol 2010; 145 Suppl 1:S137-44. [PMID: 20826037 DOI: 10.1016/j.ijfoodmicro.2010.07.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 07/27/2010] [Accepted: 07/31/2010] [Indexed: 11/18/2022]
Abstract
Bacillus anthracis is closely related to the endospore forming bacteria Bacillus cereus and Bacillus thuringiensis. For accurate detection of the life threatening pathogen B. anthracis, it is essential to distinguish between these three species. Here we present a novel multiplex real-time PCR for simultaneous specific identification of B. anthracis and discrimination of different B. anthracis virulence types. Specific B. anthracis markers were selected by whole genome comparison and different sets of primers and probes with optimal characteristic for multiplex detection of the B. anthracis chromosome, the B. anthracis pXO1 and pXO2 plasmids and an internal control (IC) were designed. The primer sets were evaluated using a panel of B. anthracis strains and exclusivity was tested using genetically closely related B. cereus strains. The robustness of final primer design was evaluated by laboratories in three different countries using five different real-time PCR thermocyclers. Testing of a panel of more than 20 anthrax strains originating from different locations around the globe, including the recent Swedish anthrax outbreak strain, showed that all strains were detected correctly.
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Affiliation(s)
- Peter R Wielinga
- National Institute for Public Health and the Environment, Centre for infectious Disease Control, Laboratory for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, PO Box 1, Bilthoven, The Netherlands.
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Qu S, Shi Q, Zhou L, Guo Z, Zhou D, Zhai J, Yang R. Ambient stable quantitative PCR reagents for the detection of Yersinia pestis. PLoS Negl Trop Dis 2010; 4:e629. [PMID: 20231881 PMCID: PMC2834737 DOI: 10.1371/journal.pntd.0000629] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 01/25/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Although assays for detecting Yersinia pestis using TaqMan probe-based real-time PCR have been developed for years, little is reported on room-temperature-stable PCR reagents, which will be invaluable for field epidemic surveillance, immediate response to public health emergencies, counter-bioterrorism investigation, etc. In this work, a set of real-time PCR reagents for rapid detection of Y. pestis was developed with extraordinary stability at 37 degrees C. METHODS/PRINCIPAL FINDINGS TaqMan-based real-time PCR assays were developed using the primers and probes targeting the 3a sequence in the chromosome and the F1 antigen gene caf1 in the plasmid pMT1of Y. pestis, respectively. Then, carbohydrate mixtures were added to the PCR reagents, which were later vacuum-dried for stability evaluation. The vacuum-dried reagents were stable at 37 degrees C for at least 49 days for a lower concentration of template DNA (10 copies/microl), and up to 79 days for higher concentrations (> or =10(2) copies/microl). The reagents were used subsequently to detect soil samples spiked with Y. pestis vaccine strain EV76, and 5x10(4) CFU per gram of soil could be detected by both 3a- and caf1-based PCR reagents. In addition, a simple and efficient method for soil sample processing is presented here. CONCLUSIONS/SIGNIFICANCE The vacuum-dried reagents for real-time PCR maintain accuracy and reproducibility for at least 49 days at 37 degrees C, indicating that they can be easily transported at room temperature for field application if the machine for performing real-time PCR is available. This dry reagent is of great significance for routine plague surveillance.
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Affiliation(s)
- Shi Qu
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qinghai Shi
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Zhou
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhaobiao Guo
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Junhui Zhai
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Wang DB, Yang R, Zhang ZP, Bi LJ, You XY, Wei HP, Zhou YF, Yu Z, Zhang XE. Detection of B. anthracis spores and vegetative cells with the same monoclonal antibodies. PLoS One 2009; 4:e7810. [PMID: 19915677 PMCID: PMC2773009 DOI: 10.1371/journal.pone.0007810] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 10/18/2009] [Indexed: 11/18/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax disease, could be used as a biothreat reagent. It is vital to develop a rapid, convenient method to detect B. anthracis. In the current study, three high affinity and specificity monoclonal antibodies (mAbs, designated 8G3, 10C6 and 12F6) have been obtained using fully washed B. anthracis spores as an immunogen. These mAbs, confirmed to direct against EA1 protein, can recognize the surface of B. anthracis spores and intact vegetative cells with high affinity and species-specificity. EA1 has been well known as a major S-layer component of B. anthracis vegetative cells, and it also persistently exists in the spore preparations and bind tightly to the spore surfaces even after rigorous washing. Therefore, these mAbs can be used to build a new and rapid immunoassay for detection of both life forms of B. anthracis, either vegetative cells or spores.
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Affiliation(s)
- Dian-Bing Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Agromicrobiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Zhi-Ping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Li-Jun Bi
- State Key Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiang-Yu You
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Hong-Ping Wei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ya-Feng Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ziniu Yu
- State Key Laboratory of Agromicrobiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xian-En Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- * E-mail:
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Koskela KA, Matero P, Blatny JM, Fykse EM, Olsen JS, Nuotio LO, Nikkari S. A multiplatform real-time polymerase chain reaction detection assay for Vibrio cholerae. Diagn Microbiol Infect Dis 2009; 65:339-44. [DOI: 10.1016/j.diagmicrobio.2009.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 06/18/2009] [Accepted: 07/07/2009] [Indexed: 10/20/2022]
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Schroeder K, Nitsche A. Multicolour, multiplex real-time PCR assay for the detection of human-pathogenic poxviruses. Mol Cell Probes 2009; 24:110-3. [PMID: 19879351 DOI: 10.1016/j.mcp.2009.10.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Revised: 10/15/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
Abstract
After eradication of variola virus, one of the most dangerous infectious diseases affecting mankind, today other poxviruses of different genera can cause infection in humans. These viruses include human-specific molluscipoxviruses as well as zoonotic orthopoxviruses and parapoxviruses. While non-variola orthopoxvirus infections mostly cause mild symptoms in immunocompetent persons, they can evoke severe disease in immunocompromised patients. Since the typical poxviral skin lesions are rarely diagnosed by physicians, PCR-based identification of suspected poxviruses is often required. To simplify the PCR-based diagnosis of human-pathogenic poxviruses, we established a multicolour multiplex real-time PCR that simultaneously detects and differentiates human-pathogenic poxviruses in one reaction. Using 5' nuclease probes labelled with FAM for orthopoxviruses, VIC for parapoxviruses and FAM and VIC for molluscipoxviruses, respectively, amplification of poxviral DNA resulted in a genus-specific reporter-dye profile. Validation with 36 human clinical specimens and DNA of pathogens causing pox-like skin lesions demonstrated the specificity of the assay. Probit analysis revealed a limit of detection of 9.7, 22.08 and 28.1 copies/assay (95% CI) for molluscipoxvirus, orthopoxvirus and parapoxvirus DNA, respectively. The combinatorial multicolour strategy applied has the potential to be used in further applications targeting even more than three pathogens.
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Affiliation(s)
- Kati Schroeder
- Robert Koch-Institut, Centre for Biological Safety 1, Nordufer 20, 13353 Berlin, Germany
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Use of molecular beacons and multi-allelic real-time PCR for detection of and discrimination between virulent Bacillus anthracis and other Bacillus isolates. J Microbiol Methods 2009; 78:45-53. [DOI: 10.1016/j.mimet.2009.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 04/10/2009] [Accepted: 04/14/2009] [Indexed: 11/22/2022]
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Matero P, Pasanen T, Laukkanen R, Tissari P, Tarkka E, Vaara M, Skurnik M. Real-time multiplex PCR assay for detection of Yersinia pestis and Yersinia pseudotuberculosis. APMIS 2009; 117:34-44. [PMID: 19161535 DOI: 10.1111/j.1600-0463.2008.00013.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A multiplex real-time polymerase chain reaction (PCR) assay was developed for the detection of Yersinia pestis and Yersinia pseudotuberculosis. The assay includes four primer pairs, two of which are specific for Y. pestis, one for Y. pestis and Y. pseudotuberculosis and one for bacteriophage lambda; the latter was used as an internal amplification control. The Y. pestis-specific target genes in the assay were ypo2088, a gene coding for a putative methyltransferase, and the pla gene coding for the plasminogen activator. In addition, the wzz gene was used as a target to specifically identify both Y. pestis and the closely related Y. pseudotuberculosis group. The primer and probe sets described for the different genes can be used either in single or in multiplex PCR assays because the individual probes were designed with different fluorochromes. The assays were found to be both sensitive and specific; the lower limit of the detection was 10-100 fg of extracted Y. pestis or Y. pseudotuberculosis total DNA. The sensitivity of the tetraplex assay was determined to be 1 cfu for the ypo2088 and pla probe labelled with FAM and JOE fluorescent dyes, respectively.
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Affiliation(s)
- Pirjo Matero
- Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland
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Abstract
Objectifs Depuis les dix dernières années, l’introduction de la biologie moléculaire et l’automatisation ont radicalement changé les pratiques dans les laboratoires de microbiologie clinique. L’amélioration de la communication entre les microbiologistes et les cliniciens ainsi que les évolutions technologiques telles que la standardisation et le développement de tests diagnostics plus rapides ont conduit à une réorganisation des laboratoires de microbiologie. Méthodes Jusqu’à présent la prescription des examens ciblait un diagnostic étiologique précis, actuellement l’évolution se fait vers le diagnostic par syndrome incluant un panel de tests regroupant les étiologies responsables d’un syndrome donné y compris les pathogènes émergents. Résultats et conclusions Dans cette revue, nous avons résumé les développements technologiques les plus récents en matière de diagnostic microbiologique adapté au diagnostic par syndrome incluant les stratégies de diagnostic exhaustif, les DNA microarray et les microarray antigéniques.
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He J, Kraft AJ, Fan J, Van Dyke M, Wang L, Bose ME, Khanna M, Metallo JA, Henrickson KJ. Simultaneous Detection of CDC Category "A" DNA and RNA Bioterrorism Agents by Use of Multiplex PCR & RT-PCR Enzyme Hybridization Assays. Viruses 2009; 1:441-459. [PMID: 20224751 PMCID: PMC2836126 DOI: 10.3390/v1030441] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 09/22/2009] [Accepted: 10/20/2009] [Indexed: 11/16/2022] Open
Abstract
Assays to simultaneously detect multiple potential agents of bioterrorism are limited. Two multiplex PCR and RT-PCR enzyme hybridization assays (mPCR-EHA, mRT-PCR-EHA) were developed to simultaneously detect many of the CDC category "A" bioterrorism agents. The "Bio T" DNA assay was developed to detect: Variola major (VM), Bacillus anthracis (BA), Yersinia pestis (YP), Francisella tularensis (FT) and Varicella zoster virus (VZV). The "Bio T" RNA assay (mRT-PCR-EHA) was developed to detect: Ebola virus (Ebola), Lassa fever virus (Lassa), Rift Valley fever (RVF), Hantavirus Sin Nombre species (HSN) and dengue virus (serotypes 1-4). Sensitivity and specificity of the 2 assays were tested by using genomic DNA, recombinant plasmid positive controls, RNA transcripts controls, surrogate (spiked) clinical samples and common respiratory pathogens. The analytical sensitivity (limit of detection (LOD)) of the DNA asssay for genomic DNA was 1x10(0)~1x10(2) copies/mL for BA, FT and YP. The LOD for VZV whole organism was 1x10(-2) TCID(50)/mL. The LOD for recombinant controls ranged from 1x10(2)~1x10(3)copies/mL for BA, FT, YP and VM. The RNA assay demonstrated LOD for RNA transcript controls of 1x10(4)~1x10(6) copies/mL without extraction and 1x10(5)~1x10(6) copies/mL with extraction for Ebola, RVF, Lassa and HSN. The LOD for dengue whole organisms was ~1x10(-4) dilution for dengue 1 and 2, 1x10(4) LD(50)/mL and 1x10(2) LD(50)/mL for dengue 3 and 4. The LOD without extraction for recombinant plasmid DNA controls was ~1x10(3) copies/mL (1.5 input copies/reaction) for Ebola, RVF, Lassa and HSN. No cross-reactivity of primers and probes used in both assays was detected with common respiratory pathogens or between targeted analytes. Clinical sensitivity was estimated using 264 surrogate clinical samples tested with the BioT DNA assay and 549 samples tested with the BioT RNA assay. The clinical specificity is 99.6% and 99.8% for BioT DNA assay and BioT RNA assay, respectively. The surrogate sensitivities of these two assays were 100% (95%CI 83-100) for FT, BA (pX02), YP, VM, VZV, dengue 2,3,4 and 95% (95%CI 75-100) for BA (pX01) and dengue 1 using spiked clinical specimens. The specificity of both BioT multiplex assays on spiked specimens was 100% (95% CI 99-100). Compared to other available assays (culture, serology, PCR, etc.) both the BioT DNA mPCR-EHA and BioT RNA mRT-PCR-EHA are rapid, sensitive and specific assays for detecting many category "A" Bioterrorism agents using a standard thermocycler.
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Affiliation(s)
- Jie He
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Andrea J. Kraft
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Jiang Fan
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Meredith Van Dyke
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Lihua Wang
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Michael E. Bose
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Marilyn Khanna
- National Institutes of Health, Bethesda, MD 20892-7616, USA; E-Mail: (M.K.)
| | - Jacob A. Metallo
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Kelly J. Henrickson
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
- Children’s Research Institute, Children’s Hospital of Wisconsin, P.O. Box 1997, Milwaukee, WI 53201-1997, USA
- Children’s Hospital of Wisconsin, P.O. Box 1997, Milwaukee, WI 53201-1997, USA
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Fykse E, Langseth B, Olsen J, Skogan G, Blatny J. Detection of bioterror agents in air samples using real-time PCR. J Appl Microbiol 2008; 105:351-8. [DOI: 10.1111/j.1365-2672.2008.03750.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kenny JH, Zhou Y, Schriefer ME, Bearden SW. Detection of viable Yersinia pestis by fluorescence in situ hybridization using peptide nucleic acid probes. J Microbiol Methods 2008; 75:293-301. [PMID: 18655809 DOI: 10.1016/j.mimet.2008.06.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 06/19/2008] [Accepted: 06/24/2008] [Indexed: 11/28/2022]
Abstract
A successful method has been developed for the detection of live Yersinia pestis, the plague bacillus, which incorporates nascent RNA synthesis. A fluorescent in situ hybridization (FISH) assay using peptide nucleic acid (PNA) probes was developed specifically to differentiate Y. pestis strains from closely related bacteria. PNA probes were chosen to target high copy mRNA of the Y. pestis caf1 gene, encoding the Fraction 1 (F1) antigen, and 16S ribosomal RNA. Among Yersinia strains tested, PNA probes Yp-16S-426 and Yp-F1-55 exhibited binding specificities of 100% and 98%, respectively. Y. pestis grown in the presence of competing bacteria, as might be encountered when recovering Y. pestis from environmental surfaces in a post-release bioterrorism event, was recognized by PNA probes and neither hybridization nor fluorescence was inhibited by competing bacterial strains which exhibited faster growth rates. Using fluorescence microscopy, individual Y. pestis bacteria were clearly differentiated from competing bacteria with an average detection sensitivity of 7.9x10(3) cells by fluorescence microscopy. In the current system, this would require an average of 2.56x10(5) viable Y. pestis organisms be recovered from a post-release environmental sample in order to achieve the minimum threshold for detection. The PNA-FISH assays described in this study allow for the sensitive and specific detection of viable Y. pestis bacteria in a timely manner.
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Affiliation(s)
- John H Kenny
- Bacterial Diseases Branch, Division of Vector-Borne Infectious Diseases, National Center for Zoonotic, Vector-Borne and Enteric Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, United States
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Hepburn MJ, Simpson AJH. Tularemia: current diagnosis and treatment options. Expert Rev Anti Infect Ther 2008; 6:231-40. [PMID: 18380605 DOI: 10.1586/14787210.6.2.231] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tularemia is an infection caused by Francisella tularensis with a worldwide distribution and diverse clinical manifestations. Limitations in both culture and serologic testing have led to substantial research into new diagnostic techniques and their clinical application, with PCR testing as the best example. This review focuses on the utility of culture, PCR and serologic testing for tularemia. In addition, we also review the evidence to support different therapeutic options for tularemia, highlighting both the most effective supporting evidence for therapeutic recommendations as well as gaps in current knowledge. We conclude the article with suggestions regarding potential areas for future research.
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Affiliation(s)
- Matthew J Hepburn
- United States Army, Defence Science and Technology Laboratory, Porton Down, UK.
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Quenelle DC, Prichard MN, Keith KA, Hruby DE, Jordan R, Painter GR, Robertson A, Kern ER. Synergistic efficacy of the combination of ST-246 with CMX001 against orthopoxviruses. Antimicrob Agents Chemother 2007; 51:4118-24. [PMID: 17724153 PMCID: PMC2151443 DOI: 10.1128/aac.00762-07] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The combination of ST-246 and hexadecyloxypropyl-cidofovir or CMX001 was evaluated for synergistic activity in vitro against vaccinia virus and cowpox virus (CV) and in vivo against CV. In cell culture the combination was highly synergistic against both viruses, and the results suggested that combined treatment with these agents might offer superior efficacy in vivo. For animal models, ST-246 was administered orally with or without CMX001 to mice lethally infected with CV. Treatments began 1, 3, or 6 days postinfection using lower dosages than previously used for single-drug treatment. ST-246 was given at 10, 3, or 1 mg/kg of body weight with or without CMX001 at 3, 1, or 0.3 mg/kg to evaluate potential synergistic interactions. Treatment beginning 6 days post-viral inoculation with ST-246 alone only increased the mean day to death at 10 or 3 mg/kg but had no effect on survival. CMX001 alone also had no effect on survival. When the combination of the two drugs was begun 6 days after viral infection using various dosages of the two, a synergistic reduction in mortality was observed. No evidence of increased toxicity was noted with the combination either in vitro or in vivo. These results indicate that combinations of ST-246 and CMX001 are synergistic both in vitro and in vivo and suggest that combination therapy using ST-246 and CMX001 for treatment of orthopoxvirus disease in humans or animals may provide an additional benefit over the use of the two drugs by themselves.
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Affiliation(s)
- Debra C Quenelle
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35233-1711, USA.
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