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Optimized Method for Bacterial Nucleic Acid Extraction from Positive Blood Culture Broth for Whole-Genome Sequencing, Resistance Phenotype Prediction, and Downstream Molecular Applications. J Clin Microbiol 2022; 60:e0101222. [PMID: 36314799 PMCID: PMC9667764 DOI: 10.1128/jcm.01012-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The application of direct metagenomic sequencing from positive blood culture broth may solve the challenges of sequencing from low-bacterial-load blood samples in patients with sepsis. Forty prospectively collected blood culture broth samples growing Gram-negative bacteria were extracted using commercially available kits to achieve high-quality DNA.
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2
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Doualeh M, Payne M, Litton E, Raby E, Currie A. Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis. Int J Mol Sci 2022; 23:ijms23094484. [PMID: 35562877 PMCID: PMC9104822 DOI: 10.3390/ijms23094484] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
Polymicrobial sepsis is associated with worse patient outcomes than monomicrobial sepsis. Routinely used culture-dependent microbiological diagnostic techniques have low sensitivity, often leading to missed identification of all causative organisms. To overcome these limitations, culture-independent methods incorporating advanced molecular technologies have recently been explored. However, contamination, assay inhibition and interference from host DNA are issues that must be addressed before these methods can be relied on for routine clinical use. While the host component of the complex sepsis host–pathogen interplay is well described, less is known about the pathogen’s role, including pathogen–pathogen interactions in polymicrobial sepsis. This review highlights the clinical significance of polymicrobial sepsis and addresses how promising alternative molecular microbiology methods can be improved to detect polymicrobial infections. It also discusses how the application of shotgun metagenomics can be used to uncover pathogen/pathogen interactions in polymicrobial sepsis cases and their potential role in the clinical course of this condition.
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Affiliation(s)
- Mariam Doualeh
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
| | - Matthew Payne
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Division of Obstetrics and Gynaecology, University of Western Australia, Perth, WA 6008, Australia
| | - Edward Litton
- Intensive Care Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Intensive Care Unit, St. John of God Hospital, Subiaco, WA 6009, Australia
| | - Edward Raby
- State Burns Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Microbiology Department, Path West Laboratory Medicine, Murdoch, WA 6150, Australia
| | - Andrew Currie
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Correspondence: ; Tel.: +61-(08)-9360-7426
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3
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Mao J, Tang S, Liang S, Pan W, Kang Y, Cheng J, Yu D, Chen J, Lou J, Zhao H, Zhou J. A new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of exponential amplification reaction. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3947-3953. [PMID: 34528948 DOI: 10.1039/d1ay00520k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Exponential amplification reaction (EXPAR) has attracted much attention due to its simple primers and high amplification efficiency, but its applications are hindered by severe non-specificity amplification. Convenient exogenous chemical modification methods modified the entire template while inhibiting both non-specific and specific amplification. In this paper, we proposed a new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of EXPAR. We phosphorothioated several bases where the sequence was prone to form transient intermolecular 3'-end hybridization, thereby inhibiting the non-specific interactions and preventing the extension of templates by DNA polymerase. The melting temperature (Tm) curve and density functional theory (DFT) proved that the stability of hydrogen bonds between phosphorothioated bases did decrease. Benefitting from this strategy, the detection limit had been improved by 3 orders of magnitude. Moreover, due to the antioxidation property of phosphorothioate, this strategy showed good stability in serum, reflecting its excellent prospects in clinical sampling and detection.
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Affiliation(s)
- Jikai Mao
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Shiyi Tang
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Sijia Liang
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
| | - Wufan Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yanlei Kang
- Zhejiang Province Key Laboratory of Smart Management & Application of Modern Agricultural Resources, School of Information Engineering, Huzhou University, Huzhou, 313000, Zhejiang Province, China
| | - Jianbo Cheng
- Yantai Univ, Sch Chem & Chem Engn, Lab Theoret & Computat Chem, Yantai 264005, China
| | - Dongdong Yu
- Hospital of Zhejiang University, Zhejiang University, Hangzhou 310000, China
| | - Jie Chen
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Jingan Lou
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Hong Zhao
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
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4
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Tasca Ribeiro VS, Tuon FF, Kraft L, Suss PH, Wollmann LC, Roderjan JG, Brito DA, Alexandrino F, Malgarin JS, Morello LG, da Costa FDA, Pillonetto M. Conventional culture method and qPCR using 16S rDNA for tissue bank: a comparison using a model of cardiac tissue contamination. J Med Microbiol 2018; 67:1571-1575. [PMID: 30207519 DOI: 10.1099/jmm.0.000837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Real-time polymerase chain reaction (qPCR) using 16S rDNA is an alternative to conventional culture-based tests. The aim of this study was to compare the conventional culture method with qPCR using 16S rDNA in a model of cardiac tissue contamination. Samples of cardiac tissue for artificial contamination with Escherichia coli and control samples were submitted for DNA extraction, which was conducted by selective and alkaline lysis and purification steps. A standard curve for 16S rDNA was constructed to determine the efficiency and analytical sensitivity of the assay in concentrations from 106 to 102 c.f.u. ml-1 using TaqMan Master Mix. 16S rDNA was detected in all contaminated samples; however, it was not detected in the the final washing step solution of the sample with a bioburden of 102 c.f.u. ml-1. Using qPCR is a potential alternative to conventional culture for microbiological safety testing of allograft tissues for biobanking, reducing the time and labour input required.
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Affiliation(s)
- Victoria Stadler Tasca Ribeiro
- 1Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, Paraná, Brazil
| | - Felipe Francisco Tuon
- 2Department of Medicine, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil.,1Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, Paraná, Brazil
| | - Letícia Kraft
- 1Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, Paraná, Brazil
| | - Paula Hansen Suss
- 1Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, Paraná, Brazil
| | - Luciana Cristina Wollmann
- 1Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, Paraná, Brazil
| | - João Gabriel Roderjan
- 1Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, Paraná, Brazil
| | - Diego Armando Brito
- 3Central Laboratory of Paraná State, Rua Sebastiana Santana Fraga, 1001, Curitiba, Paraná, Brazil
| | - Fabiana Alexandrino
- 4Molecular Biology Institute of Paraná, Rua Prof. Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil
| | - Juliane Soldi Malgarin
- 4Molecular Biology Institute of Paraná, Rua Prof. Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil
| | - Luis Gustavo Morello
- 4Molecular Biology Institute of Paraná, Rua Prof. Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil.,5Carlos Chagas Institute, Rua Prof. Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil
| | - Francisco Diniz Affonso da Costa
- 1Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, Paraná, Brazil.,2Department of Medicine, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Marcelo Pillonetto
- 2Department of Medicine, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil.,3Central Laboratory of Paraná State, Rua Sebastiana Santana Fraga, 1001, Curitiba, Paraná, Brazil
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5
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Abstract
PURPOSE OF REVIEW Bloodstream infections are a major cause of hospital and ICU admission with high morbidity and mortality; however, early and targeted antimicrobial therapy reduces mortality in high-risk patients. This article focuses on the diagnosis of bloodstream infections by PCR-based approaches at an early stage to enable prompt treatment and prevent organ dysfunction. RECENT FINDINGS PCR systems offering highly multiplexed targeting of bacterial and/or fungal pathogens (in whole blood) offer the best opportunity for clinical impact, as informed decisions can be made within 4-8 h of the blood draw. Although more rapid, these systems are typically associated with lower sensitivity and specificity than postculture detection methods which rely on microbial growth. Additionally, unlike postculture methods, detection directly from blood is not prone to misleading results because of concurrent (or previous) therapy, which limit clinical relevance. SUMMARY Rapid and accurate identification of the cause of sepsis is essential in improving patient outcomes. Early identification of these pathogens by nucleic acid detection assays directly from blood samples remains key to achieving this, particularly if taken at the time of presentation. Selection of the most suitable PCR system is typically influenced by local epidemiology and by the resources of the testing laboratory.
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Anson LW, Chau K, Sanderson N, Hoosdally S, Bradley P, Iqbal Z, Phan H, Foster D, Oakley S, Morgan M, Peto TEA, Modernizing Medical Microbiology Informatics Group Mmmig, Crook DW, Pankhurst LJ. DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing. J Med Microbiol 2018; 67:347-357. [PMID: 29458686 PMCID: PMC5882078 DOI: 10.1099/jmm.0.000664] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Speed of bloodstream infection diagnosis is vital to reduce morbidity and mortality. Whole genome sequencing (WGS) performed directly from liquid blood culture could provide single-assay species and antibiotic susceptibility prediction; however, high inhibitor and human cell/DNA concentrations limit pathogen recovery. We develop a method for the preparation of bacterial DNA for WGS-based diagnostics direct from liquid blood culture. METHODOLOGY We evaluate three commercial DNA extraction kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus. Differential centrifugation, filtration, selective lysis and solid-phase reversible immobilization bead clean-up are tested to improve human cells/DNA and inhibitor removal. Using WGS (Illumina/MinION), we assess human DNA removal, pathogen recovery, and predict species and antibiotic susceptibility inpositive blood cultures of 44 Gram-negative and 54 Staphylococcus species.Results/Key findings. BiOstic kit extractions yield the greatest mean DNA concentration, 94-301 ng µl-1, versus 0-2.5 ng µl-1 using Amplex and MolYsis kits. However, we note higher levels of inhibition (260/280 ratio 0.9-2.1) and human DNA (0.0-4.4×106 copies) in BiOstic extracts. Differential centrifugation (2000 g, 1 min) prior to BiOstic extraction reduces human DNA by 63-89 % with selective lysis minimizing by a further 62 %. Post-extraction bead clean-up lowers inhibition. Overall, 67 % of sequenced samples (Illumina MiSeq) contain <10 % human DNA, with >93 % concordance between WGS-based species and susceptibility predictions and clinical diagnosis. If >60 % of sequencing reads are human (7/98 samples) susceptibility prediction becomes compromised. Novel MinION-based WGS (n=9) currently gives rapid species identification but not susceptibility prediction. CONCLUSION Our method for DNA preparation allows WGS-based diagnosis direct from blood culture bottles, providing species and antibiotic susceptibility prediction in a single assay.
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Affiliation(s)
- Luke W Anson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Present address: Genomic Research Laboratory, Division of Infectious Diseases, University of Geneva Hospitals, Rue Gabrielle-Perret-Gentil, 4, CH-1211 Geneva 14, Switzerland
| | - Kevin Chau
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Nicholas Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Sarah Hoosdally
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Phelim Bradley
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Hang Phan
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Dona Foster
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Sarah Oakley
- Microbiology Laboratory, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Marcus Morgan
- Microbiology Laboratory, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Tim E A Peto
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | | | - Derrick W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Public Health England, Wellington House, 133-155 Waterloo Rd, Lambeth, London SE1 8UG, UK
| | - Louise J Pankhurst
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
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7
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Aloni-Grinstein R, Schuster O, Yitzhaki S, Aftalion M, Maoz S, Steinberger-Levy I, Ber R. Isolation of Francisella tularensis and Yersinia pestis from Blood Cultures by Plasma Purification and Immunomagnetic Separation Accelerates Antibiotic Susceptibility Determination. Front Microbiol 2017; 8:312. [PMID: 28293231 PMCID: PMC5329073 DOI: 10.3389/fmicb.2017.00312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/15/2017] [Indexed: 01/16/2023] Open
Abstract
The early symptoms of tularemia and plague, which are caused by Francisella tularensis and Yersinia pestis infection, respectively, are common to other illnesses, resulting in a low index of suspicion among clinicians. Moreover, because these diseases can be treated only with antibiotics, rapid isolation of the bacteria and antibiotic susceptibility testing (AST) are preferable. Blood cultures of patients may serve as a source for bacteria isolation. However, due to the slow growth rates of F. tularensis and Y. pestis on solid media, isolation by plating blood culture samples on proper agar plates may require several days. Thus, improving the isolation procedure prior to antibiotic susceptibility determination is a major clinically relevant need. In this study, we developed a rapid, selective procedure for the isolation of F. tularensis and Y. pestis from blood cultures. We examined drop-plating and plasma purification followed by immunomagnetic separation (IMS) as alternative isolation methods. We determined that replacing the classical isolation method with drop-plating is advantageous with respect to time at the expense of specificity. Hence, we also examined isolation by IMS. Sub-localization of F. tularensis within blood cultures of infected mice has revealed that the majority of the bacteria are located within the extracellular fraction, in the plasma. Y. pestis also resides within the plasma. Therefore, the plasma fraction was isolated from blood cultures and subjected to an IMS procedure using polyclonal anti-F. tularensis live vaccine strain (LVS) or anti-Y. pestis antibodies conjugated to 50-nm nano-beads. The time required to reach an inoculum of sufficient bacteria for AST was shortest when using the plasma and IMSs for both bacteria, saving up to 2 days of incubation for F. tularensis and 1 day for Y. pestis. Our isolation procedure provides a proof of concept for the clinical relevance of rapid isolation for AST from F. tularensis- and Y. pestis-infected patients.
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Affiliation(s)
- Ronit Aloni-Grinstein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological ResearchNess-Ziona, Israel
| | - Ofir Schuster
- Department of Infectious diseases, Israel Institute for Biological ResearchNess-Ziona, Israel
| | - Shmuel Yitzhaki
- Department of Infectious diseases, Israel Institute for Biological ResearchNess-Ziona, Israel
| | - Moshe Aftalion
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological ResearchNess-Ziona, Israel
| | - Sharon Maoz
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological ResearchNess-Ziona, Israel
| | - Ida Steinberger-Levy
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological ResearchNess-Ziona, Israel
| | - Raphael Ber
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological ResearchNess-Ziona, Israel
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8
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Pîrlea S, Puiu M, Răducan A, Oancea D. Permanganate-assisted removal of PCR inhibitors during the DNA Chelex extraction from stained denim samples. Int J Legal Med 2016; 131:323-331. [PMID: 27595149 DOI: 10.1007/s00414-016-1443-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/23/2016] [Indexed: 11/25/2022]
Abstract
In this study, it was demonstrated that the DNA Chelex extraction combined with the permanganate assisted-oxidation is highly efficient in removing the PCR inhibitors often found in clothing materials, such as phthalocyanine. The extraction assays were conducted in saliva, blood and epithelial cells samples mixed with three oxidation-resistant dye copper(II) α-phthalocyanine, copper(II) β-phthalocyanine and tetrasulfonated copper(II) β-phthalocyanine. After DNA amplification, all samples were able to provide full DNA profiles. The permanganate/Chelex system was tested further on denim-stained samples and displayed the same ability to remove the PCR inhibitors from the commercial textile materials.
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Affiliation(s)
- Sorina Pîrlea
- National Forensic Science Institute, Şoseaua Ştefan cel Mare 13-15, sect. 2, 020123, Bucharest, Romania
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
| | - Mihaela Puiu
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
| | - Adina Răducan
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania.
| | - Dumitru Oancea
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
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9
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Kim J, Wang HY, Kim S, Park SD, Yu K, Kim HY, Uh Y, Lee H. Evaluation of the Punch-it™ NA-Sample kit for detecting microbial DNA in blood culture bottles using PCR-reverse blot hybridization assay. J Microbiol Methods 2016; 128:24-30. [DOI: 10.1016/j.mimet.2016.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/25/2022]
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10
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Lopes ALK, Cardoso J, Dos Santos FRCC, Silva ACG, Stets MI, Zanchin NIT, Soares MJ, Krieger MA. Development of a magnetic separation method to capture sepsis associated bacteria in blood. J Microbiol Methods 2016; 128:96-101. [PMID: 27432342 DOI: 10.1016/j.mimet.2016.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 12/21/2022]
Abstract
Bloodstream infections are important public health problems, associated with high mortality due to the inability to detect the pathogen quickly in the early stages of infection. Such inability has led to a growing interest in the development of a rapid, sensitive, and specific assay to detect these pathogens. In an effort to improve diagnostic efficiency, we present here a magnetic separation method for bacteria that is based on mutated lysozyme (LysE35A) to capture S. aureus from whole blood. LysE35A-coated beads were able to bind different MSSA and MRSA isolates in the blood and also other six Gram-positive and two Gram-negative species in whole blood. This system was capable to bind bacteria at low concentrations (10CFU/ml) in spiked blood. Samples captured with the mutated lysozyme showed more responsive amplification of the 16S gene than whole blood at concentrations of 10(3)-10(5)CFU. These data demonstrate detection of S. aureus directly in blood samples, without in vitro cultivation. Our results show that capture with LysE35A-coated beads can be useful to develop a point of care diagnostic system for rapid and sensitive detection of pathogens in clinical settings.
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Affiliation(s)
- Ana Luisa Kalb Lopes
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil.
| | - Josiane Cardoso
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | | | - Ana Claudia Graziani Silva
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | - Maria Isabel Stets
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | - Nilson Ivo Tonin Zanchin
- Laboratory of Proteomic and Protein Engineering, Carlos Chagas Institute, Fiocruz, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | - Maurilio José Soares
- Laboratory of Cell Biology, Carlos Chagas Institute, Fiocruz, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | - Marco Aurélio Krieger
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
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11
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Niebuhr CN, Blasco-Costa I. Improving detection of avian malaria from host blood: a step towards a standardised protocol for diagnostics. Parasitol Res 2016; 115:3905-11. [PMID: 27249965 DOI: 10.1007/s00436-016-5157-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 05/24/2016] [Indexed: 11/30/2022]
Abstract
Avian malaria, caused by Plasmodium spp., has been linked to the mortality and population-level declines in native birds in some regions. While molecular diagnostic methods have greatly improved our ability to detect infections of both human and bird malaria, failing to identify false negatives remains an important handicap, particularly for avian malaria due to host DNA presence in the bird blood cells. In an attempt to improve the accuracy of diagnostics by PCR, we evaluated the performance of a commercial silica-membrane-based DNA extraction kit by modifying the protocol with four unpooled elution volume alternatives. Our results suggest that the best template is the DNA extract obtained from the second eluate of a first 50 μL elution step. In one case, the only band visible was from this second eluate and, thus, may not have been identified as positive for Plasmodium spp. if a different elution protocol had been followed. Our results are likely explained by the concept of size exclusion chromatography by which particles of different sizes will elute at different rates. Overall, first elution templates may consist of a lower ratio of parasite to host DNA, while second eluates may contain a higher parasite to host DNA ratio. A low ratio of parasite to host DNA is a concern in detecting chronic infections, in which birds typically carry low levels of parasitemia, making accurate diagnostics imperative when identifying reservoirs of disease that could lead to spillback events.
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Affiliation(s)
- Chris N Niebuhr
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
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12
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Abstract
Real-time PCR is the traditional face of nucleic acid detection in the diagnostic microbiology laboratory and is now generally regarded as robust enough to be widely adopted. Methods based on nucleic acid detection of this type are bringing increased accuracy to diagnosis in areas where culture is difficult and/or expensive, and these methods are often effective partners to other rapid molecular diagnostic tools such as matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS). This change in practice has particularly affected the recognition of viruses and fastidious or antibiotic-exposed bacteria, but has been also shown to be effective in the recognition of troublesome or specialised phenotypes such as antiviral resistance and transmissible antibiotic resistance in the Enterobacteriaceae. Quantitation and high-intensity sequencing (of multiple whole genomes) has brought new opportunities as well as new challenges to the microbiology community. Diagnostic microbiologists currently training might be expected to deal less with the culture-based techniques of the last half-century than with the high-volume data and complex analyses of the next.
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13
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Sodium polyanethol sulfonate (SPS) falsifies protein staining and quantification and how to solve this problem. J Microbiol Methods 2015; 118:176-81. [DOI: 10.1016/j.mimet.2015.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 10/05/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022]
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Bacterial and fungal DNA extraction from positive blood culture bottles: a manual and an automated protocol. Methods Mol Biol 2015; 1237:57-64. [PMID: 25319779 DOI: 10.1007/978-1-4939-1776-1_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
When adapting a gene amplification-based method in a routine sepsis diagnostics using a blood culture sample as a specimen type, a prerequisite for a successful and sensitive downstream analysis is the efficient DNA extraction step. In recent years, a number of in-house and commercial DNA extraction solutions have become available. Careful evaluation in respect to cell wall disruption of various microbes and subsequent recovery of microbial DNA without putative gene amplification inhibitors should be conducted prior selecting the most feasible DNA extraction solution for the downstream analysis used. Since gene amplification technologies have been developed to be highly sensitive for a broad range of microbial species, it is also important to confirm that the used sample preparation reagents and materials are bioburden-free to avoid any risks for false-positive result reporting or interference of the diagnostic process. Here, one manual and one automated DNA extraction system feasible for blood culture samples are described.
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Kim SY, Hong YJ, Hwang SM, Kim TS, Kim JS, Park KU, Song J, Kim EC. Direct identification of Gram-positive bacteria and resistance determinants from blood cultures using a microarray-based nucleic acid assay: in-depth analysis of microarray data for undetermined results. Clin Chem Lab Med 2014; 53:1013-24. [PMID: 25536666 DOI: 10.1515/cclm-2014-0669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/24/2014] [Indexed: 11/15/2022]
Abstract
BACKGROUND The Verigene Gram-Positive Blood Culture (BC-GP) nucleic acid assay (Nanosphere, Inc., Northbrook, IL, USA) is a newly developed microarray-based test with which 12 Gram-positive bacterial genes and three resistance determinants can be detected using blood culture broths. We evaluated the performance of this assay and investigated the signal characteristics of the microarray images. METHODS At the evaluation stage, we tested 80 blood cultures that were positive for various bacteria (68 bacteria covered and 12 not covered by the BC-GP panel) collected from the blood of 36 patients and 44 spiked samples. In instances where the automated system failed and errors were called, we manually inspected microarray images, measured the signal intensities of target spots, and reclassified the results. RESULTS With the manual analysis of the microarray images of 14 samples for which error calls were reported, we could obtain correct identification results for 12 samples without the need for retesting, because strong signals in the target spots were clearly discriminable from background noise. With our interpretation strategy, we could obtain 97.1% sensitivity and 100% specificity for bacterial identification by using the BC-GP assay. The two unidentified bacteria were viridans group streptococci, which produced weaker target signals. During the application stage, among 25 consecutive samples positive for Gram-positive bacteria, we identified two specimens with error calls as Streptococcus spp. by using manual analysis. CONCLUSIONS With help of the manual review of the microarray images, the BC-GP assay could successfully identify species and resistance markers for many clinically important Gram-positive bacteria.
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McCann CD, Jordan JA. Evaluation of MolYsis™ Complete5 DNA extraction method for detecting Staphylococcus aureus DNA from whole blood in a sepsis model using PCR/pyrosequencing. J Microbiol Methods 2014; 99:1-7. [PMID: 24503182 DOI: 10.1016/j.mimet.2014.01.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 01/21/2014] [Accepted: 01/22/2014] [Indexed: 11/18/2022]
Abstract
Bacterial bloodstream infections (BSI) and ensuing sepsis are important causes of morbidity and mortality. Early diagnosis and rapid treatment with appropriate antibiotics are vital for improving outcome. Nucleic acid amplification of bacteria directly from whole blood has the potential of providing a faster means of diagnosing BSI than automated blood culture. However, effective DNA extraction of commonly low levels of bacterial target from whole blood is critical for this approach to be successful. This study compared the Molzyme MolYsis™ Complete5 DNA extraction method to a previously described organic bead-based method for use with whole blood. A well-characterized Staphylococcus aureus-induced pneumonia model of sepsis in canines was used to provide clinically relevant whole blood samples. DNA extracts were assessed for purity and concentration and analyzed for bacterial rRNA gene targets using PCR and sequence-based identification. Both extraction methods yielded relatively pure DNA with median A260/280 absorbance ratios of 1.71 (MolYsis™) and 1.97 (bead-based). The organic bead-based extraction method yielded significantly higher average DNA concentrations (P<0.05) at each time point throughout the experiment, closely correlating with changes observed in white blood cell (WBC) concentrations during this same time period, while DNA concentrations of the MolYsis™ extracts closely mirrored quantitative blood culture results. Overall, S. aureus DNA was detected from whole blood samples in 70.7% (58/82) of MolYsis™ DNA extracts, and in 59.8% (49/82) of organic bead-based extracts, with peak detection rates seen at 48h for both MolYsis™ (87.0%) and organic bead-based (82.6%) methods. In summary, the MolYsis™ Complete5 DNA extraction kit proved to be the more effective method for isolating bacterial DNA directly from extracts made from whole blood.
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Affiliation(s)
- Chase D McCann
- George Washington University, School of Public Health and Health Services, Department of Epidemiology and Biostatistics, 2300 I Street NW, Washington, DC 20037, USA.
| | - Jeanne A Jordan
- George Washington University, School of Public Health and Health Services, Department of Epidemiology and Biostatistics, 2300 I Street NW, Washington, DC 20037, USA.
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Abstract
DNA isolation is a fundamental initial step for molecular genetic studies. Two quite different methodologies are described in this unit: silica spin column and phenol/chloroform extraction. Currently, the most commonly used technique is the silica-based spin column, although phenol/chloroform extraction is still widely used. This unit also presents basic procedures for extraction of DNA from both fresh tissues and formalin-fixed, paraffin-embedded (FFPE) tissue samples.
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Affiliation(s)
- Ximeng Liu
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Diaz MH, Waller JL, Napoliello RA, Islam MS, Wolff BJ, Burken DJ, Holden RL, Srinivasan V, Arvay M, McGee L, Oberste MS, Whitney CG, Schrag SJ, Winchell JM, Saha SK. Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection. PLoS One 2013; 8:e66183. [PMID: 23805203 PMCID: PMC3689704 DOI: 10.1371/journal.pone.0066183] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/02/2013] [Indexed: 12/01/2022] Open
Abstract
Identification of etiology remains a significant challenge in the diagnosis of infectious diseases, particularly in resource-poor settings. Viral, bacterial, and fungal pathogens, as well as parasites, play a role for many syndromes, and optimizing a single diagnostic system to detect a range of pathogens is challenging. The TaqMan Array Card (TAC) is a multiple-pathogen detection method that has previously been identified as a valuable technique for determining etiology of infections and holds promise for expanded use in clinical microbiology laboratories and surveillance studies. We selected TAC for use in the Aetiology of Neonatal Infection in South Asia (ANISA) study for identifying etiologies of severe disease in neonates in Bangladesh, India, and Pakistan. Here we report optimization of TAC to improve pathogen detection and overcome technical challenges associated with use of this technology in a large-scale surveillance study. Specifically, we increased the number of assay replicates, implemented a more robust RT-qPCR enzyme formulation, and adopted a more efficient method for extraction of total nucleic acid from blood specimens. We also report the development and analytical validation of ten new assays for use in the ANISA study. Based on these data, we revised the study-specific TACs for detection of 22 pathogens in NP/OP swabs and 12 pathogens in blood specimens as well as two control reactions (internal positive control and human nucleic acid control) for each specimen type. The cumulative improvements realized through these optimization studies will benefit ANISA and perhaps other studies utilizing multiple-pathogen detection approaches. These lessons may also contribute to the expansion of TAC technology to the clinical setting.
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Affiliation(s)
- Maureen H. Diaz
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jessica L. Waller
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rebecca A. Napoliello
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Md. Shahidul Islam
- Department of Microbiology, Bangladesh Institute of Child Health, Child Health Research Foundation, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Bernard J. Wolff
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Daniel J. Burken
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rhiannon L. Holden
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Velusamy Srinivasan
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Melissa Arvay
- Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - M. Steven Oberste
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Cynthia G. Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stephanie J. Schrag
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jonas M. Winchell
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Samir K. Saha
- Department of Microbiology, Bangladesh Institute of Child Health, Child Health Research Foundation, Dhaka Shishu Hospital, Dhaka, Bangladesh
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Automation of genomic DNA isolation from formalin-fixed, paraffin-embedded tissues. Pathol Res Pract 2012; 208:705-7. [DOI: 10.1016/j.prp.2012.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/07/2012] [Accepted: 08/17/2012] [Indexed: 11/19/2022]
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Hazelton BJ, Thomas LC, Unver T, Iredell JR. Rapid identification of Gram-positive pathogens and their resistance genes from positive blood culture broth using a multiplex tandem RT-PCR assay. J Med Microbiol 2012; 62:223-231. [PMID: 23139396 DOI: 10.1099/jmm.0.050385-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The early initiation of targeted antibiotic therapy in patients with bacteraemia and septic shock impacts favourably on outcomes. Rapid methods are therefore increasingly employed for bacterial identification directly from positive blood culture bottles, but with variable success. We evaluated the performance of the Gram Positive 12 multiplex tandem PCR (MT-PCR) assay (AusDiagnostics; catalogue no. 6202, version 07) containing targets for the identification of staphylococci including Staphylococcus aureus, streptococci including Streptococcus pneumoniae, enterococci including Enterococcus faecalis and Enterococcus faecium and their common antibiotic resistance genes (mecA, vanA, vanB). A total of 673 aerobic and anaerobic blood culture broths demonstrating Gram-positive cocci on microscopy were analysed in parallel with traditional phenotypic methods. Amplification of the internal control was inhibited in 79/673 (11.7 %) samples; however, MT-PCR identification was in concordance with phenotypic identification to the genus level in 96.6 % (537/556) of the remaining monomicrobial specimens and to the species level, where applicable, in 100 % (172/172) of samples. MT-PCR identification for 94.7 % (36/38) of polymicrobial samples matched traditional phenotypic identification. Meticillin and vancomycin susceptibility results determined by MT-PCR in blood culture broths demonstrated complete agreement with those determined by phenotypic methods in all 143 Staphylococcus aureus isolates and eight E. faecium isolates, respectively. Gram-positive pathogens and their key antibiotic resistance markers were reliably identified with the MT-PCR assay within 3 h of a positive blood culture result.
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Affiliation(s)
- Briony J Hazelton
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Lee C Thomas
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Tuba Unver
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Jonathan R Iredell
- Sydney Emerging Infectious Diseases Institute, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Research Excellence in Critical Infection, Westmead Millennium Institute, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
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Weller SA, Cox V, Essex-Lopresti A, Hartley MG, Parsons TM, Rachwal PA, Stapleton HL, Lukaszewski RA. Evaluation of two multiplex real-time PCR screening capabilities for the detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis in blood samples generated from murine infection models. J Med Microbiol 2012; 61:1546-1555. [DOI: 10.1099/jmm.0.049007-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Simon A. Weller
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Victoria Cox
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | | | - Margaret G. Hartley
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Tanya M. Parsons
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Phillip A. Rachwal
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Helen L. Stapleton
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
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