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Recent Studies on Advance Spectroscopic Techniques for the Identification of Microorganisms: A Review. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Rais Y, Fu Z, Drabovich AP. Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants. Clin Proteomics 2021; 18:19. [PMID: 34384361 PMCID: PMC8358260 DOI: 10.1186/s12014-021-09325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023] Open
Abstract
Molecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics may provide confirmatory diagnostic information and complimentary biological knowledge on protein abundance, post-translational modifications, protein-protein interactions, and the functional impact of the emerging mutations. Pending advances in sensitivity and throughput of mass spectrometry and liquid chromatography, shotgun and targeted proteomic assays may find their niche for the differential quantification of viral proteins in clinical and environmental samples. Targeted proteomic assays in combination with immunoaffinity enrichments also provide orthogonal tools to evaluate cross-reactivity of serology tests and facilitate development of tests with the nearly perfect diagnostic specificity, this enabling reliable testing of broader populations for the acquired immunity. The coronavirus pandemic of 2019-2021 is another reminder that the future global pandemics may be inevitable, but their impact could be mitigated with the novel tools and assays, such as mass spectrometry-based proteomics, to enable continuous monitoring of emerging viruses, and to facilitate rapid response to novel infectious diseases.
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Affiliation(s)
- Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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Parker MT, Kunjapur AM. Deployment of Engineered Microbes: Contributions to the Bioeconomy and Considerations for Biosecurity. Health Secur 2021; 18:278-296. [PMID: 32816583 DOI: 10.1089/hs.2020.0010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Engineering at microscopic scales has an immense effect on the modern bioeconomy. Microbes contribute to such disparate markets as chemical manufacturing, fuel production, crop optimization, and pharmaceutical synthesis, to name a few. Due to new and emerging synthetic biology technologies, and the sophistication and control afforded by them, we are on the brink of deploying engineered microbes to not only enhance traditional applications but also to introduce these microbes to sectors, contexts, and formats not previously attempted. In microbially managed medicine, microbial engineering holds promise for increasing efficacy, improving tissue penetration, and sustaining treatment. In the environment, the most effective areas for deployment are in the management of crops and protection of ecosystems. However, caution is warranted before introducing engineered organisms to new environments where they may proliferate without control and could cause unforeseen effects. We summarize ideas and data that can inform identification and assessment of the risks that these tools present to ensure that realistic hazards are described and unrealistic ones do not hinder advancement. Further, because modes of containment are crucial complements to deployment, we describe the state of the art in microbial biocontainment strategies, current gaps, and how these gaps might be addressed through technological advances in synthetic engineering. Collectively, this work highlights engineered microbes as a foundational and expanding facet of the bioeconomy, projects their utility in upcoming deployments outside the laboratory, and identifies knowns and unknowns that will be necessary considerations and points of focus in this endeavor.
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Affiliation(s)
- Michael T Parker
- Michael T. Parker, PhD, is an Assistant Dean, Office of the Dean, Georgetown University, Washington, DC. Aditya M. Kunjapur, PhD, is an Assistant Professor, Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| | - Aditya M Kunjapur
- Michael T. Parker, PhD, is an Assistant Dean, Office of the Dean, Georgetown University, Washington, DC. Aditya M. Kunjapur, PhD, is an Assistant Professor, Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
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McIlwain DR, Chen H, Apkarian M, Affrime M, Bock B, Kim K, Mukherjee N, Nolan GP, McNeal MM. Performance of BioFire array or QuickVue influenza A + B test versus a validation qPCR assay for detection of influenza A during a volunteer A/California/2009/H1N1 challenge study. Virol J 2021; 18:45. [PMID: 33632249 PMCID: PMC7905982 DOI: 10.1186/s12985-021-01516-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/18/2021] [Indexed: 01/01/2023] Open
Abstract
Background Influenza places a significant burden on global health and economics. Individual case management and public health efforts to mitigate the spread of influenza are both strongly impacted by our ability to accurately and efficiently detect influenza viruses in clinical samples. Therefore, it is important to understand the performance characteristics of available assays to detect influenza in a variety of settings. We provide the first report of relative performance between two products marketed to streamline detection of influenza virus in the context of a highly controlled volunteer influenza challenge study. Methods Nasopharyngeal swab samples were collected during a controlled A/California/2009/H1N1 influenza challenge study and analyzed for detection of virus shedding using a validated qRT-PCR (qPCR) assay, a sample-to-answer qRT-PCR device (BioMerieux BioFire FilmArray RP), and an immunoassay based rapid test kit (Quidel QuickVue Influenza A + B Test). Results Relative to qPCR, the sensitivity and specificity of the BioFire assay was 72.1% [63.7–79.5%, 95% confidence interval (CI)] and 93.5% (89.3–96.4%, 95% CI) respectively. For the QuickVue rapid test the sensitivity was 8.5% (4.8–13.7%, 95% CI) and specificity was 99.2% (95.6–100%, 95% CI). Conclusion Relative to qPCR, the BioFire assay had superior performance compared to rapid test in the context of a controlled influenza challenge study. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01516-0.
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Affiliation(s)
- David R McIlwain
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. .,WCCT Global, Cypress, CA, USA.
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | - Nilanjan Mukherjee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Monica M McNeal
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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Jing R, Kudinha T, Zhou ML, Xiao M, Wang H, Yang WH, Xu YC, Hsueh PR. Laboratory diagnosis of COVID-19 in China: A review of challenging cases and analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 54:17-26. [PMID: 33153907 PMCID: PMC7568515 DOI: 10.1016/j.jmii.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/03/2020] [Accepted: 10/10/2020] [Indexed: 12/24/2022]
Abstract
Since the initial emergence of coronavirus disease 2019 (COVID-19) in Wuhan, Hubei province, China, a rapid spread of the disease occurred around the world, rising to become an international global health concern at pandemic level. In the face of this medical challenge threatening humans, the development of rapid and accurate methods for early screening and diagnosis of COVID-19 became crucial to containing the emerging public health threat, and prevent further spread within the population. Despite the large number of COVID-19 confirmed cases in China, some problematic cases with inconsistent laboratory testing results, were reported. Specifically, a high false-negative rate of 41% on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by real-time reverse transcription-polymerase chain reaction (qRT-PCR) assays was observed in China. Although serological testing has been applied worldwide as a complementary method to help identify SARS-CoV-2, several limitations on its use have been reported in China. Therefore, the use of both qRT-PCR and serological testing in the diagnosis of COVID-19 in China and elsewhere, presented considerable challenges, but when used in combination, can be valuable tools in the fight against COVID-19. In this review, we give an overview of the advantages and disadvantages of different molecular techniques for SARS-CoV-2 detection that are currently used in several labs, including qRT-PCR, gene sequencing, loop-mediated isothermal amplification (LAMP), nucleic acid mass spectrometry (MS), and gene editing technique based on clustered regularly interspaced short palindromic repeats (CRISPR/Cas13) system. Then we mainly review and analyze some causes of false-negative qRT-PCR results, and how to resolve some of the diagnostic dilemma.
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Affiliation(s)
- Ran Jing
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Leeds Parade, Orange, NSW, 2800, Australia; NSW Health Pathology, Orange Pathology Lab, Orange, NSW, 2800, Australia.
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - He Wang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wen-Hang Yang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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Lipkin WI, Mishra N, Briese T. Screening for Viral Infections. ENCYCLOPEDIA OF VIROLOGY 2021. [PMCID: PMC7836304 DOI: 10.1016/b978-0-12-814515-9.00052-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This article reviews methods for diagnosis of viral infections including histopathology, culture, nucleic acid tests, and serology. We discuss the principles that underlie individual assays as well as their strengths and limitations. Our intent is to provide insights into selecting strategies for viral diagnosis and discovery that can be pursued by accessing more detailed and granular protocols.
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Peiris HN, Romero R, Vaswani K, Gomez-Lopez N, Tarca AL, Gudicha DW, Erez O, Maymon E, Reed S, Mitchell MD. Prostaglandin and prostamide concentrations in amniotic fluid of women with spontaneous labor at term with and without clinical chorioamnionitis. Prostaglandins Leukot Essent Fatty Acids 2020; 163:102195. [PMID: 33137520 PMCID: PMC8314956 DOI: 10.1016/j.plefa.2020.102195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 10/08/2020] [Accepted: 10/16/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Prostaglandins (PGs) are considered universal mediators for the process of physiological parturition. This is based on observations that amniotic fluid concentrations of PGs are elevated prior to and during the onset of labor (mostly utilizing immunoassays). Distinguishing PGs from similarly structured molecules (i.e. prostamides; PG-EA) is difficult given the cross-reactivity of available antibodies and the chemical similarity between these compounds. Herein, this limitation was overcome by utilizing mass spectrometry to determine PG and PG-EA concentrations in amniotic fluid of women with spontaneous labor at term and in those with clinical chorioamnionitis (CHAM), the most common infection-related diagnosis made in labor and delivery units worldwide. STUDY DESIGN Liquid chromatography-tandem mass spectrometry (LC MS/MS) was used to determine the PG and PG-EA content in amniotic fluid samples of women with spontaneous labor at term with (n = 14) or without (n = 28) CHAM. Controls included women who delivered at term without labor (n = 10). RESULTS PGE2, PGF2α, and 13,14-dihydro-15-keto-PGF2α (PGFM) were higher in amniotic fluid of women with spontaneous labor at term than in those without labor. PGE2, PGF2α, and PGFM were also higher in amniotic fluid of women with CHAM than in those without labor. However, PGE2-EA and PGF2α-EA were lower in amniotic fluid of women with CHAM than in those without CHAM. The ratios of PGE2 to PGE2-EA and PGF2α to PGF2α-EA were higher in amniotic fluid of women with spontaneous labor at term with or without CHAM than in those without labor; yet, the ratio of PGF2α to PGF2α-EA was greater in women with CHAM than in those without this clinical condition. CONCLUSIONS Spontaneous labor at term with or without CHAM is characterized by elevated amniotic fluid concentrations of prostaglandins (PGE2, PGF2α, and PGFM) but not prostamides. Quantification of these products by LC MS/MSlc==may potentially be of utility in identifying their physiological functions relevant to parturition. SUMMARY Prostaglandins (PGs) are critical for the onset and progression of labor. Structural similarities of PGs and prostamides (PG-EA) prevents their specific identification by immunoassay. We utilized LC MS/MS to determine PG and PG-EA content in amniotic fluid (AF) of women with spontaneous labor at term with or without CHAM and women who delivered at term without labor. Higher aamniotic ffluid PG levels were observed in women with spontaneous labor with and without CHAM compared to women delivering without labor. PG-EA levels in amniotic fluid of women with spontaneous labor and CHAM were lower than in women with spontaneous labor without CHAM but not those without labor. Ratios of PGs to PG-EAs were higher in AF of women with labor and CHAM compared to those without labor. Delineation of these products by LC MS/MS may potentially be of utility in identifying their physiological functions relevant to parturition.
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Affiliation(s)
- Hassendrini N Peiris
- Institute of Health and Biomedical Innovation, Centre for Children's Health Research, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4029, Australia
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, and Detroit, MI, United States; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, United States; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States; Detroit Medical Center, Detroit, MI, United States; Department of Obstetrics and Gynecology, Florida International University, Miami, FL, United States.
| | - Kanchan Vaswani
- Institute of Health and Biomedical Innovation, Centre for Children's Health Research, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4029, Australia
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, and Detroit, MI, United States; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States; Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, and Detroit, MI, United States; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States; Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, United States
| | - Dereje W Gudicha
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, and Detroit, MI, United States; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Offer Erez
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States; Division of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Eli Maymon
- Division of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Sarah Reed
- UQ Centre for Clinical Research, University of Queensland, QLD, Australia
| | - Murray D Mitchell
- Institute of Health and Biomedical Innovation, Centre for Children's Health Research, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4029, Australia.
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Franco-Duarte R, Černáková L, Kadam S, Kaushik KS, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Relison Tintino S, Alexandrino de Souza VC, Sharifi-Rad J, Coutinho HDM, Martins N, Rodrigues CF. Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present. Microorganisms 2019; 7:E130. [PMID: 31086084 PMCID: PMC6560418 DOI: 10.3390/microorganisms7050130] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022] Open
Abstract
Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.
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Affiliation(s)
- Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal.
| | - Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Snehal Kadam
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Karishma S Kaushik
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 14665-354, Iran.
| | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Maria Rosaria Corbo
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Katarzyna Dybka-Stępień
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Martyna Leszczewicz
- Laboratory of Industrial Biotechnology, Bionanopark Ltd, Dubois 114/116, 93-465 Lodz, Poland.
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | | | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal.
| | - Célia F Rodrigues
- LEPABE⁻Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
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Chaiyasit N, Romero R, Chaemsaithong P, Docheva N, Bhatti G, Kusanovic JP, Dong Z, Yeo L, Pacora P, Hassan SS, Erez O. Clinical chorioamnionitis at term VIII: a rapid MMP-8 test for the identification of intra-amniotic inflammation. J Perinat Med 2017; 45:539-550. [PMID: 28672752 PMCID: PMC5625338 DOI: 10.1515/jpm-2016-0344] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/09/2016] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Clinical chorioamnionitis is the most common infection/inflammatory process diagnosed in labor and delivery units worldwide. The condition is a syndrome that can be caused by (1) intra-amniotic infection, (2) intra-amniotic inflammation without demonstrable microorganisms (i.e. sterile intra-amniotic inflammation), and (3) maternal systemic inflammation that is not associated with intra-amniotic inflammation. The presence of intra-amniotic inflammation is a risk factor for adverse maternal and neonatal outcomes in a broad range of obstetrical syndromes that includes clinical chorioamnionitis at term. Although the diagnosis of intra-amniotic infection has relied on culture results, such information is not immediately available for patient management. Therefore, the diagnosis of intra-amniotic inflammation could be helpful as a proxy for intra-amniotic infection, while results of microbiologic studies are pending. A rapid test is now available for the diagnosis of intra-amniotic inflammation, based on the determination of neutrophil collagenase or matrix metalloproteinase-8 (MMP-8). The objectives of this study were (1) to evaluate the diagnostic indices of a rapid MMP-8 test for the identification of intra-amniotic inflammation/infection in patients with the diagnosis of clinical chorioamnionitis at term, and (2) to compare the diagnostic performance of a rapid MMP-8 test to that of a conventional enzyme-linked immunosorbent assay (ELISA) interleukin (IL)-6 test for patients with clinical chorioamnionitis at term. MATERIALS AND METHODS A retrospective cohort study was conducted. A transabdominal amniocentesis was performed in patients with clinical chorioamnionitis at term (n=44). Amniotic fluid was analyzed using cultivation techniques (for aerobic and anaerobic bacteria as well as genital Mycoplasmas) and broad-range polymerase chain reaction (PCR) coupled with electrospray ionization mass spectrometry (PCR/ESI-MS). Amniotic fluid IL-6 concentrations were determined by ELISA, and rapid MMP-8 results were determined by Yoon's MMP-8 Check®. Intra-amniotic inflammation was defined as an elevated amniotic fluid IL-6 concentration ≥2.6 ng/mL, and intra-amniotic infection was diagnosed by the presence of microorganisms in the amniotic fluid accompanied by intra-amniotic inflammation. The diagnostic indices of Yoon's MMP-8 Check® for the identification of intra-amniotic inflammation were calculated. In order to objectively compare Yoon's MMP-8 Check® with the ELISA IL-6 test for the identification of intra-amniotic inflammation, we used an amniotic fluid white blood cell (WBC) count ≥50 cells/mm3 to define intra-amniotic inflammation. RESULTS (1) A positive rapid MMP-8 test had a sensitivity of 82.4% (28/34), specificity of 90% (9/10), positive predictive value of 96.6% (28/29), negative predictive value of 60% (9/15), positive likelihood ratio 8.2 (95% CI 1.3-53.2), and negative likelihood ratio 0.2 (95% CI 0.1-0.4) for the identification of intra-amniotic inflammation (prevalence 77.3%); (2) a positive rapid MMP-8 test had a sensitivity of 91.7% (22/24), specificity of 65% (13/20), positive predictive value of 75.9% (22/29), negative predictive value of 86.7% (13/15), positive likelihood ratio of 2.6 (95% CI 1.4-4.8), and negative likelihood ratio of 0.1 (95% CI 0.03-0.5) for the identification of intra-amniotic infection; (3) the rapid MMP-8 test had a significantly higher specificity than the ELISA IL-6 test in the identification of intra-amniotic inflammation as determined by an amniotic fluid WBC count ≥50 cells/mm3. The sensitivity and accuracy of the rapid MMP-8 test were comparable to those of the ELISA IL-6 test; and (4) importantly, the rapid MMP-8 test had 100% sensitivity and 100% negative predictive value in the identification of neonates affected with fetal inflammatory response syndrome (FIRS). CONCLUSION The rapid diagnosis of intra-amniotic inflammation is possible by analysis of amniotic fluid using a point-of-care test for MMP-8. Patients with a positive test are at risk of delivering a neonate affected with systemic inflammation, a risk factor for adverse neonatal outcome.
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Affiliation(s)
- Noppadol Chaiyasit
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Roberto Romero
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Piya Chaemsaithong
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nikolina Docheva
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Gaurav Bhatti
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Juan Pedro Kusanovic
- Center for Research and Innovation in Maternal-Fetal Medicine (CIMAF), Department of Obstetrics and Gynecology, Sótero del Río Hospital, Santiago, Chile
- Division of Obstetrics and Gynecology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Zhong Dong
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Lami Yeo
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Percy Pacora
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
| | - Sonia S. Hassan
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Offer Erez
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
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10
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Molecular and Mass Spectrometry Detection and Identification of Causative Agents of Bloodstream Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Detection of Biofilm in Wounds as an Early Indicator for Risk for Tissue Infection and Wound Chronicity. Ann Plast Surg 2016; 76:127-31. [DOI: 10.1097/sap.0000000000000440] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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[Position on blood collection and use of convalescent plasma as a treatment option in the outbreak of severe infections]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2015; 58:1371-7. [PMID: 26487385 PMCID: PMC7079896 DOI: 10.1007/s00103-015-2256-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Jiang T, Song Y, Wei T, Li H, Du D, Zhu MJ, Lin Y. Sensitive detection of Escherichia coli O157:H7 using Pt-Au bimetal nanoparticles with peroxidase-like amplification. Biosens Bioelectron 2015; 77:687-94. [PMID: 26496223 DOI: 10.1016/j.bios.2015.10.017] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/15/2015] [Accepted: 10/06/2015] [Indexed: 01/06/2023]
Abstract
Escherichia coli O157:H7 is one of the most notorious foodborne pathogens causing serious disease at low infectious dose. To protect consumers from deadly foodborne E. coli O157:H7 infection, it is vital to develop a simple, reliable, sensitive and rapid method which can detect low level E. coli O157:H7 in foods at real-time. We have successfully developed a novel immunochromatographic assay (ICA) with enhanced sensitivity for the visual and quantitative detection of E. coli O157:H7. Sandwich-type immunoreactions were performed on the ICA, and Pt-Au bimetal nanoparticles (NPs) were accumulated on the test zone. The signal amplification is based on Pt-Au bimetal NPs possessing high peroxidase activity toward 3,3',5,5'-tetramethylbenzidine, which can produce characteristic colored bands and thus, enable visual detection of E. coli O157:H7 without instrumentation. The innovative aspect of this approach lies in the visualization and quantification of target pathogen through the detection of color intensity. Due to the excellent peroxidase activity of Pt-Au NPs, they emit strong visible color intensity in less than 1 min for visual observation even in low concentration range of E. coli O157:H7. Quantification was performed using a commercial assay meter. The sensitivity was improved more than 1000-folds compared to the conventional test strip based on colored gold-colloids. Although the feasibility was demonstrated using E. coli O157:H7 as a model analyte, this approach could be easily developed to be a universal signal amplification technique and applied to detection of a wide variety of foodborne pathogens and protein biomarkers.
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Affiliation(s)
- Tao Jiang
- School of Mechanical and Material Engineering, Washington State University, Pullman, WA 99164, United States; Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Yang Song
- School of Mechanical and Material Engineering, Washington State University, Pullman, WA 99164, United States
| | - Tianxiang Wei
- School of Mechanical and Material Engineering, Washington State University, Pullman, WA 99164, United States
| | - He Li
- School of Mechanical and Material Engineering, Washington State University, Pullman, WA 99164, United States
| | - Dan Du
- School of Mechanical and Material Engineering, Washington State University, Pullman, WA 99164, United States; Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, United States
| | - Mei-Jun Zhu
- School of Food Science, Washington State University, Pullman, WA 99164, United States.
| | - Yuehe Lin
- School of Mechanical and Material Engineering, Washington State University, Pullman, WA 99164, United States; Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, United States.
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14
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Eshoo MW, Carolan HE, Massire C, Chou DM, Crowder CD, Rounds MA, Phillipson CA, Schutzer SE, Ecker DJ. Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species. PLoS One 2015; 10:e0135828. [PMID: 26375033 PMCID: PMC4574436 DOI: 10.1371/journal.pone.0135828] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022] Open
Abstract
Ixodes pacificus ticks can harbor a wide range of human and animal pathogens. To survey the prevalence of tick-borne known and putative pathogens, we tested 982 individual adult and nymphal I. pacificus ticks collected throughout California between 2007 and 2009 using a broad-range PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) assay designed to detect a wide range of tick-borne microorganisms. Overall, 1.4% of the ticks were found to be infected with Borrelia burgdorferi, 2.0% were infected with Borrelia miyamotoi and 0.3% were infected with Anaplasma phagocytophilum. In addition, 3.0% were infected with Babesia odocoilei. About 1.2% of the ticks were co-infected with more than one pathogen or putative pathogen. In addition, we identified a novel Anaplasmataceae species that we characterized by sequencing of its 16S rRNA, groEL, gltA, and rpoB genes. Sequence analysis indicated that this organism is phylogenetically distinct from known Anaplasma species with its closest genetic near neighbors coming from Asia. The prevalence of this novel Anaplasmataceae species was as high as 21% at one site, and it was detected in 4.9% of ticks tested statewide. Based upon this genetic characterization we propose that this organism be called ‘Candidatus Cryptoplasma californiense’. Knowledge of this novel microbe will provide awareness for the community about the breadth of the I. pacificus microbiome, the concept that this bacterium could be more widely spread; and an opportunity to explore whether this bacterium also contributes to human or animal disease burden.
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Affiliation(s)
- Mark W. Eshoo
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
- * E-mail:
| | - Heather E. Carolan
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | - Christian Massire
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | - Danny M. Chou
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | - Chris D. Crowder
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | - Megan A. Rounds
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | | | - Steven E. Schutzer
- Rutgers New Jersey Medical School, Dept. of Medicine, Newark, New Jersey, United States of America
| | - David J. Ecker
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
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15
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Romero R, Miranda J, Chaiworapongsa T, Chaemsaithong P, Gotsch F, Dong Z, Ahmed AI, Yoon BH, Hassan SS, Kim CJ, Korzeniewski SJ, Yeo L, Kim YM. Sterile intra-amniotic inflammation in asymptomatic patients with a sonographic short cervix: prevalence and clinical significance. J Matern Fetal Neonatal Med 2015; 28:1343-1359. [PMID: 25123515 PMCID: PMC4372495 DOI: 10.3109/14767058.2014.954243] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 08/10/2014] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To determine the frequency and clinical significance of sterile and microbial-associated intra-amniotic inflammation in asymptomatic patients with a sonographic short cervix. METHODS Amniotic fluid (AF) samples obtained by transabdominal amniocentesis from 231 asymptomatic women with a sonographic short cervix [cervical length (CL) ≤25 mm] were analyzed using cultivation techniques (for aerobic and anaerobic as well as genital mycoplasmas) and broad-range polymerase chain reaction (PCR) coupled with electrospray ionization mass spectrometry (PCR/ESI-MS). The frequency and magnitude of intra-amniotic inflammation [defined as an AF interleukin (IL)-6 concentration ≥2.6 ng/mL], acute histologic placental inflammation, spontaneous preterm delivery (sPTD), and the amniocentesis-to-delivery interval were examined according to the results of AF cultures, PCR/ESI-MS and AF IL-6 concentrations. RESULTS Ten percent (24/231) of patients with a sonographic short cervix had sterile intra-amniotic inflammation (an elevated AF IL-6 concentration without evidence of microorganisms using cultivation and molecular methods). Sterile intra-amniotic inflammation was significantly more frequent than microbial-associated intra-amniotic inflammation [10.4% (24/231) versus 2.2% (5/231); p < 0.001]. Patients with sterile intra-amniotic inflammation had a significantly higher rate of sPTD <34 weeks of gestation [70.8% (17/24) versus 31.6% (55/174); p < 0.001] and a significantly shorter amniocentesis-to-delivery interval than patients without intra-amniotic inflammation [median 35, (IQR: 10-70) versus median 71, (IQR: 47-98) days, (p < 0.0001)]. CONCLUSION Sterile intra-amniotic inflammation is more common than microbial-associated intra-amniotic inflammation in asymptomatic women with a sonographic short cervix, and is associated with increased risk of sPTD (<34 weeks). Further investigation is required to determine the causes of sterile intra-amniotic inflammation and the mechanisms whereby this condition is associated with a short cervix and sPTD.
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Affiliation(s)
- Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Jezid Miranda
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Piya Chaemsaithong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Francesca Gotsch
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Integrata Verona, Ostetricia Ginecologia, Azienda Ospedaliera Universitaria, Verona, Italy
| | - Zhong Dong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ahmed I. Ahmed
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Bo Hyun Yoon
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Sonia S. Hassan
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chong J. Kim
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Pathology, College of Medicine Inje University, Haeundae Paik Hospital
| | - Steven J. Korzeniewski
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Lami Yeo
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yeon Mee Kim
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, USA
- Department of Pathology, College of Medicine Inje University, Haeundae Paik Hospital
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16
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Actinomyces naeslundiiLung Infection Diagnosed by Polymerase Chain Reaction Coupled with Electrospray-Ionization Mass Spectrometry. Ann Am Thorac Soc 2014; 11:1163-5. [DOI: 10.1513/annalsats.201405-219le] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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17
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Identification of occult Fusobacterium nucleatum central nervous system infection by use of PCR-electrospray ionization mass spectrometry. J Clin Microbiol 2014; 52:3462-4. [PMID: 24966358 DOI: 10.1128/jcm.01082-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic bacteria are often difficult to detect, especially after the initiation of antibiotics. We describe the application of PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) using a sample of cerebrospinal fluid to identify an anaerobic Gram-negative bacillus, Fusobacterium nucleatum, in a patient with "culture-negative" meningitis and cerebral abscesses.
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18
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Hellberg RS, Li F, Sampath R, Yasuda IJ, Carolan HE, Wolfe JM, Brown MK, Alexander RC, Williams-Hill DM, Martin WB. Rapid detection and differentiation of human noroviruses using RT-PCR coupled to electrospray ionization mass spectrometry. Food Microbiol 2014; 44:71-80. [PMID: 25084648 DOI: 10.1016/j.fm.2014.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/25/2014] [Accepted: 05/25/2014] [Indexed: 11/26/2022]
Abstract
The goal of this study was to develop an assay for the detection and differentiation of noroviruses using RT-PCR followed by electrospray ionization mass spectrometry (ESI-MS). Detection of hepatitis A virus was also considered. Thirteen primer pairs were designed for use in this assay and a reference database was created using GenBank sequences and reference norovirus samples. The assay was tested for inclusivity and exclusivity using 160 clinical norovirus samples, 3 samples of hepatitis A virus and 3 other closely related viral strains. Results showed that the assay was able to detect norovirus with a sensitivity of 92% and a specificity of 100%. Norovirus identification at the genogroup level was correct for 98% of samples detected by the assay and for 75% of a subset of samples (n = 32) compared at the genotype level. Identification of norovirus genotypes is expected to improve as more reference samples are added to the database. The assay was also capable of detecting and genotyping hepatitis A virus in all 3 samples tested. Overall, the assay developed here allows for detection and differentiation of noroviruses within one working day and may be used as a tool in surveillance efforts or outbreak investigations.
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Affiliation(s)
- Rosalee S Hellberg
- Chapman University, Schmid College of Science and Technology, Food Science and Nutrition, One University Drive, Orange, CA 92866, USA.
| | - Feng Li
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Rangarajan Sampath
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Irene J Yasuda
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Heather E Carolan
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Julia M Wolfe
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Michael K Brown
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Richard C Alexander
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Donna M Williams-Hill
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Regional Laboratory Southwest, 19701 Fairchild, Irvine, CA 92612, USA
| | - William B Martin
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Regional Laboratory Southwest, 19701 Fairchild, Irvine, CA 92612, USA
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Maggi RG, Birkenheuer AJ, Hegarty BC, Bradley JM, Levy MG, Breitschwerdt EB. Comparison of serological and molecular panels for diagnosis of vector-borne diseases in dogs. Parasit Vectors 2014; 7:127. [PMID: 24670154 PMCID: PMC3972965 DOI: 10.1186/1756-3305-7-127] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/13/2014] [Indexed: 11/25/2022] Open
Abstract
Background Canine vector-borne diseases (CVBD) are caused by a diverse array of pathogens with varying biological behaviors that result in a wide spectrum of clinical presentations and laboratory abnormalities. For many reasons, the diagnosis of canine vector-borne infectious diseases can be challenging for clinicians. The aim of the present study was to compare CVBD serological and molecular testing as the two most common methodologies used for screening healthy dogs or diagnosing sick dogs in which a vector-borne disease is suspected. Methods We used serological (Anaplasma species, Babesia canis, Bartonella henselae, Bartonella vinsonii subspecies berkhoffii, Borrelia burgdorferi, Ehrlichia canis, and SFG Rickettsia) and molecular assays to assess for exposure to, or infection with, 10 genera of organisms that cause CVBDs (Anaplasma, Babesia, Bartonella, Borrelia, Ehrlichia, Francisella, hemotropic Mycoplasma, Neorickettsia, Rickettsia, and Dirofilaria). Paired serum and EDTA blood samples from 30 clinically healthy dogs (Group I) and from 69 sick dogs suspected of having one or more canine vector-borne diseases (Groups II-IV), were tested in parallel to establish exposure to or infection with the specific CVBDs targeted in this study. Results Among all dogs tested (Groups I-IV), the molecular prevalences for individual CVBD pathogens ranged between 23.3 and 39.1%. Similarly, pathogen-specific seroprevalences ranged from 43.3% to 59.4% among healthy and sick dogs (Groups I-IV). Among these representative sample groupings, a panel combining serological and molecular assays run in parallel resulted in a 4-58% increase in the recognition of exposure to or infection with CVBD. Conclusions We conclude that serological and PCR assays should be used in parallel to maximize CVBD diagnosis.
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Affiliation(s)
- Ricardo G Maggi
- Vector Borne Disease Diagnostic Laboratory and the Intracellular Pathogens Research Laboratory, Center for Comparative Medicine and Translational Research, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Dr,, Raleigh, North Carolina 27607, USA.
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20
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Romero R, Miranda J, Chaiworapongsa T, Chaemsaithong P, Gotsch F, Dong Z, Ahmed AI, Yoon BH, Hassan SS, Kim CJ, Korzeniewski SJ, Yeo L. A novel molecular microbiologic technique for the rapid diagnosis of microbial invasion of the amniotic cavity and intra-amniotic infection in preterm labor with intact membranes. Am J Reprod Immunol 2014; 71:330-58. [PMID: 24417618 DOI: 10.1111/aji.12189] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 11/25/2013] [Indexed: 12/16/2022] Open
Abstract
PROBLEM The diagnosis of microbial invasion of the amniotic cavity (MIAC) has been traditionally performed using traditional cultivation techniques, which require growth of microorganisms in the laboratory. Shortcomings of culture methods include the time required (days) for identification of microorganisms, and that many microbes involved in the genesis of human diseases are difficult to culture. A novel technique combines broad-range real-time polymerase chain reaction with electrospray ionization time-of-flight mass spectrometry (PCR/ESI-MS) to identify and quantify genomic material from bacteria and viruses. METHOD OF STUDY AF samples obtained by transabdominal amniocentesis from 142 women with preterm labor and intact membranes (PTL) were analyzed using cultivation techniques (aerobic, anaerobic, and genital mycoplasmas) as well as PCR/ESI-MS. The prevalence and relative magnitude of intra-amniotic inflammation [AF interleukin 6 (IL-6) concentration ≥ 2.6 ng/mL], acute histologic chorioamnionitis, spontaneous preterm delivery, and perinatal mortality were examined. RESULTS (i) The prevalence of MIAC in patients with PTL was 7% using standard cultivation techniques and 12% using PCR/ESI-MS; (ii) seven of ten patients with positive AF culture also had positive PCR/ESI-MS [≥17 genome equivalents per PCR reaction well (GE/well)]; (iii) patients with positive PCR/ESI-MS (≥17 GE/well) and negative AF cultures had significantly higher rates of intra-amniotic inflammation and acute histologic chorioamnionitis, a shorter interval to delivery [median (interquartile range-IQR)], and offspring at higher risk of perinatal mortality, than women with both tests negative [90% (9/10) versus 32% (39/122) OR: 5.6; 95% CI: 1.4-22; (P < 0.001); 70% (7/10) versus 35% (39/112); (P = 0.04); 1 (IQR: <1-2) days versus 25 (IQR: 5-51) days; (P = 0.002), respectively]; (iv) there were no significant differences in these outcomes between patients with positive PCR/ESI-MS (≥17 GE/well) who had negative AF cultures and those with positive AF cultures; and (v) PCR/ESI-MS detected genomic material from viruses in two patients (1.4%). CONCLUSION (i) Rapid diagnosis of intra-amniotic infection is possible using PCR/ESI-MS; (ii) the combined use of biomarkers of inflammation and PCR/ESI-MS allows for the identification of specific bacteria and viruses in women with preterm labor and intra-amniotic infection; and (iii) this approach may allow for administration of timely and specific interventions to reduce morbidity attributed to infection-induced preterm birth.
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Affiliation(s)
- Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA, and Detroit, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
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Eshoo MW, Schutzer SE, Crowder CD, Carolan HE, Ecker DJ. Achieving molecular diagnostics for Lyme disease. Expert Rev Mol Diagn 2014; 13:875-83. [DOI: 10.1586/14737159.2013.850418] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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22
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Deyde VM, Sampath R, Gubareva LV. RT-PCR/electrospray ionization mass spectrometry approach in detection and characterization of influenza viruses. Expert Rev Mol Diagn 2014; 11:41-52. [DOI: 10.1586/erm.10.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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23
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Kaslow RA, Stanberry LR, Le Duc JW. Diagnosis, Discovery and Dissection of Viral Diseases. VIRAL INFECTIONS OF HUMANS 2014. [PMCID: PMC7122662 DOI: 10.1007/978-1-4899-7448-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard A. Kaslow
- Department of Epidemiology, University of Alabama, Birmingham School of Public Health, Birmingham, Alabama USA
| | - Lawrence R. Stanberry
- Departmant of Pediatrics, Columbia University College of Physicians and Surgeons, New York, New York USA
| | - James W. Le Duc
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas USA
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Zhu Z, Fan H, Qi X, Qi Y, Shi Z, Wang H, Cui L, Zhou M. Development and evaluation of a SYBR green-based real time RT-PCR assay for detection of the emerging avian influenza A (H7N9) virus. PLoS One 2013; 8:e80028. [PMID: 24278234 PMCID: PMC3835827 DOI: 10.1371/journal.pone.0080028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Most recently a novel avian-origin influenza A (H7N9) virus emerged in China and has been associated with lots of human infection and fatal cases. Genetic analysis of the viral genome revealed that this reassortant virus might be better adapted to humans than other avian influenza viruses. Molecular diagnostic methods are thus urgently needed in public health laboratories. In this study, a SYBR green-based one-step real time reverse transcription-PCR (RT-PCR) was developed to detect the novel H7N9 virus. The primer pairs on the basis of the hemagglutinin and neuraminidase gene sequences of H7N9 viruses amplified subtype-specific fragments with Tm values of 80.77±0.06°C for H7 and 81.20±0.17°C for N9 respectively. The standard curves showed a dynamic linear range across 6 log units of RNA copy number (106 to 101 copies/ µl) with a detection limit of 10 copies per reaction for both H7 and N9 assays by using serial ten-fold diluted in-vitro transcribed viral RNA. In addition, no cross-reactivity was observed with seasonal H1N1, H1N1 pdm09, H3N2, H5N1 and H9N2 viruses as well as other human respiratory viruses. When the assay was further evaluated in H7N9 virus infected clinical samples, positive amplification signals were obtained in all of the specimens with the accordance between H7 and N9 assays. Therefore, the established SYBR green-based real time RT-PCR assay could provide a rapid, sensitive, specific and reliable alternative approach with lower costs for high throughput screening of suspected samples from humans, animals and environments in first line public health laboratories.
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Affiliation(s)
- Zheng Zhu
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Huan Fan
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Xian Qi
- Department of Acute Infectious Diseases Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yuhua Qi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Zhiyang Shi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Hua Wang
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Lunbiao Cui
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
- * E-mail: (LC); (MZ)
| | - Minghao Zhou
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
- * E-mail: (LC); (MZ)
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Incorporation of a proteotyping approach using mass spectrometry for surveillance of influenza virus in cell-cultured strains. J Clin Microbiol 2013; 52:725-35. [PMID: 24226917 DOI: 10.1128/jcm.02315-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reemergence of deadly pandemic influenza virus strains has necessitated the development of improved methods for rapid detection and subtyping of influenza viruses that will enable more strains to be characterized at the molecular level. Representative circulating strains of human influenza viruses from primary clinical specimens were grown in cell culture, purified through polyethylene glycol precipitation, proteolytically digested with an endoproteinase, and analyzed and identified by high-resolution mass spectrometry using unique signature peptides that are characteristic of type A H1N1 and H3N2 and type B influenza viruses. This proteotyping approach enabled circulating strains of type A influenza virus to be typed and subtyped, cocirculating seasonal and pandemic H1N1 viruses to be differentiated, and the lineage of type B viruses to be determined through single-ion detection by high-resolution mass spectrometry. Results were obtained using virus titers comparable to those used in reverse transcription (RT)-PCR assays with clinical specimens grown in cell cultures. The methodology represents a more rapid and direct approach than RT-PCR and can be integrated into existing procedures currently used for the surveillance of emerging pandemic and seasonal influenza viruses.
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Abstract
Influenza viruses cause recurring epidemic outbreaks every year associated with high morbidity and mortality. Despite extensive research and surveillance efforts to control influenza outbreaks, the primary mitigation treatment for influenza is the development of yearly vaccine mixes targeted for the most prevalent virus strains. Consequently, the focus of many detection technologies has evolved toward accurate identification of subtype and understanding the evolution and molecular determinants of novel and pathogenic forms of influenza. The recent availability of potential antiviral treatments are only effective if rapid and accurate diagnostic tests for influenza epidemic management are available; thus, early detection of influenza infection is still important for prevention, containment, patient management, and infection control. This review discusses the current and emerging technologies for detection and strain identification of influenza virus and their specific gene targets, as well as their implications in patient management.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, U. S. Naval Research Laboratory, 4555 Overlook Avenue, S. W., Code 6900, Washington, DC, 20375, USA
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"Salvage microbiology": detection of bacteria directly from clinical specimens following initiation of antimicrobial treatment. PLoS One 2013; 8:e66349. [PMID: 23825537 PMCID: PMC3692526 DOI: 10.1371/journal.pone.0066349] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/08/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND PCR coupled with electrospray ionization mass spectrometry (ESI-MS) is a diagnostic approach that has demonstrated the capacity to detect pathogenic organisms from culture negative clinical samples after antibiotic treatment has been initiated. [1] We describe the application of PCR/ESI-MS for detection of bacteria in original patient specimens that were obtained after administration of antibiotic treatment in an open investigation analysis. METHODS We prospectively identified cases of suspected bacterial infection in which cultures were not obtained until after the initiation of antimicrobial treatment. PCR/ESI-MS was performed on 76 clinical specimens that were submitted for conventional microbiology testing from 47 patients receiving antimicrobial treatment. FINDINGS In our series, 72% (55/76) of cultures obtained following initiation of antimicrobial treatment were non-diagnostic (45 negative cultures; and 10 respiratory specimens with normal flora (5), yeast (4), or coagulase-negative staphylococcus (1)). PCR/ESR-MS detected organisms in 83% (39/47) of cases and 76% (58/76) of the specimens. Bacterial pathogens were detected by PCR/ESI-MS in 60% (27/45) of the specimens in which cultures were negative. Notably, in two cases of relapse of prosthetic knee infections in patients on chronic suppressive antibiotics, the previous organism was not recovered in tissue cultures taken during extraction of the infected knee prostheses, but was detected by PCR/ESI-MS. CONCLUSION Molecular methods that rely on nucleic acid amplification may offer a unique advantage in the detection of pathogens collected after initiation of antimicrobial treatment and may provide an opportunity to target antimicrobial therapy and "salvage" both individual treatment regimens as well as, in select cases, institutional antimicrobial stewardship efforts.
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A Murillo L, Hardick J, Jeng K, Gaydos CA. Evaluation of the Pan Influenza detection kit utilizing the PLEX-ID and influenza samples from the 2011 respiratory season. J Virol Methods 2013; 193:173-6. [PMID: 23764420 DOI: 10.1016/j.jviromet.2013.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 05/21/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
Abstract
A comparison study was performed between the PLEX-ID and the CDC RT-PCR method for the detection and identification of Influenza A viruses using nasopharyngeal samples (N=75) collected between January and May 2011. Overall agreement was 89.3% (67/75 kappa=0.57 95% CI 0.3-0.89). Positive percent agreement was 92.3% (60/65); negative percent agreement was 70% (7/10). H1N1 pdm09 identified: 42.6% (32/75) and 54.7% (41/75) by PLEX-ID and CDC RT-PCR, respectively. H3N2 identified: 29.3% (22/75) and 32% (24/75) of samples by PLEX-ID and CDC RT-PCR, respectively. Negatives identified: 16% (12/75) and 13.3% (10/75), by PLEX-ID and CDC RT-PCR respectively. For influenza viruses identified as H1N1 pdm09, Influenza A virus A/NEW YORK/15/2009(H1N1 pdm09) was the most prevalent genotype at 50% (16/32), followed by A/CALIFORNIA/05/2009(H1N1 pdm09) at 18.2% (6/32). Updated assay plates containing additional primers designed for H1N1 pdm09 HA and NA genes were utilized for this evaluation. Among H1N1 pdm09 samples, the HA gene was conserved in 96.9% (31/32) of samples. The NA gene was conserved in 96.9% (31/32).
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Affiliation(s)
- Luis A Murillo
- The Johns Hopkins University School of Medicine, Division of Infectious Diseases, 855 North Wolfe Street, Rangos Building, Room 530, Baltimore, MD 21205, United States.
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Jordana-Lluch E, Carolan HE, Giménez M, Sampath R, Ecker DJ, Quesada MD, Mòdol JM, Arméstar F, Blyn LB, Cummins LL, Ausina V, Martró E. Rapid diagnosis of bloodstream infections with PCR followed by mass spectrometry. PLoS One 2013; 8:e62108. [PMID: 23626775 PMCID: PMC3633912 DOI: 10.1371/journal.pone.0062108] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 03/19/2013] [Indexed: 01/30/2023] Open
Abstract
Achieving a rapid microbiological diagnosis is crucial for decreasing morbidity and mortality of patients with a bloodstream infection, as it leads to the administration of an appropriate empiric antimicrobial therapy. Molecular methods may offer a rapid alternative to conventional microbiological diagnosis involving blood culture. In this study, the performance of a new technology that uses broad-spectrum PCR coupled with mass spectrometry (PCR/ESI-MS) was evaluated for the detection of microorganisms directly from whole blood. A total of 247 whole blood samples and paired blood cultures were prospectively obtained from 175 patients with a suspicion of sepsis. Both sample types were analyzed using the PCR/ESI-MS technology, and the results were compared with those obtained by conventional identification methods. The overall agreement between conventional methods and PCR/ESI-MS performed in blood culture aliquots was 94.2% with 96.8% sensitivity and 98.5% specificity for the molecular method. When comparing conventional methods with PCR/ESI-MS performed in whole blood specimens, the overall agreement was 77.1% with 50% sensitivity and 93.8% specificity for the molecular method. Interestingly, the PCR/ESI-MS technology led to the additional identification of 13 pathogens that were not found by conventional methods. Using the PCR/ESI-MS technology the microbiological diagnosis of bloodstream infections could be anticipated in about half of the patients in our setting, including a small but significant proportion of patients newly diagnosed. Thus, this promising technology could be very useful for the rapid diagnosis of sepsis in combination with traditional methods.
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Affiliation(s)
- Elena Jordana-Lluch
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Heather E. Carolan
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Montserrat Giménez
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Rangarajan Sampath
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - David J. Ecker
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - M. Dolores Quesada
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Josep M. Mòdol
- Emergency Room, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Fernando Arméstar
- Intensive Care Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Lawrence B. Blyn
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Lendell L. Cummins
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Vicente Ausina
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Spain
- * E-mail:
| | - Elisa Martró
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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Mengelle C, Mansuy JM, Da Silva I, Guerin JL, Izopet J. Evaluation of a polymerase chain reaction-electrospray ionization time-of-flight mass spectrometry for the detection and subtyping of influenza viruses in respiratory specimens. J Clin Virol 2013; 57:222-6. [PMID: 23557709 PMCID: PMC7108247 DOI: 10.1016/j.jcv.2013.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/27/2013] [Accepted: 03/06/2013] [Indexed: 11/29/2022]
Abstract
Background PCR coupled to electrospray ionization mass spectrometry technology (PCR/ESI-TOF-MS) (PLEX-ID system, Abbott Ibis Biosciences) was developed to characterize microbial pathogens. Objectives To evaluate the performance of the PLEX-ID flu detection™ kit for detecting Influenza viruses by comparison with the multiplex RespiFinder® Kit (PathoFinder). Study design Acute-phase respiratory samples (n = 293) were analysed for this purpose. A subpopulation of influenza type A positive samples, identified with the RespiFinder® kit (n = 64), were subtyped with the RealTime ready Inf A/H1N1 Detection Set® (Roche Molecular Diagnostics) and results were compared to the PLEX-ID Flu Detection™ kit. Results 274 samples gave concordant results (93.5%, p < 0.0001): 65 influenza A-positive, 18 influenza B-positive and 191 negative samples. Of these, 7 samples were PLEX-ID positive/RespiFinder® negative (5 influenza A and 2 influenza B) and 12 were PLEX-ID positive/RespiFinder® negative (10 influenza A and 2 influenza B). PLEX-ID showed one sample as an influenza A and B co-infection while the RespiFinder® assay showed it to be influenza A-positive. The sensitivity, specificity, positive and negative predictive values of the PLEX-ID™ system were 87.4%, 96.5%, 92.2% and 94.1% respectively. Thirteen of 19 discordant samples available for retesting were investigated further with the Anyplex™II RV16 Detection kit (Seegene): seven were RespiFinder® concordant, while six were PLEX-ID™ concordant. Subtyping of 61/64 influenza A samples was concordant (95.3%): 55 were H1N1pdm09 and six were non-H1N1pdm09. Three samples gave negative PLEX-ID™ results (one H1N1pdm09 and two non-H1N1pdm09). Conclusions PCR/ESI-TOF-MS technology showed good diagnostic performances to detect and subtype influenza viruses.
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Affiliation(s)
- Catherine Mengelle
- Department of Virology, CH Toulouse, 330 Avenue de Grande Bretagne, TSA 40031, 31059 Toulouse Cedex 09, France.
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31
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Beer B, Krjutškov K, Erb R, Viltrop T, Oberacher H. A novel amplification strategy for genotyping with liquid chromatography-electrospray ionization mass spectrometry. Analyst 2013; 137:5325-33. [PMID: 23034565 DOI: 10.1039/c2an35440c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Among numerous available genotyping techniques, mass spectrometry (MS) based methods play a major role in providing high quality genotype data at reasonable costs for research and diagnostics, e.g. for pharmacogenetic applications. Ion-pair reversed-phase liquid chromatography hyphenated to electrospray ionization time-of-flight MS (ICEMS) is, for example, a powerful instrument that allows a direct characterization of complex mixtures of polymerase chain reaction (PCR) amplified DNA fragments. Current limitations of PCR-ICEMS genotyping are mainly concerned with the multiplex PCR set-up. Assay development often requires time-consuming primer design and intensive optimization of PCR conditions. To overcome this restraint, a robust amplification strategy originally combined with arrayed primer extension genotyping was transferred and adapted to ICEMS genotyping. The modifications involved limitation of the primer length, application of two universal sequences and amplification with an appropriate DNA polymerase. To demonstrate the applicability of the novel amplification strategy for ICEMS, a 23-plex pharmacogenetic genotyping assay was developed. After slight optimization steps, an efficient and quantitatively balanced amplification of all targeted markers was achieved, resulting in a convenient characterization of the multiplexed PCR fragments with ICEMS. Expenditure of time, costs and hands-on work associated with assay design and optimization was dramatically lowered compared to previous multiplex PCR-ICEMS assays. The developed 23-plex assay was applied in a pharmacogenetic study including 284 individuals (genotype call rate 99.0%). A total of 399 SNPs were retyped by Sanger sequencing (concordance rate 99.8%). The PCR-ICEMS assay turned out to be an accurate, reliable, cost-effective and a ready-to-use tool for pharmacogenetic genotyping.
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Affiliation(s)
- Beate Beer
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria
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32
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Abstract
The detection of nucleic acid is of central importance for the diagnosis of genetic diseases, infectious agents, and biowarfare agents. Traditional strategies and technologies for nucleic acid detection are time-consuming and labor-intensive. Recently, isothermal strand-displacement reaction-based lateral flow biosensors have attracted a great deal of research interest because they are sensitive, simple, fast, and easy to use. Here, we describe a lateral flow biosensor based on isothermal strand-displacement polymerase reaction and gold nanoparticles for the visual detection of nucleic acid.
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Affiliation(s)
- Lingwen Zeng
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Diagnostic performance of two highly multiplexed respiratory virus assays in a pediatric cohort. J Clin Virol 2012; 55:168-72. [PMID: 22832060 PMCID: PMC3586269 DOI: 10.1016/j.jcv.2012.06.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/26/2012] [Accepted: 06/28/2012] [Indexed: 11/20/2022]
Abstract
Background Rapid detection of respiratory viruses is important for management and infection control in hospitalized patients. Multiplex nucleic acid tests (NATs) have begun to replace conventional methods as gold standards for respiratory virus detection. Objective To compare the performance of two large multiplex NATS, ResPlex II (RPII) and Respiratory Virus Surveillance kit with electrospray ionization mass spectrometry (RVS/MS) using nasopharyngeal aspirates (NPAs) from hospitalized children who had been tested previously with conventional methods. Study design Stored residual NPAs (N = 306) were tested concomitantly by RPII and RVS/MS. Alternate NATs were used to adjudicate discordant results. Results More viruses were detected with multiplex NATs (RPII, 110; RVS/MS, 109) than conventional assays (86); diagnostic gain was primarily for fastidious viruses (coronaviruses and enteroviruses [EVs]/human rhinoviruses [HRVs]). Total positive and negative agreement between the multiplex NATs for all viruses detected was quite high (86% positive agreement, 99% negative agreement). Most individual viruses were detected with fairly equivalent accuracy by the multiplex NATs, except for adenoviruses (RPII sensitivity 40%) and human metapneumovirus (RVS/MS sensitivity 42%). RPII had the advantage of detecting EVs and HRVs, however, it demonstrated considerable EV/HRV cross-reactivity (29 HRV-positive specimens by real-time PCR were positive for EV by RPII and 21 specimens positive for HRV only by RT-PCR were dual positive for EV/HRV by RPII). RPII also had reduced sensitivity for HRV detection (in 36 specimens, HRV was detected by RT-PCR but not by RPII). Conclusions Both multiplex NATs were promising, but had notable limitations.
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Afshari A, Schrenzel J, Ieven M, Harbarth S. Bench-to-bedside review: Rapid molecular diagnostics for bloodstream infection--a new frontier? CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2012; 16:222. [PMID: 22647543 PMCID: PMC3580598 DOI: 10.1186/cc11202] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Among critically ill patients, the diagnosis of bloodstream infection poses a major challenge. Current standard bacterial identification based on blood culture platforms is intrinsically time-consuming and slow. The continuous evolvement of molecular techniques has the potential of providing a faster, more sensitive and direct identification of causative pathogens without prior need for cultivation. This may ultimately impact clinical decision-making and antimicrobial treatment. This review summarises the currently available technologies, their strengths and limitations and the obstacles that have to be overcome in order to develop a satisfactory bedside point-of-care diagnostic tool for detection of bloodstream infection.
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Wolk DM, Kaleta EJ, Wysocki VH. PCR-electrospray ionization mass spectrometry: the potential to change infectious disease diagnostics in clinical and public health laboratories. J Mol Diagn 2012; 14:295-304. [PMID: 22584138 PMCID: PMC7106027 DOI: 10.1016/j.jmoldx.2012.02.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 02/04/2012] [Accepted: 02/09/2012] [Indexed: 12/18/2022] Open
Abstract
During the past 20 years, microbial detection methods that are genetically based, such as real-time PCR and peptide nucleic acid fluorescent hybridization, coexisted with traditional microbiological methods and were typically based on the identification of individual genetic targets. For these methods to be successful, a potential cause of infection must be suspected. More recently, multiplex PCR and multiplex RT-PCR were used to enable more broad-range testing based on panels of suspected pathogens. PCR–electrospray ionization mass spectrometry (PCR-ESI/MS) has emerged as a technology that is capable of identifying nearly all known human pathogens either from microbial isolates or directly from clinical specimens. Assay primers are strategically designed to target one or more of the broad pathogen categories: bacterial, mycobacterial, fungal, or viral. With broad-range amplification followed by detection of mixed amplicons, the method can identify genetic evidence of known and unknown pathogens. This unique approach supports a higher form of inquiry, asking the following question: What is the genetic evidence of known or unknown pathogens in the patient sample? This approach has advantages over traditional assays that commonly target the presence or absence of one or more pathogens with known genetic composition. This review considers the breadth of the published literature and explores the possibilities, advantages, and limitations for implementation of PCR-ESI/MS in diagnostic laboratories.
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Affiliation(s)
- Donna M Wolk
- Division of Clinical Microbiology, Department of Pathology/BIO5 Institute, University of Arizona, Tucson, AZ 85724, USA.
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Cordey S, Thomas Y, Suter P, Kaiser L. Pilot Evaluation of RT-PCR/Electrospray Ionization Mass Spectrometry (PLEX-ID/Flu assay) on Influenza-Positive Specimens. Open Virol J 2012; 6:64-7. [PMID: 22611461 PMCID: PMC3355350 DOI: 10.2174/1874357901206010064] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/12/2012] [Accepted: 03/22/2012] [Indexed: 12/27/2022] Open
Abstract
The PLEX-ID/Flu assay has been recently developed to enable the detection and typing of influenza viruses based on the RT-PCR/electrospray ionization mass spectrometry technology.This novel assay was evaluated for typing performance on 201 positive influenza A or B nasopharyngeal swab specimens (NPS) detected by real-time RT-PCR during the 2010-2011 season. The PLEX-ID/Flu assay detected and characterized 91.3% and 95.3% of all influenza A and B samples, respectively. All non-typeable influenza A and B specimens by the assay showed low viral loads with threshold cycle values ≥ 33. Taken together, and although our results need to be confirmed by further prospective studies, the PLEX-ID/Flu assay detected positively and gave a typing result for 93% of all NPS detected positively by real-time RT-PCR, thus suggesting a potential role for influenza virus surveillance among other techniques.
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Affiliation(s)
- Samuel Cordey
- Swiss National Reference Centre for Emerging Viral Diseases, University of Geneva Hospitals, Geneva, Switzerland
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38
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Eshoo MW, Crowder CC, Rebman AW, Rounds MA, Matthews HE, Picuri JM, Soloski MJ, Ecker DJ, Schutzer SE, Aucott JN. Direct molecular detection and genotyping of Borrelia burgdorferi from whole blood of patients with early Lyme disease. PLoS One 2012; 7:e36825. [PMID: 22590620 PMCID: PMC3348129 DOI: 10.1371/journal.pone.0036825] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 04/16/2012] [Indexed: 11/20/2022] Open
Abstract
Direct molecular tests in blood for early Lyme disease can be insensitive due to low amount of circulating Borrelia burgdorferi DNA. To address this challenge, we have developed a sensitive strategy to both detect and genotype B. burgdorferi directly from whole blood collected during the initial patient visit. This strategy improved sensitivity by employing 1.25 mL of whole blood, a novel pre-enrichment of the entire specimen extract for Borrelia DNA prior to a multi-locus PCR and electrospray ionization mass spectrometry detection assay. We evaluated the assay on blood collected at the initial presentation from 21 endemic area patients who had both physician-diagnosed erythema migrans (EM) and positive two-tiered serology either at the initial visit or at a follow-up visit after three weeks of antibiotic therapy. Results of this DNA analysis showed detection of B. burgdorferi in 13 of 21 patients (62%). In most cases the new assay also provided the B. burgdorferi genotype. The combined results of our direct detection assay with initial physician visit serology resulted in the detection of early Lyme disease in 19 of 21 (90%) of patients at the initial visit. In 5 of 21 cases we demonstrate the ability to detect B. burgdorferi in early Lyme disease directly from whole blood specimens prior to seroconversion.
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MESH Headings
- Antibodies, Bacterial/blood
- Antibodies, Bacterial/immunology
- Borrelia burgdorferi/genetics
- Borrelia burgdorferi/immunology
- DNA, Bacterial/blood
- DNA, Bacterial/genetics
- DNA, Bacterial/immunology
- Female
- Follow-Up Studies
- Genotype
- Glossitis, Benign Migratory/blood
- Glossitis, Benign Migratory/drug therapy
- Glossitis, Benign Migratory/genetics
- Glossitis, Benign Migratory/immunology
- Glossitis, Benign Migratory/microbiology
- Humans
- Lyme Disease/blood
- Lyme Disease/drug therapy
- Lyme Disease/genetics
- Lyme Disease/immunology
- Lyme Disease/microbiology
- Male
- Polymerase Chain Reaction/methods
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Affiliation(s)
- Mark W Eshoo
- Ibis Biosciences Inc, an Abbott Company, Carlsbad, California, United States of America.
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Hartmann EM, Halden RU. Analytical methods for the detection of viruses in food by example of CCL-3 bioagents. Anal Bioanal Chem 2012; 404:2527-37. [PMID: 22526652 DOI: 10.1007/s00216-012-5974-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 03/24/2012] [Accepted: 03/26/2012] [Indexed: 12/26/2022]
Abstract
This critical review presents challenges and strategies in the detection of viral contaminants in food products. Adenovirus, caliciviruses, enteroviruses, and hepatitis A are emerging contaminant viruses. These viruses contaminate a variety of food products, including fruits, vegetables, shellfish, and ready-to-eat processed foods. The diversity of targets and sample matrices presents unique challenges to virus monitoring that have been addressed by a wide array of processing and detection methods. This review covers sample acquisition and handling, virus recovery/concentration, and the determination of targets using molecular biology and mass-spectrometric approaches. The concentration methods discussed include precipitation, antibody-based concentration, and filtration; the detection methods discussed include microscopy, polymerase chain reaction, nucleic acid sequence-based amplification, and mass spectrometry.
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Affiliation(s)
- E M Hartmann
- The Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85006-5701, USA
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Lie P, Liu J, Fang Z, Dun B, Zeng L. A lateral flow biosensor for detection of nucleic acids with high sensitivity and selectivity. Chem Commun (Camb) 2012; 48:236-8. [DOI: 10.1039/c1cc15878c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Al-Khaldi SF, Mossoba MM, Allard MM, Lienau EK, Brown ED. Bacterial identification and subtyping using DNA microarray and DNA sequencing. Methods Mol Biol 2012; 881:73-95. [PMID: 22639211 DOI: 10.1007/978-1-61779-827-6_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.
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Affiliation(s)
- Sufian F Al-Khaldi
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA.
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Kammerer PE, Montiel S, Kriner P, Bojorquez I, Bejarano Ramirez V, Vazquez-Erlbeck M, Azziz-Baumgartner E, Blair PJ, Hawksworth AW, Faix DJ, Nava ML, Lopez LW, Palacios E, Flores R, Fonseca-Ford M, Phippard A, Lopez K, Johnson J, Bustamante Moreno JG, Russell KL, Waterman SH. Influenza-like illness surveillance on the California-Mexico border, 2004-2009. Influenza Other Respir Viruses 2011; 6:358-66. [PMID: 22212638 PMCID: PMC5779811 DOI: 10.1111/j.1750-2659.2011.00316.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Since 2004, the Naval Health Research Center, with San Diego and Imperial counties, has collaborated with the US Centers for Disease Control and Prevention to conduct respiratory disease surveillance in the US-Mexico border region. In 2007, the Secretariat of Health, Mexico and the Institute of Public Health of Baja California joined the collaboration. OBJECTIVES The identification of circulating respiratory pathogens in respiratory specimens from patients with influenza-like illness (ILI). METHODS Demographic, symptom information and respiratory swabs were collected from enrollees who met the case definition for ILI. Specimens underwent PCR testing and culture in virology and bacteriology. RESULTS From 2004 through 2009, 1855 persons were sampled. Overall, 36% of the participants had a pathogen identified. The most frequent pathogen was influenza (25%), with those aged 6-15 years the most frequently affected. In April 2009, a young female participant from Imperial County, California, was among the first documented cases of 2009 H1N1. Additional pathogens included influenza B, adenovirus, parainfluenza virus, respiratory syncytial virus, enterovirus, herpes simplex virus, Streptococcus pneumoniae, and Streptococcus pyogenes. CONCLUSIONS The US-Mexico border is one of the busiest in the world, with a large number of daily crossings. Due to its traffic, this area is an ideal location for surveillance sites. We identified a pathogen in 36% of the specimens tested, with influenza A the most common pathogen. A number of other viral and bacterial respiratory pathogens were identified. An understanding of the incidence of respiratory pathogens in border populations is useful for development of regional vaccination and disease prevention responses.
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Ho YP, Reddy PM. Advances in mass spectrometry for the identification of pathogens. MASS SPECTROMETRY REVIEWS 2011; 30:1203-24. [PMID: 21557290 PMCID: PMC7168406 DOI: 10.1002/mas.20320] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 08/06/2010] [Accepted: 08/06/2010] [Indexed: 05/25/2023]
Abstract
Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.
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Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan.
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Abstract
From the emergence of Hendra virus and Menangle virus in Australia to the global pandemics of severe acute respiratory syndrome and influenza viruses (both H5N1 and H1N1), there has been a surge of zoonotic virus outbreaks in the last two decades. Although the drivers for virus emergence remain poorly understood, the rate of discovery of new viruses is accelerating. This is due to a combination of true emergence of new pathogens and the advance of new technologies making rapid detection and characterisation possible. While molecular approaches will continue to lead the way in virus discovery, other technological platforms are required to increase the chance of success. The lessons learnt in the last 20 years confirm that the One Health approach, involving inclusive collaborations between physicians, veterinarians and other health and environmental professionals, will be the key to combating future zoonotic disease outbreaks.
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Affiliation(s)
- Lin-Fa Wang
- CSIRO Livestock Industries, Australian Animal Health Laboratory.
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Ketteler M, Martin KJ, Cozzolino M, Goldsmith D, Sharma A, Khan S, Dumas E, Amdahl M, Marx S, Audhya P. Paricalcitol versus cinacalcet plus low-dose vitamin D for the treatment of secondary hyperparathyroidism in patients receiving haemodialysis: study design and baseline characteristics of the IMPACT SHPT study. Nephrol Dial Transplant 2011; 27:1942-9. [PMID: 21931122 PMCID: PMC3339443 DOI: 10.1093/ndt/gfr531] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background. Paricalcitol and cinacalcet are common therapies for patients on haemodialysis with secondary hyperparathyroidism (SHPT). We conducted a multi-centre study in 12 countries to compare the safety and efficacy of paricalcitol and cinacalcet for the treatment of SHPT. Methods. Patients aged ≥18 years with Stage 5 chronic kidney disease receiving maintenance haemodialysis and with intact parathyroid hormone (iPTH) 300–800 pg/mL, calcium 8.4–10.0 mg/dL (2.09–2.49 mmol/L) and phosphorus ≤6.5 mg/dL (2.09 mmol/L) were randomized within two strata defined by the mode of paricalcitol administration to treatment with paricalcitol- (intra-venous, US and Russian sites, IV stratum; oral, non-US and non-Russian sites, oral stratum) or cinacalcet-centred therapy. The primary endpoint is the proportion of patients in each treatment group who achieve a mean iPTH value of 150–300 pg/mL during Weeks 21–28 of treatment. Assuming efficacy response rates of 36 and 66% for cinacalcet and paricalcitol, respectively, and a 20% discontinuation rate, 124 subjects in each stratum were estimated to provide 81% power to detect a 30% absolute difference in the primary endpoint. Results. Of 746 patients screened, 272 (mean age, 63 years; mean iPTH, 509 pg/mL) were randomized. Mean duration of haemodialysis at baseline was 3.7 years. Comorbidities included hypertension (90.4%), Type 2 diabetes (40.4%), congestive heart failure (17.3%), coronary artery disease (34.6%) and gastrointestinal disorders (75%). Conclusions. The study participants are representative of a multinational cohort of patients on haemodialysis with elevated iPTH. The study results will provide valuable information on the best available treatment of SHPT in patients on haemodialysis.
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Gu Z, Hall TA, Frinder M, Walsh TJ, Hayden RT. Evaluation of repetitive sequence PCR and PCR-mass spectrometry for the identification of clinically relevant Candida species. Med Mycol 2011; 50:259-65. [PMID: 21859387 DOI: 10.3109/13693786.2011.600341] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The application of molecular diagnostic methods may improve the timeliness and accuracy with which fungi are identified. A total of 76 well-characterized reference strains of clinically relevant Candida species and 61 clinical Candida isolates were tested by repetitive sequence PCR (rep-PCR) and PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) and results compared against internal transcribed spacer (ITS) ribosomal RNA gene sequencing as a reference standard. Both rep-PCR and PCR/ESI-MS correctly identified 51 isolates to the species level. When method performance was evaluated based only on genospecies included in the reference libraries, both methods yielded an accuracy of 98.1%. It may be concluded that rep-PCR and PCR/ESI-MS are highly effective at identifying clinical isolates of Candida to the species level. These methods hold promise for improving the speed and accuracy of identification of Candida spp. in clinical mycology laboratories.
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Affiliation(s)
- Zhengming Gu
- Department of Pathology, St. Jude Children's Research Hospital , Memphis, TN, USA
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Kaleta EJ, Clark AE, Cherkaoui A, Wysocki VH, Ingram EL, Schrenzel J, Wolk DM. Comparative analysis of PCR-electrospray ionization/mass spectrometry (MS) and MALDI-TOF/MS for the identification of bacteria and yeast from positive blood culture bottles. Clin Chem 2011; 57:1057-67. [PMID: 21576270 PMCID: PMC7108470 DOI: 10.1373/clinchem.2011.161968] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Emerging technologies for rapid identification of microbes demonstrate a shift from traditional biochemical and molecular testing algorithms toward methods using mass spectrometry (MS) for the semiquantitative analysis of microbial proteins and genetic elements. This study was performed to assess the diagnostic accuracy of 2 such technologies, PCR–electrospray ionization (ESI)/MS and MALDI-TOF/MS, with respect to phenotypic and biochemical profiling as a reference standard method. A positive challenge set of blood culture bottles was used to compare PCR-ESI/MS and MALDI-TOF/MS performance on a matched set of samples. METHODS We performed characterization of bloodstream infections from blood cultures using the Ibis T5000 PCR-ESI/MS and the Bruker MALDI Biotyper 2.0 (MALDI-TOF/MS) platforms for microbial identification. Diagnostic accuracy was determined by independent comparison of each method to phenotypic and biochemical characterization with Vitek2 analysis as the reference standard identification. RESULTS The diagnostic accuracy, represented as positive agreement, at the genus level was 0.965 (0.930–0.984) for PCR-ESI/MS and 0.969 (0.935–0.987) for MALDI-TOF/MS, and at the species level was 0.952 (0.912–0.974) with PCR-ESI/MS and 0.943 (0.902–0.968) for MALDI-TOF/MS. No statistically significant difference was found between PCR-ESI/MS and MALDI-TOF/MS in the ability to rapidly identify microorganisms isolated from blood culture. CONCLUSIONS Our results demonstrate that PCR-ESI/MS and MALDI-TOF/MS are equivalent in their ability to characterize bloodstream infections with respect to the reference standard, and highlight key differences in the methods that allow for each method to have a unique niche as a tool for rapid identification of microbes in blood cultures.
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Affiliation(s)
- Erin J Kaleta
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
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Endimiani A, Hujer KM, Hujer AM, Kurz S, Jacobs MR, Perlin DS, Bonomo RA. Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia? Clin Infect Dis 2011; 52 Suppl 4:S373-83. [PMID: 21460299 PMCID: PMC3106236 DOI: 10.1093/cid/cir054] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hospital-acquired pneumonia represents one of the most difficult treatment challenges in infectious diseases. Many studies suggest that the timely administration of appropriate, pathogen-directed therapy can be lifesaving. Because results of culture and antimicrobial susceptibility testing can take 48 h or longer, physicians currently rely on clinical, epidemiological, and demographic factors to assist with the choice of empiric therapy for antibiotic-resistant pathogens. At present, a number of rapid molecular tests are being developed that identify pathogens and the presence of genetic determinants of antimicrobial resistance (eg, GeneXpert [Cepheid], ResPlex [Qiagen], FilmArray [Idaho Technologies], and Microarray [Check-Points]). In this review, the potential impact that molecular diagnostics has to identify and characterize pathogens that cause hospital-acquired bacterial pneumonia at an early stage is examined. In addition, a perspective on a novel technology, polymerase chain reaction followed by electrospray ionization mass spectrometry, is presented, and its prospective use in the diagnosis of pneumonia is also discussed. The complexities of the pulmonary microbiome represent a novel challenge to clinicians, but many questions still remain even as these technologies improve.
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Affiliation(s)
- Andrea Endimiani
- Department of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Kristine M. Hujer
- Department of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Andrea M. Hujer
- Department of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Sebastian Kurz
- Department of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | | | - David S. Perlin
- Public Health Research Institute
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Robert A. Bonomo
- Department of Medicine
- Department of Pharmacology
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
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Keeping Track of Viruses. MICROBIAL FORENSICS 2011. [PMCID: PMC7148630 DOI: 10.1016/b978-0-12-382006-8.00009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
This chapter reviews methods of isolating, identifying, and tracking viruses with potential applications to microbial forensic investigations. Viruses are the most abundant biological entities on earth. These obligate parasites infect every form of life, from archaea and eubacteria to fungi, plants, and animals. Viruses play key roles in global ecology—they form a vast reservoir of genetic diversity, influence the composition and evolution of host populations, and affect the cycling of chemical compounds through the environment. Research has focused on the tiny fraction that causes disease in humans, domestic animals, and crops; sequencing surveys have suggested that the majority of viruses are completely unknown. The ability of viruses to jump species barriers, move between habitats, and circle the globe rapidly underscores the importance of continued vigilance for naturally emerging or deliberately engineered outbreaks. Viruses are extremely simple “life” forms without metabolic capacity, organelles, translational machinery, or autonomous replicative potential. Virus particles constitute a minimal set of components, primarily those required to deliver the genome to the target cell and initiate replication. Consequently, virus particles (or virions) are extremely small, most in the range of 20 to 200 nm in diameter. Virions are diverse not only in size but also in composition, morphology, and genome characteristics. Virus particles may be irregular in shape or possess a distinct symmetry, such as helical or icosahedral. Particles may be surrounded by a host-derived membrane, termed “enveloped,” or a tight protein shell, termed “nonenveloped.”
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Abstract
The threat posed by terrorism remains many years ahead. Bioterrorism remains a real threat, but because actual incidents remain at a low level, complacency is a constant enemy; hence the continuing background of false alarms may indeed be beneficial, encouraging responding agencies to keep practiced and alert. The Australian Federal Police (AFP) model of an integrated intelligence and forensic approach is a useful model for other nations of similar size or maturity to consider as a measured contribution to a whole of government approach to threats posed by bioterrorism. The Australian microbial forensic capability is reliant on the combined and coordinated efforts of numerous government facilities, departments, and agencies within law enforcement and public health at the state, territory, and commonwealth levels, as well as the private sector. It is a shining example of how a coordinated effort can provide a comprehensive capability that does well to protect the Australian community. The AFP and Australian Chemical, Biological, Radiological and Nuclear Data Center also work closely with international law enforcement partners in the United Kingdom, Canada, and the United States. The contribution of these and other international partners can be understated in the ongoing united effort to protect the citizens and assets of Australia and other countries against bioterrorism.
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