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Evaluation of co-circulating pathogens and microbiome from COVID-19 infections. PLoS One 2022; 17:e0278543. [PMID: 36455065 PMCID: PMC9714956 DOI: 10.1371/journal.pone.0278543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
Co-infections or secondary infections with SARS-CoV-2 have the potential to affect disease severity and morbidity. Additionally, the potential influence of the nasal microbiome on COVID-19 illness is not well understood. In this study, we analyzed 203 residual samples, originally submitted for SARS-CoV-2 testing, for the presence of viral, bacterial, and fungal pathogens and non-pathogens using a comprehensive microarray technology, the Lawrence Livermore Microbial Detection Array (LLMDA). Eighty-seven percent of the samples were nasopharyngeal samples, and 23% of the samples were oral, nasal and oral pharyngeal swabs. We conducted bioinformatics analyses to examine differences in microbial populations of these samples, as a proxy for the nasal and oral microbiome, from SARS-CoV-2 positive and negative specimens. We found 91% concordance with the LLMDA relative to a diagnostic RT-qPCR assay for detection of SARS-CoV-2. Sixteen percent of all the samples (32/203) revealed the presence of an opportunistic bacterial or frank viral pathogen with the potential to cause co-infections. The two most detected bacteria, Streptococcus pyogenes and Streptococcus pneumoniae, were present in both SARS-CoV-2 positive and negative samples. Human metapneumovirus was the most prevalent viral pathogen in the SARS-CoV-2 negative samples. Sequence analysis of 16S rRNA was also conducted to evaluate bacterial diversity and confirm LLMDA results.
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2
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Sampieri A, Monroy-Contreras R, Asanov A, Vaca L. Design of Hydrogel Silk-Based Microarrays and Molecular Beacons for Reagentless Point-of-Care Diagnostics. Front Bioeng Biotechnol 2022; 10:881679. [PMID: 35957640 PMCID: PMC9361048 DOI: 10.3389/fbioe.2022.881679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
We have developed a novel microarray system based on three technologies: 1) molecular beacons designed to interact with DNA targets at room temperature (25–27°C), 2) tridimensional silk-based microarrays containing the molecular beacons immersed in the silk hydrogel, and 3) shallow angle illumination, which uses separated optical pathways for excitation and emission. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing, and stringency control, and measure only end-point results, our microarray technology provides enhanced signal-to-background ratio (achieved by separating the optical pathways for excitation and emission, resulting in reduced stray light), performs analysis rapidly in one step without the need for labeling DNA targets, and measures the entire course of association kinetics between target DNA and the molecular beacons. To illustrate the benefits of our technology, we conducted microarray assays designed for the identification of influenza viruses. We show that in a single microarray slide, we can identify the virus subtype according to the molecular beacons designed for hemagglutinin (H1, H2, and H3) and neuraminidase (N1, N2). We also show the identification of human and swine influenza using sequence-specific molecular beacons. This microarray technology can be easily implemented for reagentless point-of-care diagnostics of several contagious diseases, including coronavirus variants responsible for the current pandemic.
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Affiliation(s)
- Alicia Sampieri
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
| | - Ricardo Monroy-Contreras
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
| | | | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
- *Correspondence: Luis Vaca,
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3
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Zaczek-Moczydlowska MA, Beizaei A, Dillon M, Campbell K. Current state-of-the-art diagnostics for Norovirus detection: Model approaches for point-of-care analysis. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.06.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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4
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Afouda P, Dubourg G, Raoult D. Archeomicrobiology applied to environmental samples. Microb Pathog 2020; 143:104140. [DOI: 10.1016/j.micpath.2020.104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
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5
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Malfatti MA, Kuhn EA, Murugesh DK, Mendez ME, Hum N, Thissen JB, Jaing CJ, Loots GG. Manipulation of the Gut Microbiome Alters Acetaminophen Biodisposition in Mice. Sci Rep 2020; 10:4571. [PMID: 32165665 PMCID: PMC7067795 DOI: 10.1038/s41598-020-60982-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 02/19/2020] [Indexed: 12/30/2022] Open
Abstract
The gut microbiota is a vast and diverse microbial community that has co-evolved with its host to perform a variety of essential functions involved in the utilization of nutrients and the processing of xenobiotics. Shifts in the composition of gut microbiota can disturb the balance of organisms which can influence the biodisposition of orally administered drugs. To determine how changes in the gut microbiome can alter drug disposition, the pharmacokinetics (PK), and biodistribution of acetaminophen were assessed in C57Bl/6 mice after treatment with the antibiotics ciprofloxacin, amoxicillin, or a cocktail of ampicillin/neomycin. Altered PK, and excretion profiles of acetaminophen were observed in antibiotic exposed animals. Plasma Cmax was significantly decreased in antibiotic treated animals suggesting decreased bioavailability. Urinary metabolite profiles revealed decreases in acetaminophen-sulfate metabolite levels in both the amoxicillin and ampicillin/neomycin treated animals. The ratio between urinary and fecal excretion was also altered in antibiotic treated animals. Analysis of gut microbe composition revealed that changes in microbe content in antibiotic treated animals was associated with changes in acetaminophen biodisposition. These results suggest that exposure to amoxicillin or ampicillin/neomycin can alter the biodisposition of acetaminophen and that these alterations could be due to changes in gut microbiome composition.
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Affiliation(s)
- Michael A Malfatti
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
| | - Edward A Kuhn
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Deepa K Murugesh
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Melanie E Mendez
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.,School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Nicholas Hum
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.,School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - James B Thissen
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Crystal J Jaing
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Gabriela G Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.,School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
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6
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Feng J, Wang Y, Jin R, Hao G. A universal random DNA amplification and labeling strategy for microarray to detect multiple pathogens of aquatic animals. J Virol Methods 2019; 275:113761. [PMID: 31693912 DOI: 10.1016/j.jviromet.2019.113761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 11/28/2022]
Abstract
Diseases caused by bacteria, fungi, and viruses pose a great threat to aquaculture. As DNA microarrays can be used to detect multiple pathogens, here we reported an array with the potential to simultaneously detect 13 bacterial and 11 viral pathogens of aquatic animals. The array included 853 oligonucleotide probes (20-40 mer) complementary to various virus-specific sequences and four chromosomal loci (16S rRNA, gyrB, dnaJ, and recA) of bacteria. Multiplex PCR, phi29 DNA polymerase, and a Klenow fragment-based method were evaluated for amplifying and labeling the nucleic acid of pathogens. While array hybridization signals were most intense using pathogen sequences amplified by multiplex PCR, the phi29 DNA polymerase method was more convenient and ideal since it did not require sequence-specific primers that could bias against detecting novel pathogens. The feasibility of the phi29 DNA polymerase-based microarray strategy was also demonstrated by detecting multiple unknown pathogens from four samples of diseased fish and shrimps.
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Affiliation(s)
- Junli Feng
- Institute of Seafood, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yi Wang
- Institute of Seafood, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Renyao Jin
- Institute of Seafood, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Guijie Hao
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China.
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Mosquito-Borne Viruses and Insect-Specific Viruses Revealed in Field-Collected Mosquitoes by a Monitoring Tool Adapted from a Microbial Detection Array. Appl Environ Microbiol 2019; 85:AEM.01202-19. [PMID: 31350319 DOI: 10.1128/aem.01202-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
Several mosquito-borne diseases affecting humans are emerging or reemerging in the United States. The early detection of pathogens in mosquito populations is essential to prevent and control the spread of these diseases. In this study, we tested the potential applicability of the Lawrence Livermore Microbial Detection Array (LLMDA) to enhance biosurveillance by detecting microbes present in Aedes aegypti, Aedes albopictus, and Culex mosquitoes, which are major vector species globally, including in Texas. The sensitivity and reproducibility of the LLMDA were tested in mosquito samples spiked with different concentrations of dengue virus (DENV), revealing a detection limit of >100 but <1,000 PFU/ml. Additionally, field-collected mosquitoes from Chicago, IL, and College Station, TX, of known infection status (West Nile virus [WNV] and Culex flavivirus [CxFLAV] positive) were tested on the LLMDA to confirm its efficiency. Mosquito field samples of unknown infection status, collected in San Antonio, TX, and the Lower Rio Grande Valley (LRGV), TX, were run on the LLMDA and further confirmed by PCR or quantitative PCR (qPCR). The analysis of the field samples with the LLMDA revealed the presence of cell-fusing agent virus (CFAV) in A. aegypti populations. Wolbachia was also detected in several of the field samples (A. albopictus and Culex spp.) by the LLMDA. Our findings demonstrated that the LLMDA can be used to detect multiple arboviruses of public health importance, including viruses that belong to the Flavivirus, Alphavirus, and Orthobunyavirus genera. Additionally, insect-specific viruses and bacteria were also detected in field-collected mosquitoes. Another strength of this array is its ability to detect multiple viruses in the same mosquito pool, allowing for the detection of cocirculating pathogens in an area and the identification of potential ecological associations between different viruses. This array can aid in the biosurveillance of mosquito-borne viruses circulating in specific geographical areas.IMPORTANCE Viruses associated with mosquitoes have made a large impact on public and veterinary health. In the United States, several viruses, including WNV, DENV, and chikungunya virus (CHIKV), are responsible for human disease. From 2015 to 2018, imported Zika cases were reported in the United States, and in 2016 to 2017, local Zika transmission occurred in the states of Texas and Florida. With globalization and a changing climate, the frequency of outbreaks linked to arboviruses will increase, revealing a need to better detect viruses in vector populations. With the capacity of the LLMDA to detect viruses, bacteria, and fungi, this study highlights its ability to broadly screen field-collected mosquitoes and contribute to the surveillance and management of arboviral diseases.
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Vila AR, Briceño C, McAloose D, Seimon TA, Armién AG, Mauldin EA, Be NA, Thissen JB, Hinojosa A, Quezada M, Paredes J, Avendaño I, Silva A, Uhart MM. Putative parapoxvirus-associated foot disease in the endangered huemul deer (Hippocamelus bisulcus) in Bernardo O'Higgins National Park, Chile. PLoS One 2019; 14:e0213667. [PMID: 30995215 PMCID: PMC6469779 DOI: 10.1371/journal.pone.0213667] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
The huemul (Hippocamelus bisulcus) is an endangered cervid endemic to southern Argentina and Chile. Here we report foot lesions in 24 huemul from Bernardo O’Higgins National Park, Chile, between 2005 and 2010. Affected deer displayed variably severe clinical signs, including lameness and soft tissue swelling of the limbs proximal to the hoof or in the interdigital space, ulceration of the swollen tissues, and some developed severe proliferative tissue changes that caused various types of abnormal wear, entrapment, and/or displacement of the hooves and/or dewclaws. Animals showed signs of intense pain and reduced mobility followed by loss of body condition and recumbency, which often preceded death. The disease affected both genders and all age categories. Morbidity and mortality reached 80% and 40%, respectively. Diagnostics were restricted to a limited number of cases from which samples were available. Histology revealed severe papillomatous epidermal hyperplasia and superficial dermatitis. Electron microscopy identified viral particles consistent with viruses in the Chordopoxvirinae subfamily. The presence of parapoxvirus DNA was confirmed by a pan-poxvirus PCR assay, showing high identity (98%) with bovine papular stomatitis virus and pseudocowpoxvirus. This is the first report of foot disease in huemul deer in Chile, putatively attributed to poxvirus. Given the high morbidity and mortality observed, this virus might pose a considerable conservation threat to huemul deer in Chilean Patagonia. Moreover, this report highlights a need for improved monitoring of huemul populations and synergistic, rapid response efforts to adequately address disease events that threaten the species.
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Affiliation(s)
| | - Cristóbal Briceño
- ConserLab, Department of Preventive Medicine, Faculty of Animal and Veterinary Sciences, Universidad de Chile, Santiago, Chile
| | - Denise McAloose
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, United States of America
| | - Tracie A. Seimon
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, United States of America
| | - Anibal G. Armién
- Ultrastructural Pathology Unit, Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN, United States of America
| | - Elizabeth A. Mauldin
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States of America
| | - Nicholas A. Be
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - James B. Thissen
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Ana Hinojosa
- Departamento de Áreas Silvestres Protegidas, Corporación Nacional Forestal, Chillán, Chile
| | - Manuel Quezada
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - José Paredes
- Departamento de Áreas Silvestres Protegidas, Corporación Nacional Forestal, Punta Arenas, Chile
| | - Iván Avendaño
- Departamento de Áreas Silvestres Protegidas, Corporación Nacional Forestal, Punta Arenas, Chile
| | - Alejandra Silva
- Departamento de Áreas Silvestres Protegidas, Corporación Nacional Forestal, Punta Arenas, Chile
| | - Marcela M. Uhart
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- * E-mail:
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9
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Thissen JB, Be NA, McLoughlin K, Gardner S, Rack PG, Shapero MH, Rowland RRR, Slezak T, Jaing CJ. Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis. PLoS One 2019; 14:e0212045. [PMID: 30735540 PMCID: PMC6368325 DOI: 10.1371/journal.pone.0212045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/25/2019] [Indexed: 12/23/2022] Open
Abstract
Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. In this study, the Axiom Microbiome Array was evaluated to determine its sensitivity, specificity and utility in microbiome analysis of veterinary clinical samples. The array contains probes designed to detect more than 12,000 species of viruses, bacteria, fungi, protozoa and archaea, yielding the most comprehensive microbial detection platform built to date. The array was able to detect Shigella and Aspergillus at 100 genome copies, and vaccinia virus DNA at 1,000 genome copies. The Axiom Microbiome Array made correct species-level calls in mock microbial community samples. When tested against serum, tissue, and fecal samples from pigs experimentally co-infected with porcine reproductive and respiratory syndrome virus and porcine circovirus type 2, the microarray correctly detected these two viruses and other common viral and bacterial microbiome species. This cost-effective and high-throughput microarray is an efficient tool to rapidly analyze large numbers of clinical and environmental samples for the presence of multiple viral and bacterial pathogens.
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Affiliation(s)
- James B. Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Nicholas A. Be
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Kevin McLoughlin
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Shea Gardner
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Paul G. Rack
- Thermo Fisher Scientific, Santa Clara, California, United States of America
| | - Michael H. Shapero
- Thermo Fisher Scientific, Santa Clara, California, United States of America
| | - Raymond R. R. Rowland
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Tom Slezak
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Crystal J. Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
- * E-mail:
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10
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Hameed S, Xie L, Ying Y. Conventional and emerging detection techniques for pathogenic bacteria in food science: A review. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.05.020] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Kim Y, Pierce CM, Robinson LA. Impact of viral presence in tumor on gene expression in non-small cell lung cancer. BMC Cancer 2018; 18:843. [PMID: 30134863 PMCID: PMC6106745 DOI: 10.1186/s12885-018-4748-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 08/14/2018] [Indexed: 12/26/2022] Open
Abstract
Background In our recent study, most non-small-lung cancer (NSCLC) tumor specimens harbored viral DNA but it was absent in non-neoplastic lung. However, their targets and roles in the tumor cells remain poorly understood. We analyzed gene expression microarrays to identify genes and pathways differentially altered between virus-infected and uninfected NSCLC tumors. Methods Gene expression microarrays of 30 primary and 9 metastatic NSCLC patients were preprocessed through a series of quality control analyses. Linear Models for Microarray Analysis and Gene Set Enrichment Analysis were used to assess differential expression. Results Various genes and gene sets had significantly altered expressions between virus-infected and uninfected NSCLC tumors. Notably, 22 genes on the viral carcinogenesis pathway were significantly overexpressed in virus-infected primary tumors, along with three oncogenic gene sets. A total of 12 genes, as well as seven oncogenic and 133 immunologic gene sets, were differentially altered in squamous cell carcinomas, depending on the virus. In adenocarcinoma, 14 differentially expressed genes (DEGs) were identified, but no oncogenic and immunogenic gene sets were significantly altered. In bronchioloalveolar carcinoma, several genes were highly overexpressed in virus-infected specimens, but not statistically significant. Only five of 69 DEGs (7.2%) from metastatic tumor analysis overlapped with 1527 DEGs from the primary tumor analysis, indicating differences in host cellular targets and the viral impact between primary and metastatic NSCLC. Conclusions The differentially expressed genes and gene sets were distinctive among infected viral types, histological subtypes, and metastatic disease status of NSCLC. These results support the hypothesis that tumor viruses play a role in NSCLC by regulating host genes in tumor cells during NSCLC differentiation and progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4748-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youngchul Kim
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, 33612-9416, Florida, USA.
| | - Christine M Pierce
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, 33612-9416, Florida, USA.,Center for Immunization and Infection Research in Cancer, Moffitt Cancer Center, Tampa, 33612-9416, Florida, USA.,Division of Thoracic Oncology, Moffitt Cancer Center, Tampa, Florida, 33612-9416, USA
| | - Lary A Robinson
- Center for Immunization and Infection Research in Cancer, Moffitt Cancer Center, Tampa, 33612-9416, Florida, USA.,Division of Thoracic Oncology, Moffitt Cancer Center, Tampa, Florida, 33612-9416, USA
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12
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Varughese EA, Brinkman NE, Anneken EM, Cashdollar JL, Fout GS, Furlong ET, Kolpin DW, Glassmeyer ST, Keely SP. Estimating virus occurrence using Bayesian modeling in multiple drinking water systems of the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:1330-1339. [PMID: 29734610 PMCID: PMC6075686 DOI: 10.1016/j.scitotenv.2017.10.267] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 05/11/2023]
Abstract
Drinking water treatment plants rely on purification of contaminated source waters to provide communities with potable water. One group of possible contaminants are enteric viruses. Measurement of viral quantities in environmental water systems are often performed using polymerase chain reaction (PCR) or quantitative PCR (qPCR). However, true values may be underestimated due to challenges involved in a multi-step viral concentration process and due to PCR inhibition. In this study, water samples were concentrated from 25 drinking water treatment plants (DWTPs) across the US to study the occurrence of enteric viruses in source water and removal after treatment. The five different types of viruses studied were adenovirus, norovirus GI, norovirus GII, enterovirus, and polyomavirus. Quantitative PCR was performed on all samples to determine presence or absence of these viruses in each sample. Ten DWTPs showed presence of one or more viruses in source water, with four DWTPs having treated drinking water testing positive. Furthermore, PCR inhibition was assessed for each sample using an exogenous amplification control, which indicated that all of the DWTP samples, including source and treated water samples, had some level of inhibition, confirming that inhibition plays an important role in PCR-based assessments of environmental samples. PCR inhibition measurements, viral recovery, and other assessments were incorporated into a Bayesian model to more accurately determine viral load in both source and treated water. Results of the Bayesian model indicated that viruses are present in source water and treated water. By using a Bayesian framework that incorporates inhibition, as well as many other parameters that affect viral detection, this study offers an approach for more accurately estimating the occurrence of viral pathogens in environmental waters.
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Affiliation(s)
- Eunice A Varughese
- USEPA, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, United States.
| | - Nichole E Brinkman
- USEPA, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, United States.
| | - Emily M Anneken
- USEPA, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, United States.
| | - Jennifer L Cashdollar
- USEPA, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, United States.
| | - G Shay Fout
- USEPA, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, United States.
| | - Edward T Furlong
- USGS, National Water Quality Laboratory, Denver Federal Center, Bldg 95, Denver, CO 80225, United States.
| | - Dana W Kolpin
- USGS, 400 S. Clinton St, Rm 269, Federal Building, Iowa City, IA 52240, United States.
| | - Susan T Glassmeyer
- USEPA, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, United States.
| | - Scott P Keely
- USEPA, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, United States.
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13
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Karouia F, Peyvan K, Pohorille A. Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth. Biotechnol Adv 2017; 35:905-932. [PMID: 28433608 DOI: 10.1016/j.biotechadv.2017.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis.
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Affiliation(s)
- Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA; NASA Ames Research Center, Flight Systems Implementation Branch, Moffett Field, CA 94035, USA.
| | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA.
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14
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Lin S, Liang R, Zhang T, Yuan Y, Shen S, Ye H. Microarray analysis of the transcriptome of theEscherichia coli(E. coli) regulated by cinnamaldehyde (CMA). FOOD AGR IMMUNOL 2017. [DOI: 10.1080/09540105.2017.1300875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Songyi Lin
- College of Food Science and Technology, Jilin University, Changchun, People’s Republic of China
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, People’s Republic of China
| | - Rong Liang
- College of Food Science and Technology, Jilin University, Changchun, People’s Republic of China
| | - Tiehua Zhang
- College of Food Science and Technology, Jilin University, Changchun, People’s Republic of China
| | - Yuan Yuan
- College of Food Science and Technology, Jilin University, Changchun, People’s Republic of China
| | - Suxia Shen
- College of Food Science and Technology, Jilin University, Changchun, People’s Republic of China
| | - Haiqing Ye
- College of Food Science and Technology, Jilin University, Changchun, People’s Republic of China
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15
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Robinson LA, Jaing CJ, Pierce Campbell C, Magliocco A, Xiong Y, Magliocco G, Thissen JB, Antonia S. Molecular evidence of viral DNA in non-small cell lung cancer and non-neoplastic lung. Br J Cancer 2016; 115:497-504. [PMID: 27415011 PMCID: PMC4985355 DOI: 10.1038/bjc.2016.213] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 01/02/2023] Open
Abstract
Background: Although ∼20% of human cancers are caused by microorganisms, only suspicion exists for a microbial cause of lung cancer. Potential infectious agents were investigated in non-small cell lung cancer (NSCLC) and non-neoplastic lung. Methods: Seventy NSCLC tumours (33 squamous cell carcinomas, 17 adenocarcinomas, 10 adenocarcinomas with lepidic spread, and 10 oligometastases) and 10 non-neoplastic lung specimens were evaluated for molecular evidence of microorganisms. Tissues were subjected to the Lawrence Livermore Microbial Detection Array, an oncovirus panel of the International Agency for Research on Cancer, and human papillomavirus (HPV) genotyping. Associations were examined between microbial prevalence, clinical characteristics, and p16 and EGFR expression. Results: Retroviral DNA was observed in 85% squamous cell carcinomas, 47% adenocarcinomas, and 10% adenocarcinomas with lepidic spread. Human papillomavirus DNA was found in 69% of squamous cell carcinomas with 30% containing high-risk HPV types. No significant viral DNA was detected in non-neoplastic lung. Patients with tumours containing viral DNA experienced improved long-term survival compared with patients with viral DNA-negative tumours. Conclusions: Most squamous cell carcinomas and adenocarcinomas contained retroviral DNA and one-third of squamous cell carcinomas contained high-risk HPV DNA. Viral DNA was absent in non-neoplastic lung. Trial results encourage further study of the viral contribution to lung carcinogenesis.
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Affiliation(s)
- Lary A Robinson
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, Florida 33612-9416, USA.,Center for Infection Research in Cancer (CIRC), Moffitt Cancer Center, Tampa, Florida 33612-9416, USA
| | - Crystal J Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94559-9698, USA
| | - Christine Pierce Campbell
- Center for Infection Research in Cancer (CIRC), Moffitt Cancer Center, Tampa, Florida 33612-9416, USA.,Department of Epidemiology, Moffitt Cancer Center, Tampa, Florida 33612-9416, USA
| | - Anthony Magliocco
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida 33612-9416, USA
| | - Yin Xiong
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida 33612-9416, USA
| | - Genevra Magliocco
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida 33612-9416, USA
| | - James B Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94559-9698, USA
| | - Scott Antonia
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, Florida 33612-9416, USA
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16
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Medina-Sánchez M, Ibarlucea B, Pérez N, Karnaushenko DD, Weiz SM, Baraban L, Cuniberti G, Schmidt OG. High-Performance Three-Dimensional Tubular Nanomembrane Sensor for DNA Detection. NANO LETTERS 2016; 16:4288-96. [PMID: 27266478 DOI: 10.1021/acs.nanolett.6b01337] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report an ultrasensitive label-free DNA biosensor with fully on-chip integrated rolled-up nanomembrane electrodes. The hybridization of complementary DNA strands (avian influenza virus subtype H1N1) is selectively detected down to attomolar concentrations, an unprecedented level for miniaturized sensors without amplification. Impedimetric DNA detection with such a rolled-up biosensor shows 4 orders of magnitude sensitivity improvement over its planar counterpart. Furthermore, it is observed that the impedance response of the proposed device is contrary to the expected behavior due to its particular geometry. To further investigate this difference, a thorough model analysis of the measured signal and the electric field calculation is performed, revealing enhanced electron hopping/tunneling along the DNA chains due to an enriched electric field inside the tube. Likewise, conformational changes of DNA might also contribute to this effect. Accordingly, these highly integrated three-dimensional sensors provide a tool to study electrical properties of DNA under versatile experimental conditions and open a new avenue for novel biosensing applications (i.e., for protein, enzyme detection, or monitoring of cell behavior under in vivo like conditions).
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Affiliation(s)
- Mariana Medina-Sánchez
- Institute for Integrative Nanosciences, IFW Dresden , Helmholtzstraße 20, 01069 Dresden, Germany
| | - Bergoi Ibarlucea
- Institute of Materials Science and Max Bergmann Center for Biomaterials, Center for Advancing Electronics Dresden (CfAED), Dresden University of Technology , 01062 Dresden, Germany
| | - Nicolás Pérez
- Institute for Integrative Nanosciences, IFW Dresden , Helmholtzstraße 20, 01069 Dresden, Germany
| | - Dmitriy D Karnaushenko
- Institute for Integrative Nanosciences, IFW Dresden , Helmholtzstraße 20, 01069 Dresden, Germany
| | - Sonja M Weiz
- Institute for Integrative Nanosciences, IFW Dresden , Helmholtzstraße 20, 01069 Dresden, Germany
| | - Larysa Baraban
- Institute of Materials Science and Max Bergmann Center for Biomaterials, Center for Advancing Electronics Dresden (CfAED), Dresden University of Technology , 01062 Dresden, Germany
| | - Gianaurelio Cuniberti
- Institute of Materials Science and Max Bergmann Center for Biomaterials, Center for Advancing Electronics Dresden (CfAED), Dresden University of Technology , 01062 Dresden, Germany
| | - Oliver G Schmidt
- Institute for Integrative Nanosciences, IFW Dresden , Helmholtzstraße 20, 01069 Dresden, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology , Reichenhainer Straße 70, 09107 Chemnitz, Germany
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17
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Wilson WC, Daniels P, Ostlund EN, Johnson DE, Oberst RD, Hairgrove TB, Mediger J, McIntosh MT. Diagnostic Tools for Bluetongue and Epizootic Hemorrhagic Disease Viruses Applicable to North American Veterinary Diagnosticians. Vector Borne Zoonotic Dis 2016; 15:364-73. [PMID: 26086557 DOI: 10.1089/vbz.2014.1702] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This review provides an overview of current and potential new diagnostic tests for bluetongue (BT) and epizootic hemorrhagic disease (EHD) viruses compiled from international participants of the Orbivirus Gap Analysis Workshop, Diagnostic Group. The emphasis of this review is on diagnostic tools available to North American veterinary diagnosticians. Standard diagnostic tests are readily available for BT/EHD viruses, and there are described tests that are published in the World Organization for Animal Health (OIE) Terrestrial Manual. There is however considerable variation in the diagnostic approach to these viruses. Serological assays are well established, and many laboratories are experienced in running these assays. Numerous nucleic acid amplification assays are also available for BT virus (BTV) and EHD virus (EHDV). Although there is considerable experience with BTV reverse-transcriptase PCR (RT-PCR), there are no standards or comparisons of the protocols used by various state and federal veterinary diagnostic laboratories. Methods for genotyping BTV and EHDV isolates are available and are valuable tools for monitoring and analyzing circulating viruses. These methods include RT-PCR panels or arrays, RT-PCR and sequencing of specific genome segments, or the use of next-generation sequencing. In addition to enabling virus characterization, use of advanced molecular detection methods, including DNA microarrays and next-generation sequencing, significantly enhance the ability to detect unique virus strains that may arise through genetic drift, recombination, or viral genome segment reassortment, as well as incursions of new virus strains from other geographical areas.
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Affiliation(s)
- William C Wilson
- 1 Arthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research , USDA, ARS, Manhattan, Kansas
| | - Peter Daniels
- 2 CSIRO Australian Animal Health Laboratory , Geelong, Australia
| | - Eileen N Ostlund
- 3 National Veterinary Services Laboratories, USDA, APHIS, VS, Science, Technology and Analysis Services , Ames, Iowa
| | - Donna E Johnson
- 3 National Veterinary Services Laboratories, USDA, APHIS, VS, Science, Technology and Analysis Services , Ames, Iowa
| | - Richard D Oberst
- 4 Kansas Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas
| | | | - Jessica Mediger
- 6 Department of Veterinary and Biomedical Sciences, South Dakota State University , Brookings, South Dakota
| | - Michael T McIntosh
- 7 Foreign Animal Disease Diagnostic Laboratory, USDA, APHIS, VS, STAS, NVSL, Plum Island Disease Center , Greenport, New York
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18
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Yu C, Wales SQ, Mammel MK, Hida K, Kulka M. Optimizing a custom tiling microarray for low input detection and identification of unamplified virus targets. J Virol Methods 2016; 234:54-64. [PMID: 27033182 DOI: 10.1016/j.jviromet.2016.03.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 03/04/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022]
Abstract
Viruses are major pathogens causing foodborne illnesses and are often present at low levels in foods, thus requiring sensitive techniques for their detection in contaminated foods. The lack of efficient culture methods for many foodborne viruses and the potential for multi-species viral contamination have driven investigation toward non-amplification based methods for virus detection and identification. A custom DNA microarray (FDA_EVIR) was assessed for its sensitivity in the detection and identification of low-input virus targets, human hepatitis A virus, norovirus, and coxsackievirus, individually and in combination. Modifications to sample processing were made to accommodate low input levels of unamplified virus targets, which included addition of carrier cDNA, RNase treatment, and optimization of DNase I-mediated target fragmentation. Amplification-free detection and identification of foodborne viruses were achieved in the range of 250-500 copies of virus RNA. Alternative data analysis methods were employed to distinguish the genotypes of the viruses particularly at lower levels of target input and the single probe-based analysis approach made it possible to identify a minority species in a multi-virus complex. The oligonucleotide array is shown to be a promising platform to detect foodborne viruses at low levels close to what are anticipated in food or environmental samples.
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Affiliation(s)
- Christine Yu
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Samantha Q Wales
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Mark K Mammel
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Kaoru Hida
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Michael Kulka
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA.
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19
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Miller S, Karaoz U, Brodie E, Dunbar S. Solid and Suspension Microarrays for Microbial Diagnostics. METHODS IN MICROBIOLOGY 2015; 42:395-431. [PMID: 38620236 PMCID: PMC7172482 DOI: 10.1016/bs.mim.2015.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.
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Affiliation(s)
- Steve Miller
- Clinical Microbiology Laboratory, University of California, San Francisco, California, USA
| | - Ulas Karaoz
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Eoin Brodie
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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20
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Stramer SL, Dodd RY, Chiu CY. Advances in testing technology to ensure transfusion safety - NAT and beyond. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/voxs.12152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- S. L. Stramer
- American Red Cross Biomedical Services; Gaithersburg MD USA
| | - R. Y. Dodd
- Research and Development; American Red Cross Biomedical Services; Rockville MD USA
| | - C. Y. Chiu
- Laboratory Medicine and Medicine/Infectious Diseases; UCSF School of Medicine; San Francisco CA USA
- UCSF-Abbott Viral Diagnostics and Discovery Center; UCSF School of Medicine; San Francisco CA USA
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21
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Tellez J, Jaing C, Wang J, Green R, Chen M. Detection of Epstein-Barr virus (EBV) in human lymphoma tissue by a novel microbial detection array. Biomark Res 2014; 2:24. [PMID: 25635226 PMCID: PMC4310026 DOI: 10.1186/s40364-014-0024-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 11/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious agents are estimated to play a causative role in approximately 20% of cancers worldwide. Viruses, notably the Epstein-Barr virus (EBV), are associated with 10-15% of B-cell lymphomas and are found at a higher frequency in immunosuppressed patients. In this study, we screened human lymphoma tissues using a novel Lawrence Livermore Microbial Detection Array (LLMDA), a comprehensive detection system that contains probes for all sequenced viruses and bacteria. This technology has been applied to identify pathogen-associated diseases. RESULTS We evaluated samples from 58 cases with various lymphoid tissue disorders using LLMDA. These included 30 B-cell lymphomas (9 indolent and 21 aggressive type), 2 T-cell lymphomas and 2 NK/T cell lymphomas, 4 plasmacytomas as well as 8 specimens of benign lymphoid tissue. Five of 21 high-grade B-cell lymphomas were positive for Epstein-Barr virus-encoded small RNA (EBER+), while all the indolent B-cell lymphomas were EBER-. Similarly, both NK/T cell lymphomas were EBER+, and the benign tissues were EBER-. We also screened 10 cases of post-transplant lymphoproliferative disorder (PTLD). Five of these cases (4 B-cell lymphomas and 1 NK/T cell lymphoma) were EBER+, and the remaining five cases were EBER-. CONCLUSIONS We have confirmed the reliability of the LLMDA methods by detecting EBV in EBV-positive lymphomas while observing no false-positive results in EBV-negative lymphomas. The LLMDA technique provides a sensitive and alternative method for identifying known viral pathogen associated with tumors and may prove useful for future clinical identification of novel cancer-associated viral pathogens.
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Affiliation(s)
- Joseph Tellez
- Deptartment of Pathology and Laboratory Medicine, University of California, Davis Medical Center, PATH Bldg. 4400V Street, Sacramento, CA 95817 USA
| | - Crystal Jaing
- Applied Genomics, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | - Jun Wang
- Department of Pathology and Laboratory Medicine, Loma Linda University Medical Center, Loma Linda, CA 92354 USA
| | - Ralph Green
- Deptartment of Pathology and Laboratory Medicine, University of California, Davis Medical Center, PATH Bldg. 4400V Street, Sacramento, CA 95817 USA
| | - Mingyi Chen
- Deptartment of Pathology and Laboratory Medicine, University of California, Davis Medical Center, PATH Bldg. 4400V Street, Sacramento, CA 95817 USA
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22
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Rosenstierne MW, McLoughlin KS, Olesen ML, Papa A, Gardner SN, Engler O, Plumet S, Mirazimi A, Weidmann M, Niedrig M, Fomsgaard A, Erlandsson L. The microbial detection array for detection of emerging viruses in clinical samples--a useful panmicrobial diagnostic tool. PLoS One 2014; 9:e100813. [PMID: 24963710 PMCID: PMC4070998 DOI: 10.1371/journal.pone.0100813] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/29/2014] [Indexed: 11/30/2022] Open
Abstract
Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travel, climate change and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. Many of these viruses cause similar disease symptoms as other emerging viruses or common infections, making these unexpected pathogens difficult to diagnose. Broad-spectrum pathogen detection microarrays containing probes for all sequenced viruses and bacteria can provide rapid identification of viruses, guiding decisions about treatment and appropriate case management. We report a modified Whole Transcriptome Amplification (WTA) method that increases unbiased amplification, particular of RNA viruses. Using this modified WTA method, we tested the specificity and sensitivity of the Lawrence Livermore Microbial Detection Array (LLMDA) against a wide range of emerging viruses present in both non-clinical and clinical samples using two different microarray data analysis methods.
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Affiliation(s)
- Maiken W. Rosenstierne
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| | - Kevin S. McLoughlin
- Global Security, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Majken Lindholm Olesen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Papa
- Department of Microbiology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Shea N. Gardner
- Global Security, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Olivier Engler
- Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland
| | - Sebastien Plumet
- Virology department, French Army Forces Biomedical Institute (IRBA), Marseille, France
| | - Ali Mirazimi
- Swedish Institute for Communicable Disease Control, Solna, Sweden
- National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | | | - Anders Fomsgaard
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lena Erlandsson
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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