The Experts below are selected from a list of 29889 Experts worldwide ranked by ideXlab platform
Kevin Mcloughlin - One of the best experts on this subject based on the ideXlab platform.
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the Microbial Detection array for Detection of emerging viruses in clinical samples a useful panMicrobial diagnostic tool
PLOS ONE, 2014Co-Authors: Maiken W Rosenstierne, Kevin Mcloughlin, Majken Lindholm Olesen, Shea N Gardner, Olivier Engler, Manfred Weidmann, Ali Mirazimi, Sébastien Plumet, Anna Papa, Matthias NiedrigAbstract: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 nonclinical and clinical samples using two different microarray data analysis methods.
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Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.
Scientific reports, 2014Co-Authors: Alison Devault, Kevin Mcloughlin, Shea N Gardner, Crystal Jaing, James B. Thissen, Teresita M. Porter, Jacob Enk, Jonathan E. Allen, Monica K. Borucki, Sharon N. DewitteAbstract:Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of Microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis (“Black Death” plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.
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Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray.
Journal of virological methods, 2014Co-Authors: James B. Thissen, Kevin Mcloughlin, Shea N Gardner, Tom Slezak, Shalini Mabery, Crystal JaingAbstract: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. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA was able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate Detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.
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Detection of Adventitious Viruses from Biologicals Using a Broad-Spectrum Microbial Detection Array
PDA journal of pharmaceutical science and technology, 2011Co-Authors: Crystal Jaing, Kevin Mcloughlin, Shea N Gardner, James B. Thissen, Tom SlezakAbstract:CONFERENCE PROCEEDING Proceedings of the PDA/FDA Adventitious Viruses in Biologics: Detection and Mitigation Strategies Workshop in Bethesda, MD, USA; December 1-3, 2010 Guest Editors: Arifa Khan (Bethesda, MD), Patricia Hughes (Bethesda, MD) and Michael Wiebe (San Francisco, CA) We designed the Lawrence Livermore Microbial Detection Array (LLMDA), which contains 388,000 DNA probes. This array can detect any sequenced viruses or bacteria within 24 h. In addition, the oligonucleotide probes were selected to enable Detection of novel, divergent species with homology to sequenced organisms. We recently used this array to identify an adventitious virus from a vaccine product. We have also used this array to detect viral and bacterial infections from various human clinical samples. Broad-spectrum Microbial Detection microarrays are efficient and cost-effective tools to rapidly screen cell bank samples, raw materials, vaccine samples, and clinical samples to ensure drug, food, and health safety in the United States and worldwide.
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Microarrays for Pathogen Detection and Analysis
Briefings in functional genomics, 2011Co-Authors: Kevin McloughlinAbstract:DNA microarrays have emerged as a viable platform for Detection of pathogenic organisms in clinical and environmental samples. These Microbial Detection arrays occupy a middle ground between low cost, narrowly focused assays such as multiplex PCR and more expensive, broad-spectrum technologies like high-throughput sequencing. While pathogen Detection arrays have been used primarily in a research context, several groups are aggressively working to develop arrays for clinical diagnostics, food safety testing, environmental monitoring and biodefense. Statistical algorithms that can analyze data from Microbial Detection arrays and provide easily interpretable results are absolutely required in order for these efforts to succeed. In this article, we will review the most promising array designs and analysis algorithms that have been developed to date, comparing their strengths and weaknesses for pathogen Detection and discovery.
Crystal Jaing - One of the best experts on this subject based on the ideXlab platform.
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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
Applied and Environmental Microbiology, 2019Co-Authors: Estelle Martin, Crystal Jaing, James B. Thissen, Monica K. Borucki, Selene Garcialuna, Mona Hwang, Megan Wise De Valdez, Gabriel L Hamer, Matthias FrankAbstract: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 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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Detection of Epstein-Barr virus (EBV) in human lymphoma tissue by a novel Microbial Detection array.
Biomarker research, 2014Co-Authors: Joseph Tellez, Crystal Jaing, Jun Wang, Ralph Green, Mingyi ChenAbstract: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. 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-. 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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Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.
Scientific reports, 2014Co-Authors: Alison Devault, Kevin Mcloughlin, Shea N Gardner, Crystal Jaing, James B. Thissen, Teresita M. Porter, Jacob Enk, Jonathan E. Allen, Monica K. Borucki, Sharon N. DewitteAbstract:Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of Microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis (“Black Death” plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.
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Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray.
Journal of virological methods, 2014Co-Authors: James B. Thissen, Kevin Mcloughlin, Shea N Gardner, Tom Slezak, Shalini Mabery, Crystal JaingAbstract: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. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA was able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate Detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.
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Comprehensive Analysis Of Microbial Signatures For Lymphomagenesis Using a Novel Microbial Detection Array
Blood, 2013Co-Authors: Crystal Jaing, Jun Wang, Ralph Green, Mingyi ChenAbstract:Introduction Infectious agents are estimated to play a causative role in approximately 20% of cancers worldwide. Viral infections, 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 with B-cell malignancy. The risks posed by these pathogens increases with age. Early Detection can impact treatment options and may play a critical role in patient survival. We report the use of the Lawrence Livermore Microbial Detection Array (LLMDA), a highly sensitive and comprehensive Detection system that contains probes for all known sequenced viruses and bacteria designed to identify pathogen-associated diseases. Our study focuses on detecting pathogens that may be associated with lymphomas, in order to develop appropriate therapeutic treatment strategies for pathogen-associated B-cell lymphomas. Methods The LLMDA is a pan-Microbial Detection Array (MDA) capable of detecting all known viruses (including phages), bacteria and plasmids and uses a novel statistical analysis method to identify organisms from complex mixtures hybridized to the array. The LLMDA contains a more comprehensive bacterial and viral target spectrum, more probes per target and is based on more updated sequence data than other existing Microbial Detection/discovery arrays. Family-specific probes representing complete genomes of all sequenced bacteria and viruses, conserved segments of these genomes, and plasmids were selected. Probes possess adequate sequence variation to allow Detection of divergent species with homology to sequenced organisms. Using the LLMDA we tested indolent and aggressive stage B cell lymphomas and normal tissues as controls. We demonstrated the system’s accuracy by investigating the pathogen profiles of previously analyzed post-transplant lymphoproliferative disorder (PTLD) tumors. We also applied the technique to fresh frozen and formalin fixed, paraffin-embedded (FFPE) tissues to evaluate the range of sample types amenable to the LLMDA analysis. Results We evaluated tissue from 34 lymphoma cases using LLMDA. These included 30 B cell (9 indolent and 21 aggressive stage), 2 T cell and 2 NKT cell, 4 plasmacytomas as well as 8 specimens of benign lymphoid tissue. Five of 21 aggressive stage B cell lymphomas were EBER+, and all the indolent stage B cell lymphomas were EBER-. Both NKT cell lymphomas were EBER+, and the T cell lymphomas and benign tissues were EBER-. Five of the PTLD cases (4 B cell lymphomas and 1 NKT cell lymphoma) were EBER+ and 5 were EBER-. Finally, two of the FFPE tissues (1 B cell lymphoma and 1 NKT cell lymphoma) were EBER+ and 1 EBER-, in conformity with the previously analysis of EBER status in these samples. We have confirmed the accuracy of the technique by detecting EBV in EBV-positive lymphomas while observing no false-positive results in EBV-negative lymphomas Conclusions We have confirmed the LLMDA’s efficacy for detecting viruses in pathogen-associated disease. This technique may provide a powerful and sensitive method for identifying known viral pathogens associated with tumors and may also prove useful for the discovery of novel tumor-associated viruses. Disclosures: No relevant conflicts of interest to declare.
Shea N Gardner - One of the best experts on this subject based on the ideXlab platform.
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the Microbial Detection array for Detection of emerging viruses in clinical samples a useful panMicrobial diagnostic tool
PLOS ONE, 2014Co-Authors: Maiken W Rosenstierne, Kevin Mcloughlin, Majken Lindholm Olesen, Shea N Gardner, Olivier Engler, Manfred Weidmann, Ali Mirazimi, Sébastien Plumet, Anna Papa, Matthias NiedrigAbstract: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 nonclinical and clinical samples using two different microarray data analysis methods.
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Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.
Scientific reports, 2014Co-Authors: Alison Devault, Kevin Mcloughlin, Shea N Gardner, Crystal Jaing, James B. Thissen, Teresita M. Porter, Jacob Enk, Jonathan E. Allen, Monica K. Borucki, Sharon N. DewitteAbstract:Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of Microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis (“Black Death” plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.
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Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray.
Journal of virological methods, 2014Co-Authors: James B. Thissen, Kevin Mcloughlin, Shea N Gardner, Tom Slezak, Shalini Mabery, Crystal JaingAbstract: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. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA was able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate Detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.
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Detection of Adventitious Viruses from Biologicals Using a Broad-Spectrum Microbial Detection Array
PDA journal of pharmaceutical science and technology, 2011Co-Authors: Crystal Jaing, Kevin Mcloughlin, Shea N Gardner, James B. Thissen, Tom SlezakAbstract:CONFERENCE PROCEEDING Proceedings of the PDA/FDA Adventitious Viruses in Biologics: Detection and Mitigation Strategies Workshop in Bethesda, MD, USA; December 1-3, 2010 Guest Editors: Arifa Khan (Bethesda, MD), Patricia Hughes (Bethesda, MD) and Michael Wiebe (San Francisco, CA) We designed the Lawrence Livermore Microbial Detection Array (LLMDA), which contains 388,000 DNA probes. This array can detect any sequenced viruses or bacteria within 24 h. In addition, the oligonucleotide probes were selected to enable Detection of novel, divergent species with homology to sequenced organisms. We recently used this array to identify an adventitious virus from a vaccine product. We have also used this array to detect viral and bacterial infections from various human clinical samples. Broad-spectrum Microbial Detection microarrays are efficient and cost-effective tools to rapidly screen cell bank samples, raw materials, vaccine samples, and clinical samples to ensure drug, food, and health safety in the United States and worldwide.
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A Microbial Detection array (MDA) for viral and bacterial Detection
BMC Genomics, 2010Co-Authors: Shea N Gardner, Crystal J Jaing, Kevin S Mcloughlin, Tom R SlezakAbstract:Background Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. Methods We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other Microbial Detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable Detection of divergent species with homology to sequenced organisms, and to have no significant matches to the human genome sequence. Results In blinded testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Conclusions The MDA can be used to identify the suite of viruses and bacteria present in complex samples.
Tom Slezak - One of the best experts on this subject based on the ideXlab platform.
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Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray.
Journal of virological methods, 2014Co-Authors: James B. Thissen, Kevin Mcloughlin, Shea N Gardner, Tom Slezak, Shalini Mabery, Crystal JaingAbstract: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. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA was able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate Detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.
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Detection of Adventitious Viruses from Biologicals Using a Broad-Spectrum Microbial Detection Array
PDA journal of pharmaceutical science and technology, 2011Co-Authors: Crystal Jaing, Kevin Mcloughlin, Shea N Gardner, James B. Thissen, Tom SlezakAbstract:CONFERENCE PROCEEDING Proceedings of the PDA/FDA Adventitious Viruses in Biologics: Detection and Mitigation Strategies Workshop in Bethesda, MD, USA; December 1-3, 2010 Guest Editors: Arifa Khan (Bethesda, MD), Patricia Hughes (Bethesda, MD) and Michael Wiebe (San Francisco, CA) We designed the Lawrence Livermore Microbial Detection Array (LLMDA), which contains 388,000 DNA probes. This array can detect any sequenced viruses or bacteria within 24 h. In addition, the oligonucleotide probes were selected to enable Detection of novel, divergent species with homology to sequenced organisms. We recently used this array to identify an adventitious virus from a vaccine product. We have also used this array to detect viral and bacterial infections from various human clinical samples. Broad-spectrum Microbial Detection microarrays are efficient and cost-effective tools to rapidly screen cell bank samples, raw materials, vaccine samples, and clinical samples to ensure drug, food, and health safety in the United States and worldwide.
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A Microbial Detection array (MDA) for viral and bacterial Detection
BMC genomics, 2010Co-Authors: Shea N Gardner, Kevin Mcloughlin, Crystal Jaing, Tom SlezakAbstract:Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other Microbial Detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable Detection of divergent species with homology to sequenced organisms, and to have no significant matches to the human genome sequence. In blinded testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. The MDA can be used to identify the suite of viruses and bacteria present in complex samples.
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Bioinformatics Methods for Microbial Detection and Forensic Diagnostic Design
Microbial Forensics, 2005Co-Authors: Tom Slezak, Steven L. SalzbergAbstract:Publisher Summary This chapter reviews bioinformatics techniques that are used for the Detection and identication of Microbial samples, and for further analysis of sequence information derived from Microbial organisms. It begins with an overview of laboratory techniques used to create the diagnostic and forensic data, and then describes methods for sequencing, assembling, and analyzing genomic data. Algorithms for large-scale genome alignment and comparison, followed by methods for modeling protein structure are considered. The goal of bioinformatics in Microbial forensics and diagnostics is to support the rapid identification of Microbial samples, at a variety of levels of resolution (family, species, strain, and isolate). Techniques to accomplish this are based upon accurate determination and comparison of genomic sequence of high quality, combined with detailed analysis of the sequence to determine gene composition, protein structure, and the functional organization of the mechanisms of transmission and virulence. The chapter concludes with real-life examples demonstrating working systems for Detection and analysis of the Microbial pathogens, using both DNA and protein Detection methods.
James B. Thissen - One of the best experts on this subject based on the ideXlab platform.
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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
Applied and Environmental Microbiology, 2019Co-Authors: Estelle Martin, Crystal Jaing, James B. Thissen, Monica K. Borucki, Selene Garcialuna, Mona Hwang, Megan Wise De Valdez, Gabriel L Hamer, Matthias FrankAbstract: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 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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Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.
Scientific reports, 2014Co-Authors: Alison Devault, Kevin Mcloughlin, Shea N Gardner, Crystal Jaing, James B. Thissen, Teresita M. Porter, Jacob Enk, Jonathan E. Allen, Monica K. Borucki, Sharon N. DewitteAbstract:Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of Microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis (“Black Death” plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.
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Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray.
Journal of virological methods, 2014Co-Authors: James B. Thissen, Kevin Mcloughlin, Shea N Gardner, Tom Slezak, Shalini Mabery, Crystal JaingAbstract: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. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA was able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate Detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.
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Detection of Adventitious Viruses from Biologicals Using a Broad-Spectrum Microbial Detection Array
PDA journal of pharmaceutical science and technology, 2011Co-Authors: Crystal Jaing, Kevin Mcloughlin, Shea N Gardner, James B. Thissen, Tom SlezakAbstract:CONFERENCE PROCEEDING Proceedings of the PDA/FDA Adventitious Viruses in Biologics: Detection and Mitigation Strategies Workshop in Bethesda, MD, USA; December 1-3, 2010 Guest Editors: Arifa Khan (Bethesda, MD), Patricia Hughes (Bethesda, MD) and Michael Wiebe (San Francisco, CA) We designed the Lawrence Livermore Microbial Detection Array (LLMDA), which contains 388,000 DNA probes. This array can detect any sequenced viruses or bacteria within 24 h. In addition, the oligonucleotide probes were selected to enable Detection of novel, divergent species with homology to sequenced organisms. We recently used this array to identify an adventitious virus from a vaccine product. We have also used this array to detect viral and bacterial infections from various human clinical samples. Broad-spectrum Microbial Detection microarrays are efficient and cost-effective tools to rapidly screen cell bank samples, raw materials, vaccine samples, and clinical samples to ensure drug, food, and health safety in the United States and worldwide.