1
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Kok CR, Bram Z, Thissen JB, Horseman TS, Fong KSK, Reichert-Scrivner SA, Paguirigan C, O'Connor K, Thompson K, Scheiber AE, Mabery S, Ngauy V, Uyehara CF, Be NA. The military gear microbiome: risk factors surrounding the warfighter. Appl Environ Microbiol 2024; 90:e0117623. [PMID: 38170999 PMCID: PMC10807412 DOI: 10.1128/aem.01176-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024] Open
Abstract
Combat extremity wounds are highly susceptible to contamination from surrounding environmental material. This bioburden could be partially transferred from materials in immediate proximity to the wound, including fragments of the uniform and gear. However, the assessment of the microbial bioburden present on military gear during operational conditions of deployment or training is relatively unexplored. Opportunistic pathogens that can survive on gear represent risk factors for infection following injury, especially following combat blasts, where fibers and other materials are embedded in wounded tissue. We utilized 16S rRNA sequencing to assess the microbiome composition of different military gear types (boot, trouser, coat, and canteen) from two operational environments (training in Hawai'i and deployed in Indonesia) across time (days 0 and 14). We found that microbiome diversity, stability, and composition were dependent on gear type, training location, and sampling timepoint. At day 14, species diversity was significantly higher in Hawai'i samples compared to Indonesia samples for boot, coat, and trouser swabs. In addition, we observed the presence of potential microbial risk factors, as opportunistic pathogenic species, such as Acinetobacter, Pseudomonas, and Staphylococcus, were found to be present in all sample types and in both study sites. These study outcomes will be used to guide the design of antimicrobial materials and uniforms and for infection control efforts following combat blasts and other injuries, thereby improving treatment guidance during military training and deployment.IMPORTANCECombat extremity wounds are vulnerable to contamination from environments of proximity to the warfighter, leading to potential detrimental outcomes such as infection and delayed wound healing. Therefore, microbial surveillance of such environments is necessary to aid the advancement of military safety and preparedness through clinical diagnostics, treatment protocols, and uniform material design.
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Affiliation(s)
- Car Reen Kok
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | | | - James B. Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Timothy S. Horseman
- Tripler Army Medical Center, Honolulu, Hawaii, USA
- School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | | | | | | | | | | | - Shalini Mabery
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Viseth Ngauy
- Tripler Army Medical Center, Honolulu, Hawaii, USA
| | | | - Nicholas A. Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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2
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Kok CR, Mulakken N, Thissen JB, Grey SF, Avila-Herrera A, Upadhyay MM, Lisboa FA, Mabery S, Elster EA, Schobel SA, Be NA. Targeted metagenomic assessment reflects critical colonization in battlefield injuries. Microbiol Spectr 2023; 11:e0252023. [PMID: 37874143 PMCID: PMC10714869 DOI: 10.1128/spectrum.02520-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/18/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Microbial contamination in combat wounds can lead to opportunistic infections and adverse outcomes. However, current microbiological detection has a limited ability to capture microbial functional genes. This work describes the application of targeted metagenomic sequencing to profile wound bioburden and capture relevant wound-associated signatures for clinical utility. Ultimately, the ability to detect such signatures will help guide clinical decisions regarding wound care and management and aid in the prediction of wound outcomes.
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Affiliation(s)
- Car Reen Kok
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Nisha Mulakken
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - James B. Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Scott F. Grey
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Meenu M. Upadhyay
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Felipe A. Lisboa
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Shalini Mabery
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Eric A. Elster
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Seth A. Schobel
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Nicholas A. Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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3
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McGowan J, Borucki M, Omairi H, Varghese M, Vellani S, Chakravarty S, Fan S, Chattopadhyay S, Siddiquee M, Thissen JB, Mulakken N, Moon J, Kimbrel J, Tiwari AK, Taylor RT, Kang DW, Jaing C, Chakravarti R, Chattopadhyay S. SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection. Viruses 2022; 14:2032. [PMID: 36146835 PMCID: PMC9503862 DOI: 10.3390/v14092032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
Wastewater-based epidemiology (WBE) is a popular tool for the early indication of community spread of infectious diseases. WBE emerged as an effective tool during the COVID-19 pandemic and has provided meaningful information to minimize the spread of infection. Here, we present a combination of analyses using the correlation of viral gene copies with clinical cases, sequencing of wastewater-derived RNA for the viral mutants, and correlative analyses of the viral gene copies with the bacterial biomarkers. Our study provides a unique platform for potentially using the WBE-derived results to predict the spread of COVID-19 and the emergence of new variants of concern. Further, we observed a strong correlation between the presence of SARS-CoV-2 and changes in the microbial community of wastewater, particularly the significant changes in bacterial genera belonging to the families of Lachnospiraceae and Actinomycetaceae. Our study shows that microbial biomarkers could be utilized as prediction tools for future infectious disease surveillance and outbreak responses. Overall, our comprehensive analyses of viral spread, variants, and novel bacterial biomarkers will add significantly to the growing body of literature on WBE and COVID-19.
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Affiliation(s)
- Jenna McGowan
- Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Monica Borucki
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Hicham Omairi
- Department of Civil and Environmental Engineering, University of Toledo College of Engineering, Toledo, OH 43607, USA
| | - Merina Varghese
- Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Shahnaz Vellani
- Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Sukanya Chakravarty
- Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Shumin Fan
- Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Srestha Chattopadhyay
- College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Mashuk Siddiquee
- Department of Civil and Environmental Engineering, University of Toledo College of Engineering, Toledo, OH 43607, USA
| | - James B. Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Nisha Mulakken
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Joseph Moon
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Jeffrey Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Amit K. Tiwari
- College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606, USA
- Center for Medical Bio-Allied Health Sciences Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Roger Travis Taylor
- Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Dae-Wook Kang
- Department of Civil and Environmental Engineering, University of Toledo College of Engineering, Toledo, OH 43607, USA
| | - Crystal Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Ritu Chakravarti
- Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Saurabh Chattopadhyay
- Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
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Urbaniak C, Morrison MD, Thissen JB, Karouia F, Smith DJ, Mehta S, Jaing C, Venkateswaran K. Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station. Microbiome 2022; 10:100. [PMID: 35765106 PMCID: PMC9241228 DOI: 10.1186/s40168-022-01293-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/19/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months. METHODS Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results. RESULTS Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 105 cfu/m2 CONCLUSIONS: Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity. Video Abstract.
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Affiliation(s)
- Camilla Urbaniak
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Michael D Morrison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - James B Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Fathi Karouia
- KBRwyle, NASA Ames Research Center, Moffett Field, Mountain View, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - David J Smith
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, Mountain View, CA, USA
| | - Satish Mehta
- JesTech, NASA-Johnson Space Center, Houston, TX, USA
| | - Crystal Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA.
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5
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Morrison MD, Thissen JB, Karouia F, Mehta S, Urbaniak C, Venkateswaran K, Smith DJ, Jaing C. Investigation of Spaceflight Induced Changes to Astronaut Microbiomes. Front Microbiol 2021; 12:659179. [PMID: 34149649 PMCID: PMC8207296 DOI: 10.3389/fmicb.2021.659179] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/05/2021] [Indexed: 12/26/2022] Open
Abstract
The International Space Station (ISS) is a uniquely enclosed environment that has been continuously occupied for the last two decades. Throughout its operation, protecting the health of the astronauts on-board has been a high priority. The human microbiome plays a significant role in maintaining human health, and disruptions in the microbiome have been linked to various diseases. To evaluate the effects of spaceflight on the human microbiome, body swabs and saliva samples were collected from four ISS astronauts on consecutive expeditions. Astronaut samples were analyzed using shotgun metagenomic sequencing and microarrays to characterize the microbial biodiversity before, during, and after the astronauts’ time onboard the ISS. Samples were evaluated at an individual and population level to identify changes in microbial diversity and abundance. No significant changes in the number or relative abundance of taxa were observed between collection time points when samples from all four astronauts were analyzed together. When the astronauts’ saliva samples were analyzed individually, the saliva samples of some astronauts showed significant changes in the relative abundance of taxa during and after spaceflight. The relative abundance of Prevotella in saliva samples increased during two astronauts’ time onboard the ISS while the relative abundance of other commensal taxa such as Neisseria, Rothia, and Haemophilus decreased. The abundance of some antimicrobial resistance genes within the saliva samples also showed significant changes. Most notably, elfamycin resistance gene significantly increased in all four astronauts post-flight and a CfxA6 beta-lactam marker significantly increased during spaceflight but returned to normal levels post-flight. The combination of both shotgun metagenomic sequencing and microarrays showed the benefit of both technologies in monitoring microbes on board the ISS. There were some changes in each astronaut’s microbiome during spaceflight, but these changes were not universal for all four astronauts. Two antimicrobial resistance gene markers did show a significant change in abundance in the saliva samples of all four astronauts across their collection times. These results provide insight for future ISS microbial monitoring studies and targets for antimicrobial resistance screenings.
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Affiliation(s)
- Michael D Morrison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - James B Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Fathi Karouia
- KBRwyle, NASA Ames Research Center, Moffett Field, CA, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States.,Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States
| | - Satish Mehta
- JesTech, NASA Johnson Space Center, Houston, TX, United States
| | - Camilla Urbaniak
- Biotechnology and Planetary Protection Group, NASA-Jet Propulsion Laboratory, Pasadena, CA, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, NASA-Jet Propulsion Laboratory, Pasadena, CA, United States
| | - David J Smith
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, United States
| | - Crystal Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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6
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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: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Borucki MK, Collette NM, Coffey LL, Van Rompay KKA, Hwang MH, Thissen JB, Allen JE, Zemla AT. Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence. PLoS One 2019; 14:e0225699. [PMID: 31809512 PMCID: PMC6897431 DOI: 10.1371/journal.pone.0225699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 11/11/2019] [Indexed: 11/19/2022] Open
Abstract
The question of how Zika virus (ZIKV) changed from a seemingly mild virus to a human pathogen capable of microcephaly and sexual transmission remains unanswered. The unexpected emergence of ZIKV's pathogenicity and capacity for sexual transmission may be due to genetic changes, and future changes in phenotype may continue to occur as the virus expands its geographic range. Alternatively, the sheer size of the 2015-16 epidemic may have brought attention to a pre-existing virulent ZIKV phenotype in a highly susceptible population. Thus, it is important to identify patterns of genetic change that may yield a better understanding of ZIKV emergence and evolution. However, because ZIKV has an RNA genome and a polymerase incapable of proofreading, it undergoes rapid mutation which makes it difficult to identify combinations of mutations associated with viral emergence. As next generation sequencing technology has allowed whole genome consensus and variant sequence data to be generated for numerous virus samples, the task of analyzing these genomes for patterns of mutation has become more complex. However, understanding which combinations of mutations spread widely and become established in new geographic regions versus those that disappear relatively quickly is essential for defining the trajectory of an ongoing epidemic. In this study, multiscale analysis of the wealth of genomic data generated over the course of the epidemic combined with in vivo laboratory data allowed trends in mutations and outbreak trajectory to be assessed. Mutations were detected throughout the genome via deep sequencing, and many variants appeared in multiple samples and in some cases become consensus. Similarly, amino acids that were previously consensus in pre-outbreak samples were detected as low frequency variants in epidemic strains. Protein structural models indicate that most of the mutations associated with the epidemic transmission occur on the exposed surface of viral proteins. At the macroscale level, consensus data was organized into large and interactive databases to allow the spread of individual mutations and combinations of mutations to be visualized and assessed for temporal and geographical patterns. Thus, the use of multiscale modeling for identifying mutations or combinations of mutations that impact epidemic transmission and phenotypic impact can aid the formation of hypotheses which can then be tested using reverse genetics.
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Affiliation(s)
- Monica K. Borucki
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Nicole M. Collette
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Lark L. Coffey
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Koen K. A. Van Rompay
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
| | - Mona H. Hwang
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - James B. Thissen
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Jonathan E. Allen
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Adam T. Zemla
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Thissen JB, Isshiki M, Jaing C, Nagao Y, Lebron Aldea D, Allen JE, Izui M, Slezak TR, Ishida T, Sano T. A novel variant of torque teno virus 7 identified in patients with Kawasaki disease. PLoS One 2018; 13:e0209683. [PMID: 30592753 PMCID: PMC6310298 DOI: 10.1371/journal.pone.0209683] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/09/2018] [Indexed: 11/18/2022] Open
Abstract
Kawasaki disease (KD), first identified in 1967, is a pediatric vasculitis of unknown etiology that has an increasing incidence in Japan and many other countries. KD can cause coronary artery aneurysms. Its epidemiological characteristics, such as seasonality and clinical picture of acute systemic inflammation with prodromal intestinal/respiratory symptoms, suggest an infectious etiology for KD. Interestingly, multiple host genotypes have been identified as predisposing factors for KD. To explore experimental methodology for identifying etiological agent(s) for KD and to optimize epidemiological study design (particularly the sample size) for future studies, we conducted a pilot study. For a 1-year period, we prospectively enrolled 11 patients with KD. To each KD patient, we assigned two control individuals (one with diarrhea and the other with respiratory infections), matched for age, sex, and season of diagnosis. During the acute phase of disease, we collected peripheral blood, nasopharyngeal aspirate, and feces. We also determined genotypes, to identify those that confer susceptibility to KD. There was no statistically significant difference in the frequency of the risk genotypes between KD patients and control subjects. We also used unbiased metagenomic sequencing to analyze these samples. Metagenomic sequencing and PCR detected torque teno virus 7 (TTV7) in two patients with KD (18%), but not in control subjects (P = 0.111). Sanger sequencing revealed that the TTV7 found in the two KD patients contained almost identical variants in nucleotide and identical changes in resulting amino acid, relative to the reference sequence. Additionally, we estimated the sample size that would be required to demonstrate a statistical correlation between TTV7 and KD. Future larger scale studies with carefully optimized metagenomic sequencing experiments and adequate sample size are warranted to further examine the association between KD and potential pathogens, including TTV7.
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Affiliation(s)
- James B. Thissen
- Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Crystal Jaing
- Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Yoshiro Nagao
- Department of Pediatrics, Japan Community Health Care Organization Osaka Hospital, Osaka, Japan
| | - Dayanara Lebron Aldea
- Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Jonathan E. Allen
- Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Masafumi Izui
- Department of Pediatrics, Japan Community Health Care Organization Osaka Hospital, Osaka, Japan
| | - Thomas R. Slezak
- Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Tetsuya Sano
- Department of Pediatrics, Japan Community Health Care Organization Osaka Hospital, Osaka, Japan
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11
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Feng SF, Jaing C, Thissen JB, Wang C, Duncan P. Modeling an approach to define sensitivity of viral detection in sample matrices-examples with microarray readout. PDA J Pharm Sci Technol 2018; 68:589-94. [PMID: 25475633 DOI: 10.5731/pdajpst.2014.01011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Advances in viral detection technologies have the potential to increase the safety assurance of medicines produced in biological production systems. However, taking full advantage of these technological advances in the regulated testing environment will require protocols for standardization and performance testing. The most essential performance characteristics of detection methods for these applications include sensitivity, breadth of detection, and consistency. We have evaluated an approach to establishing the suitability of advanced nucleic-acid-based detection systems for characterization of cell substrates and production cultures. This approach is based on selecting relevant challenge viruses, their preparation and characterization, their application to a sample preparation workflow, and quantitation of their recovery by an independent means as well as the advanced detection readout. This approach helps us evaluate the suitability of the workflow for handling diverse sample matrices across manufacturing platforms for vaccines and other biological products, and also suggests a means by which technology users, developers, and regulators may consider the critical performance attributes of novel detection technologies. We have applied this workflow to a novel microarray-based viral detection system in collaboration with Lawrence Livermore National Laboratory. This system is appealing because of the rapid turnaround of results compared to some other advanced detection technologies.
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Affiliation(s)
- Szi Fei Feng
- Merck Research Laboratories, Sumneytown Pike, West Point, PA, USA; and
| | - Crystal Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - James B Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christopher Wang
- Merck Research Laboratories, Sumneytown Pike, West Point, PA, USA; and
| | - Paul Duncan
- Merck Research Laboratories, Sumneytown Pike, West Point, PA, USA; and
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12
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Jaing C, Rowland RRR, Allen JE, Certoma A, Thissen JB, Bingham J, Rowe B, White JR, Wynne JW, Johnson D, Gaudreault NN, Williams DT. Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses. Sci Rep 2017; 7:10115. [PMID: 28860602 PMCID: PMC5579198 DOI: 10.1038/s41598-017-10186-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/04/2017] [Indexed: 11/09/2022] Open
Abstract
African swine fever virus (ASFV) is a macrophage-tropic virus responsible for ASF, a transboundary disease that threatens swine production world-wide. Since there are no vaccines available to control ASF after an outbreak, obtaining an understanding of the virus-host interaction is important for developing new intervention strategies. In this study, a whole transcriptomic RNA-Seq method was used to characterize differentially expressed genes in pigs infected with a low pathogenic ASFV isolate, OUR T88/3 (OURT), or the highly pathogenic Georgia 2007/1 (GRG). After infection, pigs infected with OURT showed no or few clinical signs; whereas, GRG produced clinical signs consistent with acute ASF. RNA-Seq detected the expression of ASFV genes from the whole blood of the GRG, but not the OURT pigs, consistent with the pathotypes of these strains and the replication of GRG in circulating monocytes. Even though GRG and OURT possess different pathogenic properties, there was significant overlap in the most upregulated host genes. A small number of differentially expressed microRNAs were also detected in GRG and OURT pigs. These data confirm previous studies describing the response of macrophages and lymphocytes to ASFV infection, as well as reveal unique gene pathways upregulated in response to infection with GRG.
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Affiliation(s)
- Crystal Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America.
| | - Raymond R R Rowland
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Jonathan E Allen
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Andrea Certoma
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - James B Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - John Bingham
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Brenton Rowe
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - John R White
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - James W Wynne
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Dayna Johnson
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Natasha N Gaudreault
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - David T Williams
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
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13
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Ober RA, Thissen JB, Jaing CJ, Cino-Ozuna AG, Rowland RRR, Niederwerder MC. Increased microbiome diversity at the time of infection is associated with improved growth rates of pigs after co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2). Vet Microbiol 2017; 208:203-211. [PMID: 28888639 DOI: 10.1016/j.vetmic.2017.06.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/20/2017] [Accepted: 06/20/2017] [Indexed: 01/30/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are two of the most important pathogens affecting the swine industry worldwide. Co-infections are common on a global scale, resulting in pork production losses through reducing weight gain and causing respiratory disease in growing pigs. Our initial work demonstrated that the fecal microbiome was associated with clinical outcome of pigs 70days post-infection (dpi) with PRRSV and PCV2. However, it remained uncertain if microbiome characteristics could predispose response to viral infection. The purpose of this study was to determine if microbiome characteristics present at the time of virus exposure were associated with outcome after co-infection. Using the Lawrence Livermore Microbial Detection Array, we profiled the microbiome in feces prior to infection from pigs identified retrospectively as having high or low growth rates after co-infection. High growth rate pigs had less severe interstitial pneumonia, reduced virus replication, and a significant increase in average daily weight gain throughout the study. At the level of the fecal microbiome, high growth rate pigs had increased microbial diversity on both a family and species level. Shifts in the microbiome composition of high growth rate pigs included reduced Methanobacteriaceae species, increased Ruminococcaceae species, and increased Streptococcaceae species when compared to low growth rate pigs. The results indicate that both microbiome diversity and composition at the time of virus exposure may play a role in the subsequent response of pigs to PRRSV/PCV2 co-infection.
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Affiliation(s)
- Rebecca A Ober
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University,1800 Denison Avenue, Manhattan, KS 66506, USA
| | - James B Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory,7000 East Avenue, Livermore, CA 94550, USA
| | - Crystal J Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory,7000 East Avenue, Livermore, CA 94550, USA
| | - Ada G Cino-Ozuna
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University,1800 Denison Avenue, Manhattan, KS 66506, USA; Kansas State Veterinary Diagnostic Laboratory, Kansas State University,1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Raymond R R Rowland
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University,1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University,1800 Denison Avenue, Manhattan, KS 66506, USA; Kansas State Veterinary Diagnostic Laboratory, Kansas State University,1800 Denison Avenue, Manhattan, KS 66506, USA.
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14
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Robinson LA, Jaing CJ, Campbell CP, Magliocco A, Xiong Y, Magliocco G, Thissen JB, Antonia S. Reply to: Comment on 'Molecular evidence of viral DNA in non-small cell lung cancer and non-neoplastic lung'. Br J Cancer 2017; 116:e6. [PMID: 27764846 PMCID: PMC5294469 DOI: 10.1038/bjc.2016.339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Lary A Robinson
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL 33612-9416, USA
- Center for Infection Research in Cancer (CIRC), Moffitt Cancer Center, Tampa, FL 33612-9416, USA
| | - Crystal J Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94559-9698, USA
| | - Christine Pierce Campbell
- Center for Infection Research in Cancer (CIRC), Moffitt Cancer Center, Tampa, FL 33612-9416, USA
- Department of Epidemiology, Moffitt Cancer Center, Tampa, FL 33612-9416, USA
| | - Anthony Magliocco
- Department of Pathology, Moffitt Cancer Center, Tampa, FL 33612-9416, USA
| | - Yin Xiong
- Department of Pathology, Moffitt Cancer Center, Tampa, FL 33612-9416, USA
| | - Genevra Magliocco
- Department of Pathology, Moffitt Cancer Center, Tampa, FL 33612-9416, USA
| | - James B Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94559-9698, USA
| | - Scott Antonia
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL 33612-9416, USA
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15
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Jaing CJ, McLoughlin KS, Thissen JB, Zemla A, Gardner SN, Vergez LM, Bourguet F, Mabery S, Fofanov VY, Koshinsky H, Jackson PJ. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing. PLoS One 2016; 11:e0163458. [PMID: 27668749 PMCID: PMC5036845 DOI: 10.1371/journal.pone.0163458] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/08/2016] [Indexed: 11/19/2022] Open
Abstract
Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. Genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.
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Affiliation(s)
- Crystal J. Jaing
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
- * E-mail:
| | - Kevin S. McLoughlin
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - James B. Thissen
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Adam Zemla
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shea N. Gardner
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Lisa M. Vergez
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Feliza Bourguet
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shalini Mabery
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | | | | | - Paul J. Jackson
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Niederwerder MC, Jaing CJ, Thissen JB, Cino-Ozuna AG, McLoughlin KS, Rowland RRR. Microbiome associations in pigs with the best and worst clinical outcomes following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2). Vet Microbiol 2016; 188:1-11. [PMID: 27139023 DOI: 10.1016/j.vetmic.2016.03.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/17/2023]
Abstract
On a world-wide basis, co-infections involving porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are common and contribute to a range of polymicrobial disease syndromes in swine. Both viruses compromise host defenses, resulting in increased susceptibility to infections by primary and secondary pathogens that can affect growth performance as well as increased morbidity and mortality. An experimental population of 95 pigs was co-infected with PRRSV and PCV2. At 70days post-infection (dpi), 20 representative pigs were selected as having the best or worst clinical outcome based on average daily gain (ADG) and the presence of clinical disease. Worst clinical outcome pigs had prolonged and greater levels of viremia as measured by qPCR. Serum, lung and fecal samples collected at 70 dpi were analyzed using a comprehensive DNA microarray technology, the Lawrence Livermore Microbial Detection Array, to detect over 8000 microbes. Bacterial species, such as Bacillus cereus, were detected at a higher rate in the serum of worst performing pigs. At the level of the fecal microbiome, the overall microbial diversity was lower in the worst clinical outcome group. The results reinforce the importance of pathogen load in determining clinical outcome and suggest an important role of microbial diversity as a contributing factor in disease.
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Affiliation(s)
- Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA; Kansas State Veterinary Diagnostic Laboratory, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA.
| | - Crystal J Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - James B Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Ada Giselle Cino-Ozuna
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA; Kansas State Veterinary Diagnostic Laboratory, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Kevin S McLoughlin
- Computations Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Raymond R R Rowland
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
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18
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Gardner SN, Frey KG, Redden CL, Thissen JB, Allen JE, Allred AF, Dyer MD, Mokashi VP, Slezak TR. Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing. BMC Res Notes 2015; 8:682. [PMID: 26572552 PMCID: PMC4647626 DOI: 10.1186/s13104-015-1530-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/28/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Historically, identification of causal agents of disease has relied heavily on the ability to culture the organism in the laboratory and/or the use of pathogen-specific antibodies or sequence-based probes. However, these methods can be limiting: Even highly sensitive PCR-based assays must be continually updated due to signature degradation as new target strains and near neighbors are sequenced. Thus, there has been a need for assays that do not suffer as greatly from these limitations and/or biases. Recent advances in library preparation technologies for Next-Generation Sequencing (NGS) are focusing on the use of targeted amplification and targeted enrichment/capture to ensure that the most highly discriminating regions of the genomes of known targets (organism-unique regions and/or regions containing functionally important genes or phylogenetically-discriminating SNPs) will be sequenced, regardless of the complex sample background. RESULTS In the present study, we have assessed the feasibility of targeted sequence enhancement via amplification to facilitate detection of a bacterial pathogen present in low copy numbers in a background of human genomic material. Our results indicate that the targeted amplification of signature regions can effectively identify pathogen genomic material present in as little as 10 copies per ml in a complex sample. Importantly, the correct species and strain calls could be made in amplified samples, while this was not possible in unamplified samples. CONCLUSIONS The results presented here demonstrate the efficacy of a targeted amplification approach to biothreat detection, using multiple highly-discriminative amplicons per biothreat organism that provide redundancy in case of variation in some primer regions. Importantly, strain level discrimination was possible at levels of 10 genome equivalents. Similar results could be obtained through use of panels focused on the identification of amplicons targeted for specific genes or SNPs instead of, or in addition to, those targeted for specific organisms (ongoing gene-targeting work to be reported later). Note that without some form of targeted enhancement, the enormous background present in complex clinical and environmental samples makes it highly unlikely that sufficient coverage of key pathogen(s) present in the sample will be achieved with current NGS technology to guarantee that the most highly discriminating regions will be sequenced.
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Affiliation(s)
- Shea N Gardner
- Bioinformatics, Global Security Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-174, Livermore, CA, 94550, USA.
| | - Kenneth G Frey
- Naval Medical Research Center, NMRC-Frederick, 8400 Research Plaza, Fort Detrick, MD, 21702, USA. .,Henry M. Jackson Foundation, 6720-A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA.
| | - Cassie L Redden
- Naval Medical Research Center, NMRC-Frederick, 8400 Research Plaza, Fort Detrick, MD, 21702, USA. .,Henry M. Jackson Foundation, 6720-A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA.
| | - James B Thissen
- Bioinformatics, Global Security Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-174, Livermore, CA, 94550, USA.
| | - Jonathan E Allen
- Bioinformatics, Global Security Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-174, Livermore, CA, 94550, USA.
| | - Adam F Allred
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, Building 200, South San Francisco, CA, 94080, USA.
| | - Matthew D Dyer
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, Building 200, South San Francisco, CA, 94080, USA.
| | - Vishwesh P Mokashi
- Naval Medical Research Center, NMRC-Frederick, 8400 Research Plaza, Fort Detrick, MD, 21702, USA.
| | - Tom R Slezak
- Bioinformatics, Global Security Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-174, Livermore, CA, 94550, USA.
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Jaing C, Thissen JB, Gardner S, McLoughlin K, Slezak T, Bossart GD, Fair PA. Pathogen surveillance in wild bottlenose dolphins Tursiops truncatus. Dis Aquat Organ 2015; 116:83-91. [PMID: 26480911 DOI: 10.3354/dao02917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The number and prevalence of diseases is rapidly increasing in the marine ecosystem. Although there is an increase in the number of marine diseases observed world-wide, current understanding of the pathogens associated with marine mammals is limited. An important need exists to develop and apply platforms for rapid detection and characterization of pathogenic agents to assess, prevent and respond to disease outbreaks. In this study, a broad-spectrum molecular detection technology capable of detecting all sequenced microbial organisms, the Lawrence Livermore Microbial Detection Array, was used to assess the microbial agents that could be associated with wild Atlantic dolphins. Blowhole, gastric, and fecal samples from 8 bottlenose dolphins were collected in Charleston, SC, as part of the dolphin assessment effort. The array detected various microbial agents from the dolphin samples. Clostridium perfringens was most prevalent in the samples surveyed using the microarray. This pathogen was also detected using microbiological culture techniques. Additionally, Campylobacter sp., Staphylococcus sp., Erwinia amylovora, Helicobacter pylori, and Frankia sp. were also detected in more than one dolphin using the microarray, but not in culture. This study provides the first survey of pathogens associated with 3 tissue types in dolphins using a broad-spectrum microbial detection microarray and expands insight on the microbial community profile in dolphins.
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Affiliation(s)
- Crystal Jaing
- Physical & Life Sciences Directorate, Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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20
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Jaing CJ, Thissen JB, Gardner SN, McLoughlin KS, Hullinger PJ, Monday NA, Niederwerder MC, Rowland RRR. Application of a pathogen microarray for the analysis of viruses and bacteria in clinical diagnostic samples from pigs. J Vet Diagn Invest 2015; 27:313-25. [PMID: 25855363 DOI: 10.1177/1040638715578484] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many of the disease syndromes challenging the commercial swine industry involve the analysis of complex problems caused by polymicrobial, emerging or reemerging, and transboundary pathogens. This study investigated the utility of the Lawrence Livermore Microbial Detection Array (Lawrence Livermore National Laboratory, Livermore, California), designed to detect 8,101 species of microbes, in the evaluation of known and unknown microbes in serum, oral fluid, and tonsil from pigs experimentally coinfected with Porcine reproductive and respiratory syndrome virus (PRRSV) and Porcine circovirus-2 (PCV-2). The array easily identified PRRSV and PCV-2, but at decreased sensitivities compared to standard polymerase chain reaction detection methods. The oral fluid sample was the most informative, possessing additional signatures for several swine-associated bacteria, including Streptococcus sp., Clostridium sp., and Staphylococcus sp.
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Affiliation(s)
- Crystal J Jaing
- Physical & Life Sciences Directorate (Jaing, Thissen, Hullinger), Computations Directorate (Gardner, McLoughlin), Lawrence Livermore National Laboratory, Livermore, CADepartment of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS (Monday, Niederwerder, Rowland)
| | - James B Thissen
- Physical & Life Sciences Directorate (Jaing, Thissen, Hullinger), Computations Directorate (Gardner, McLoughlin), Lawrence Livermore National Laboratory, Livermore, CADepartment of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS (Monday, Niederwerder, Rowland)
| | - Shea N Gardner
- Physical & Life Sciences Directorate (Jaing, Thissen, Hullinger), Computations Directorate (Gardner, McLoughlin), Lawrence Livermore National Laboratory, Livermore, CADepartment of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS (Monday, Niederwerder, Rowland)
| | - Kevin S McLoughlin
- Physical & Life Sciences Directorate (Jaing, Thissen, Hullinger), Computations Directorate (Gardner, McLoughlin), Lawrence Livermore National Laboratory, Livermore, CADepartment of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS (Monday, Niederwerder, Rowland)
| | - Pam J Hullinger
- Physical & Life Sciences Directorate (Jaing, Thissen, Hullinger), Computations Directorate (Gardner, McLoughlin), Lawrence Livermore National Laboratory, Livermore, CADepartment of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS (Monday, Niederwerder, Rowland)
| | - Nicholas A Monday
- Physical & Life Sciences Directorate (Jaing, Thissen, Hullinger), Computations Directorate (Gardner, McLoughlin), Lawrence Livermore National Laboratory, Livermore, CADepartment of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS (Monday, Niederwerder, Rowland)
| | - Megan C Niederwerder
- Physical & Life Sciences Directorate (Jaing, Thissen, Hullinger), Computations Directorate (Gardner, McLoughlin), Lawrence Livermore National Laboratory, Livermore, CADepartment of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS (Monday, Niederwerder, Rowland)
| | - Raymond R R Rowland
- Physical & Life Sciences Directorate (Jaing, Thissen, Hullinger), Computations Directorate (Gardner, McLoughlin), Lawrence Livermore National Laboratory, Livermore, CADepartment of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS (Monday, Niederwerder, Rowland)
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Be NA, Thissen JB, Fofanov VY, Allen JE, Rojas M, Golovko G, Fofanov Y, Koshinsky H, Jaing CJ. Metagenomic analysis of the airborne environment in urban spaces. Microb Ecol 2015; 69:346-55. [PMID: 25351142 PMCID: PMC4312561 DOI: 10.1007/s00248-014-0517-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 10/09/2014] [Indexed: 05/04/2023]
Abstract
The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. Whole metagenome sequencing was applied to DNA extracted from air filters obtained during periods from each of the four seasons. The composition of bacteria, plants, fungi, invertebrates, and viruses demonstrated distinct temporal shifts. Bacillus thuringiensis serovar kurstaki was detected in samples known to be exposed to aerosolized spores, illustrating the potential utility of this approach for identification of intentionally introduced microbial agents. Together, these data demonstrate the temporally dependent metagenomic complexity of urban aerosols and the potential of genomic analytical techniques for biosurveillance and monitoring of threats to public health.
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Affiliation(s)
- Nicholas A. Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | - James B. Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | | | - Jonathan E. Allen
- Computation/Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Mark Rojas
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | - George Golovko
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | - Yuriy Fofanov
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | | | - Crystal J. Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
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Thissen JB, McLoughlin K, Gardner S, Gu P, Mabery S, Slezak T, Jaing C. Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray. J Virol Methods 2014; 201:73-8. [DOI: 10.1016/j.jviromet.2014.01.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 01/14/2014] [Accepted: 01/21/2014] [Indexed: 11/26/2022]
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Be NA, Thissen JB, Gardner SN, McLoughlin KS, Fofanov VY, Koshinsky H, Ellingson SR, Brettin TS, Jackson PJ, Jaing CJ. Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing. PLoS One 2013; 8:e73455. [PMID: 24039948 PMCID: PMC3767809 DOI: 10.1371/journal.pone.0073455] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 07/03/2013] [Indexed: 11/19/2022] Open
Abstract
Bacillus anthracis is the potentially lethal etiologic agent of anthrax disease, and is a significant concern in the realm of biodefense. One of the cornerstones of an effective biodefense strategy is the ability to detect infectious agents with a high degree of sensitivity and specificity in the context of a complex sample background. The nature of the B. anthracis genome, however, renders specific detection difficult, due to close homology with B. cereus and B. thuringiensis. We therefore elected to determine the efficacy of next-generation sequencing analysis and microarrays for detection of B. anthracis in an environmental background. We applied next-generation sequencing to titrated genome copy numbers of B. anthracis in the presence of background nucleic acid extracted from aerosol and soil samples. We found next-generation sequencing to be capable of detecting as few as 10 genomic equivalents of B. anthracis DNA per nanogram of background nucleic acid. Detection was accomplished by mapping reads to either a defined subset of reference genomes or to the full GenBank database. Moreover, sequence data obtained from B. anthracis could be reliably distinguished from sequence data mapping to either B. cereus or B. thuringiensis. We also demonstrated the efficacy of a microbial census microarray in detecting B. anthracis in the same samples, representing a cost-effective and high-throughput approach, complementary to next-generation sequencing. Our results, in combination with the capacity of sequencing for providing insights into the genomic characteristics of complex and novel organisms, suggest that these platforms should be considered important components of a biosurveillance strategy.
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Affiliation(s)
- Nicholas A. Be
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - James B. Thissen
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Shea N. Gardner
- Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Kevin S. McLoughlin
- Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | | | | | - Sally R. Ellingson
- Department of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Thomas S. Brettin
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Paul J. Jackson
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Crystal J. Jaing
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
- * E-mail:
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Jaing C, Gardner S, McLoughlin K, Thissen JB, Slezak T. Detection of adventitious viruses from biologicals using a broad-spectrum microbial detection array. PDA J Pharm Sci Technol 2011; 65:668-674. [PMID: 22294595 DOI: 10.5731/pdajpst.2011.00838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
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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Affiliation(s)
- Crystal Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA
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Lenhoff RJ, Naraghi-Arani P, Thissen JB, Olivas J, Carillo AC, Chinn C, Rasmussen M, Messenger SM, Suer LD, Smith SM, Tammero LFB, Vitalis EA, Slezak TR, Hullinger PJ, Hindson BJ, Hietala SK, Crossley BM, McBride MT. Multiplexed molecular assay for rapid exclusion of foot-and-mouth disease. J Virol Methods 2008; 153:61-9. [PMID: 18634827 DOI: 10.1016/j.jviromet.2008.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Revised: 05/29/2008] [Accepted: 06/03/2008] [Indexed: 10/21/2022]
Abstract
A nucleic acid-based multiplexed assay was developed that combines detection of foot-and-mouth disease virus (FMDV) with rule-out assays for two other foreign animal diseases and four domestic animal diseases that cause vesicular or ulcerative lesions indistinguishable from FMDV infection in cattle, sheep and swine. The FMDV "look-alike" diagnostic assay panel contains 5 PCR and 12 reverse transcriptase PCR (RT-PCR) signatures for a total of 17 simultaneous PCR amplifications for 7 diseases plus incorporating 4 internal assay controls. It was developed and optimized to amplify both DNA and RNA viruses simultaneously in a single tube and employs Luminex liquid array technology. Assay development including selection of appropriate controls, a comparison of signature performance in single and multiplex testing against target nucleic acids, as well of limits of detection for each of the individual signatures is presented. While this assay is a prototype and by no means a comprehensive test for FMDV "look-alike" viruses, an assay of this type is envisioned to have benefit to a laboratory network in routine surveillance and possibly for post-outbreak proof of freedom from foot-and-mouth disease.
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Affiliation(s)
- Raymond J Lenhoff
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-371, P.O. Box 808, Livermore, CA 94550, United States
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