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Nelson S, Hofacre K, Calfee MW, Serre S, Benard E, Graham C, Oudejans L, Mickelsen L, Tang J, Bansleben D, Taft S, James R, Shah S. Evaluation of two methods for detection of viable Bacillus anthracis simulant spores in maritime environmental samples. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:257. [PMID: 36595073 PMCID: PMC9913613 DOI: 10.1007/s10661-022-10772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Analytical methods exist to detect biothreat agents in environmental samples during a response to biological contamination incidents. However, the coastal zone facilities and assets of the US Coast Guard (USCG), including response boats in diverse geographical areas and maritime environmental conditions, can pose complex and unique challenges for adapting existing analytical detection methods. The traditional culture (TC) and the rapid viability polymerase chain reaction (RV-PCR) methods were evaluated for their compatibility for maritime environmental surface and grab sample analysis to detect spores of Bacillus thuringiensis subspecies kurstaki (Btk), a surrogate for Bacillus anthracis. The representative samples collected from a USCG installation included surfaces, such as aluminum on boats, nonskid tread on decks of watercraft, computer touchscreens, and concrete piers, and grab samples of boat washdown water, soil, vegetation, and gravel from surrounding areas. Replicate samples were spiked with Btk spores at two to three tenfold increasing levels and analyzed. Out of a total of 150 samples collected and analyzed, the TC method gave 10 false-positive and 19 false-negative results, while the RV-PCR method-based analysis resulted in 0 false-positive and 26 false-negative results. An abundance of microbial background and particulates in some samples interfered with true results, while both methods gave similar results for samples with low microbial background and particulates. Improved and high-throughput sample processing methods are needed for analysis of complex environmental samples.
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Affiliation(s)
| | | | - M Worth Calfee
- Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, Durham, NC, USA
| | - Shannon Serre
- Office of Land and Emergency Management, CBRN Consequence Management Advisory Division, US Environmental Protection Agency, Research Triangle Park, Durham, NC, USA
| | | | | | - Lukas Oudejans
- Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, Durham, NC, USA
| | - Leroy Mickelsen
- Office of Land and Emergency Management, CBRN Consequence Management Advisory Division, US Environmental Protection Agency, Research Triangle Park, Durham, NC, USA
| | | | | | - Sarah Taft
- Office of Research and Development, US Environmental Protection Agency, Cincinnati, OH, USA
| | - Ryan James
- Battelle Memorial Institute, Columbus, OH, USA
| | - Sanjiv Shah
- Homeland Security and Materials Management Division, Center for Environmental Solutions and Emergency Response, Office of Research and Development, US Environmental Protection Agency, Washington, DC, USA.
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2
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McMullen JG, Lennon JT. Mark-recapture of microorganisms. Environ Microbiol 2023; 25:150-157. [PMID: 36310117 DOI: 10.1111/1462-2920.16267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 01/21/2023]
Affiliation(s)
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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3
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McDonald ND, Rhea KA, Davies JP, Zacharko JL, Berk KL, Buckley PE. Evaluating the persistence and stability of a DNA-barcoded microbial system in a mock home environment. Synth Biol (Oxf) 2022; 7:ysac016. [PMID: 36046153 PMCID: PMC9423098 DOI: 10.1093/synbio/ysac016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 08/04/2022] [Accepted: 08/11/2022] [Indexed: 12/01/2023] Open
Abstract
Recent advancements in engineered microbial systems capable of deployment in complex environments have enabled the creation of unique signatures for environmental forensics operations. These microbial systems must be robust, able to thrive in specific environments of interest and contain molecular signatures, enabling the detection of the community across conditions. Furthermore, these systems must balance biocontainment concerns with the stability and persistence required for environmental forensics. Here we evaluate the stability and persistence of a recently described microbial system composed of germination-deficient Bacillus subtilis and Saccharomyces cerevisiae spores containing nonredundant DNA barcodes in a controlled simulated home environment. These spore-based microbial communities were found to be persistent in the simulated environment across 30-day periods and across multiple surface types. To improve the repeatability and reproducibility in detecting the DNA barcodes, we evaluated several spore lysis and sampling processes paired with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) -CRISPR-associated proteins (Cas) detection (Sherlock). Finally, having optimized the detectability of the spores, we demonstrate that we can detect the spores transferring across multiple material types. Together, we further demonstrate the utility of a recently described microbial forensics system and highlight the importance of independent validation and verification of synthetic biology tools and applications. Graphical Abstract.
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Affiliation(s)
- Nathan D McDonald
- United States Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Katherine A Rhea
- United States Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - John P Davies
- United States Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Julie L Zacharko
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Kimberly L Berk
- United States Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Patricia E Buckley
- United States Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
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4
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Bernhards CB, Liem AT, Berk KL, Roth PA, Gibbons HS, Lux MW. Putative Phenotypically Neutral Genomic Insertion Points in Prokaryotes. ACS Synth Biol 2022; 11:1681-1685. [PMID: 35271248 PMCID: PMC9016761 DOI: 10.1021/acssynbio.1c00531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
The barriers to effective
genome editing in diverse prokaryotic
organisms have been falling at an accelerated rate. As editing becomes
easier in more organisms, quickly identifying genomic locations to
insert new genetic functions without disrupting organism fitness becomes
increasingly useful. When the insertion is noncoding DNA for applications
such as information storage or barcoding, a neutral insertion point
can be especially important. Here we describe an approach to identify
putatively neutral insertion sites in prokaryotes. An algorithm (targetFinder)
finds convergently transcribed genes with gap sizes within a specified
range, and looks for annotations within the gaps. We report putative
editing targets for 10 common synthetic biology chassis organisms,
including coverage of available RNA-seq data, and provide software
to apply to others. We further experimentally evaluate the neutrality
of six identified targets in Escherichia coli through
insertion of a DNA barcode. We anticipate this information and the
accompanying tool will prove useful for synthetic biologists seeking
neutral insertion points for genome editing.
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Affiliation(s)
- Casey B. Bernhards
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- Excet, Inc., Springfield, Virginia 22150, United States
| | - Alvin T. Liem
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Kimberly L. Berk
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Pierce A. Roth
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Henry S. Gibbons
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Matthew W. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
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5
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Bernhards CB, Lux MW, Katoski SE, Goralski TDP, Liem AT, Gibbons HS. barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection. BMC Bioinformatics 2021; 22:98. [PMID: 33648451 PMCID: PMC7919090 DOI: 10.1186/s12859-021-04019-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/11/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Tracking dispersal of microbial populations in the environment requires specific detection methods that discriminate between the target strain and all potential natural and artificial interferents, including previously utilized tester strains. Recent work has shown that genomic insertion of short identification tags, called "barcodes" here, allows detection of chromosomally tagged strains by real-time PCR. Manual design of these barcodes is feasible for small sets, but expansion of the technique to larger pools of distinct and well-functioning assays would be significantly aided by software-guided design. RESULTS Here we introduce barCoder, a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode "modules" that consist of binding sites for primers and probes, and appropriate spacer sequences. Each module is designed to yield optimal PCR amplification and unique identification. Optimal amplification includes metrics such as ideal melting temperature and G+C content, appropriate spacing, and minimal stem-loop formation; unique identification includes low BLAST hits against the target organism, previously generated barcode modules, and databases (such as NCBI). We tested the ability of our algorithm to suggest appropriate barcodes by generating 12 modules for Bacillus thuringiensis serovar kurstaki-a simulant for the potential biowarfare agent Bacillus anthracis-and three each for other potential target organisms with variable G+C content. Real-time PCR detection assays directed at barcodes were specific and yielded minimal cross-reactivity with a panel of near-neighbor and potential contaminant materials. CONCLUSIONS The barCoder algorithm facilitates the generation of synthetically barcoded biological simulants by (a) eliminating the task of creating modules by hand, (b) minimizing optimization of PCR assays, and (c) reducing effort wasted on non-unique barcode modules.
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Affiliation(s)
- Casey B Bernhards
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA.,Excet, Inc., Springfield, VA, 22150, USA
| | - Matthew W Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Sarah E Katoski
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Tyler D P Goralski
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Alvin T Liem
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA.,DCS Corporation, Abingdon, MD, 21009, USA
| | - Henry S Gibbons
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA.
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Qian J, Lu ZX, Mancuso CP, Jhuang HY, Del Carmen Barajas-Ornelas R, Boswell SA, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Pettit ME, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver PA, Rudner DZ, Springer M. Barcoded microbial system for high-resolution object provenance. Science 2020; 368:1135-1140. [PMID: 32499444 DOI: 10.1126/science.aba5584] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 02/22/2024]
Abstract
Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.
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Affiliation(s)
- Jason Qian
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Zhi-Xiang Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher P Mancuso
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Han-Ying Jhuang
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Sarah A Boswell
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Victoria Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Akhila Sonti
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Kole Sedlack
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Lior Artzi
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Giyoung Jung
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mohammad Arammash
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mary E Pettit
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Melfi
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lorena Lyon
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Siân V Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Baym
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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7
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Hess KL, Jewell CM. Phage display as a tool for vaccine and immunotherapy development. Bioeng Transl Med 2020; 5:e10142. [PMID: 31989033 PMCID: PMC6971447 DOI: 10.1002/btm2.10142] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/15/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Bacteriophages, or phages, are viruses that specifically infect bacteria and coopt the cellular machinery to create more phage proteins, eventually resulting in the release of new phage particles. Phages are heavily utilized in bioengineering for applications ranging from tissue engineering scaffolds to immune signal delivery. Of specific interest to vaccines and immunotherapies, phages have demonstrated an ability to activate both the innate and adaptive immune systems. The genome of these viral particles can be harnessed for DNA vaccination, or the surface proteins can be exploited for antigen display. More specifically, genes that encode an antigen of interest can be spliced into the phage genome, allowing antigenic proteins or peptides to be displayed by fusion to phage capsid proteins. Phages therefore present antigens to immune cells in a highly ordered and repetitive manner. This review discusses the use of phage with adjuvanting activity as antigen delivery vehicles for vaccination against infectious disease and cancer.
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Affiliation(s)
- Krystina L. Hess
- U.S. Army Combat Capabilities Development Command Chemical Biological CenterAberdeen Proving GroundMaryland
| | - Christopher M. Jewell
- Fischell Department of BioengineeringUniversity of MarylandCollege ParkMaryland
- Robert E. Fischell Institute for Biomedical DevicesCollege ParkMaryland
- Department of Microbiology and ImmunologyUniversity of Maryland Medical SchoolBaltimoreMaryland
- Marlene and Stewart Greenebaum Cancer CenterBaltimoreMaryland
- U.S. Department of Veterans AffairsBaltimoreMaryland
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Competitive Fitness of Essential Gene Knockdowns Reveals a Broad-Spectrum Antibacterial Inhibitor of the Cell Division Protein FtsZ. Antimicrob Agents Chemother 2018; 62:AAC.01231-18. [PMID: 30297366 PMCID: PMC6256756 DOI: 10.1128/aac.01231-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/01/2018] [Indexed: 12/26/2022] Open
Abstract
To streamline the elucidation of antibacterial compounds' mechanism of action, comprehensive high-throughput assays interrogating multiple putative targets are necessary. However, current chemogenomic approaches for antibiotic target identification have not fully utilized the multiplexing potential of next-generation sequencing. Here, we used Illumina sequencing of transposon insertions to track the competitive fitness of a Burkholderia cenocepacia library containing essential gene knockdowns. Using this method, we characterized a novel benzothiadiazole derivative, 10126109 (C109), with antibacterial activity against B. cenocepacia, for which whole-genome sequencing of low-frequency spontaneous drug-resistant mutants had failed to identify the drug target. By combining the identification of hypersusceptible mutants and morphology screening, we show that C109 targets cell division. Furthermore, fluorescence microscopy of bacteria harboring green fluorescent protein (GFP) cell division protein fusions revealed that C109 prevents divisome formation by altering the localization of the essential cell division protein FtsZ. In agreement with this, C109 inhibited both the GTPase and polymerization activities of purified B. cenocepacia FtsZ. C109 displayed antibacterial activity against Gram-positive and Gram-negative cystic fibrosis pathogens, including Mycobacterium abscessus C109 effectively cleared B. cenocepacia infection in the Caenorhabditis elegans model and exhibited additive interactions with clinically relevant antibiotics. Hence, C109 is an enticing candidate for further drug development.
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A Standard Method To Inactivate Bacillus anthracis Spores to Sterility via Gamma Irradiation. Appl Environ Microbiol 2018; 84:AEM.00106-18. [PMID: 29654186 DOI: 10.1128/aem.00106-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022] Open
Abstract
In 2015, a laboratory of the United States Department of Defense (DoD) inadvertently shipped preparations of gamma-irradiated spores of Bacillus anthracis that contained live spores. In response, a systematic evidence-based method for preparing, concentrating, irradiating, and verifying the inactivation of spore materials was developed. We demonstrate the consistency of spore preparations across multiple biological replicates and show that two different DoD institutions independently obtained comparable dose-inactivation curves for a monodisperse suspension of B. anthracis spores containing 3 × 1010 CFU. Spore preparations from three different institutions and three strain backgrounds yielded similar decimal reduction (D10) values and irradiation doses required to ensure sterility (DSAL) to the point at which the probability of detecting a viable spore is 10-6 Furthermore, spores of a genetically tagged strain of B. anthracis strain Sterne were used to show that high densities of dead spores suppress the recovery of viable spores. Together, we present an integrated method for preparing, irradiating, and verifying the inactivation of spores of B. anthracis for use as standard reagents for testing and evaluating detection and diagnostic devices and techniques.IMPORTANCE The inadvertent shipment by a U.S. Department of Defense (DoD) laboratory of live Bacillus anthracis (anthrax) spores to U.S. and international destinations revealed the need to standardize inactivation methods for materials derived from biological select agents and toxins (BSAT) and for the development of evidence-based methods to prevent the recurrence of such an event. Following a retrospective analysis of the procedures previously employed to generate inactivated B. anthracis spores, a study was commissioned by the DoD to provide data required to support the production of inactivated spores for the biodefense community. The results of this work are presented in this publication, which details the method by which spores can be prepared, irradiated, and tested, such that the chance of finding residual living spores in any given preparation is 1/1,000,000. These irradiated spores are used to test equipment and methods for the detection of agents of biological warfare and bioterrorism.
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Abstract
Surrogate microorganisms, in short surrogates, are an essential part of pathogen research. Compared to surrogates used in controlled laboratory environments, surrogates for field release are restricted by concerns about human and environmental safety. For field research of food-borne pathogens, strains of an attenuated pathogen or strains of genetically close non-pathogenic species have been used as surrogates. Genetic modification is usually performed to attenuate virulence, through for examples deletion of genes of virulence and transcriptional regulators and removal of virulence plasmids, and to facilitate detection and monitoring through observing antibiotic resistance, fluorescence, and bioluminescence. For field research of a biological warfare agent Bacillus anthracis, strains of genetically close non-pathogenic species or strains of genetically distant non-pathogenic species have been used, mostly without any genetic modification. Recently, we constructed strains of Bacillus thuringiensis as surrogates for B. anthracis, demonstrating that strain engineering could significantly enhance the utility of surrogates, and that the application of a simple genetic circuit could significantly impact surrogate safety. Thus far, enormous potential of biotechnology has not been exploited enough due to safety concerns regarding the field release of genetically engineered microorganisms. However, synthetic biology is rapidly developing, providing new concepts for biocontainment as well as ingenious genetic circuits and devices, which should be applied in future research of field-use surrogates.
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Affiliation(s)
- Sangjin Park
- a Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology , Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon , Republic of Korea.,b The 5th R&D Institute, Agency for Defense Development (ADD) , Daejeon , Republic of Korea
| | - Chang-Hwan Kim
- b The 5th R&D Institute, Agency for Defense Development (ADD) , Daejeon , Republic of Korea
| | - Seong Tae Jeong
- b The 5th R&D Institute, Agency for Defense Development (ADD) , Daejeon , Republic of Korea
| | - Sang Yup Lee
- a Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology , Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon , Republic of Korea
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Abakpa GO, Umoh VJ, Kamaruzaman S, Ibekwe M. Fingerprints of resistant Escherichia coli O157:H7 from vegetables and environmental samples. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:80-86. [PMID: 28543177 DOI: 10.1002/jsfa.8441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/04/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Some routes of transmission of Escherichia coli O157:H7 to fresh produce include contaminated irrigation water and manure polluted soils. The aim of the present study was to determine the genetic relationships of E. coli O157:H7 isolated from some produce growing region in Nigeria using enterobacterial repetitive intergenic consensus (ERIC) DNA fingerprinting analysis. A total of 440 samples comprising leafy greens, irrigation water, manure and soil were obtained from vegetable producing regions in Kano and Plateau States, Nigeria. Genes coding for the quinolone resistance-determinant (gyrA) and plasmid (pCT) coding for multidrug resistance (MDR) were determined using polymerase chain reaction (PCR) in 16 isolates that showed MDR. RESULTS Cluster analysis of the ERIC-PCR profiles based on band sizes revealed six main clusters from the sixteen isolates analysed. The largest cluster (cluster 3) grouped isolates from vegetables and manure at a similarity coefficient of 0.72. CONCLUSION The present study provides data that support the potential transmission of resistant strains of E. coli O157:H7 from vegetables and environmental sources to humans with potential public health implications, especially in developing countries. © 2017 Society of Chemical Industry.
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Affiliation(s)
| | - Veronica J Umoh
- Department of Biological Sciences, Akwa Ibom State University, Mkpat Enin LGA, Akwa Ibom State, Nigeria
| | - Sijam Kamaruzaman
- Department of Agrobio, Universiti Putra, Serdang, Selangor, Malaysia
| | - Mark Ibekwe
- USDA-ARS-US Salinity Laboratory, Riverside, CA, USA
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12
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Construction of Bacillus thuringiensis Simulant Strains Suitable for Environmental Release. Appl Environ Microbiol 2017; 83:AEM.00126-17. [PMID: 28258144 DOI: 10.1128/aem.00126-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 02/24/2017] [Indexed: 12/15/2022] Open
Abstract
For a surrogate bacterium to be used in outdoor studies, it is important to consider environmental and human safety and ease of detection. Recently, Bacillus thuringiensis, a popular bioinsecticide bacterium, has been gaining attention as a surrogate bacterium for use in biodefense. In this study, we constructed simulant strains of B. thuringiensis with enhanced characteristics for environmental studies. Through transposon mutagenesis, pigment genes were inserted into the chromosome, producing yellow-colored colonies for easy detection. To prevent persistence of spores in the environment, a genetic circuit was designed to produce a spore without sporulation capability. Two loxP sites were inserted, one on each side of the spo0A gene, which encodes a sporulation master regulator, and a sporulation-dependent Cre expression cassette was inserted into the chromosome. This genetic circuit successfully deleted spo0A during sporulation, producing spores that lacked the spo0A gene. In addition, two major α/β-type small acid-soluble spore protein (SASP) genes, predicted by synteny analysis, were deleted. The spores of the mutant strain showed increased UV-C sensitivity and quickly lost viability when tested in a solar simulator. When the spores of the mutant strain were administered to the lungs of BALB/c mice, cells were quickly removed from the body, suggesting enhanced in vivo safety. All strains constructed in this study contain no antibiotic resistance markers and all heterologous genes were inserted into the chromosome, which are useful features for simulants to be released into the environment.IMPORTANCEB. thuringiensis has recently been receiving increasing attention as a good spore simulant in biodefense research. However, few studies were done to properly address many important features of B. thuringiensis as a simulant in environmental studies. Since spores can persist in the environment for years after release, environmental contamination is a big problem, especially when genetically engineered strains are used. To solve these problems, we report here the development of B. thuringiensis simulant strains that are capable of forming yellow colonies for easy detection, incapable of forming spores more than once due to a genetic circuit, and lacking in two major SASP genes. The genetic circuit to produce a spore without sporulation capability, together with the deletion of SASP genes, ensures the environmental and human safety of the simulant strains developed in this study. All of these features will allow wider use of B. thuringiensis as a simulant for Bacillus anthracis in environmental release studies.
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13
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Aerosol and Surface Deposition Characteristics of Two Surrogates for Bacillus anthracis Spores. Appl Environ Microbiol 2016; 82:6682-6690. [PMID: 27613681 DOI: 10.1128/aem.02052-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/22/2016] [Indexed: 01/22/2023] Open
Abstract
Spores of an acrystalliferous derivative of Bacillus thuringiensis subsp. kurstaki, termed Btcry-, are morphologically, aerodynamically, and structurally indistinguishable from Bacillus anthracis spores. Btcry- spores were dispersed in a large, open-ended barn together with spores of Bacillus atrophaeus subsp. globigii, a historically used surrogate for Bacillus anthracis Spore suspensions (2 × 1012 CFU each of B. atrophaeus subsp. globigii and Btcry-) were aerosolized in each of five spray events using a backpack misting device incorporating an air blower; a wind of 4.9 to 7.6 m s-1 was also flowing through the barn in the same direction. Filter air samplers were situated throughout the barn to assess the aerosol density of the spores during each release. Trays filled with a surfactant in aqueous buffer were placed on the floor near the filter samplers to assess spore deposition. Spores were also recovered from arrays of solid surfaces (concrete, aluminum, and plywood) that had been laid on the floor and set up as a wall at the end of the barn. B. atrophaeus subsp. globigii spores were found to remain airborne for significantly longer periods, and to be deposited on horizontal surfaces at lower densities, than Btcry- spores, particularly near the spray source. There was a 6-fold-higher deposition of Btcry- spores than of B. atrophaeus subsp. globigii spores on vertical surfaces relative to the surrounding airborne density. This work is relevant for selecting the best B. anthracis surrogate for the prediction of human exposure, hazard assessment, and hazard management following a malicious release of B. anthracis IMPORTANCE: There is concern that pathogenic bacteria could be maliciously disseminated in the air to cause human infection and disruption of normal life. The threat from spore-forming organisms, such as the causative agent of anthrax, is particularly serious. In order to assess the extent of this risk, it is important to have a surrogate organism that can be used to replicate the dispersal characteristics of the threat agent accurately. This work compares the aerosol dispersal and deposition behaviors of the surrogates Btcry- and B. atrophaeus subsp. globigii Btcry- spores remained in the air for a shorter time, and were markedly more likely to adhere to vertical surfaces, than B. atrophaeus subsp. globigii spores.
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Liljegren JC, Brown DF, Lunden MM, Silcott D. Particle Deposition onto People in a Transit Venue. Health Secur 2016; 14:237-49. [DOI: 10.1089/hs.2016.0010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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15
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Bishop AH, Robinson CV. Bacillus thuringiensis HD-1 Cry- : development of a safe, non-insecticidal simulant for Bacillus anthracis. J Appl Microbiol 2014; 117:654-62. [PMID: 24903218 DOI: 10.1111/jam.12560] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 05/28/2014] [Accepted: 05/31/2014] [Indexed: 11/26/2022]
Abstract
AIMS A representative simulant for spores of Bacillus anthracis is needed for field testing. Bacillus thuringiensis is gaining recognition as a suitable organism. A strain that does not form the insecticidal, parasporal crystals that are characteristic of this species is a more accurate physical representative of B. anthracis spores. We developed noninsecticidal derivatives of two isolates of B. thuringiensis HD-1. METHODS AND RESULTS Two plasmid-cured derivatives of B. thuringiensis HD-1, unable to make crystal toxins ('Cry(-) '), were isolated. These isolates and the existing Cry(-) strain, B. thuringiensis Al Hakam, were probed with PCR assays against the known insecticidal genes cry, vip and cyt. Their genomic DNA was sequenced to demonstrate a lack of insecticidal genes. This was confirmed by bioassays against a number of invertebrate species. Real-time PCR assays were developed to identify the B. thuringiensis HD-1 Cry(-) derivatives and an effective differential and selective medium was assessed. CONCLUSIONS All three Cry(-) isolates are devoid of known insecticidal determinants. The B. thuringiensis HD-1 Cry(-) derivatives can easily be recovered from soil and identified by PCR with some selectivity. SIGNIFICANCE AND IMPACT OF THE STUDY The B. thuringiensis HD-1 Cry(-) derivatives represent accurate, nongenetically manipulated simulants for B. anthracis with excellent human and environmental safety records.
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Affiliation(s)
- A H Bishop
- Detection Department, Defence Science and Technology Laboratory, Salisbury, Wiltshire, UK
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Bacillus thuringiensis as a surrogate for Bacillus anthracis in aerosol research. World J Microbiol Biotechnol 2013; 30:1453-61. [PMID: 24338558 DOI: 10.1007/s11274-013-1576-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
Abstract
Characterization of candidate surrogate spores prior to experimental use is critical to confirm that the surrogate characteristics are as closely similar as possible to those of the pathogenic agent of interest. This review compares the physical properties inherent to spores of Bacillus anthracis (Ba) and Bacillus thuringiensis (Bt) that impact their movement in air and interaction with surfaces, including size, shape, density, surface morphology, structure and hydrophobicity. Also evaluated is the impact of irradiation on the physical properties of both Bacillus species. Many physical features of Bt and Ba have been found to be similar and, while Bt is considered typically non-pathogenic, it is in the B. cereus group, as is Ba. When cultured and sporulated under similar conditions, both microorganisms share a similar cylindrical pellet shape, an aerodynamic diameter of approximately 1 μm (in the respirable size range), have an exosporium with a hairy nap, and have higher relative hydrophobicities than other Bacillus species. While spore size, morphology, and other physical properties can vary among strains of the same species, the variations can be due to growth/sporulation conditions and may, therefore, be controlled. Growth and sporulation conditions are likely among the most important factors that influence the representativeness of one species, or preparation, to another. All Bt spores may, therefore, not be representative of all Ba spores. Irradiated spores do not appear to be a good surrogate to predict the behavior of non-irradiated spores due to structural damage caused by the irradiation. While the use of Bt as a surrogate for Ba in aerosol testing appears to be well supported, this review does not attempt to narrow selection between Bt strains. Comparative studies should be performed to test the hypothesis that viable Ba and Bt spores will behave similarly when suspended in the air (as an aerosol) and to compare the known microscale characteristics versus the macroscale response.
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Omotade TO, Heffron JD, Klimko CP, Marchand CL, Miller LL, Halasahoris SA, Bozue JA, Welkos SL, Cote CK. D-cycloserine or similar physiochemical compounds may be uniquely suited for use in Bacillus anthracis spore decontamination strategies. J Appl Microbiol 2013; 115:1343-56. [PMID: 23927578 DOI: 10.1111/jam.12322] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/18/2013] [Accepted: 07/30/2013] [Indexed: 02/06/2023]
Abstract
AIMS As observed in the aftermath of the anthrax attacks of 2001, decontamination and remediation of a site contaminated by the accidental or intentional release of Bacillus anthracis spores is difficult, costly and potentially damaging to the environment. The identification of novel strategies that neutralize the threat of spores while minimizing environmental damage remains a high priority. We investigated the efficacy of d-cycloserine (DCS), an antibiotic and inhibitor of the spore-associated enzyme (alanine racemase) responsible for converting l-alanine to d-alanine, as a spore germination enhancer and antimicrobial agent. METHODS AND RESULTS We characterized the impact of DCS exposure on both germinating spores and vegetative cells of fully virulent B. anthracis by evaluating spore germination kinetics, determining the minimum inhibitory concentrations (MICs) required to affect growth of the bacteria and performing macrophage viability assays. DCS enhanced germination induced by l-alanine and also efficiently killed the newly germinated spores. Furthermore, DCS proved nontoxic to macrophages at concentrations that provided protection from the killing effects of spores. Similar tests were conducted with Bacillus thuringiensis (subspecies kurstaki and Al Hakam) to determine its potential as a possible surrogate for B. anthracis field trials. Bacillus thuringiensis spores responded in a similar manner to B. anthracis spores when exposed to DCS. CONCLUSIONS These results further support that DCS augments the germination response of spores in the presence of l-alanine but also reveal that DCS is bactericidal towards germinating spores. SIGNIFICANCE AND IMPACT OF THE STUDY DCS (or similar compounds) may be uniquely suited for use as part of decontamination strategies by augmenting the induction of spore germination and then rendering the germinated spores nonviable.
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Affiliation(s)
- T O Omotade
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, USA
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Janezic KJ, Ferry B, Hendricks EW, Janiga BA, Johnson T, Murphy S, Roberts ME, Scott SM, Theisen AN, Hung KF, Daniel SL. Phenotypic and Genotypic Characterization of Escherichia coli Isolated from Untreated Surface Waters. Open Microbiol J 2013; 7:9-19. [PMID: 23539437 PMCID: PMC3606946 DOI: 10.2174/1874285801307010009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 11/22/2022] Open
Abstract
A common member of the intestinal microbiota in humans and animals is Escherichia coli. Based on the presence of virulence factors, E. coli can be potentially pathogenic. The focus of this study was to isolate E. coli from untreated surface waters (37 sites) in Illinois and Missouri and determine phenotypic and genotypic diversity among isolates. Water samples positive for fecal coliforms based on the Colisure® test were streaked directly onto Eosin Methylene Blue (EMB) agar (37°C) or transferred to EC broth (44.5°C). EC broth cultures producing gas were then streaked onto EMB agar. Forty-five isolates were identified as E. coli using API 20E and Enterotube II identification systems, and some phenotypic variation was observed in metabolism and fermentation. Antibiotic susceptibility of each isolate was also determined using the Kirby-Bauer Method. Differential responses to 10 antimicrobial agents were seen with 7, 16, 2, and 9 of the isolates resistant to ampicillin, cephalothin, tetracycline, and triple sulfonamide, respectively. All of the isolates were susceptible or intermediate to amoxicillin, ciprofloxacin, polymyxin B, gentamicin, imipenem, and nalidixic acid. Genotypic variation was assessed through multiplex Polymerase Chain Reaction for four virulence genes (stx1 and stx2 [shiga toxin], eaeA [intimin]; and hlyA [enterohemolysin]) and one housekeeping gene (uidA [β-D-glucuronidase]). Genotypic variation was observed with two of the isolates possessing the virulence gene (eaeA) for intimin. These findings increase our understanding of the diversity of E. coli in the environment which will ultimately help in the assessment of this organism and its role in public health.
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Affiliation(s)
- Kristopher J Janezic
- Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois 61920, USA
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Emanuel PA, Buckley PE, Sutton TA, Edmonds JM, Bailey AM, Rivers BA, Kim MH, Ginley WJ, Keiser CC, Doherty RW, Kragl FJ, Narayanan FE, Katoski SE, Paikoff S, Leppert SP, Strawbridge JB, VanReenen DR, Biberos SS, Moore D, Phillips DW, Mingioni LR, Melles O, Ondercin DG, Hirsh B, Bieschke KM, Harris CL, Omberg KM, Rastogi VK, Van Cuyk S, Gibbons HS. Detection and tracking of a novel genetically tagged biological simulant in the environment. Appl Environ Microbiol 2012; 78:8281-8. [PMID: 23001670 PMCID: PMC3497391 DOI: 10.1128/aem.02006-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 09/12/2012] [Indexed: 11/20/2022] Open
Abstract
A variant of Bacillus thuringiensis subsp. kurstaki containing a single, stable copy of a uniquely amplifiable DNA oligomer integrated into the genome for tracking the fate of biological agents in the environment was developed. The use of genetically tagged spores overcomes the ambiguity of discerning the test material from pre-existing environmental microflora or from previously released background material. In this study, we demonstrate the utility of the genetically "barcoded" simulant in a controlled indoor setting and in an outdoor release. In an ambient breeze tunnel test, spores deposited on tiles were reaerosolized and detected by real-time PCR at distances of 30 m from the point of deposition. Real-time PCR signals were inversely correlated with distance from the seeded tiles. An outdoor release of powdered spore simulant at Aberdeen Proving Ground, Edgewood, MD, was monitored from a distance by a light detection and ranging (LIDAR) laser. Over a 2-week period, an array of air sampling units collected samples were analyzed for the presence of viable spores and using barcode-specific real-time PCR assays. Barcoded B. thuringiensis subsp. kurstaki spores were unambiguously identified on the day of the release, and viable material was recovered in a pattern consistent with the cloud track predicted by prevailing winds and by data tracks provided by the LIDAR system. Finally, the real-time PCR assays successfully differentiated barcoded B. thuringiensis subsp. kurstaki spores from wild-type spores under field conditions.
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Affiliation(s)
- Peter A. Emanuel
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | | | - Tiffany A. Sutton
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Jason M. Edmonds
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Andrew M. Bailey
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Bryan A. Rivers
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
- Science Applications International, Inc., Aberdeen Proving Ground, Maryland, USA
| | - Michael H. Kim
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - William J. Ginley
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | | | - Robert W. Doherty
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - F. Joseph Kragl
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Fiona E. Narayanan
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Sarah E. Katoski
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
- Science Applications International, Inc., Aberdeen Proving Ground, Maryland, USA
| | - Sari Paikoff
- Defense Threat Reduction Agency, Fort Belvoir, Virginia, USA
| | - Samuel P. Leppert
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - John B. Strawbridge
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - Daniel R. VanReenen
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - Sally S. Biberos
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - Douglas Moore
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - Douglas W. Phillips
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - Lisa R. Mingioni
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - Ogba Melles
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - Daniel G. Ondercin
- Joint Program Executive Office for Chemical and Biological Defense, Aberdeen Proving Ground, Maryland, USA
| | - Beth Hirsh
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | | | - Crystal L. Harris
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | | | - Vipin K. Rastogi
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | | | - Henry S. Gibbons
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
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