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Dedes G, Drosten H, Götz S, Dickmann J, Sarosiek C, Pankuch M, Krah N, Rit S, Bashkirov V, Schulte RW, Johnson RP, Parodi K, DeJongh E, Landry G. Comparative accuracy and resolution assessment of two prototype proton computed tomography scanners. Med Phys 2022; 49:4671-4681. [PMID: 35396739 DOI: 10.1002/mp.15657] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/14/2022] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Improving the accuracy of relative stopping power (RSP) in proton therapy may allow reducing range margins. Proton computed tomography (pCT) has been shown to provide state-of-the-art RSP accuracy estimation, and various scanner prototypes have recently been built. The different approaches used in scanner design are expected to impact spatial resolution and RSP accuracy. PURPOSE The goal of this study was to perform the first direct comparison, in terms of spatial resolution and RSP accuracy, of two pCT prototype scanners installed at the same facility and by using the same image reconstruction algorithm. METHODS A phantom containing cylindrical inserts of known RSP was scanned at the phase-II pCT prototype of the U.S. pCT collaboration and at the commercially oriented ProtonVDA scanner. Following distance-driven binning filtered backprojection reconstruction, the radial edge spread function of high-density inserts was used to estimate the spatial resolution. RSP accuracy was evaluated by the mean absolute percent error (MAPE) over the inserts. No direct imaging dose estimation was possible, which prevented a comparison of the two scanners in terms of RSP noise. RESULTS In terms of RSP accuracy, both scanners achieved the same MAPE of 0.72% when excluding the porous sinus insert from the evaluation. The ProtonVDA scanner reached a better overall MAPE when all inserts and the body of the phantom were accounted for (0.81%), compared to the phase-II scanner (1.14%). The spatial resolution with the phase-II scanner was found to be 0.61 lp/mm, while for the ProtonVDA scanner somewhat lower at 0.46 lp/mm. CONCLUSIONS The comparison between two prototype pCT scanners operated in the same clinical facility showed that they both fulfill the requirement of an RSP accuracy of about 1%. Their spatial resolution performance reflects the different design choices of either a scanner with full tracking capabilities (phase-II) or of a more compact tracker system which only provides the positions of protons but not their directions (ProtonVDA). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- G Dedes
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität München, Am Coulombwall 1, Garching b. München, 85748, Germany
| | - H Drosten
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität München, Am Coulombwall 1, Garching b. München, 85748, Germany
| | - S Götz
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität München, Am Coulombwall 1, Garching b. München, 85748, Germany
| | - J Dickmann
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität München, Am Coulombwall 1, Garching b. München, 85748, Germany
| | - C Sarosiek
- Department of Physics, Northern Illinois University, 1425 W. Lincoln Highway DeKalb, Illinois, IL, 60115, United States of America
| | - M Pankuch
- Northwestern Medicine Chicago Proton Center, 4455 Weaver Parkway, Warrenville, Illinois, IL, 60555, United States of America
| | - N Krah
- University of Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1294, LYON, F-69373, France
| | - S Rit
- University of Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1294, LYON, F-69373, France
| | - V Bashkirov
- Division of Biomedical Engineering Sciences, Loma Linda University, Loma Linda, California, CA 92354, United States of America
| | - R W Schulte
- Division of Biomedical Engineering Sciences, Loma Linda University, Loma Linda, California, CA 92354, United States of America
| | - R P Johnson
- Department of Physics, U.C. Santa Cruz, 1156 High Street Santa Cruz, California, CA, 95064, United States of America
| | - K Parodi
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität München, Am Coulombwall 1, Garching b. München, 85748, Germany
| | - E DeJongh
- ProtonVDA LLC, 1700 Park Street STE 208, Naperville, Illinois, IL, 60563, United States of America
| | - G Landry
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität München, Am Coulombwall 1, Garching b. München, 85748, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, 81377, Germany.,German Cancer Consortium (DKTK), Munich, 81377, Germany
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Volz L, Collins-Fekete CA, Bär E, Brons S, Graeff C, Johnson RP, Runz A, Sarosiek C, Schulte RW, Seco J. The accuracy of helium ion CT based particle therapy range prediction: an experimental study comparing different particle and x-ray CT modalities. Phys Med Biol 2021; 66:10.1088/1361-6560/ac33ec. [PMID: 34706355 PMCID: PMC8792995 DOI: 10.1088/1361-6560/ac33ec] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 09/06/2021] [Accepted: 10/27/2021] [Indexed: 11/12/2022]
Abstract
This work provides a quantitative assessment of helium ion CT (HeCT) for particle therapy treatment planning. For the first time, HeCT based range prediction accuracy in a heterogeneous tissue phantom is presented and compared to single-energy x-ray CT (SECT), dual-energy x-ray CT (DECT) and proton CT (pCT). HeCT and pCT scans were acquired using the US pCT collaboration prototype particle CT scanner at the Heidelberg Ion-Beam Therapy Center. SECT and DECT scans were done with a Siemens Somatom Definition Flash and converted to RSP. A Catphan CTP404 module was used to study the RSP accuracy of HeCT. A custom phantom of 20 cm diameter containing several tissue equivalent plastic cubes was used to assess the spatial resolution of HeCT and compare it to DECT. A clinically realistic heterogeneous tissue phantom was constructed using cranial slices from a pig head placed inside a cylindrical phantom (ø150 mm). A proton beam (84.67 mm range) depth-dose measurement was acquired using a stack of GafchromicTM EBT-XD films in a central dosimetry insert in the phantom. CT scans of the phantom were acquired with each modality, and proton depth-dose estimates were simulated based on the reconstructions. The RSP accuracy of HeCT for the plastic phantom was found to be 0.3 ± 0.1%. The spatial resolution for HeCT of the cube phantom was 5.9 ± 0.4 lp cm-1for central, and 7.6 ± 0.8 lp cm-1for peripheral cubes, comparable to DECT spatial resolution (7.7 ± 0.3 lp cm-1and 7.4 ± 0.2 lp cm-1, respectively). For the pig head, HeCT, SECT, DECT and pCT predicted range accuracy was 0.25%, -1.40%, -0.45% and 0.39%, respectively. In this study, HeCT acquired with a prototype system showed potential for particle therapy treatment planning, offering RSP accuracy, spatial resolution, and range prediction accuracy comparable to that achieved with a commercial DECT scanner. Still, technical improvements of HeCT are needed to enable clinical implementation.
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Affiliation(s)
- L Volz
- Department of Biomedical Physics in Radiation Oncology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - C-A Collins-Fekete
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - E Bär
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
- Department of Radiotherapy Physics, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - S Brons
- Heidelberg Ion-Beam Therapy Center, Universitäts Klinikum Heidelberg, Heidelberg, Germany
| | - C Graeff
- Biophysics, GSI Helmholtz Center for Heavy Ion Research GmbH, Darmstadt, Germany
| | - R P Johnson
- Department of Physics, University of California at Santa Cruz, Santa Cruz, United States of America
| | - A Runz
- Department of Medical Physics in Radiation Therapy, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - C Sarosiek
- Department of Physics, Northern Illinois University, DeKalb, United States of America
| | - R W Schulte
- Department of Basic Sciences, Division of Biomedical Engineering Sciences, Loma Linda University, Loma Linda, United States of America
| | - J Seco
- Department of Biomedical Physics in Radiation Oncology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
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3
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Labbé G, Kruczkiewicz P, Robertson J, Mabon P, Schonfeld J, Kein D, Rankin MA, Gopez M, Hole D, Son D, Knox N, Laing CR, Bessonov K, Taboada EN, Yoshida C, Ziebell K, Nichani A, Johnson RP, Van Domselaar G, Nash JHE. Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel. Microb Genom 2021; 7. [PMID: 34554082 PMCID: PMC8715432 DOI: 10.1099/mgen.0.000651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Indexed: 11/18/2022] Open
Abstract
Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results. The BioHansel tool was developed to provide an organism-agnostic tool for hierarchical SNP-based genotyping. The tool identifies split k-mers that distinguish predefined lineages in whole genome sequencing (WGS) data using SNP-based genotyping schemes. BioHansel uses the Aho-Corasick algorithm to type isolates from assembled genomes or raw read sequence data in a matter of seconds, with limited computational resources. This makes BioHansel ideal for use by public health agencies that rely on WGS methods for surveillance of bacterial pathogens. Genotyping results are evaluated using a quality assurance module which identifies problematic samples, such as low-quality or contaminated datasets. Using existing hierarchical SNP schemes for Mycobacterium tuberculosis and Salmonella Typhi, we compare the genotyping results obtained with the k-mer-based tools BioHansel and SKA, with those of the organism-specific tools TBProfiler and genotyphi, which use gold-standard reference-mapping approaches. We show that the genotyping results are fully concordant across these different methods, and that the k-mer-based tools are significantly faster. We also test the ability of the BioHansel quality assurance module to detect intra-lineage contamination and demonstrate that it is effective, even in populations with low genetic diversity. We demonstrate the scalability of the tool using a dataset of ~8100 S. Typhi public genomes and provide the aggregated results of geographical distributions as part of the tool’s output. BioHansel is an open source Python 3 application available on PyPI and Conda repositories and as a Galaxy tool from the public Galaxy Toolshed. In a public health context, BioHansel enables rapid and high-resolution classification of bacterial pathogens with low genetic diversity.
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Affiliation(s)
- Geneviève Labbé
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | | | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Philip Mabon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Justin Schonfeld
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Daniel Kein
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Marisa A Rankin
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Matthew Gopez
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Darian Hole
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David Son
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Natalie Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chad R Laing
- National Centres for Animal Disease Lethbridge Laboratory, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Anil Nichani
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,National Centres for Animal Disease Lethbridge Laboratory, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - John H E Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Toronto, Ontario, Canada
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Dickmann J, Sarosiek C, Rykalin V, Pankuch M, Rit S, Detrich N, Coutrakon G, Johnson RP, Schulte RW, Parodi K, Landry G, Dedes G. Experimental realization of dynamic fluence field optimization for proton computed tomography. ACTA ACUST UNITED AC 2020; 65:195001. [DOI: 10.1088/1361-6560/ab9f5f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada. Microb Genom 2020; 6. [PMID: 32496181 PMCID: PMC7371104 DOI: 10.1099/mgen.0.000376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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] [Indexed: 01/06/2023] Open
Abstract
Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.
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Affiliation(s)
- Lu Ya Ruth Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | | | - Chad R Laing
- National Centre for Animal Disease, Canadian Food Inspection Agency, Lethbridge, Alberta, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
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Niu YD, Liu H, Johnson RP, McAllister TA, Stanford K. Effect of a bacteriophage T5virus on growth of Shiga toxigenic Escherichia coli and Salmonella strains in individual and mixed cultures. Virol J 2020; 17:3. [PMID: 31910855 PMCID: PMC6947960 DOI: 10.1186/s12985-019-1269-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 09/18/2019] [Accepted: 12/10/2019] [Indexed: 02/03/2023] Open
Abstract
A previously isolated a bacteriophage, vB_EcoS_AKFV33 of T5virus, demonstrated great potential in biocontrol of Shiga toxigenic Escherichia coli (STEC) O157. This study further evaluated its potential as a biocontrol agent in broth culture against other important non-O157 serogroups of STEC and Salmonella. AKFV33 was capable of lysing isolates of STEC serogroups O26 (n = 1), O145 (n = 1) and Salmonella enterica serovars (n = 6). In a broth culture microplate system, efficacy of AKFV33 for killing STEC O26:H11, O145:NM and Salmonella was improved (P < 0.05) at a lower multiplicity of infection and sampling time (6–10 h), when STEC O157:H7 was also included in the culture. This phage was able to simultaneously reduce numbers of STEC and Salmonella in mixtures with enhanced activity (P < 0.05) against O157:H7 and O26:H11, offering great promise for control of multiple zoonotic pathogens at both pre and post-harvest.
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Affiliation(s)
- Yan D Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Hui Liu
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, N1G 3W4, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada
| | - Kim Stanford
- Alberta Agriculture and Forestry, Agriculture Centre, Lethbridge, AB, T1J 4V6, Canada
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Platnich JM, Chung H, Lau A, Sandall CF, Bondzi-Simpson A, Chen HM, Komada T, Trotman-Grant AC, Brandelli JR, Chun J, Beck PL, Philpott DJ, Girardin SE, Ho M, Johnson RP, MacDonald JA, Armstrong GD, Muruve DA. Shiga Toxin/Lipopolysaccharide Activates Caspase-4 and Gasdermin D to Trigger Mitochondrial Reactive Oxygen Species Upstream of the NLRP3 Inflammasome. Cell Rep 2019; 25:1525-1536.e7. [PMID: 30404007 DOI: 10.1016/j.celrep.2018.09.071] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 06/04/2018] [Accepted: 09/21/2018] [Indexed: 01/11/2023] Open
Abstract
The non-canonical caspase-4 and canonical NLRP3 inflammasomes are both activated by intracellular lipopolysaccharide (LPS), but the crosstalk between these two pathways remains unclear. Shiga toxin 2 (Stx2)/LPS complex, from pathogenic enterohemorrhagic Escherichia coli, activates caspase-4, gasdermin D (GSDMD), and the NLRP3 inflammasome in human THP-1 macrophages, but not mouse macrophages that lack the Stx receptor CD77. Stx2/LPS-mediated IL-1β secretion and pyroptosis are dependent on mitochondrial reactive oxygen species (ROS) downstream of the non-canonical caspase-4 inflammasome and cleaved GSDMD, which is enriched at the mitochondria. Blockade of caspase-4 activation and ROS generation as well as GSDMD deficiency significantly reduces Stx2/LPS-induced IL-1β production and pyroptosis. The NLRP3 inflammasome plays a significant role in amplifying Stx2/LPS-induced GSDMD cleavage and pyroptosis, with significant reduction of these responses in NLRP3-deficient THP-1 cells. Together, these data show that Stx2/LPS complex activates the non-canonical inflammasome and mitochondrial ROS upstream of the NLRP3 inflammasome to promote cytokine maturation and pyroptosis.
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Affiliation(s)
- Jaye M Platnich
- Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Hyunjae Chung
- Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Arthur Lau
- Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Christina F Sandall
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Adom Bondzi-Simpson
- Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Huey-Miin Chen
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Takanori Komada
- Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | | | - Jeremy R Brandelli
- Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Justin Chun
- Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Paul L Beck
- Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - May Ho
- Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Roger P Johnson
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, ON, Canada
| | - Justin A MacDonald
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Glen D Armstrong
- Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Daniel A Muruve
- Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.
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Dickmann J, Wesp P, Rädler M, Rit S, Pankuch M, Johnson RP, Bashkirov V, Schulte RW, Parodi K, Landry G, Dedes G. Prediction of image noise contributions in proton computed tomography and comparison to measurements. ACTA ACUST UNITED AC 2019; 64:145016. [DOI: 10.1088/1361-6560/ab2474] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Labbé G, Rankin MA, Robertson J, Moffat J, Giang E, Lee LK, Ziebell K, MacKinnon J, Laing CR, Parmley EJ, Agunos A, Daignault D, Bekal S, Chui L, MacDonald KA, Hoang L, Slavic D, Ramsay D, Pollari F, Nash JHE, Johnson RP. Targeting discriminatory SNPs in Salmonella enterica serovar Heidelberg genomes using RNase H2-dependent PCR. J Microbiol Methods 2018; 157:81-87. [PMID: 30592979 DOI: 10.1016/j.mimet.2018.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 11/08/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 11/16/2022]
Abstract
We report a novel RNase H2-dependent PCR (rhPCR) genotyping assay for a small number of discriminatory single-nucleotide polymorphisms (SNPs) that identify lineages and sub-lineages of the highly clonal pathogen Salmonella Heidelberg (SH). Standard PCR primers targeting numerous SNP locations were initially designed in silico, modified to be RNase H2-compatible, and then optimized by laboratory testing. Optimization often required repeated cycling through variations in primer design, assay conditions, reagent concentrations and selection of alternative SNP targets. The final rhPCR assay uses 28 independent rhPCR reactions to target 14 DNA bases that can distinguish 15 possible lineages and sub-lineages of SH. On evaluation, the assay correctly identified the 12 lineages and sub-lineages represented in a panel of 75 diverse SH strains. Non-specific amplicons were observed in 160 (15.2%) of the 1050 reactions, but due to their low intensity did not compromise assay performance. Furthermore, in silico analysis of 500 closed genomes from 103 Salmonella serovars and laboratory rhPCR testing of five prevalent Salmonella serovars including SH indicated the assay can identify Salmonella isolates as SH, since only SH isolates generated amplicons from all 14 target SNPs. The genotyping results can be fully correlated with whole genome sequencing (WGS) data in silico. This fast and economical assay, which can identify SH isolates and classify them into related or unrelated lineages and sub-lineages, has potential applications in outbreak identification, source attribution and microbial source tracking.
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Affiliation(s)
- Geneviève Labbé
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Marisa A Rankin
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Jonathan Moffat
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Elissa Giang
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Lok Kan Lee
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Joanne MacKinnon
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Chad R Laing
- National Centres for Animal Disease Lethbridge Laboratory, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - E Jane Parmley
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Agnes Agunos
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Danielle Daignault
- National Microbiology Laboratory, Public Health Agency of Canada, St-Hyacinthe, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Linda Chui
- Provincial Laboratory for Public Health-Alberta Public Laboratories, Edmonton, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kimberley A MacDonald
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; British Columbia Centre for Disease Control, Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
| | - Linda Hoang
- British Columbia Centre for Disease Control, Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
| | - Durda Slavic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | - Danielle Ramsay
- Ministère de l'Agriculture, des Pêcheries, et de l'Alimentation du Québec, Québec, Canada
| | - Frank Pollari
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John H E Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Toronto, Ontario, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada.
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10
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Shang L, Smith AJ, Duan L, Perkey KE, Wietgrefe S, Zupancic M, Southern PJ, Johnson RP, Carlis JV, Haase AT. Vaccine-Associated Maintenance of Epithelial Integrity Correlated With Protection Against Virus Entry. J Infect Dis 2018; 218:1272-1283. [PMID: 29401315 PMCID: PMC6455945 DOI: 10.1093/infdis/jiy062] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/29/2018] [Indexed: 12/13/2022] Open
Abstract
To identify the mechanisms by which human immunodeficiency virus type 1 (HIV-1) might penetrate the epithelial barrier during sexual transmission to women and the mechanisms of vaccine-associated protection against entry, we characterized early epithelial responses to vaginal inoculation of simian immunodeficiency virus strain mac251 (SIVmac251) in naive or SIVmac239Δnef-vaccinated rhesus macaques. Vaginal inoculation induced an early stress response in the cervicovaginal epithelium, which was associated with impaired epithelial integrity, damaged barrier function, and virus and bacterial translocation. In vaccinated animals, early stress responses were suppressed, and the maintenance of epithelial barrier integrity correlated with prevention of virus entry. These vaccine-protective effects were associated with a previously described mucosal system for locally producing and concentrating trimeric gp41 antibodies at the mucosal interface and with formation of SIV-specific immune complexes that block the stress responses via binding to the epithelial receptor FCGR2B and subsequent inhibitory signaling. Thus, blocking virus entry may be one protective mechanism by which locally concentrated non-neutralizing Ab might prevent HIV sexual transmission to women.
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Affiliation(s)
- L Shang
- Department of Microbiology and Immunology, Medical School, Minneapolis
| | - A J Smith
- Department of Microbiology and Immunology, Medical School, Minneapolis
| | - L Duan
- Department of Microbiology and Immunology, Medical School, Minneapolis
| | - K E Perkey
- Department of Microbiology and Immunology, Medical School, Minneapolis
| | - S Wietgrefe
- Department of Microbiology and Immunology, Medical School, Minneapolis
| | - M Zupancic
- Department of Microbiology and Immunology, Medical School, Minneapolis
| | - P J Southern
- Department of Microbiology and Immunology, Medical School, Minneapolis
| | - R P Johnson
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia
| | - J V Carlis
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis
| | - A T Haase
- Department of Microbiology and Immunology, Medical School, Minneapolis
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Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study. Front Microbiol 2018; 9:2040. [PMID: 30233526 PMCID: PMC6127291 DOI: 10.3389/fmicb.2018.02040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 06/20/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023] Open
Abstract
In this study, fecal samples were collected from a closed beef herd in Alberta, Canada from 2012 to 2015. To limit serotype bias, which was observed in enrichment broth cultures, Verotoxigenic Escherichia coli (VTEC) were isolated directly from samples using a hydrophobic grid-membrane filter verotoxin immunoblot assay. Overall VTEC isolation rates were similar for three different cohorts of yearling heifers on both an annual (68.5 to 71.8%) and seasonal basis (67.3 to 76.0%). Across all three cohorts, O139:H19 (37.1% of VTEC-positive samples), O22:H8 (15.8%) and O?(O108):H8 (15.4%) were among the most prevalent serotypes. However, isolation rates for serotypes O139:H19, O130:H38, O6:H34, O91:H21, and O113:H21 differed significantly between cohort-years, as did isolation rates for some serotypes within a single heifer cohort. There was a high level of VTEC serotype diversity with an average of 4.3 serotypes isolated per heifer and 65.8% of the heifers classified as "persistent shedders" of VTEC based on the criteria of >50% of samples positive and ≥4 consecutive samples positive. Only 26.8% (90/336) of the VTEC isolates from yearling heifers belonged to the human disease-associated seropathotypes A (O157:H7), B (O26:H11, O111:NM), and C (O22:H8, O91:H21, O113:H21, O137:H41, O2:H6). Conversely, seropathotypes B (O26:NM, O111:NM) and C (O91:H21, O2:H29) strains were dominant (76.0%, 19/25) among VTEC isolates from month-old calves from this herd. Among VTEC from heifers, carriage rates of vt1, vt2, vt1+vt2, eae, and hlyA were 10.7, 20.8, 68.5, 3.9, and 88.7%, respectively. The adhesin gene saa was present in 82.7% of heifer strains but absent from all of 13 eae+ve strains (from serotypes/intimin types O157:H7/γ1, O26:H11/β1, O111:NM/θ, O84:H2/ζ, and O182:H25/ζ). Phylogenetic relationships inferred from wgMLST and pan genome-derived core SNP analysis showed that strains clustered by phylotype and serotype. Further, VTEC strains of the same serotype usually shared the same suite of antibiotic resistance and virulence genes, suggesting the circulation of dominant clones within this distinct herd. This study provides insight into the diverse and dynamic nature of VTEC populations within groups of cattle and points to a broad spectrum of human health risks associated with these E. coli strains.
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Affiliation(s)
- Lu Ya Ruth Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada
| | | | - Chad R Laing
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada
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12
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Shang L, Smith AJ, Reilly CS, Duan L, Perkey KE, Wietgrefe S, Zupancic M, Southern PJ, Johnson RP, Carlis JV, Haase AT. Vaccine-modified NF-kB and GR signaling in cervicovaginal epithelium correlates with protection. Mucosal Immunol 2018; 11:512-522. [PMID: 28792003 PMCID: PMC5807226 DOI: 10.1038/mi.2017.69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 11/28/2016] [Accepted: 06/19/2017] [Indexed: 02/04/2023]
Abstract
Cervicovaginal epithelium plays a critical role in determining the outcome of virus transmission in the female reproductive tract (FRT) by initiating or suppressing transmission-facilitating mucosal immune responses in naïve and SIVmac239Δnef-vaccinated animals, respectively. In this study, we examined the very early responses of cervical epithelium within 24 h after vaginal exposure to SIV in naive and SIVmac239Δnef-vaccinated rhesus macaques. Using both ex vivo and in vivo experimental systems, we found that vaginal exposure to SIV rapidly induces a broad spectrum of pro-inflammatory responses in the epithelium associated with a reciprocal regulation of NF-kB and glucocorticoid receptor (GR) signaling pathways. Conversely, maintenance of high-level GR expression and suppression of NF-kB expression in the epithelium were associated with an immunologically quiescent state in the FRT mucosa and protection against vaginal challenge in SIVmac239Δnef-vaccinated animals. We show that the immunologically quiescent state is induced by FCGR2B-immune complexes interactions that modify the reciprocal regulation of NF-kB and GR signaling pathways. Our results suggest that targeting the balance of NF-kB and GR signaling in early cervicovaginal epithelium responses could moderate mucosal inflammation and target cell availability after vaginal infection, thereby providing a complementary approach to current prevention strategies.
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Affiliation(s)
- L Shang
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - A J Smith
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - C S Reilly
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - L Duan
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - K E Perkey
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - S Wietgrefe
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - M Zupancic
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - P J Southern
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - R P Johnson
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - J V Carlis
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - A T Haase
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
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13
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Falardeau J, Johnson RP, Pagotto F, Wang S. Occurrence, characterization, and potential predictors of verotoxigenic Escherichia coli, Listeria monocytogenes, and Salmonella in surface water used for produce irrigation in the Lower Mainland of British Columbia, Canada. PLoS One 2017; 12:e0185437. [PMID: 28953937 PMCID: PMC5617201 DOI: 10.1371/journal.pone.0185437] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 06/12/2017] [Accepted: 09/12/2017] [Indexed: 11/19/2022] Open
Abstract
Produce has become a major source of foodborne illness, and may become contaminated through surface water irrigation. The objectives of this study were to (i) determine the frequency of verotoxigenic E. coli (VTEC), Listeria monocytogenes, and Salmonella in surface waters used for irrigation in the Lower Mainland of British Columbia, (ii) assess the suitability of fecal coliforms and generic E. coli as hygiene indicators, and (iii) investigate the correlations of environmental factors with pathogen occurrence. Water samples were collected semi-monthly for 18 months from seven irrigation ditches across the Serpentine and Sumas watersheds. VTEC colonies on water filters were detected using a verotoxin colony immunoblot, and the presence of virulence genes vt1 and vt2 was ascertained via multiplex PCR. Detection of L. monocytogenes and Salmonella was completed using standard, Health Canada Compendium of Analytical Methods. Fecal coliforms and generic E. coli were enumerated by 3M™ Petrifilm™ and filtration methods, and meteorological and geographic data were collected from government records. VTEC, L. monocytogenes, and Salmonella were detected in 4.93%, 10.3%, and 2.69% of 223 samples, respectively. L. monocytogenes occurrence was greatest in the Serpentine watershed (χ2; p < 0.05), and was most common during the winter and fall (Fisher exact test; p < 0.05). Site dependence of VTEC and Salmonella occurrence was observed within watersheds (Fisher's exact test; p < 0.10). Pathogen occurrence correlated with fecal coliform counts (r = 0.448), while VTEC occurrence also correlated with precipitation over the five days before sampling (r = 0.239). The density of upstream livestock correlated with VTEC (rs = 0.812), and L. monocytogenes (rs = 0.841) detection. These data show that foodborne pathogens are present in the waters used for irrigation in the Lower Mainland of British Columbia, but their frequency may depend on spatial and temporal factors.
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Affiliation(s)
- Justin Falardeau
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Franco Pagotto
- Listeriosis Reference Service, Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada
| | - Siyun Wang
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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14
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Dedes G, De Angelis L, Rit S, Hansen D, Belka C, Bashkirov V, Johnson RP, Coutrakon G, Schubert KE, Schulte RW, Parodi K, Landry G. Application of fluence field modulation to proton computed tomography for proton therapy imaging. ACTA ACUST UNITED AC 2017; 62:6026-6043. [DOI: 10.1088/1361-6560/aa7734] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Opie S, Loomis E, Peralta P, Shimada T, Johnson RP. Strength and Viscosity Effects on Perturbed Shock Front Stability in Metals. Phys Rev Lett 2017; 118:195501. [PMID: 28548523 DOI: 10.1103/physrevlett.118.195501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Indexed: 06/07/2023]
Abstract
Computational modeling and experimental measurements on metal samples subject to a laser-driven, ablative Richtmyer-Meshkov instability showed differences between viscosity and strength effects. In particular, numerical and analytical solutions, coupled with measurements of fed-through perturbations, generated by perturbed shock fronts onto initially flat surfaces, show promise as a validation method for models of deviatoric response in the postshocked material. Analysis shows that measurements of shock perturbation amplitudes at low sample thickness-to-wavelength ratios are not enough to differentiate between strength and viscosity effects, but that surface displacement data of the fed-through perturbations appears to resolve the ambiguity. Additionally, analytical and numerical results show shock front perturbation evolution dependence on initial perturbation amplitude and wavelength is significantly different in viscous and materials with strength, suggesting simple experimental geometry changes should provide data supporting one model or the other.
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Affiliation(s)
- S Opie
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - E Loomis
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - P Peralta
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - T Shimada
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R P Johnson
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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16
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Ziebell K, Chui L, King R, Johnson S, Boerlin P, Johnson RP. Subtyping of Canadian isolates of Salmonella Enteritidis using Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) alone and in combination with Pulsed-Field Gel Electrophoresis (PFGE) and phage typing. J Microbiol Methods 2017; 139:29-36. [PMID: 28456552 DOI: 10.1016/j.mimet.2017.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 02/17/2017] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
Abstract
Salmonella enterica subspecies enterica serovar Enteritidis (SE) is one of the most common causes of human salmonellosis and in Canada currently accounts for over 40% of human cases. Reliable subtyping of isolates is required for outbreak detection and source attribution. However, Pulsed-Field Gel Electrophoresis (PFGE), the current standard subtyping method for Salmonella spp., is compromised by the high genetic homogeneity of SE. Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) was introduced to supplement PFGE, although there is a lack of data on the ability of MLVA to subtype Canadian isolates of SE. Three subtyping methods, PFGE, MLVA and phage typing were compared for their discriminatory power when applied to three panels of Canadian SE isolates: Panel 1: 70 isolates representing the diversity of phage types (PTs) and PFGE subtypes within these PTs; Panel 2: 214 apparently unrelated SE isolates of the most common PTs; and Panel 3: 27 isolates from 10 groups of epidemiologically related strains. For Panel 2 isolates, four MLVA subtypes were shared among 74% of unrelated isolates and in Panel 3 isolates, one MLVA subtype accounted for 62% of the isolates. For all panels, combining results from PFGE, MLVA and PT gave the best discrimination, except in Panel 1, where the combination of PT and PFGE was equally as high, due to the selection criteria for this panel. However, none of these methods is sufficiently discriminatory alone for reliable outbreak detection or source attribution, and must be applied together to achieve sufficient discrimination for practical purposes. Even then, some large clusters were not differentiated adequately. More discriminatory methods are required for reliable subtyping of this genetically highly homogeneous serovar. This need will likely be met by whole genome sequence analysis given the recent promising reports and as more laboratories implement this tool for outbreak response and surveillance.
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Affiliation(s)
- Kim Ziebell
- National Microbiology Laboratory at Guelph, PHAC, Guelph, ON, Canada
| | - Linda Chui
- Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Robin King
- Alberta Agriculture and Forestry, Edmonton, AB, Canada
| | - Suzanne Johnson
- National Microbiology Laboratory at Guelph, PHAC, Guelph, ON, Canada
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Roger P Johnson
- National Microbiology Laboratory at Guelph, PHAC, Guelph, ON, Canada.
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17
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Plautz TE, Bashkirov V, Giacometti V, Hurley RF, Johnson RP, Piersimoni P, Sadrozinski HFW, Schulte RW, Zatserklyaniy A. An evaluation of spatial resolution of a prototype proton CT scanner. Med Phys 2017; 43:6291. [PMID: 27908179 DOI: 10.1118/1.4966028] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To evaluate the spatial resolution of proton CT using both a prototype proton CT scanner and Monte Carlo simulations. METHODS A custom cylindrical edge phantom containing twelve tissue-equivalent inserts with four different compositions at varying radial displacements from the axis of rotation was developed for measuring the modulation transfer function (MTF) of a prototype proton CT scanner. Two scans of the phantom, centered on the axis of rotation, were obtained with a 200 MeV, low-intensity proton beam: one scan with steps of 4°, and one scan with the phantom continuously rotating. In addition, Monte Carlo simulations of the phantom scan were performed using scanners idealized to various degrees. The data were reconstructed using an iterative projection method with added total variation superiorization based on individual proton histories. Edge spread functions in the radial and azimuthal directions were obtained using the oversampling technique. These were then used to obtain the modulation transfer functions. The spatial resolution was defined by the 10% value of the modulation transfer function (MTF10%) in units of line pairs per centimeter (lp/cm). Data from the simulations were used to better understand the contributions of multiple Coulomb scattering in the phantom and the scanner hardware, as well as the effect of discretization of proton location. RESULTS The radial spatial resolution of the prototype proton CT scanner depends on the total path length, W, of the proton in the phantom, whereas the azimuthal spatial resolution depends both on W and the position, u-, at which the most-likely path uncertainty is evaluated along the path. For protons contributing to radial spatial resolution, W varies with the radial position of the edge, whereas for protons contributing to azimuthal spatial resolution, W is approximately constant. For a pixel size of 0.625 mm, the radial spatial resolution of the image reconstructed from the fully idealized simulation data ranged between 6.31 ± 0.36 lp/cm for W = 197 mm i.e., close to the center of the phantom, and 13.79 ± 0.36 lp/cm for W = 97 mm, near the periphery of the phantom. The azimuthal spatial resolution ranged from 6.99 ± 0.23 lp/cm at u- = 75 mm (near the center) to 11.20 ± 0.26 lp/cm at u- = 20 mm (near the periphery). Multiple Coulomb scattering limits the radial spatial resolution for path lengths greater than approximately 130 mm, and the azimuthal spatial resolution for positions of evaluation greater than approximately 40 mm for W = 199 mm. The radial spatial resolution of the image reconstructed from data from the 4° stepped experimental scan ranged from 5.11 ± 0.61 lp/cm for W = 197 mm to 8.58 ± 0.50 lp/cm for W = 97 mm. In the azimuthal direction, the spatial resolution ranged from 5.37 ± 0.40 lp/cm at u- = 75 mm to 7.27 ± 0.39 lp/cm at u- = 20 mm. The continuous scan achieved the same spatial resolution as that of the stepped scan. CONCLUSIONS Multiple Coulomb scattering in the phantom is the limiting physical factor of the achievable spatial resolution of proton CT; additional loss of spatial resolution in the prototype system is associated with scattering in the proton tracking system and inadequacies of the proton path estimate used in the iterative reconstruction algorithm. Improvement in spatial resolution may be achievable by improving the most likely path estimate by incorporating information about high and low density materials, and by minimizing multiple Coulomb scattering in the proton tracking system.
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Affiliation(s)
- Tia E Plautz
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, Santa Cruz, California 95064
| | - V Bashkirov
- Department of Basic Science, Loma Linda University, Loma Linda, California 92354
| | - V Giacometti
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong NSW 2522, Australia
| | - R F Hurley
- Department of Basic Science, Loma Linda University, Loma Linda, California 92354
| | - R P Johnson
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, Santa Cruz, California 95064
| | - P Piersimoni
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94143
| | - H F-W Sadrozinski
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, Santa Cruz, California 95064
| | - R W Schulte
- Department of Basic Science, Loma Linda University, Loma Linda, California 92354
| | - A Zatserklyaniy
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, Santa Cruz, California 95064
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18
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Shang L, Duan L, Perkey KE, Wietgrefe S, Zupancic M, Smith AJ, Southern PJ, Johnson RP, Haase AT. Epithelium-innate immune cell axis in mucosal responses to SIV. Mucosal Immunol 2017; 10:508-519. [PMID: 27435105 PMCID: PMC5250613 DOI: 10.1038/mi.2016.62] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 06/18/2016] [Indexed: 02/04/2023]
Abstract
In the SIV (simian immunodeficiency virus)-rhesus macaque model of HIV-1 (human immunodeficiency virus type I) transmission to women, one hallmark of the mucosal response to exposure to high doses of SIV is CD4 T-cell recruitment that fuels local virus expansion in early infection. In this study, we systematically analyzed the cellular events and chemoattractant profiles in cervical tissues that precede CD4 T-cell recruitment. We show that vaginal exposure to the SIV inoculum rapidly induces chemokine expression in cervical epithelium including CCL3, CCL20, and CXCL8. The chemokine expression is associated with early recruitment of macrophages and plasmacytoid dendritic cells that are co-clustered underneath the cervical epithelium. Production of chemokines CCL3 and CXCL8 by these cells in turn generates a chemokine gradient that is spatially correlated with the recruitment of CD4 T cells. We further show that the protection of SIVmac239Δnef vaccination against vaginal challenge is correlated with the absence of this epithelium-innate immune cell-CD4 T-cell axis response in the cervical mucosa. Our results reveal a critical role for cervical epithelium in initiating early mucosal responses to vaginal infection, highlight an important role for macrophages in target cell recruitment, and provide further evidence of a paradoxical dampening effect of a protective vaccine on these early mucosal responses.
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Affiliation(s)
- L Shang
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - L Duan
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - K E Perkey
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - S Wietgrefe
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - M Zupancic
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - A J Smith
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - P J Southern
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - R P Johnson
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - A T Haase
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
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19
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Pollari F, Christidis T, Pintar KDM, Nesbitt A, Farber J, Lavoie MC, Gill A, Kirsch P, Johnson RP. Evidence for the benefits of food chain interventions on E. coli O157:H7/NM prevalence in retail ground beef and human disease incidence: A success story. Can J Public Health 2017; 108:e71-e78. [PMID: 31820420 DOI: 10.17269/cjph.108.5655] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 09/30/2016] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Human infection with Escherichia coli O157:H7/NM has historically been associated with consumption of undercooked ground beef. The purpose of this paper is to investigate the correlation of the decline in E. coli O157:H7/NM infections in Canada with the introduction of control efforts in ground beef by industry. METHODS The human incidence of E. coli O157:H7/NM, prevalence in ground beef and interventions from 1996 to 2014 were analyzed. Pathogen prevalence data were obtained from federal government and industry surveillance and inspection/compliance programs. A survey of the largest ground beef producers in Canada was conducted to identify when interventions were implemented. RESULTS The incidence of E. coli O157:H7/NM infections in Canada declined from ≈4 cases/100 000 to ≈1 case/100000 from 2000 to 2010. Verotoxigenic Escherichia coli (VTEC) prevalence in ground beef sold at retail declined from about 30% around the year 2000 to <2% since 2012. Other measures of the prevalence of E. coli, VTEC, and E. coli O157:H7/NM in beef and ground beef also declined. The number and types of interventions implemented in the major beef processing establishments in Canada increased from 1996 to 2016. CONCLUSION The observed decline in human illnesses and pathogen levels in relation to retail meats was associated with the introduction of control efforts by industry, federal and provincial/territorial governments, and the general population. Industry-led changes in beef processing along with the introduction of food safety policies, regulations, and public education have led to improved food safety in Canada.
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Affiliation(s)
- Frank Pollari
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, 130 Colonnade Road, Ottawa, ON, K1A 0K9, Canada
| | - Tanya Christidis
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, 130 Colonnade Road, Ottawa, ON, K1A 0K9, Canada
| | - Katarina D M Pintar
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, 130 Colonnade Road, Ottawa, ON, K1A 0K9, Canada.
| | - Andrea Nesbitt
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, 130 Colonnade Road, Ottawa, ON, K1A 0K9, Canada
| | - Jeff Farber
- Department of Food Science, University of Cuelph, Guelph, ON, Canada
| | | | | | | | - Roger P Johnson
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Ottawa, ON, Canada
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Bashkirov VA, Schulte RW, Hurley RF, Johnson RP, Sadrozinski HFW, Zatserklyaniy A, Plautz T, Giacometti V. Novel scintillation detector design and performance for proton radiography and computed tomography. Med Phys 2016; 43:664-74. [PMID: 26843230 DOI: 10.1118/1.4939255] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Proton computed tomography (pCT) will enable accurate prediction of proton and ion range in a patient while providing the benefit of lower radiation exposure than in x-ray CT. The accuracy of the range prediction is essential for treatment planning in proton or ion therapy and depends upon the detector used to evaluate the water-equivalent path length (WEPL) of a proton passing through the object. A novel approach is presented for an inexpensive WEPL detector for pCT and proton radiography. METHODS A novel multistage detector with an aperture of 10 × 37.5 cm was designed to optimize the accuracy of the WEPL measurements while simplifying detector construction and the performance requirements of its components. The design of the five-stage detector was optimized through simulations based on the geant4 detector simulation toolkit, and the fabricated prototype was calibrated in water-equivalent millimeters with 200 MeV protons in the research beam line of the clinical proton synchrotron at Loma Linda University Medical Center. A special polystyrene step phantom was designed and built to speed up and simplify the calibration procedure. The calibrated five-stage detector was tested in the 200 MeV proton beam as part of the pCT head scanner, using a water phantom and polystyrene slabs to verify the WEPL reconstruction accuracy. RESULTS The beam-test results demonstrated excellent performance of the new detector, in good agreement with the simulation results. The WEPL measurement accuracy is about 3.0 mm per proton in the 0-260 mm WEPL range required for a pCT head scan with a 200 MeV proton beam. CONCLUSIONS The new multistage design approach to WEPL measurements for proton CT and radiography has been prototyped and tested. The test results show that the design is competitive with much more expensive calorimeter and range-counter designs.
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Affiliation(s)
- V A Bashkirov
- Department of Basic Science, Loma Linda University, 11175 Campus Street, Loma Linda, California 92354
| | - R W Schulte
- Department of Basic Science, Loma Linda University, 11175 Campus Street, Loma Linda, California 92354
| | - R F Hurley
- Department of Basic Science, Loma Linda University, 11175 Campus Street, Loma Linda, California 92354
| | - R P Johnson
- Physics Department, University of California, 1156 High Street, Santa Cruz, California 95064
| | - H F-W Sadrozinski
- Physics Department, University of California, 1156 High Street, Santa Cruz, California 95064
| | - A Zatserklyaniy
- Physics Department, University of California, 1156 High Street, Santa Cruz, California 95064
| | - T Plautz
- Physics Department, University of California, 1156 High Street, Santa Cruz, California 95064
| | - V Giacometti
- Centre for Medical Radiation Physics, University of Wollongong, NSW 2522, Australia
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Sadrozinski HFW, Geoghegan T, Harvey E, Johnson RP, Plautz TE, Zatserklyaniy A, Bashkirov V, Hurley RF, Piersimoni P, Schulte RW, Karbasi P, Schubert KE, Schultze B, Giacometti V. Operation of the Preclinical Head Scanner for Proton CT. Nucl Instrum Methods Phys Res A 2016; 831:394-399. [PMID: 27818559 PMCID: PMC5094456 DOI: 10.1016/j.nima.2016.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report on the operation and performance tests of a preclinical head scanner developed for proton computed tomography (pCT). After extensive preclinical testing, pCT is intended to be employed in support of proton therapy treatment planning and pre-treatment verification in patients undergoing particle-beam therapy. In order to assess the performance of the scanner, we have performed CT scans with 200 MeV protons from both the synchrotron of the Loma Linda University Medical Center (LLUMC) and the cyclotron of the Northwestern Medicine Chicago Proton Center (NMCPC). The very high sustained rate of data acquisition, exceeding one million protons per second, allowed a full 360° scan to be completed in less than 7 minutes. The reconstruction of various phantoms verified accurate reconstruction of the proton relative stopping power (RSP) and the spatial resolution in a variety of materials. The dose for an image with better than 1% uncertainty in the RSP is found to be close to 1 mGy.
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Affiliation(s)
| | - T Geoghegan
- SCIPP, U.C. Santa Cruz, Santa Cruz, CA 95064, USA
| | - E Harvey
- SCIPP, U.C. Santa Cruz, Santa Cruz, CA 95064, USA
| | - R P Johnson
- SCIPP, U.C. Santa Cruz, Santa Cruz, CA 95064, USA
| | - T E Plautz
- SCIPP, U.C. Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - V Bashkirov
- Division of Radiation Research, Loma Linda University, Loma Linda, CA 92354, USA
| | - R F Hurley
- Division of Radiation Research, Loma Linda University, Loma Linda, CA 92354, USA
| | - P Piersimoni
- Division of Radiation Research, Loma Linda University, Loma Linda, CA 92354, USA
| | - R W Schulte
- Division of Radiation Research, Loma Linda University, Loma Linda, CA 92354, USA
| | - P Karbasi
- School of Engineering and Computer Science, Baylor University, Waco, TX 76798, USA
| | - K E Schubert
- School of Engineering and Computer Science, Baylor University, Waco, TX 76798, USA
| | - B Schultze
- School of Engineering and Computer Science, Baylor University, Waco, TX 76798, USA
| | - V Giacometti
- Center for Medical Radiation Physics, University of Wollongong, NSW, Australia
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22
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Leon-Velarde CG, Happonen L, Pajunen M, Leskinen K, Kropinski AM, Mattinen L, Rajtor M, Zur J, Smith D, Chen S, Nawaz A, Johnson RP, Odumeru JA, Griffiths MW, Skurnik M. Yersinia enterocolitica-Specific Infection by Bacteriophages TG1 and ϕR1-RT Is Dependent on Temperature-Regulated Expression of the Phage Host Receptor OmpF. Appl Environ Microbiol 2016; 82:5340-53. [PMID: 27342557 PMCID: PMC4988191 DOI: 10.1128/aem.01594-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/17/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Bacteriophages present huge potential both as a resource for developing novel tools for bacterial diagnostics and for use in phage therapy. This potential is also valid for bacteriophages specific for Yersinia enterocolitica To increase our knowledge of Y. enterocolitica-specific phages, we characterized two novel yersiniophages. The genomes of the bacteriophages vB_YenM_TG1 (TG1) and vB_YenM_ϕR1-RT (ϕR1-RT), isolated from pig manure in Canada and from sewage in Finland, consist of linear double-stranded DNA of 162,101 and 168,809 bp, respectively. Their genomes comprise 262 putative coding sequences and 4 tRNA genes and share 91% overall nucleotide identity. Based on phylogenetic analyses of their whole-genome sequences and large terminase subunit protein sequences, a genus named Tg1virus within the family Myoviridae is proposed, with TG1 and ϕR1-RT (R1RT in the ICTV database) as member species. These bacteriophages exhibit a host range restricted to Y. enterocolitica and display lytic activity against the epidemiologically significant serotypes O:3, O:5,27, and O:9 at and below 25°C. Adsorption analyses of lipopolysaccharide (LPS) and OmpF mutants demonstrate that these phages use both the LPS inner core heptosyl residues and the outer membrane protein OmpF as phage receptors. Based on RNA sequencing and quantitative proteomics, we also demonstrate that temperature-dependent infection is due to strong repression of OmpF at 37°C. In addition, ϕR1-RT was shown to be able to enter into a pseudolysogenic state. Together, this work provides further insight into phage-host cell interactions by highlighting the importance of understanding underlying factors which may affect the abundance of phage host receptors on the cell surface. IMPORTANCE Only a small number of bacteriophages infecting Y. enterocolitica, the predominant causative agent of yersiniosis, have been previously described. Here, two newly isolated Y. enterocolitica phages were studied in detail, with the aim of elucidating the host cell receptors required for infection. Our research further expands the repertoire of phages available for consideration as potential antimicrobial agents or as diagnostic tools for this important bacterial pathogen.
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Affiliation(s)
- Carlos G Leon-Velarde
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Lotta Happonen
- Department of Clinical Sciences Lund, Infection Medicine, Lund University, Lund, Sweden Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Maria Pajunen
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Katarzyna Leskinen
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Andrew M Kropinski
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura Mattinen
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Monika Rajtor
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Joanna Zur
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Darren Smith
- Applied Sciences, University of Northumbria, Newcastle upon Tyne, United Kingdom
| | - Shu Chen
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | - Ayesha Nawaz
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Roger P Johnson
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Joseph A Odumeru
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Mansel W Griffiths
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
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Stanford K, Johnson RP, Alexander TW, McAllister TA, Reuter T. Influence of Season and Feedlot Location on Prevalence and Virulence Factors of Seven Serogroups of Escherichia coli in Feces of Western-Canadian Slaughter Cattle. PLoS One 2016; 11:e0159866. [PMID: 27482711 PMCID: PMC4970752 DOI: 10.1371/journal.pone.0159866] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 05/20/2016] [Accepted: 07/08/2016] [Indexed: 11/19/2022] Open
Abstract
Pooled feces collected over two years from 1749 transport trailers hauling western-Canadian slaughter cattle were analysed by PCR for detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157. Sequential immunomagnetic separation was then used to collect bacterial isolates (n = 1035) from feces positive for target serogroups. Isolated bacteria were tested by PCR to confirm serogroup and the presence of eae, ehxA, stx1, and stx2 virulence genes. Based on PCR screening, serogroup prevalence in feces ranged from 7.0% (O145) to 94.4% (O103) with at least 3 serogroups present in 79.5% of samples. Origin of cattle affected serogroup PCR prevalence and O157 was most prevalent in feces from south-west Alberta (P < 0.001). All serogroups demonstrated seasonal variations in PCR prevalence, with O26, O45, O103, O121, and O157 least prevalent (P < 0.001) in cooler winter months, while uncommon serogroups O111 and O145 increased in prevalence during winter (P < 0.001). However, isolates collected during winter were predominantly from serogroups O103 and O45. No seasonal variation was noted in proportion of isolates which were Shiga toxin containing E. coli (STEC; P = 0.18) or positive for Shiga toxin and eae (enterohemorrhagic E. coli; EHEC; P = 0.29). Isolates of serogroups O111, O145, and O157 were more frequently EHEC than were others, although 37.6–54.3% of isolates from other serogroups were also EHEC. Shiga-toxin genes present also varied by geographic origin of cattle (P < 0.05) in all serogroups except O157. As cattle within feedlots are sourced from multiple regions, locational differences in serogroup prevalence and virulence genes imply existence of selection pressures for E. coli and their virulence in western-Canadian cattle. Factors which reduce carriage or expression of virulence genes, particularly in non-O157 serogroups, should be investigated.
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Affiliation(s)
- Kim Stanford
- Alberta Agriculture and Forestry, Lethbridge, Alberta, Canada
- * E-mail:
| | | | | | | | - Tim Reuter
- Alberta Agriculture and Forestry, Lethbridge, Alberta, Canada
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Abstract
Patients who do not recognise their disabilities are extremely difficult to treat and manage. This paper describes a method by which feedback about errors was provided for a patient who could not acknowledge that his intellectual function was impaired following a severe head injury. This brought about a shift in his attitude and aided his successful resettlement. The nature of denial following brain injury is discussed.
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25
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Wang J, Stanford K, McAllister TA, Johnson RP, Chen J, Hou H, Zhang G, Niu YD. Biofilm Formation, Virulence Gene Profiles, and Antimicrobial Resistance of Nine Serogroups of Non-O157 Shiga Toxin–ProducingEscherichia coli. Foodborne Pathog Dis 2016; 13:316-24. [DOI: 10.1089/fpd.2015.2099] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jiaying Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Kim Stanford
- Alberta Agriculture and Forestry, Lethbridge, Alberta, Canada
| | | | - Roger P. Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongman Hou
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Gongliang Zhang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Yan D. Niu
- Alberta Agriculture and Forestry, Lethbridge, Alberta, Canada
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26
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Nadya S, Delaquis P, Chen J, Allen K, Johnson RP, Ziebell K, Laing C, Gannon V, Bach S, Topp E. Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape. Front Cell Infect Microbiol 2016; 6:36. [PMID: 27092297 PMCID: PMC4820441 DOI: 10.3389/fcimb.2016.00036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/14/2016] [Indexed: 11/13/2022] Open
Abstract
A hydrophobic grid membrane filtration-Shiga toxin immunoblot method was used to examine the prevalence of Shiga toxin-producing Escherichia coli (STEC) in four watersheds located in the Lower Mainland of British Columbia, Canada, a region characterized by rapid urbanization and intensive agricultural activity. STEC were recovered from 21.6, 23.2, 19.5, and 9.2% of surface water samples collected monthly from five sites in each watershed over a period of 1 year. Overall prevalence was subject to seasonal variation however, ranging between 13.3% during fall months and 34.3% during winter months. STEC were also recovered from 23.8% of sediment samples collected in one randomly selected site. One hundred distinct STEC isolates distributed among 29 definitive and 4 ambiguous or indeterminate serotypes were recovered from water and sediments, including isolates from Canadian "priority" serogroups O157 (3), O26 (4), O103 (5), and O111 (7). Forty seven isolates were further characterized by analysis of whole genome sequences to detect Shiga toxin gene (stx 1 and stx 2), intimin gene (eaeA) allelic variants and acquired virulence factors. These analyses collectively showed that surface waters from the region support highly diverse STEC populations that include strains with virulence factors commonly associated with human pathotypes. The present work served to characterize the microbiological hazard implied by STEC to support future assessments of risks to public health arising from non-agricultural and agricultural uses of surface water resources in the region.
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Affiliation(s)
- Stephanie Nadya
- Food, Nutrition and Health, Faculty of Land and Food Systems, University of British ColumbiaVancouver, BC, Canada
| | - Pascal Delaquis
- Agriculture and Agri-Food Canada, Summerland Research and Development CentreSummerland, BC, Canada
| | - Jessica Chen
- Food, Nutrition and Health, Faculty of Land and Food Systems, University of British ColumbiaVancouver, BC, Canada
| | - Kevin Allen
- Food, Nutrition and Health, Faculty of Land and Food Systems, University of British ColumbiaVancouver, BC, Canada
| | - Roger P. Johnson
- Public Health Agency of Canada, National Microbiology Laboratory at GuelphGuelph, ON, Canada
| | - Kim Ziebell
- Public Health Agency of Canada, National Microbiology Laboratory at GuelphGuelph, ON, Canada
| | - Chad Laing
- Laboratory for Foodborne Zoonoses, Public Health Agency of CanadaLethbridge, AB, Canada
| | - Victor Gannon
- Laboratory for Foodborne Zoonoses, Public Health Agency of CanadaLethbridge, AB, Canada
| | - Susan Bach
- Agriculture and Agri-Food Canada, Summerland Research and Development CentreSummerland, BC, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development CentreLondon, ON, Canada
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27
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Zelyas N, Poon A, Patterson-Fortin L, Johnson RP, Lee W, Chui L. Assessment of commercial chromogenic solid media for the detection of non-O157 Shiga toxin-producing Escherichia coli (STEC). Diagn Microbiol Infect Dis 2016; 85:302-308. [PMID: 27157987 DOI: 10.1016/j.diagmicrobio.2016.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 01/07/2016] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 11/30/2022]
Abstract
Detection of Shiga toxin-producing Escherichia coli (STEC) has evolved significantly since the introduction of sorbitol-MacConkey agar. This study compares four chromogenic media (CHROMagar™ STEC, Rainbow® O157 agar, CHROMagar™ O157, and Colorex® O157) in their identification of non-O157 STEC. When 161 non-O157 STEC were directly inoculated onto each medium, detection rates on CHROMagar™ STEC, Rainbow® O157 agar, CHROMagar™ O157 and Colorex® O157 were 90%, 70%, 3.7% and 6.8%, respectively. Tellurite minimal inhibitory concentrations (MICs) correlated with growth on CHROMagar™ STEC as 20 of 22 isolates with poor or no growth had MICs ≤1μg/mL. Stool spiking experiments revealed that CHROMagar™ STEC had the highest recovery of the six most common non-O157 STEC, ranging from 30% (in mucoid stool) to 98% (in watery stool). When using clinical stool samples, CHROMagar™ STEC had a sensitivity, specificity, positive predictive value, and negative predictive value of 84.6%, 87%, 13.9%, and 99.6%, respectively.
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Affiliation(s)
- Nathan Zelyas
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Alan Poon
- Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada
| | | | - Roger P Johnson
- Public Health Agency of Canada, National Microbiology Laboratory@Guelph, Guelph, ON, Canada
| | - Winki Lee
- Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada
| | - Linda Chui
- Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
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Eguale T, Engidawork E, Gebreyes WA, Asrat D, Alemayehu H, Medhin G, Johnson RP, Gunn JS. Fecal prevalence, serotype distribution and antimicrobial resistance of Salmonellae in dairy cattle in central Ethiopia. BMC Microbiol 2016; 16:20. [PMID: 26879347 PMCID: PMC4754838 DOI: 10.1186/s12866-016-0638-2] [Citation(s) in RCA: 34] [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: 07/20/2015] [Accepted: 02/09/2016] [Indexed: 11/10/2022] Open
Abstract
Background Salmonellae are major worldwide zoonotic pathogens infecting a wide range of vertebrate species including humans. Consumption of contaminated dairy products and contact with dairy cattle represent a common source of non-typhoidal Salmonella infection in humans. Despite a large number of small-scale dairy farms in Addis Ababa and its surrounding districts, little is known about the status of Salmonella in these farms. Results Salmonella was recovered from the feces of at least one animal in 7.6 % (10/132) of the dairy farms. Out of 1203 fecal samples examined, 30 were positive for Salmonella resulting in a weighted animal level prevalence of 2.3 %. Detection of diarrhea in an animal and in a farm was significantly associated with animal level (p = 0.012) and herd level (p < 0.001) prevalence of Salmonella. Animal level prevalence of Salmonella was significantly associated with age (p = 0.023) and study location; it was highest among those under 6 months of age and in farms from Adaa district and Addis Ababa (p < 0.001). Nine different serotypes were identified using standard serological agglutination tests. The most frequently recovered serotypes were Salmonella Typhimurium (23.3 %), S. Saintpaul (20 %), S. Kentucky (16.7 %) and S. Virchow (16.7 %). All isolates were resistant or intermediately resistant to at least one of the 18 drugs tested. Twenty-six (86.7 %), 19 (63.3 %), 18 (60 %), 16 (53.3 %) of the isolates were resistant to streptomycin, nitrofurantoin, sulfisoxazole and tetracycline , respectively. Resistance to 2 drugs was detected in 27 (90 %) of the isolates. Resistance to 3 or more drugs was detected in 21 (70 %) of the isolates, while resistance to 7 or more drugs was detected in 11 (36.7 %) of the isolates. The rate of occurrence of multi-drug resistance (MDR) in Salmonella strains isolated from dairy farms in Addis Ababa was significantly higher than those isolated from farms outside of Addis Ababa (p = 0.009). MDR was more common in S. Kentucky, S. Virchow and S. Saintpaul. Conclusion Isolation of Salmonella serotypes commonly known for causing human salmonellosis that are associated with an MDR phenotype in dairy farms in close proximity with human population is a major public health concern. These findings imply the need for a strict pathogen reduction strategy.
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Affiliation(s)
- Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Ephrem Engidawork
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Churchill Avenue, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Wondwossen A Gebreyes
- Department of Veterinary Preventive Medicine, The Ohio State University, 1920 Coffey Rd., Columbus, OH, 43210, USA.
| | - Daniel Asrat
- Department of Microbiology, Immunology & Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Churchill Avenue, P.O. Box 9086, Addis Ababa, Ethiopia.
| | - Haile Alemayehu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Girmay Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Roger P Johnson
- Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3W4, Canada.
| | - John S Gunn
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Biomedical Research Tower, 460 West 12th, Columbus, OH, 43210-1214, USA.
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29
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Labbé G, Edirmanasinghe R, Ziebell K, Nash JHE, Bekal S, Parmley EJ, Mulvey MR, Johnson RP. Complete Genome and Plasmid Sequences of Three Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human and Food Sources. Genome Announc 2016; 4:e01526-15. [PMID: 26769926 PMCID: PMC4714108 DOI: 10.1128/genomea.01526-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/18/2015] [Indexed: 11/20/2022]
Abstract
Isolates of Salmonella enterica subsp. enterica serovar Heidelberg are often associated with poultry products and may cause severe human illness. Here, we report the fully assembled genome and plasmid sequences of three S. Heidelberg strains with phage types 9, 29, and 41.
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Affiliation(s)
- Geneviève Labbé
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Romaine Edirmanasinghe
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kim Ziebell
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John H E Nash
- National Microbiology Laboratory at Toronto, Public Health Agency of Canada, Toronto, Ontario, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - E Jane Parmley
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Roger P Johnson
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
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30
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Wang J, Niu YD, Chen J, Anany H, Ackermann HW, Johnson RP, Ateba CN, Stanford K, McAllister TA. Feces of feedlot cattle contain a diversity of bacteriophages that lyse non-O157 Shiga toxin-producing Escherichia coli. Can J Microbiol 2015; 61:467-75. [PMID: 26011668 DOI: 10.1139/cjm-2015-0163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 01/01/2023]
Abstract
This study aimed to isolate and characterize bacteriophages that lyse non-O157 Shiga toxin-producing Escherichia coli (STEC) from cattle feces. Of 37 non-O157 STEC-infecting phages isolated, those targeting O26 (AXO26A, AYO26A, AYO26B), O103 (AXO103A, AYO103A), O111 (AXO111A, AYO111A), O121 (AXO121A, AXO121B), and O145 (AYO145A, AYO145B) were further characterized. Transmission electron microscopy showed that the 11 isolates belonged to 3 families and 6 genera: the families Myoviridae (types rV5, T4, ViI, O1), Siphoviridae (type T5), and Podoviridae (type T7). Genome size of the phages as determined by pulsed-field gel electrophoresis ranged from 38 to 177 kb. Excluding phages AXO26A, AYO103A, AYO145A, and AYO145B, all other phages were capable of lysing more than 1 clinically important strain from serogroups of O26, O91, O103, O111, O113, O121, and O128, but none exhibited infectivity across all serogroups. Moreover, phages AYO26A, AXO121A, and AXO121B were also able to lyse 4 common phage types of STEC O157:H7. Our findings show that a diversity of non-O157 STEC-infecting phages are harbored in bovine feces. Phages AYO26A, AYO26B, AXO103A, AXO111A, AYO111A, AXO121A, and AXO121B exhibited a broad host range against a number of serogroups of STEC and have potential for the biocontrol of STEC in the environment.
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Affiliation(s)
- Jiaying Wang
- a College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China.,c Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Yan D Niu
- b Alberta Agriculture and Rural Development, Lethbridge, AB T1J 4V6, Canada
| | - Jinding Chen
- a College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Hany Anany
- d Department of Food Science, Canadian Research Institute for Food Safety, Guelph, ON N1G 2W1, Canada.,e Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Hans-W Ackermann
- f Département de microbiologie, Faculté de médecine, Université Laval, Québec, QC G1K 7P4, Canada
| | - Roger P Johnson
- g Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada
| | - Collins N Ateba
- h Department of Biological Sciences, Faculty of Agriculture Science and Technology, North West University-Mafikeng Campus, North West, Mmabatho 2735, South Africa
| | - Kim Stanford
- b Alberta Agriculture and Rural Development, Lethbridge, AB T1J 4V6, Canada
| | - Tim A McAllister
- c Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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Dudnikov V, Johnson RP, Murrey S, Pinnisi T, Piller C, Santana M, Stockli M, Welton R, Johnson C, Turvey M. Improving efficiency of negative ion production in ion source with saddle antenna. Rev Sci Instrum 2014; 85:02B111. [PMID: 24593551 DOI: 10.1063/1.4833021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Extraction of negative ions from a saddle antenna radio-frequency surface plasma source is considered. Several versions of new plasma generators with different antennas and magnetic field configurations were tested in the smal Oak Ridge National Laboratory Spallation Neutron Source Test Stand. The efficiency of positive ion generation in plasma has been improved to 200 mA/cm(2) kW from 2.5 mA/cm(2) kW. A small oven was developed for cesiation by cesium compounds and alloy decomposition. After cesiation, a current of negative ions to the collector was increased from 1 mA to 10 mA with 1.5 kW RF power in the plasma and longitudinal magnetic field Bl ∼ 250 G. The specific efficiency of H(-) production was increased to 20 mA/cm(2) kW from 2.5 mA/cm(2) kW.
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Affiliation(s)
- V Dudnikov
- Muons, Inc., Batavia, Illinois 60510, USA
| | | | - S Murrey
- ORNL, Oak Ridge, Tennessee 37831, USA
| | - T Pinnisi
- ORNL, Oak Ridge, Tennessee 37831, USA
| | - C Piller
- ORNL, Oak Ridge, Tennessee 37831, USA
| | - M Santana
- ORNL, Oak Ridge, Tennessee 37831, USA
| | - M Stockli
- ORNL, Oak Ridge, Tennessee 37831, USA
| | - R Welton
- ORNL, Oak Ridge, Tennessee 37831, USA
| | - C Johnson
- Physics Department, Wisconsin University of Madison, Wisconsin 53706, USA
| | - M Turvey
- Engineering Department, University of Florida, Gainesville, Florida 32611, USA
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Chung M, Collura MG, Flanagan G, Freemire B, Hanlet PM, Jana MR, Johnson RP, Kaplan DM, Leonova M, Moretti A, Popovic M, Schwarz T, Tollestrup A, Torun Y, Yonehara K. Pressurized H2 RF cavities in ionizing beams and magnetic fields. Phys Rev Lett 2013; 111:184802. [PMID: 24237526 DOI: 10.1103/physrevlett.111.184802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Indexed: 06/02/2023]
Abstract
A major technological challenge in building a muon cooling channel is operating rf cavities in multitesla external magnetic fields. We report the first proof-of-principle experiment of a high pressure gas-filled rf cavity for use with intense ionizing beams and strong external magnetic fields. rf power consumption by beam-induced plasma is investigated with hydrogen and deuterium gases with pressures between 20 and 100 atm and peak rf gradients between 5 and 50 MV/m. The low pressure case agrees well with an analytical model based on electron and ion mobilities. Varying concentrations of oxygen gas are investigated to remove free electrons from the cavity and reduce the rf power consumption. Measurements of the electron attachment time to oxygen and rate of ion-ion recombination are also made. Additionally, we demonstrate the operation of the gas-filled rf cavity in a solenoidal field of up to 3 T, finding no major magnetic field dependence. All these results indicate that a high pressure gas-filled cavity is a viable technology for muon ionization cooling.
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Affiliation(s)
- M Chung
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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Kropinski AM, Waddell T, Meng J, Franklin K, Ackermann HW, Ahmed R, Mazzocco A, Yates J, Lingohr EJ, Johnson RP. The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5. Virol J 2013; 10:76. [PMID: 23497209 PMCID: PMC3606486 DOI: 10.1186/1743-422x-10-76] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 02/28/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Bacteriophages (phages) have been used extensively as analytical tools to type bacterial cultures and recently for control of zoonotic foodborne pathogens in foods and in animal reservoirs. METHODS We examined the host range, morphology, genome and proteome of the lytic E. coli O157 phage rV5, derived from phage V5, which is a member of an Escherichia coli O157:H7 phage typing set. RESULTS Phage rV5 is a member of the Myoviridae family possessing an icosahedral head of 91 nm between opposite apices. The extended tail measures 121 x 17 nm and has a sheath of 44 x 20 nm and a 7 nm-wide core in the contracted state. It possesses a 137,947 bp genome (43.6 mol%GC) which encodes 233 ORFs and six tRNAs. Until recently this virus appeared to be phylogenetically isolated with almost 70% of its gene products ORFans. rV5 is closely related to coliphages Delta and vB-EcoM-FY3, and more distantly related to Salmonella phages PVP-SE1 and SSE-121, Cronobacter sakazakii phage vB_CsaM_GAP31, and coliphages phAPEC8 and phi92. A complete shotgun proteomic analysis was carried out on rV5, extending what had been gleaned from the genomic analyses. Host range studies revealed that rV5 is active against several other E. coli.
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Affiliation(s)
- Andrew M Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Tom Waddell
- Abbott Point of Care, 185 Corkstown Road, Ottawa, ON, K2H 8V4, Canada
| | - Juncai Meng
- Merck Research Laboratories, 126E Lincoln Avenue, Rahway, NJ, 07065, USA
| | - Kristyn Franklin
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - Hans-Wolfgang Ackermann
- Département de Microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Québec, QC, G1K 7P4, Canada
| | - Rafiq Ahmed
- Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Amanda Mazzocco
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - John Yates
- The Scripps Research Institute, Department of Cell Biology, Proteomic Mass Spectrometry Laboratory, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Erika J Lingohr
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - Roger P Johnson
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
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Roth M, Jung D, Falk K, Guler N, Deppert O, Devlin M, Favalli A, Fernandez J, Gautier D, Geissel M, Haight R, Hamilton CE, Hegelich BM, Johnson RP, Merrill F, Schaumann G, Schoenberg K, Schollmeier M, Shimada T, Taddeucci T, Tybo JL, Wagner F, Wender SA, Wilde CH, Wurden GA. Bright laser-driven neutron source based on the relativistic transparency of solids. Phys Rev Lett 2013; 110:044802. [PMID: 25166169 DOI: 10.1103/physrevlett.110.044802] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Indexed: 06/03/2023]
Abstract
Neutrons are unique particles to probe samples in many fields of research ranging from biology to material sciences to engineering and security applications. Access to bright, pulsed sources is currently limited to large accelerator facilities and there has been a growing need for compact sources over the recent years. Short pulse laser driven neutron sources could be a compact and relatively cheap way to produce neutrons with energies in excess of 10 MeV. For more than a decade experiments have tried to obtain neutron numbers sufficient for applications. Our recent experiments demonstrated an ion acceleration mechanism based on the concept of relativistic transparency. Using this new mechanism, we produced an intense beam of high energy (up to 170 MeV) deuterons directed into a Be converter to produce a forward peaked neutron flux with a record yield, on the order of 10(10) n/sr. We present results comparing the two acceleration mechanisms and the first short pulse laser generated neutron radiograph.
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Affiliation(s)
- M Roth
- Institut für Kernphysik, Technische Universität Darmstadt, Schloßgartenstrasse 9, D-64289 Darmstadt, Germany and Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D Jung
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - K Falk
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - N Guler
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - O Deppert
- Institut für Kernphysik, Technische Universität Darmstadt, Schloßgartenstrasse 9, D-64289 Darmstadt, Germany
| | - M Devlin
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - A Favalli
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - J Fernandez
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D Gautier
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M Geissel
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - R Haight
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C E Hamilton
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - B M Hegelich
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R P Johnson
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - F Merrill
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - G Schaumann
- Institut für Kernphysik, Technische Universität Darmstadt, Schloßgartenstrasse 9, D-64289 Darmstadt, Germany
| | - K Schoenberg
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M Schollmeier
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - T Shimada
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - T Taddeucci
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - J L Tybo
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - F Wagner
- Institut für Kernphysik, Technische Universität Darmstadt, Schloßgartenstrasse 9, D-64289 Darmstadt, Germany
| | - S A Wender
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C H Wilde
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - G A Wurden
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Kropinski AM, Lingohr EJ, Moyles DM, Ojha S, Mazzocco A, She YM, Bach SJ, Rozema EA, Stanford K, McAllister TA, Johnson RP. Endemic bacteriophages: a cautionary tale for evaluation of bacteriophage therapy and other interventions for infection control in animals. Virol J 2012; 9:207. [PMID: 22985539 PMCID: PMC3496638 DOI: 10.1186/1743-422x-9-207] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/31/2012] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND One of the most effective targets for control of zoonotic foodborne pathogens in the farm to fork continuum is their elimination in food animals destined for market. Phage therapy for Escherichia coli O157:H7 in ruminants, the main animal reservoir of this pathogen, is a popular research topic. Since phages active against this pathogen may be endemic in host animals and their environment, they may emerge during trials of phage therapy or other interventions, rendering interpretation of trials problematic. METHODS During separate phage therapy trials, sheep and cattle inoculated with 109 to 1010 CFU of E. coli O157:H7 soon began shedding phages dissimilar in plaque morphology to the administered therapeutic phages. None of the former was previously identified in the animals or in their environment. The dissimilar "rogue" phage was isolated and characterized by host range, ultrastructure, and genomic and proteomic analyses. RESULTS The "rogue" phage (Phage vB_EcoS_Rogue1) is distinctly different from the administered therapeutic Myoviridae phages, being a member of the Siphoviridae (head: 53 nm; striated tail: 152x8 nm). It has a 45.8 kb genome which is most closely related to coliphage JK06, a member of the "T1-like viruses" isolated in Israel. Detailed bioinformatic analysis reveals that the tail of these phages is related to the tail genes of coliphage lambda. The presence of "rogue" phages resulting from natural enrichments can pose problems in the interpretation of phage therapeutic studies. Similarly, evaluation of any interventions for foodborne or other bacterial pathogens in animals may be compromised unless tests for such phages are included to identify their presence and potential impact.
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Affiliation(s)
- Andrew M Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, N1G 2 W1, Canada
| | - Erika J Lingohr
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
| | - Dianne M Moyles
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, N1G 2 W1, Canada
| | - Shivani Ojha
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
| | - Amanda Mazzocco
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
| | - Yi-Min She
- Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, ON, K1A 0 K9, Canada
| | - Susan J Bach
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, BC, V0H 1Z0, Canada
| | - Erica A Rozema
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Alberta Agriculture and Rural Development, Agriculture Centre, Lethbridge, AB, T1J 4 V6, Canada
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Kim Stanford
- Alberta Agriculture and Rural Development, Agriculture Centre, Lethbridge, AB, T1J 4 V6, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Roger P Johnson
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
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Billingsley JM, Rajakumar PA, Salisch NC, Kuzmichev YV, Hong HS, Connole MA, Reeves RK, Kang H, Li W, Johnson RP. Maturation of protective immunity induced by SIVΔnef correlates with differential expression of transcription factors in SIV-specific CD8+ T cells. Retrovirology 2012. [PMCID: PMC3441477 DOI: 10.1186/1742-4690-9-s2-p33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Dudnikov V, Johnson RP, Murray S, Pennisi T, Piller C, Santana M, Stockli M, Welton R. Surface plasma source with saddle antenna radio frequency plasma generator. Rev Sci Instrum 2012; 83:02A712. [PMID: 22380221 DOI: 10.1063/1.3672111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A prototype RF H(-) surface plasma source (SPS) with saddle (SA) RF antenna is developed which will provide better power efficiency for high pulsed and average current, higher brightness with longer lifetime and higher reliability. Several versions of new plasma generators with small AlN discharge chambers and different antennas and magnetic field configurations were tested in the plasma source test stand. A prototype SA SPS was installed in the Spallation Neutron Source (SNS) ion source test stand with a larger, normal-sized SNS AlN chamber that achieved unanalyzed peak currents of up to 67 mA with an apparent efficiency up to 1.6 mA∕kW. Control experiments with H(-) beam produced by SNS SPS with internal and external antennas were conducted. A new version of the RF triggering plasma gun has been designed. A saddle antenna SPS with water cooling is fabricated for high duty factor testing.
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Affiliation(s)
- V Dudnikov
- Muons, Inc., Batavia, Illinios 60510, USA.
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Ackermann M, Ajello M, Albert A, Atwood WB, Baldini L, Ballet J, Barbiellini G, Bastieri D, Bechtol K, Bellazzini R, Berenji B, Blandford RD, Bloom ED, Bonamente E, Borgland AW, Bregeon J, Brigida M, Bruel P, Buehler R, Burnett TH, Buson S, Caliandro GA, Cameron RA, Cañadas B, Caraveo PA, Casandjian JM, Cecchi C, Charles E, Chekhtman A, Chiang J, Ciprini S, Claus R, Cohen-Tanugi J, Conrad J, Cutini S, de Angelis A, de Palma F, Dermer CD, Digel SW, do Couto e Silva E, Drell PS, Drlica-Wagner A, Falletti L, Favuzzi C, Fegan SJ, Ferrara EC, Fukazawa Y, Funk S, Fusco P, Gargano F, Gasparrini D, Gehrels N, Germani S, Giglietto N, Giordano F, Giroletti M, Glanzman T, Godfrey G, Grenier IA, Guiriec S, Gustafsson M, Hadasch D, Hayashida M, Hays E, Hughes RE, Jeltema TE, Jóhannesson G, Johnson RP, Johnson AS, Kamae T, Katagiri H, Kataoka J, Knödlseder J, Kuss M, Lande J, Latronico L, Lionetto AM, Llena Garde M, Longo F, Loparco F, Lott B, Lovellette MN, Lubrano P, Madejski GM, Mazziotta MN, McEnery JE, Mehault J, Michelson PF, Mitthumsiri W, Mizuno T, Monte C, Monzani ME, Morselli A, Moskalenko IV, Murgia S, Naumann-Godo M, Norris JP, Nuss E, Ohsugi T, Okumura A, Omodei N, Orlando E, Ormes JF, Ozaki M, Paneque D, Parent D, Pesce-Rollins M, Pierbattista M, Piron F, Pivato G, Porter TA, Profumo S, Rainò S, Razzano M, Reimer A, Reimer O, Ritz S, Roth M, Sadrozinski HFW, Sbarra C, Scargle JD, Schalk TL, Sgrò C, Siskind EJ, Spandre G, Spinelli P, Strigari L, Suson DJ, Tajima H, Takahashi H, Tanaka T, Thayer JG, Thayer JB, Thompson DJ, Tibaldo L, Tinivella M, Torres DF, Troja E, Uchiyama Y, Vandenbroucke J, Vasileiou V, Vianello G, Vitale V, Waite AP, Wang P, Winer BL, Wood KS, Wood M, Yang Z, Zimmer S, Kaplinghat M, Martinez GD. Constraining dark matter models from a combined analysis of Milky Way satellites with the Fermi Large Area Telescope. Phys Rev Lett 2011; 107:241302. [PMID: 22242987 DOI: 10.1103/physrevlett.107.241302] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/06/2011] [Indexed: 05/31/2023]
Abstract
Satellite galaxies of the Milky Way are among the most promising targets for dark matter searches in gamma rays. We present a search for dark matter consisting of weakly interacting massive particles, applying a joint likelihood analysis to 10 satellite galaxies with 24 months of data of the Fermi Large Area Telescope. No dark matter signal is detected. Including the uncertainty in the dark matter distribution, robust upper limits are placed on dark matter annihilation cross sections. The 95% confidence level upper limits range from about 10(-26) cm3 s(-1) at 5 GeV to about 5×10(-23) cm3 s(-1) at 1 TeV, depending on the dark matter annihilation final state. For the first time, using gamma rays, we are able to rule out models with the most generic cross section (∼3×10(-26) cm3 s(-1) for a purely s-wave cross section), without assuming additional boost factors.
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Affiliation(s)
- M Ackermann
- W. W. Hansen Experimental Physics Laboratory, Kavli Institute for Particle Astrophysics and Cosmology, Department of Physics, Stanford University, Stanford, California 94305, USA
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Offermann DT, Flippo KA, Gaillard SA, Gautier DC, Letzring S, Cobble JC, Wurden G, Johnson RP, Shimada T, Montgomery DS, Gonzales RP, Hurry T, Archuleta F, Schmitt MJ, Reid SM, Bartal T, Wei MS, Higginson DP, Beg FN, Geissel M, Schollmeier M. Carbon ion beam focusing using laser irradiated, heated diamond hemispherical shells. ACTA ACUST UNITED AC 2010. [DOI: 10.1088/1742-6596/244/2/022053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abdo AA, Ackermann M, Ajello M, Atwood WB, Baldini L, Ballet J, Barbiellini G, Bastieri D, Bechtol K, Bellazzini R, Berenji B, Blandford RD, Bloom ED, Bonamente E, Borgland AW, Bouvier A, Brandt TJ, Bregeon J, Brez A, Brigida M, Bruel P, Buehler R, Burnett TH, Buson S, Caliandro GA, Cameron RA, Caraveo PA, Carrigan S, Casandjian JM, Cecchi C, Celik O, Charles E, Chaty S, Chekhtman A, Cheung CC, Chiang J, Ciprini S, Claus R, Cohen-Tanugi J, Conrad J, Corbel S, Corbet R, DeCesar ME, den Hartog PR, Dermer CD, de Palma F, Digel SW, Donato D, do Couto e Silva E, Drell PS, Dubois R, Dubus G, Dumora D, Favuzzi C, Fegan SJ, Ferrara EC, Fortin P, Frailis M, Fuhrmann L, Fukazawa Y, Funk S, Fusco P, Gargano F, Gasparrini D, Gehrels N, Germani S, Giglietto N, Giordano F, Giroletti M, Glanzman T, Godfrey G, Grenier IA, Grondin MH, Grove JE, Guiriec S, Hadasch D, Harding AK, Hayashida M, Hays E, Healey SE, Hill AB, Horan D, Hughes RE, Itoh R, Jean P, Jóhannesson G, Johnson AS, Johnson RP, Johnson TJ, Johnson WN, Kamae T, Katagiri H, Kataoka J, Kerr M, Knödlseder J, Koerding E, Kuss M, Lande J, Latronico L, Lee SH, Lemoine-Goumard M, Garde ML, Longo F, Loparco F, Lott B, Lovellette MN, Lubrano P, Makeev A, Mazziotta MN, McConville W, McEnery JE, Mehault J, Michelson PF, Mizuno T, Moiseev AA, Monte C, Monzani ME, Morselli A, Moskalenko IV, Murgia S, Nakamori T, Naumann-Godo M, Nestoras I, Nolan PL, Norris JP, Nuss E, Ohno M, Ohsugi T, Okumura A, Omodei N, Orlando E, Ormes JF, Ozaki M, Paneque D, Panetta JH, Parent D, Pelassa V, Pepe M, Pesce-Rollins M, Piron F, Porter TA, Rainò S, Rando R, Ray PS, Razzano M, Razzaque S, Rea N, Reimer A, Reimer O, Reposeur T, Ripken J, Ritz S, Romani RW, Roth M, Sadrozinski HFW, Sander A, Parkinson PMS, Scargle JD, Schinzel FK, Sgrò C, Shaw MS, Siskind EJ, Smith DA, Smith PD, Sokolovsky KV, Spandre G, Spinelli P, Stawarz Ł, Strickman MS, Suson DJ, Takahashi H, Takahashi T, Tanaka T, Tanaka Y, Thayer JB, Thayer JG, Thompson DJ, Tibaldo L, Torres DF, Tosti G, Tramacere A, Uchiyama Y, Usher TL, Vandenbroucke J, Vasileiou V, Vilchez N, Vitale V, Waite AP, Wallace E, Wang P, Winer BL, Wolff MT, Wood KS, Yang Z, Ylinen T, Ziegler M, Maehara H, Nishiyama K, Kabashima F, Bach U, Bower GC, Falcone A, Forster JR, Henden A, Kawabata KS, Koubsky P, Mukai K, Nelson T, Oates SR, Sakimoto K, Sasada M, Shenavrin VI, Shore SN, Skinner GK, Sokoloski J, Stroh M, Tatarnikov AM, Uemura M, Wahlgren GM, Yamanaka M. Gamma-ray emission concurrent with the nova in the symbiotic binary V407 Cygni. Science 2010; 329:817-21. [PMID: 20705855 DOI: 10.1126/science.1192537] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Novae are thermonuclear explosions on a white dwarf surface fueled by mass accreted from a companion star. Current physical models posit that shocked expanding gas from the nova shell can produce x-ray emission, but emission at higher energies has not been widely expected. Here, we report the Fermi Large Area Telescope detection of variable gamma-ray emission (0.1 to 10 billion electron volts) from the recently detected optical nova of the symbiotic star V407 Cygni. We propose that the material of the nova shell interacts with the dense ambient medium of the red giant primary and that particles can be accelerated effectively to produce pi(0) decay gamma-rays from proton-proton interactions. Emission involving inverse Compton scattering of the red giant radiation is also considered and is not ruled out.
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Affiliation(s)
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- Space Science Division, Naval Research Laboratory, Washington, DC 20375, USA
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Stanford K, McAllister TA, Niu YD, Stephens TP, Mazzocco A, Waddell TE, Johnson RP. Oral delivery systems for encapsulated bacteriophages targeted at Escherichia coli O157:H7 in feedlot cattle. J Food Prot 2010; 73:1304-12. [PMID: 20615343 DOI: 10.4315/0362-028x-73.7.1304] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacteriophages are natural predators of bacteria and may mitigate Escherichia coli O157:H7 in cattle and their environment. As bacteriophages targeted to E. coli O157:H7 (phages) lose activity at low pH, protection from gastric acidity may enhance efficacy of orally administered phages. Polymer encapsulation of four phages, wV8, rV5, wV7, and wV11, and exposure to pH 3.0 for 20 min resulted in an average 13.6% recovery of phages after release from encapsulation at pH 7.2. In contrast, untreated phages under similar conditions had a complete loss of activity. Steers (n = 24) received 10(11) CFU of naladixic acid-resistant E. coli O157:H7 on day 0 and were housed in six pens of four steers. Two pens were control (naladixic acid-resistant E. coli O157:H7 only), and the remaining pens received polymer-encapsulated phages (Ephage) on days -1, 1, 3, 6, and 8. Two pens received Ephage orally in gelatin capsules (bolus; 10(10) PFU per steer per day), and the remaining two pens received Ephage top-dressed on their feed (feed; estimated 10(11) PFU per steer per day). Shedding of E. coli O157:H7 was monitored for 10 weeks by collecting fecal grab and hide swab samples. Acceptable activity of mixed phages at delivery to steers was found for bolus and feed, averaging 1.82 and 1.13 x 10(9) PFU/g, respectively. However, Ephage did not reduce shedding of naladixic acid-resistant E. coli O157:H7, although duration of shedding was reduced by 14 days (P < 0.1) in bolus-fed steers as compared with control steers. Two successful systems for delivery of Ephage were developed, but a better understanding of phage-E. coli O157:H7 ecology is required to make phage therapy a viable strategy for mitigation of this organism in feedlot cattle.
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Affiliation(s)
- K Stanford
- Alberta Agriculture and Rural Development, Agriculture Centre, Lethbridge, Alberta, Canada.
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Abstract
Results of 1,579 observations of cars entering or exiting campus parking lots showed direct relationships between seat belt wearing and the intrusiveness of the engineering device designed to induce belt usage, and between device intrusiveness and system defeat. For example, all drivers with working interlocks or unlimited buzzer reminders were wearing a seat belt; but 62% of the systems with interlocks or unlimited buzzers had been defeated, and only 15.9% of the drivers in these cars were wearing a seat belt. The normative data indicated marked ineffectiveness of the negative reinforcement contingencies implied by current seat belt inducement systems; but suggested that unlimited buzzer systems would be the optimal system currently available if contingencies were developed to discourage the disconnection and circumvention of such systems. Positive reinforcement strategies are discussed that would be quite feasible for large-scale promotion of seat belt usage.
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Affiliation(s)
- E S Geller
- Virginia Polytechnic Institute and State University
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Abdo AA, Ackermann M, Ajello M, Atwood WB, Baldini L, Ballet J, Barbiellini G, Bastieri D, Baughman BM, Bechtol K, Bellazzini R, Berenji B, Blandford RD, Bloom ED, Bonamente E, Borgland AW, Bregeon J, Brez A, Brigida M, Bruel P, Burnett TH, Buson S, Caliandro GA, Cameron RA, Caraveo PA, Casandjian JM, Cavazzuti E, Cecchi C, Celik O, Charles E, Chekhtman A, Cheung CC, Chiang J, Ciprini S, Claus R, Cohen-Tanugi J, Cominsky LR, Conrad J, Cutini S, Dermer CD, de Angelis A, de Palma F, Digel SW, Di Bernardo G, do Couto e Silva E, Drell PS, Drlica-Wagner A, Dubois R, Dumora D, Farnier C, Favuzzi C, Fegan SJ, Focke WB, Fortin P, Frailis M, Fukazawa Y, Funk S, Fusco P, Gaggero D, Gargano F, Gasparrini D, Gehrels N, Germani S, Giebels B, Giglietto N, Giommi P, Giordano F, Glanzman T, Godfrey G, Grenier IA, Grondin MH, Grove JE, Guillemot L, Guiriec S, Gustafsson M, Hanabata Y, Harding AK, Hayashida M, Hughes RE, Itoh R, Jackson MS, Jóhannesson G, Johnson AS, Johnson RP, Johnson TJ, Johnson WN, Kamae T, Katagiri H, Kataoka J, Kawai N, Kerr M, Knödlseder J, Kocian ML, Kuehn F, Kuss M, Lande J, Latronico L, Lemoine-Goumard M, Longo F, Loparco F, Lott B, Lovellette MN, Lubrano P, Madejski GM, Makeev A, Mazziotta MN, McConville W, McEnery JE, Meurer C, Michelson PF, Mitthumsiri W, Mizuno T, Moiseev AA, Monte C, Monzani ME, Morselli A, Moskalenko IV, Murgia S, Nolan PL, Norris JP, Nuss E, Ohsugi T, Omodei N, Orlando E, Ormes JF, Paneque D, Panetta JH, Parent D, Pelassa V, Pepe M, Pesce-Rollins M, Piron F, Porter TA, Rainò S, Rando R, Razzano M, Reimer A, Reimer O, Reposeur T, Ritz S, Rochester LS, Rodriguez AY, Roth M, Ryde F, Sadrozinski HFW, Sanchez D, Sander A, Saz Parkinson PM, Scargle JD, Sellerholm A, Sgrò C, Shaw MS, Siskind EJ, Smith DA, Smith PD, Spandre G, Spinelli P, Starck JL, Strickman MS, Strong AW, Suson DJ, Tajima H, Takahashi H, Takahashi T, Tanaka T, Thayer JB, Thayer JG, Thompson DJ, Tibaldo L, Torres DF, Tosti G, Tramacere A, Uchiyama Y, Usher TL, Vasileiou V, Vilchez N, Vitale V, Waite AP, Wang P, Winer BL, Wood KS, Ylinen T, Ziegler M. Spectrum of the isotropic diffuse gamma-ray emission derived from first-year Fermi Large Area Telescope data. Phys Rev Lett 2010; 104:101101. [PMID: 20366411 DOI: 10.1103/physrevlett.104.101101] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Indexed: 05/29/2023]
Abstract
We report on the first Fermi Large Area Telescope (LAT) measurements of the so-called "extragalactic" diffuse gamma-ray emission (EGB). This component of the diffuse gamma-ray emission is generally considered to have an isotropic or nearly isotropic distribution on the sky with diverse contributions discussed in the literature. The derivation of the EGB is based on detailed modeling of the bright foreground diffuse Galactic gamma-ray emission, the detected LAT sources, and the solar gamma-ray emission. We find the spectrum of the EGB is consistent with a power law with a differential spectral index gamma = 2.41 +/- 0.05 and intensity I(>100 MeV) = (1.03 +/- 0.17) x 10(-5) cm(-2) s(-1) sr(-1), where the error is systematics dominated. Our EGB spectrum is featureless, less intense, and softer than that derived from EGRET data.
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Affiliation(s)
- A A Abdo
- Space Science Division, Naval Research Laboratory, Washington, D.C. 20375, USA
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Abdo AA, Ackermann M, Ajello M, Atwood WB, Baldini L, Ballet J, Barbiellini G, Bastieri D, Bechtol K, Bellazzini R, Berenji B, Bloom ED, Bonamente E, Borgland AW, Bouvier A, Bregeon J, Brez A, Brigida M, Bruel P, Burnett TH, Buson S, Caliandro GA, Cameron RA, Caraveo PA, Carrigan S, Casandjian JM, Cecchi C, Celik O, Chekhtman A, Chiang J, Ciprini S, Claus R, Cohen-Tanugi J, Conrad J, Dermer CD, de Angelis A, de Palma F, Digel SW, do Couto E Silva E, Drell PS, Drlica-Wagner A, Dubois R, Dumora D, Edmonds Y, Essig R, Farnier C, Favuzzi C, Fegan SJ, Focke WB, Fortin P, Frailis M, Fukazawa Y, Funk S, Fusco P, Gargano F, Gasparrini D, Gehrels N, Germani S, Giglietto N, Giordano F, Glanzman T, Godfrey G, Grenier IA, Grove JE, Guillemot L, Guiriec S, Gustafsson M, Hadasch D, Harding AK, Horan D, Hughes RE, Jackson MS, Jóhannesson G, Johnson AS, Johnson RP, Johnson WN, Kamae T, Katagiri H, Kataoka J, Kawai N, Kerr M, Knödlseder J, Kuss M, Lande J, Latronico L, Llena Garde M, Longo F, Loparco F, Lott B, Lovellette MN, Lubrano P, Makeev A, Mazziotta MN, McEnery JE, Meurer C, Michelson PF, Mitthumsiri W, Mizuno T, Moiseev AA, Monte C, Monzani ME, Morselli A, Moskalenko IV, Murgia S, Nolan PL, Norris JP, Nuss E, Ohsugi T, Omodei N, Orlando E, Ormes JF, Ozaki M, Paneque D, Panetta JH, Parent D, Pelassa V, Pepe M, Pesce-Rollins M, Piron F, Rainò S, Rando R, Razzano M, Reimer A, Reimer O, Reposeur T, Ripken J, Ritz S, Rodriguez AY, Roth M, Sadrozinski HFW, Sander A, Parkinson PMS, Scargle JD, Schalk TL, Sellerholm A, Sgrò C, Siskind EJ, Smith DA, Smith PD, Spandre G, Spinelli P, Starck JL, Strickman MS, Suson DJ, Tajima H, Takahashi H, Tanaka T, Thayer JB, Thayer JG, Tibaldo L, Torres DF, Uchiyama Y, Usher TL, Vasileiou V, Vilchez N, Vitale V, Waite AP, Wang P, Winer BL, Wood KS, Ylinen T, Ziegler M. Fermi large area telescope search for photon lines from 30 to 200 GeV and dark matter implications. Phys Rev Lett 2010; 104:091302. [PMID: 20366979 DOI: 10.1103/physrevlett.104.091302] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Indexed: 05/29/2023]
Abstract
Dark matter (DM) particle annihilation or decay can produce monochromatic gamma rays readily distinguishable from astrophysical sources. gamma-ray line limits from 30 to 200 GeV obtained from 11 months of Fermi Large Area Space Telescope data from 20-300 GeV are presented using a selection based on requirements for a gamma-ray line analysis, and integrated over most of the sky. We obtain gamma-ray line flux upper limits in the range 0.6-4.5x10{-9} cm{-2} s{-1}, and give corresponding DM annihilation cross-section and decay lifetime limits. Theoretical implications are briefly discussed.
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Affiliation(s)
- A A Abdo
- Space Science Division, Naval Research Laboratory, Washington, DC 20375, USA
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Abstract
BACKGROUND Pathogenic HIV and SIV infections characteristically deplete central memory CD4(+) T cells and induce chronic immune activation, but it is controversial whether this also occurs after vaccination with attenuated SIVs and whether depletion or activation of CD4(+) T-cell play roles in protection against wild-type virus challenge. METHODS Rhesus macaques were vaccinated with SIVmac239Deltanef and quantitative and phenotypic polychromatic flow cytometry analyses were performed on mononuclear cells from blood, lymph nodes and rectal biopsies. RESULTS Animals vaccinated with SIVmac239Deltanef demonstrated no loss of CD4(+) T cells in any tissue, and in fact CCR5(+) and CD28(+)CD95(+) central memory CD4(+) T cells were significantly increased. In contrast, CD4(+) T-cell numbers and CCR5 expression significantly declined in unvaccinated controls challenged with SIVmac239. Also, intracellular Ki67 increased acutely as much as 3-fold over baseline in all tissues after SIVmac239Deltanef vaccination then declined following primary infection. CONCLUSION We demonstrated in this study that SIVmac239Deltanef vaccination did not deplete CD4(+) T cells but transiently activated and expanded the memory cell population. However, increases in numbers and activation of memory CD4(+) T cells did not appear to influence protective immunity.
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Affiliation(s)
- R K Reeves
- Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, MA 01772-9102, USA
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Abdo AA, Ackermann M, Ajello M, Anderson B, Atwood WB, Axelsson M, Baldini L, Ballet J, Barbiellini G, Bastieri D, Baughman BM, Bechtol K, Bellazzini R, Berenji B, Blandford RD, Bloom ED, Bonamente E, Borgland AW, Bregeon J, Brez A, Brigida M, Bruel P, Burnett TH, Caliandro GA, Cameron RA, Caraveo PA, Casandjian JM, Cecchi C, Charles E, Chekhtman A, Cheung CC, Chiang J, Ciprini S, Claus R, Cohen-Tanugi J, Conrad J, Dereli H, Dermer CD, de Angelis A, de Palma F, Digel SW, Di Bernardo G, Dormody M, do Couto e Silva E, Drell PS, Dubois R, Dumora D, Edmonds Y, Farnier C, Favuzzi C, Fegan SJ, Focke WB, Frailis M, Fukazawa Y, Funk S, Fusco P, Gaggero D, Gargano F, Gehrels N, Germani S, Giebels B, Giglietto N, Giordano F, Glanzman T, Godfrey G, Grenier IA, Grondin MH, Grove JE, Guillemot L, Guiriec S, Hanabata Y, Harding AK, Hayashida M, Hays E, Hughes RE, Jóhannesson G, Johnson AS, Johnson RP, Johnson TJ, Johnson WN, Kamae T, Katagiri H, Kataoka J, Kawai N, Kerr M, Knödlseder J, Kocian ML, Kuehn F, Kuss M, Lande J, Latronico L, Longo F, Loparco F, Lott B, Lovellette MN, Lubrano P, Madejski GM, Makeev A, Mazziotta MN, McConville W, McEnery JE, Meurer C, Michelson PF, Mitthumsiri W, Mizuno T, Moiseev AA, Monte C, Monzani ME, Morselli A, Moskalenko IV, Murgia S, Nolan PL, Nuss E, Ohsugi T, Okumura A, Omodei N, Orlando E, Ormes JF, Paneque D, Panetta JH, Parent D, Pelassa V, Pepe M, Pesce-Rollins M, Piron F, Porter TA, Rainò S, Rando R, Razzano M, Reimer A, Reimer O, Reposeur T, Ritz S, Rodriguez AY, Roth M, Ryde F, Sadrozinski HFW, Sanchez D, Sander A, Saz Parkinson PM, Scargle JD, Sellerholm A, Sgrò C, Smith DA, Smith PD, Spandre G, Spinelli P, Starck JL, Stecker FW, Striani E, Strickman MS, Strong AW, Suson DJ, Tajima H, Takahashi H, Tanaka T, Thayer JB, Thayer JG, Thompson DJ, Tibaldo L, Torres DF, Tosti G, Tramacere A, Uchiyama Y, Usher TL, Vasileiou V, Vilchez N, Vitale V, Waite AP, Wang P, Winer BL, Wood KS, Ylinen T, Ziegler M. Fermi large area telescope measurements of the diffuse gamma-ray emission at intermediate galactic latitudes. Phys Rev Lett 2009; 103:251101. [PMID: 20366246 DOI: 10.1103/physrevlett.103.251101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Indexed: 05/29/2023]
Abstract
The diffuse galactic gamma-ray emission is produced by cosmic rays (CRs) interacting with the interstellar gas and radiation field. Measurements by the Energetic Gamma-Ray Experiment Telescope (EGRET) instrument on the Compton Gamma-Ray Observatory indicated excess gamma-ray emission greater, > or approximately equal to 1 GeV relative to diffuse galactic gamma-ray emission models consistent with directly measured CR spectra (the so-called "EGRET GeV excess"). The Large Area Telescope (LAT) instrument on the Fermi Gamma-Ray Space Telescope has measured the diffuse gamma-ray emission with improved sensitivity and resolution compared to EGRET. We report on LAT measurements for energies 100 MeV to 10 GeV and galactic latitudes 10 degrees < or = |b| < or = 20 degrees. The LAT spectrum for this region of the sky is well reproduced by a diffuse galactic gamma-ray emission model that is consistent with local CR spectra and inconsistent with the EGRET GeV excess.
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Affiliation(s)
- A A Abdo
- Space Science Division, Naval Research Laboratory, Washington, DC 20375, USA
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Abdo AA, Ackermann M, Ajello M, Atwood WB, Axelsson M, Baldini L, Ballet J, Barbiellini G, Bastieri D, Baughman BM, Bechtol K, Bellazzini R, Berenji B, Blandford RD, Bloom ED, Bonamente E, Borgland AW, Bregeon J, Brez A, Brigida M, Bruel P, Burnett TH, Caliandro GA, Cameron RA, Caraveo PA, Casandjian JM, Cecchi C, Celik O, Charles E, Chaty S, Chekhtman A, Cheung CC, Chiang J, Ciprini S, Claus R, Cohen-Tanugi J, Conrad J, Cutini S, Dermer CD, de Palma F, Digel SW, Dormody M, do Couto e Silva E, Drell PS, Dubois R, Dumora D, Farnier C, Favuzzi C, Fegan SJ, Focke WB, Frailis M, Fukazawa Y, Fusco P, Gargano F, Gasparrini D, Gehrels N, Germani S, Giebels B, Giglietto N, Giordano F, Glanzman T, Godfrey G, Grenier IA, Grove JE, Guillemot L, Guiriec S, Hanabata Y, Harding AK, Hayashida M, Hays E, Horan D, Hughes RE, Jóhannesson G, Johnson AS, Johnson RP, Johnson TJ, Johnson WN, Kamae T, Katagiri H, Kawai N, Kerr M, Knödlseder J, Kuehn F, Kuss M, Lande J, Latronico L, Lemoine-Goumard M, Longo F, Loparco F, Lott B, Lovellette MN, Lubrano P, Makeev A, Mazziotta MN, McConville W, McEnery JE, Meurer C, Michelson PF, Mitthumsiri W, Mizuno T, Moiseev AA, Monte C, Monzani ME, Morselli A, Moskalenko IV, Murgia S, Nolan PL, Norris JP, Nuss E, Ohsugi T, Omodei N, Orlando E, Ormes JF, Paneque D, Panetta JH, Parent D, Pelassa V, Pepe M, Pierbattista M, Piron F, Porter TA, Rainò S, Rando R, Razzano M, Rea N, Reimer A, Reimer O, Reposeur T, Ritz S, Rochester LS, Rodriguez AY, Romani RW, Roth M, Ryde F, Sadrozinski HFW, Sanchez D, Sander A, Saz Parkinson PM, Sgrò C, Smith DA, Smith PD, Spandre G, Spinelli P, Starck JL, Strickman MS, Suson DJ, Tajima H, Takahashi H, Tanaka T, Thayer JB, Thayer JG, Thompson DJ, Tibaldo L, Torres DF, Tosti G, Tramacere A, Uchiyama Y, Usher TL, Vasileiou V, Vilchez N, Vitale V, Wang P, Webb N, Winer BL, Wood KS, Ylinen T, Ziegler M. Detection of high-energy gamma-ray emission from the globular cluster 47 Tucanae with Fermi. Science 2009; 325:845-8. [PMID: 19679807 DOI: 10.1126/science.1177023] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We report the detection of gamma-ray emissions above 200 megaelectron volts at a significance level of 17sigma from the globular cluster 47 Tucanae, using data obtained with the Large Area Telescope onboard the Fermi Gamma-ray Space Telescope. Globular clusters are expected to emit gamma rays because of the large populations of millisecond pulsars that they contain. The spectral shape of 47 Tucanae is consistent with gamma-ray emission from a population of millisecond pulsars. The observed gamma-ray luminosity implies an upper limit of 60 millisecond pulsars present in 47 Tucanae.
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Affiliation(s)
- A A Abdo
- Space Science Division, Naval Research Laboratory, Washington, DC 20375, USA
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Henig A, Kiefer D, Markey K, Gautier DC, Flippo KA, Letzring S, Johnson RP, Shimada T, Yin L, Albright BJ, Bowers KJ, Fernández JC, Rykovanov SG, Wu HC, Zepf M, Jung D, Liechtenstein VK, Schreiber J, Habs D, Hegelich BM. Enhanced laser-driven ion acceleration in the relativistic transparency regime. Phys Rev Lett 2009; 103:045002. [PMID: 19659362 DOI: 10.1103/physrevlett.103.045002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2009] [Indexed: 05/28/2023]
Abstract
We report on the acceleration of ion beams from ultrathin diamondlike carbon foils of thickness 50, 30, and 10 nm irradiated by ultrahigh contrast laser pulses at intensities of approximately 7 x 10;{19} W/cm;{2}. An unprecedented maximum energy of 185 MeV (15 MeV/u) for fully ionized carbon atoms is observed at the optimum thickness of 30 nm. The enhanced acceleration is attributed to self-induced transparency, leading to strong volumetric heating of the classically overdense electron population in the bulk of the target. Our experimental results are supported by both particle-in-cell (PIC) simulations and an analytical model.
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Affiliation(s)
- A Henig
- Max-Planck-Institut für Quantenoptik, Garching, Germany.
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Abdo AA, Ackermann M, Ajello M, Anderson B, Atwood WB, Axelsson M, Baldini L, Ballet J, Barbiellini G, Baring MG, Bastieri D, Baughman BM, Bechtol K, Bellazzini R, Berenji B, Bignami GF, Blandford RD, Bloom ED, Bonamente E, Borgland AW, Bregeon J, Brez A, Brigida M, Bruel P, Burnett TH, Caliandro GA, Cameron RA, Caraveo PA, Casandjian JM, Cecchi C, Celik O, Chekhtman A, Cheung CC, Chiang J, Ciprini S, Claus R, Cohen-Tanugi J, Conrad J, Cutini S, Dermer CD, de Angelis A, de Luca A, de Palma F, Digel SW, Dormody M, do Couto e Silva E, Drell PS, Dubois R, Dumora D, Farnier C, Favuzzi C, Fegan SJ, Fukazawa Y, Funk S, Fusco P, Gargano F, Gasparrini D, Gehrels N, Germani S, Giebels B, Giglietto N, Giommi P, Giordano F, Glanzman T, Godfrey G, Grenier IA, Grondin MH, Grove JE, Guillemot L, Guiriec S, Gwon C, Hanabata Y, Harding AK, Hayashida M, Hays E, Hughes RE, Jóhannesson G, Johnson RP, Johnson TJ, Johnson WN, Kamae T, Katagiri H, Kataoka J, Kawai N, Kerr M, Knödlseder J, Kocian ML, Kuss M, Lande J, Latronico L, Lemoine-Goumard M, Longo F, Loparco F, Lott B, Lovellette MN, Lubrano P, Madejski GM, Makeev A, Marelli M, Mazziotta MN, McConville W, McEnery JE, Meurer C, Michelson PF, Mitthumsiri W, Mizuno T, Monte C, Monzani ME, Morselli A, Moskalenko IV, Murgia S, Nolan PL, Norris JP, Nuss E, Ohsugi T, Omodei N, Orlando E, Ormes JF, Paneque D, Parent D, Pelassa V, Pepe M, Pesce-Rollins M, Pierbattista M, Piron F, Porter TA, Primack JR, Rainò S, Rando R, Ray PS, Razzano M, Rea N, Reimer A, Reimer O, Reposeur T, Ritz S, Rochester LS, Rodriguez AY, Romani RW, Ryde F, Sadrozinski HFW, Sanchez D, Sander A, Saz Parkinson PM, Scargle JD, Sgrò C, Siskind EJ, Smith DA, Smith PD, Spandre G, Spinelli P, Starck JL, Strickman MS, Suson DJ, Tajima H, Takahashi H, Takahashi T, Tanaka T, Thayer JG, Thompson DJ, Tibaldo L, Tibolla O, Torres DF, Tosti G, Tramacere A, Uchiyama Y, Usher TL, Van Etten A, Vasileiou V, Vilchez N, Vitale V, Waite AP, Wang P, Watters K, Winer BL, Wolff MT, Wood KS, Ylinen T, Ziegler M. Detection of 16 gamma-ray pulsars through blind frequency searches using the Fermi LAT. Science 2009; 325:840-4. [PMID: 19574346 DOI: 10.1126/science.1175558] [Citation(s) in RCA: 237] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Pulsars are rapidly rotating, highly magnetized neutron stars emitting radiation across the electromagnetic spectrum. Although there are more than 1800 known radio pulsars, until recently only seven were observed to pulse in gamma rays, and these were all discovered at other wavelengths. The Fermi Large Area Telescope (LAT) makes it possible to pinpoint neutron stars through their gamma-ray pulsations. We report the detection of 16 gamma-ray pulsars in blind frequency searches using the LAT. Most of these pulsars are coincident with previously unidentified gamma-ray sources, and many are associated with supernova remnants. Direct detection of gamma-ray pulsars enables studies of emission mechanisms, population statistics, and the energetics of pulsar wind nebulae and supernova remnants.
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Affiliation(s)
- A A Abdo
- Space Science Division, Naval Research Laboratory, Washington, DC 20375, USA
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Bach SJ, Johnson RP, Stanford K, McAllister TA. Bacteriophages reduce Escherichia coli O157:H7 levels in experimentally inoculated sheep. Can J Anim Sci 2009. [DOI: 10.4141/cjas08083] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacteriophage biocontrol has potential as a means of mitigating the prevalence of Escherichia coli O157:H7 in ruminants. The efficacy of oral administration of bacteriophages for reducing fecal shedding of E. coli O157:H7 by sheep was evaluated using 20 Canadian Arcott rams (50.0 ± 3.0) housed in four rooms (n = 5) in a contained facility. The rams had ad libitum access to drinking water and a pelleted barley-based total mixed ration, delivered once daily. Experimental treatments consisted of administration of E. coli O157:H7 (O157), E. coli O157:H7+bacteriophages (O157+phage), bacteriophages (phage), and control (CON). Oral inoculation of the rams with 109 CFU of a mixture of four nalidixic acid-resistant strains of E. coli O157:H7 was performed on day 0. A mixture of 1010 PFU of bacteriophages P5, P8 and P11 was administered on days -2, -1, 0, 6 and 7. Fecal samples collected on 14 occasions over 21 d were analyzed for E. coli O157:H7, total E. coli, total coliforms and bacteriophages. Sheep in treatment O157+phage shed fewer (P < 0.05) E. coli O157:H7 than did sheep in treatment O157. Populations of total coliforms and total E. coli were similar (P < 0.05) among treatments, implying that bacteriophage lysis of non-target E. coli and coliform bacteria in the gastrointestinal tract did not occur. Bacteriophage numbers declined rapidly over 21 d, which likely reduced the chance of collision between bacteria and bacteriophage. Oral administration of bacteriophages reduced shedding of E. coli O157:H7 by sheep, but a delivery system that would protect bacteriophages during passage through the intestine may increase the effectiveness of this strategy as well as allow phage to be administered in the feed.Key words: Escherichia coli O157:H7, bacteriophage, sheep, environment, coliforms
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