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Xu J, Bai X, Zhang X, Yuan B, Lin L, Guo Y, Cui Y, Liu J, Cui H, Ren X, Wang J, Yuan Y. Development and application of DETECTR-based rapid detection for pathogenic Bacillusanthracis. Anal Chim Acta 2023; 1247:340891. [PMID: 36781250 DOI: 10.1016/j.aca.2023.340891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/02/2023]
Abstract
Bacillus anthracis (B. anthracis) is a gram-positive bacterium responsible for the acute disease anthrax. Rapid and reliable identification of pathogenic B. anthracis is important in the detection of natural infectious disease cases or bio-threats. Herein, a DNA endonuclease targeted CRISPR trans reporter (DETECTR) detection platform based on recombinase polymerase amplification (RPA) was studied. The DETECTR system targeted three sequences from B. anthracis (the BA_5345 chromosomal specific marker, the protective antigen gene pag A from pXO1 plasmid and the capsule-biosynthesis-related gene cap A from pXO2 plasmid). We developed a rapid (<40 min), easy-to-implement and accurate identification method for of B. anthracis nucleic acid with near two-copies sensitivity. The combination of tripartite primer sets is effective for the reliable identification of B. anthracis but also for fast screening of pathogenic strains. More importantly, DETECTR correctly detected simulated clinical blood samples and firstly detected positive samples collected from the location of world War-II site, preserved at north-east China (45°36'55.940″ N, 126°38'33.738″ E) with high sensitivity and specificity. Our study provides insight into the DETECTR-based detection of B. anthracis. We present a novel screening and diagnostic option for pathogenic B. anthracis that can be performed on a user-friendly portable device. Based on its proven reliability, sensitivity, specificity and simplicity, our proposed method can be readily adapted to detect pathogenic B. anthracis, anthrax and biothreats.
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Affiliation(s)
- Jianhao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Xinru Bai
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Lei Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Jinxiong Liu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Hongyu Cui
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Xiangang Ren
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
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Bacilli in the International Space Station. Microorganisms 2022; 10:microorganisms10122309. [PMID: 36557562 PMCID: PMC9782108 DOI: 10.3390/microorganisms10122309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Astronauts remote from Earth, not least those who will inhabit the Moon or Mars, are vulnerable to disease due to their reduced immunity, isolation from clinical support, and the disconnect from any buffering capacity provided by the Earth. Here, we explore potential risks for astronaut health, focusing on key aspects of the biology of Bacillus anthracis and other anthrax-like bacilli. We examine aspects of Bacillus cereus group genetics in relation to their evolutionary biology and pathogenicity; a new clade of the Bacillus cereus group, close related to B. anthracis, has colonized the International Space Station (ISS), is still present, and could in theory at least acquire pathogenic plasmids from the other B. cereus group strains. The main finding is that the genomic sequence alignments of the B. cereus group ISS strains revealed a high sequence identity, indicating they originated from the same strain and that a close look to the genetic variations among the strains suggesting they lived, or they are living, in a vegetative form in the ISS enough time to accumulate genetic variations unique for each single strains.
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Ochai SO, Crafford JE, Hassim A, Byaruhanga C, Huang YH, Hartmann A, Dekker EH, van Schalkwyk OL, Kamath PL, Turner WC, van Heerden H. Immunological Evidence of Variation in Exposure and Immune Response to Bacillus anthracis in Herbivores of Kruger and Etosha National Parks. Front Immunol 2022; 13:814031. [PMID: 35237267 PMCID: PMC8882864 DOI: 10.3389/fimmu.2022.814031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Exposure and immunity to generalist pathogens differ among host species and vary across spatial scales. Anthrax, caused by a multi-host bacterial pathogen, Bacillus anthracis, is enzootic in Kruger National Park (KNP), South Africa and Etosha National Park (ENP), Namibia. These parks share many of the same potential host species, yet the main anthrax host in one (greater kudu (Tragelaphus strepsiceros) in KNP and plains zebra (Equus quagga) in ENP) is only a minor host in the other. We investigated species and spatial patterns in anthrax mortalities, B. anthracis exposure, and the ability to neutralize the anthrax lethal toxin to determine if observed host mortality differences between locations could be attributed to population-level variation in pathogen exposure and/or immune response. Using serum collected from zebra and kudu in high and low incidence areas of each park (18- 20 samples/species/area), we estimated pathogen exposure from anti-protective antigen (PA) antibody response using enzyme-linked immunosorbent assay (ELISA) and lethal toxin neutralization with a toxin neutralization assay (TNA). Serological evidence of pathogen exposure followed mortality patterns within each system (kudus: 95% positive in KNP versus 40% in ENP; zebras: 83% positive in ENP versus 63% in KNP). Animals in the high-incidence area of KNP had higher anti-PA responses than those in the low-incidence area, but there were no significant differences in exposure by area within ENP. Toxin neutralizing ability was higher for host populations with lower exposure prevalence, i.e., higher in ENP kudus and KNP zebras than their conspecifics in the other park. These results indicate that host species differ in their exposure to and adaptive immunity against B. anthracis in the two parks. These patterns may be due to environmental differences such as vegetation, rainfall patterns, landscape or forage availability between these systems and their interplay with host behavior (foraging or other risky behaviors), resulting in differences in exposure frequency and dose, and hence immune response.
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Affiliation(s)
- Sunday O. Ochai
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Jan E. Crafford
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Charles Byaruhanga
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Yen-Hua Huang
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, United States
| | - Axel Hartmann
- Etosha Ecological Institute, Ministry of Environment, Forestry and Tourism, Okaukuejo, Namibia
| | - Edgar H. Dekker
- Office of the State Veterinarian, Department of Agriculture, Forestry and Fisheries, Government of South Africa, Skukuza, South Africa
| | - O. Louis van Schalkwyk
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
- Office of the State Veterinarian, Department of Agriculture, Forestry and Fisheries, Government of South Africa, Skukuza, South Africa
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, United States
| | - Wendy C. Turner
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, United States
| | - Henriette van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
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Jelinkova P, Hrdy J, Markova J, Dresler J, Pajer P, Pavlis O, Branich P, Borilova G, Reichelova M, Babak V, Reslova N, Kralik P. Development and Inter-Laboratory Validation of Diagnostics Panel for Detection of Biothreat Bacteria Based on MOL-PCR Assay. Microorganisms 2020; 9:microorganisms9010038. [PMID: 33374468 PMCID: PMC7823616 DOI: 10.3390/microorganisms9010038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Early detection of biohazardous bacteria that can be misused as biological weapons is one of the most important measures to prevent the spread and outbreak of biological warfare. For this reason, many instrument platforms need to be introduced into operation in the field of biological warfare detection. Therefore the purpose of this study is to establish a new detection panel for biothreat bacteria (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella spp.) and confirm it by collaborative validation by using a multiplex oligonucleotide ligation followed by polymerase chain reaction and hybridization to microspheres by MagPix detection platform (MOL-PCR). Appropriate specific sequences in bacterial DNA were selected and tested to assemble the detection panel, and MOLigo probes (short specific oligonucleotides) were designed to show no cross-reactivity when tested between bacteria and to decrease the background signal measurement on the MagPix platform. During testing, sensitivity was assessed for all target bacteria using serially diluted DNA and was determined to be at least 0.5 ng/µL. For use as a diagnostic kit and easier handling, the storage stability of ligation premixes (MOLigo probe mixes) was tested. This highly multiplex method can be used for rapid screening to prevent outbreaks arising from the use of bacterial strains for bioterrorism, because time of analysis take under 4 h.
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Affiliation(s)
- Pavlina Jelinkova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
- Correspondence:
| | - Jakub Hrdy
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jirina Markova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
| | - Jiri Dresler
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic; (J.D.); (P.P.); (O.P.)
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic; (J.D.); (P.P.); (O.P.)
| | - Oto Pavlis
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic; (J.D.); (P.P.); (O.P.)
| | - Pavel Branich
- Military Veterinary Institute, Opavska 29, 748 01 Hlucin, Czech Republic;
| | - Gabriela Borilova
- Department of Meat Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; (G.B.); (P.K.)
| | - Marketa Reichelova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
- Collection of Animal Pathogenic Microorganisms, Department of Bacteriology, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - Vladimir Babak
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
| | - Nikol Reslova
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic;
| | - Petr Kralik
- Department of Meat Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; (G.B.); (P.K.)
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DiEuliis D, Ellington AD, Gronvall GK, Imperiale MJ. Does Biotechnology Pose New Catastrophic Risks? Curr Top Microbiol Immunol 2019; 424:107-119. [PMID: 31463535 DOI: 10.1007/82_2019_177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Advances in biotechnology in the twenty-first century, fueled in large part by the field of synthetic biology, have greatly accelerated capabilities to manipulate and re-program bacteria, viruses, and other organisms. These genetic engineering capabilities are driving innovation and progress in drug manufacturing, bioremediation, and tissue engineering, as well as biosecurity preparedness. However, biotechnology is largely dual use, holding the potential of misuse for deliberate harm along with positive applications; defenses against those threats need to be anticipated and prepared. This chapter describes the challenges of managing dual-use capabilities enabled by modern biotechnology and synthetic biology and highlights a framework tool developed by a National Academies committee to aid analysis of the security effects of new scientific discoveries and prioritization of concerns. The positive aspects of synthetic biology in preparedness are also detailed, and policy directions are highlighted for taking advantage of the positive aspects of these emerging technologies while minimizing risks.
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Affiliation(s)
| | | | - Gigi Kwik Gronvall
- Johns Hopkins Center for Health Security, Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, USA
| | - Michael J Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, USA.
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Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ. Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. MICROBIOME 2018; 6:197. [PMID: 30396371 PMCID: PMC6219074 DOI: 10.1186/s40168-018-0582-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.
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Affiliation(s)
- Jacquelyn S Meisel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Daniel J Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Brian Brubach
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Victoria Cepeda-Espinoza
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Jessica Chopyk
- School of Public Health, University of Maryland, College Park, College Park, MD, USA
| | - Héctor Corrada-Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Marcus Fedarko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Jay Ghurye
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Kiran Javkar
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Nathan D Olson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nidhi Shah
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Sarah M Allard
- School of Public Health, University of Maryland, College Park, College Park, MD, USA
| | - Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA
| | - Alexis Brown
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - J Gregory Caporaso
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Sean Conlan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Samuel P Forry
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
- CosmosID, Inc., Rockville, MD, USA
| | - Jason Kralj
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Paul M Luethy
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Donald K Milton
- Maryland Institute for Applied Environmental Health, School of Public Health, University of Maryland, College Park, College Park, MD, USA
| | - Brian D Ondov
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Preheim
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | | | - M J Rosovitz
- National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA
| | - Eric G Sakowski
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Daniel D Sommer
- National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA
| | | | - Gherman Uritskiy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sean X Zhang
- Division of Medical Microbiology, Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Todd J Treangen
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
- Present address: Department of Computer Science - MS-132, Rice University, P.O. Box 1892, Houston, TX, 77005-1892, USA.
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Be NA, Avila-Herrera A, Allen JE, Singh N, Checinska Sielaff A, Jaing C, Venkateswaran K. Whole metagenome profiles of particulates collected from the International Space Station. MICROBIOME 2017; 5:81. [PMID: 28716113 PMCID: PMC5514531 DOI: 10.1186/s40168-017-0292-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/27/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized. METHODS This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared. RESULTS Species-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes, it was found that a larger number of relevant gene categories were observed in the ISS relative to the cleanroom. Strain-level cross-sample comparisons were made for Corynebacterium, Bacillus, and Aspergillus showing possible distinctions in the dominant strain between samples. CONCLUSION Species-level analyses demonstrated distinct differences between the ISS and cleanroom samples, indicating that the cleanroom population is not necessarily reflective of space habitation environments. The overall population of viable microorganisms and the functional diversity inherent to this unique closed environment are of critical interest with respect to future space habitation. Observations and studies such as these will be important to evaluating the conditions required for long-term health of human occupants in such environments.
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Affiliation(s)
- Nicholas A Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Aram Avila-Herrera
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jonathan E Allen
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Nitin Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Aleksandra Checinska Sielaff
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
- Present Address: Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Crystal Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station. mSystems 2017; 2:mSystems00021-17. [PMID: 28680972 PMCID: PMC5487513 DOI: 10.1128/msystems.00021-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/23/2017] [Indexed: 12/30/2022] Open
Abstract
The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions. In an ongoing Microbial Observatory investigation of the International Space Station (ISS), 11 Bacillus strains (2 from the Kibo Japanese experimental module, 4 from the U.S. segment, and 5 from the Russian module) were isolated and their whole genomes were sequenced. A comparative analysis of the 16S rRNA gene sequences of these isolates showed the highest similarity (>99%) to the Bacillus anthracis-B. cereus-B. thuringiensis group. The fatty acid composition, polar lipid profile, peptidoglycan type, and matrix-assisted laser desorption ionization–time of flight profiles were consistent with the B. cereus sensu lato group. The phenotypic traits such as motile rods, enterotoxin production, lack of capsule, and resistance to gamma phage/penicillin observed in ISS isolates were not characteristics of B. anthracis. Whole-genome sequence characterizations showed that ISS strains had the plcR non-B. anthracis ancestral “C” allele and lacked anthrax toxin-encoding plasmids pXO1 and pXO2, excluding their identification as B. anthracis. The genetic identities of all 11 ISS isolates characterized via gyrB analyses arbitrarily identified them as members of the B. cereus group, but traditional DNA-DNA hybridization (DDH) showed that the ISS isolates are similar to B. anthracis (88% to 90%) but distant from the B. cereus (42%) and B. thuringiensis (48%) type strains. The DDH results were supported by average nucleotide identity (>98.5%) and digital DDH (>86%) analyses. However, the collective phenotypic traits and genomic evidence were the reasons to exclude the ISS isolates from B. anthracis. Nevertheless, multilocus sequence typing and whole-genome single nucleotide polymorphism analyses placed these isolates in a clade that is distinct from previously described members of the B. cereus sensu lato group but closely related to B. anthracis. IMPORTANCE The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions.
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Kabir MS, Hsieh YH, Simpson S, Kerdahi K, Sulaiman IM. Evaluation of Two Standard and Two Chromogenic Selective Media for Optimal Growth and Enumeration of Isolates of 16 Unique Bacillus Species. J Food Prot 2017; 80:952-962. [PMID: 28467187 DOI: 10.4315/0362-028x.jfp-16-441] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The genus Bacillus is a group of gram-positive endospore-forming bacteria that can cause food poisoning and diarrheal illness in humans. A wide range of food products have been linked to foodborne outbreaks associated with these opportunistic pathogens. The U.S. Food and Drug Administration recommends (in their Bacteriological Analytical Manual) the use of Bacara or mannitol egg yolk polymyxin (MYP) agar plates and the most-probable-number (MPN) method for enumeration and confirmation of Bacillus cereus and related species isolated from foods, sporadic cases, outbreaks, and routine environmental surveillance samples. We performed a comparative analysis of two chromogenic media (Bacara and Brilliance) and two traditional media (MYP and polymyxin egg yolk mannitol bromothymol blue agar [PEMBA]) for the isolation and enumeration of 16 Bacillus species under modified growth conditions that included pH, temperature, and dilution factor. A total of 50 environmental, food, and American Type Culture Collection reference isolates from 16 distinct Bacillus species were evaluated. A food adulteration experiment also was carried out by artificially adulterating two baby food matrices with two isolates each of B. cereus and Bacillus thuringiensis . Our results clearly indicated that chromogenic plating media (Bacara and Brilliance) are better than conventional standard media (MYP and PEMBA) for the detection and enumeration of B. cereus in foods and other official regulatory samples. The comparison of the two chromogenic media also indicated that Brilliance medium to be more efficient and selective for the isolation of Bacillus.
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Affiliation(s)
- M Shahjahan Kabir
- U.S. Food and Drug Administration, Southeast Regional Laboratory, 60 Eight Street, Atlanta, Georgia 30309, USA
| | - Ying-Hsin Hsieh
- U.S. Food and Drug Administration, Southeast Regional Laboratory, 60 Eight Street, Atlanta, Georgia 30309, USA
| | - Steven Simpson
- U.S. Food and Drug Administration, Southeast Regional Laboratory, 60 Eight Street, Atlanta, Georgia 30309, USA
| | - Khalil Kerdahi
- U.S. Food and Drug Administration, Southeast Regional Laboratory, 60 Eight Street, Atlanta, Georgia 30309, USA
| | - Irshad M Sulaiman
- U.S. Food and Drug Administration, Southeast Regional Laboratory, 60 Eight Street, Atlanta, Georgia 30309, USA
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Liu Y, Lai Q, Du J, Shao Z. Genetic diversity and population structure of the Bacillus cereus group bacteria from diverse marine environments. Sci Rep 2017; 7:689. [PMID: 28386130 PMCID: PMC5429728 DOI: 10.1038/s41598-017-00817-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/20/2017] [Indexed: 11/25/2022] Open
Abstract
The phylogenetic diversity of marine bacteria belonged to the Bacillus cereus group has not been well investigated. Here, we present the genetic diversity and population structure of 71 bacteria from diverse marine environments, using a multilocus sequence typing (MLST) approach and the analyses of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) based on some representative genomic sequences. The MLST analysis demonstrated that these isolates were highly diverse and a wide distribution in marine environments and some of them showed niche specificity to some extent. They were assigned to 27 sequence types (STs) with 23 novel STs. Phylogenetic analysis of 82 bacteria containing 11 type strains based on MLST discriminated them as 20 clusters including 10 new ones. Both the dDDH and ANI results supported the proposition that each of 20 clusters represented one independent species, including 10 putative novel species. Values of 98.3% of MLST similarity and 96.2% of ANI were proposed as the standard for the species definition of this group. In summary, the first insight into the phylogenetic diversity of the group bacteria from marine environments will contribute to better understanding of their ecological role and evolution in contrast with terrestrial environments.
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Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China.
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Jończyk-Matysiak E, Kłak M, Weber-Dąbrowska B, Borysowski J, Górski A. Possible use of bacteriophages active against Bacillus anthracis and other B. cereus group members in the face of a bioterrorism threat. BIOMED RESEARCH INTERNATIONAL 2014; 2014:735413. [PMID: 25247187 PMCID: PMC4163355 DOI: 10.1155/2014/735413] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/25/2014] [Accepted: 07/25/2014] [Indexed: 12/14/2022]
Abstract
Anthrax is an infectious fatal disease with epidemic potential. Nowadays, bioterrorism using Bacillus anthracis is a real possibility, and thus society needs an effective weapon to neutralize this threat. The pathogen may be easily transmitted to human populations. It is easy to store, transport, and disseminate and may survive for many decades. Recent data strongly support the effectiveness of bacteriophage in treating bacterial diseases. Moreover, it is clear that bacteriophages should be considered a potential incapacitative agent against bioterrorism using bacteria belonging to B. cereus group, especially B. anthracis. Therefore, we have reviewed the possibility of using bacteriophages active against Bacillus anthracis and other species of the B. cereus group in the face of a bioterrorism threat.
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Affiliation(s)
- Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Marlena Kłak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, The Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Department of Clinical Immunology, Transplantation Institute, The Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland
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