DOCSLIB.ORG

A Major-Capsid-Protein-Based Multiplex PCR Assay for Rapid

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Major-Capsid-Protein-Based Multiplex PCR Assay for Rapid Archives of Virology (2019) 164:819–830 https://doi.org/10.1007/s00705-019-04148-6 ORIGINAL ARTICLE A major‑capsid‑protein‑based multiplex PCR assay for rapid identifcation of selected virulent bacteriophage types Yannick Born1 · Leandra E. Knecht1,2 · Mirjam Eigenmann1 · Michel Bolliger1 · Jochen Klumpp2 · Lars Fieseler1 Received: 27 September 2018 / Accepted: 14 December 2018 / Published online: 23 January 2019 © The Author(s) 2019 Abstract Bacteriophages represent a promising alternative for controlling pathogenic bacteria. They are ubiquitous in the environment, and their isolation is usually simple and fast. However, not every phage is suitable for biocontrol applications. It must be virulent (i.e., strictly lytic), non-transducing, and safe. We have developed a method for identifying selected types of virulent phages at an early stage of the isolation process to simplify the search for suitable candidates. Using the major capsid pro- tein (MCP) as a phylogenetic marker, we designed degenerate primers for the identifcation of Felix O1-, GJ1-, N4-, SP6-, T4-, T7-, and Vi1-like phages in multiplex PCR setups with single phage plaques as templates. Performance of the MCP PCR assay was evaluated with a set of 26 well-characterized phages. Neither false-positive nor false-negative results were obtained. In addition, 154 phages from enrichment cultures from various environmental samples were subjected to MCP PCR analysis. Eight of them, specifc for Salmonella enterica, Escherichia coli, or Erwinia amylovora, belonged to one of the selected phage types. Their PCR-based identifcation was successfully confrmed by pulsed-feld gel electrophoresis of the phage genomes, electron microscopy, and sequencing of the amplifed mcp gene fragment. The MCP PCR assay was shown to be a simple method for preliminary assignment of new phages to a certain group and thus to identify candidates for biocontrol immediately after their isolation. Given that sufcient sequence data are available, this method can be extended to any phage group of interest. Introduction for application as a biocontrol agent. In general, biocontrol phages need to be virulent (i.e., strictly lytic) and non-trans- Bacteriophages (phages) are viruses that infect only bacte- ducing, and they should not carry genes known to encode ria. Due to the rise of antibiotic resistance in many relevant toxins. They also must be stable during storage and appli- bacterial pathogens, interest in phage research is steadily cation. Finally, they need to be propagatable to high titers increasing. Because of their unique properties, phages are on non-pathogenic production strains [2]. Phage biocontrol promising alternatives for the control of bacteria. The major has been successfully applied in food pre- and postharvest advantage is their host specifcity, which enables a targeted to control the major foodborne pathogens Salmonella enter- treatment of a pathogen. In addition, phages are self-lim- ica, shiga-toxin-producing E. coli (STEC), Campylobacter iting and natural [1]. However, not every phage is suited jejuni, Listeria monocytogenes, and Staphylococcus aureus [2]. Likewise, phages have been used to control plant infec- tions caused by Xanthomonas spp. or Erwinia amylovora Handling Editor: Tim Skern. [3], and they have been applied in aquaculture to treat bacte- Electronic supplementary material The online version of this rial infections of fsh and shellfsh [4]. article (https ://doi.org/10.1007/s0070 5-019-04148 -6) contains The total number of phages on Earth is enormous and supplementary material, which is available to authorized users. exceeds an estimated 1031 virions [5, 6]. Given this vast * Lars Fieseler number, it is likely that there is a phage specifc for any [email protected] host that meets all the demands on a biocontrol phage. In general, phages can be easily isolated from environmental 1 Institute of Food and Beverage Innovation, Zurich University samples. Protocols for isolation of tailed phages (members of Applied Sciences, 8820 Wädenswil, Switzerland of the order Caudovirales) typically involve an enrichment 2 Institute of Food, Nutrition and Health, ETH Zurich, Zurich, step followed by plating using the soft-agar overlay method Switzerland Vol.:(0123456789)1 3 820 Y. Born et al. [7, 8]. Standard enrichments are usually performed with a the virulent Vi1-like phages share a myovirus morphology, single bacterial strain, while protocols adjusted towards iso- with genomes of ca. 155-160 kb in size, and they belong to lation of polyvalent phages include sequential enrichment the new family Ackermannviridae [28, 29]. The Vi1-like with several host strains [7, 9]. Both methods normally yield phage LIMEstone1 has been shown to signifcantly reduce numerous isolates. However, the subsequent characterization the incidence and severity of soft rot on potato tubers caused of all isolates to avoid redundancy and to identify virulent by Dickeya solani [30]. Likewise, contamination with E. coli candidates is time consuming and laborious. O157:H7 on various foods has been shown to be reduced The increase in the number of completely sequenced by EcoShield™, a commercial product composed of three phage genomes in the past years has enabled comparisons phages, one of which (ECML-4) is a member of the genus of whole genome sequences, which has revealed evolution- Vi1virus [31, 32]. However, some Vi1-like phages have been ary relationships among diferent phage groups. Although reported to be generalized transducers [33] – a characteristic clearer parameters to defne genera, subfamilies, and fami- that is incompatible with its use in phage biocontrol and lies still need to be established, new phage subfamilies and needs to be clarifed beforehand. genera have been proposed on the basis of molecular rela- The established groups of FO1-, GJ1-, N4-, SP6-, T4-, tionships (e.g., phages with 40% homologous proteins are T7-, and Vi1-like phages all comprise strictly lytic phages, members of the same genus) [10]. Importantly, members and representatives of each group have been successfully of the same subfamily or genus usually share a lifestyle applied to control pathogenic bacteria. An early assignment and approximate genome size [11]. For example, a group of a new phage to one of these groups could therefore enable of strictly lytic phages is formed by myoviruses related preselection to accelerate phage isolation and characteriza- to Salmonella phage Felix O1 (FO1) with genomes of ca. tion. Genome sequencing allows identifcation of the phylo- 85-90 kb in size. They are classifed as members of the sub- genetic relationships of a new isolate, but it is still associated family Ounavirinae [12]. The FO1-like Salmonella phages with high costs and complex data analysis. In order to cir- Mushroom and FO1a are components of commercially cumvent the need for complete sequencing, molecular mark- available phage cocktails (IntestiPhage™ and PhageGuard ers (signature genes) could be studied instead. These mark- S™, respectively) [13, 14]. GJ1-like phages are also viru- ers should be universally encoded by all tailed phages, and, lent myoviruses. ΦEcoM-GJ1 infects enterotoxigenic E. coli more importantly, the phylogenetic groups formed by com- O149:H10:F4 strains [15]. Other phages related to GJ1, such parisons of whole genome sequences and the corresponding as the E. amylovora phage vB_EamM-Y2 or Pectobacte- markers need to be identical. There are several candidates rium carotovorum phage PM1 have similar genome sizes for such signature genes, and their usefulness as molecular of ca. 55 kb as well as broad host ranges and have been markers has already been demonstrated. For example, the shown to efectively limit the growth of their target bacteria grouping of Vi1-like phages has been corroborated by phy- in vitro as well as in vivo [16, 17]. The strictly lytic N4-like logenetic analysis of single signature genes (major capsid phages belong to the family Podoviridae and have genomes protein [MCP], DNA polymerase, DNA ligase, terminase of approximately 70-75 kb in size [18]. The N4-like Escheri- large subunit) [29]. A phylogenetic tree of the former sub- chia phage EC1-UPM reduces the severity of colibacillosis family “Felixounavirinae” constructed by analysis of con- in chickens caused by E. coli O78:K80 strains [19]. SP6- catenated protein sequences (MCP, tail sheath protein, portal like phages are virulent podoviruses of one genus (Sp6virus) protein) also confrmed clustering based on whole-genome with genomes of ca. 45 kb in size [20]. The SP6-like Salmo- comparisons [34]. Signature genes have also been used to nella phage UAB_Phi78, which displays a broad host range study viral diversity in environmental samples. For exam- on strains of Salmonella enterica subsp. enterica serovars ple, the diversity of T7-like cyanoviruses has been analyzed Typhimurium and Enteritidis, was part of a cocktail that with the help of three signature genes (DNA polymerase, greatly reduced Salmonella contamination on various food MCP, photosynthesis gene psbA), and these viruses have surfaces [21]. The relatively small and strictly lytic T7-like been specifcally isolated using degenerate primers targeting viruses (ca. 40 kb) also belong to one genus (T7virus) in the DNA polymerase gene [35]. In a comprehensive study the family Podoviridae. At their tail spikes, many T7-like of phages infecting enterobacteria, Grose and Casjens [11] phages have enzymes that hydrolyze bacterial exopolysac- showed that the chance of assigning
Load more

Recommended publications
  • Entwicklung Einer Software Zur Identifizierung Neuartiger Und
    Entwicklung einer Software zur Identifizierung neuartiger und bekannter Infektionserreger in klinischen Proben Dissertation zur Erlangung des Doktorgrades an der Fakult¨at fur¨ Mathematik, Informatik und Naturwissenschaften Fachbereich Biologie der Universit¨at Hamburg vorgelegt von Malik Alawi Hamburg, 2020 Vorsitzender der Prufungskommission¨ Dr. PD Andreas Pommerening-R¨oser Gutachter Professor Dr. Adam Grundhoff Professor Dr. Stefan Kurtz Datum der Disputation 30. April 2021 Abstract Sequencing of diagnostic samples is widely considered a key technology that may fun- damentally improve infectious disease diagnostics. The approach can not only identify pathogens already known to cause a specific disease, but may also detect pathogens that have not been previously attributed to this disease, as well as completely new, previously unknown pathogens. Therefore, it may significantly increase the level of preparedness for future outbreaks of emerging pathogens. This study describes the development and application of methods for the identification of pathogenic agents in diagnostic samples. The methods have been successfully applied multiple times under clinical conditions. The corresponding results have been published within the scope of this thesis. Finally, the methods were made available to the scientific community as an open source bioinformatics tool. The novel software was validated by conventional diagnostic methods and it was compared to established analysis pipelines using authentic clinical samples. It is able to identify pathogens from different diagnostic entities and often classifies viral agents down to strain level. Furthermore, the method is capable of assembling complete viral genomes, even from samples containing multiple closely related viral strains of the same viral family. In addition to an improved method for taxonomic classification, the software offers functionality which is not present in established analysis pipelines.
    [Show full text]
  • On the Stability of Sequences Inserted Into Viral Genomes Anouk Willemsen1,*,† and Mark P
    Virus Evolution, 2019, 5(2): vez045 doi: 10.1093/ve/vez045 Review article On the stability of sequences inserted into viral genomes Anouk Willemsen1,*,† and Mark P. Zwart2,*,‡ 1Laboratory MIVEGEC (UMR CNRS IRD University of Montpellier), Centre National de la Recherche Scientifique (CNRS), 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France and 2Netherlands Institute of Ecology (NIOO-KNAW), Postbus 50, 6700 AB, Wageningen, The Netherlands *Corresponding author: E-mail: [email protected]; [email protected] †http://orcid.org/0000-0002-8511-3244 ‡http://orcid.org/0000-0003-4361-7636 Abstract Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large num- ber of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population.
    [Show full text]
  • The Landscape of Viral Associations in Human Cancers Marc Zapatka1*, Ivan Borozan2*, Daniel S
    bioRxiv preprint doi: https://doi.org/10.1101/465757; this version posted September 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The landscape of viral associations in human cancers Marc Zapatka1*, Ivan Borozan2*, Daniel S. Brewer4,5*, Murat Iskar1*, Adam Grundhoff6, Malik Alawi6,7, Nikita Desai8,9, Holger Sültmann10,16, Holger Moch11, PCAWG Pathogens Working Group, ICGC/TCGA Pan-cancer Analysis of Whole Genomes Network, Colin S. Cooper3,4, Roland Eils12,13, Vincent Ferretti14,15, Peter Lichter1,16 1 Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. 2 Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada 3 The Institute of Cancer Research, London, UK. 4 Norwich Medical School, University of East Anglia, Norwich, UK 5 Earlham Institute, Norwich, UK. 6 Virus Genomics, Heinrich-Pette-Institute, Hamburg, Germany 7 Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 8 Division of Cancer Studies, King's College London, London, UK 9 Cancer Systems Biology Laboratory, The Francis Crick Institute, London, UK 10 Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany 11 Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Zürich, Switzerland 12 Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. 13 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University and BioQuant Center, Heidelberg, Germany 14 Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada 15 Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Canada.
    [Show full text]
  • Ab Komplet 6.07.2018
    CONTENTS 1. Welcome addresses 2 2. Introduction 3 3. Acknowledgements 10 4. General information 11 5. Scientific program 16 6. Abstracts – oral presentations 27 7. Abstracts – poster sessions 99 8. Participants 419 1 EMBO Workshop Viruses of Microbes 2018 09 – 13 July 2018 | Wrocław, Poland 1. WELCOME ADDRESSES Welcome to the Viruses of Microbes 2018 EMBO Workshop! We are happy to welcome you to Wrocław for the 5th meeting of the Viruses of Microbes series. This series was launched in the year 2010 in Paris, and was continued in Brussels (2012), Zurich (2014), and Liverpool (2016). This year our meeting is co-organized by two partner institutions: the University of Wrocław and the Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences. The conference venue (University of Wrocław, Uniwersytecka 7-10, Building D) is located in the heart of Wrocław, within the old, historic part of the city. This creates an opportunity to experience the over 1000-year history of the city, combined with its current positive energy. The Viruses of Microbes community is constantly growing. More and more researchers are joining it, and they represent more and more countries worldwide. Our goal for this meeting was to create a true global platform for networking and exchanging ideas. We are most happy to welcome representatives of so many countries and continents. To accommodate the diversity and expertise of the scientists and practitioners gathered by VoM2018, the leading theme of this conference is “Biodiversity and Future Application”. With the help of your contribution, this theme was developed into a program covering a wide range of topics with the strongest practical aspect.
    [Show full text]
  • Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID-19 Pandemic: a Repo
    Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person
    [Show full text]
  • Taxonomy of Prokaryotic Viruses: 2017 Update from the ICTV Bacterial and Archaeal Viruses Subcommittee
    Archives of Virology (2018) 163:1125–1129 https://doi.org/10.1007/s00705-018-3723-z VIROLOGY DIVISION NEWS Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee Evelien M. Adriaenssens1 · Johannes Wittmann2 · Jens H. Kuhn3 · Dann Turner4 · Matthew B. Sullivan5 · Bas E. Dutilh6,7 · Ho Bin Jang5 · Leonardo J. van Zyl8 · Jochen Klumpp9 · Malgorzata Lobocka10 · Andrea I. Moreno Switt11 · Janis Rumnieks12 · Robert A. Edwards13 · Jumpei Uchiyama14 · Poliane Alfenas‑Zerbini15 · Nicola K. Petty16 · Andrew M. Kropinski17 · Jakub Barylski18 · Annika Gillis19 · Martha R. C. Clokie20 · David Prangishvili21 · Rob Lavigne22 · Ramy Karam Aziz23 · Siobain Dufy24 · Mart Krupovic21 · Minna M. Poranen25 · Petar Knezevic26 · Francois Enault27 · Yigang Tong28 · Hanna M. Oksanen25 · J. Rodney Brister29 Received: 1 December 2017 / Accepted: 15 January 2018 / Published online: 22 January 2018 © Springer-Verlag GmbH Austria, part of Springer Nature 2018 The prokaryotic virus community is represented at the Inter- 1. Changes in subcommittee membership. During the national Committee on Taxonomy of Viruses (ICTV) by the past year we have lost two members. Dr. Hans-Wolfgang Bacterial and Archaeal Viruses Subcommittee. Since our Ackermann, a life member of the ICTV, the father of cau- last report [5], the committee composition has changed, dovirus taxonomy [1] and an electron microscopist extraor- and a large number of taxonomic proposals (TaxoProps) dinaire [2–4], lamentably died and will be gravely missed. were submitted to the ICTV Executive Committee (EC) for In addition, Dr. Jens H. Kuhn, who, in spite of protestations approval. about not being a genuine phage biologist, proved invaluable Handling Editor: Sead Sabanadzovic. Electronic supplementary material The online version of this article (http​s://doi.org/10.1007​/s007​05-018-3723​-z) contains supplementary material, which is available to authorized users.
    [Show full text]
  • 1 Taxonomy of Prokaryotic Viruses: 2017 Update from the ICTV
    Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Evelien M. Adriaenssens1, Johannes Wittmann2, Jens H. Kuhn3, Dann Turner4, Matthew B. Sullivan5, Bas E. Dutilh6,7, Ho Bin Jang5, Leonardo J. van Zyl8, Jochen Klumpp9, Malgorzata Lobocka10, Andrea I. Moreno Switt11, Janis Rumnieks12, Robert A. Edwards13, Jumpei Uchiyama14, Poliane Alfenas-Zerbini15, Andrew M. Kropinski16, Jakub Barylski17, Annika Gillis18, Martha R. C. Clokie19, David Prangishvili20, Rob Lavigne21, Ramy Karam Aziz22, Siobain Duffy23, Mart Krupovic20, Minna M. Poranen24, Petar Knezevic25, Francois Enault26, Yigang Tong27, Hanna M. Oksanen24, J. Rodney Brister28 1 Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom. orcid.org/0000-0003-4826-5406 2 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124 Braunschweig, Germany. orcid.org/0000-0002-7275-9927 3 Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. orcid.org/0000- 0002-7800-6045 4 Faculty of Health and Applied Sciences (UWE Bristol), Frenchay Campus, Bristol, BS16 1QY, United Kingdom. orcid.org/0000-0002-0249-4513 5 Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA. orcid.org/0000-0003-4040-9831 6 Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands. 7 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. orcid.org/0000-0003-2329-7890 8 Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa. orcid.org/0000-0001-9364-8671 9 Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland.
    [Show full text]
  • The Gut Virome of Healthy Children During the First Year of Life Is Diverse and Dynamic
    bioRxiv preprint doi: https://doi.org/10.1101/2020.10.07.329565; this version posted October 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 The gut virome of healthy children during the first 2 year of life is diverse and dynamic 3 4 Blanca Taboada1, Patricia Morán2, Angélica Serrano-Vázquez2, Pavel Iša1, Liliana Rojas- 5 Velázquez2, Horacio Pérez-Juárez2, Susana López1, Javier Torres3*, Cecilia Ximenez2*, 6 Carlos F. Arias1*. 7 1Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 8 2001, Cuernavaca, Morelos, México. 9 2Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad 10 Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, Ciudad de México. 11 3Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital 12 Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 13 Cuauhtémoc, Ciudad de México, México. 14 15 *Corresponding authors: 16 Carlos F. Arias: [email protected] (CFA); 17 Cecilia Ximénez: [email protected] (CX); 18 Javier Torres: [email protected] (JT) 19 20 21 22 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.07.329565; this version posted October 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license.
    [Show full text]
  • Gut Mucosal Virome Alterations in Ulcerative Colitis Gut: First Published As 10.1136/Gutjnl-2018-318131 on 6 March 2019
    Gut microbiota ORIGINAL ARTICLE Gut mucosal virome alterations in ulcerative colitis Gut: first published as 10.1136/gutjnl-2018-318131 on 6 March 2019. Downloaded from T,ao Zuo 1,2,3 Xiao-Juan Lu,4 Yu Zhang,5 Chun Pan Cheung,2,3 Siu Lam,2,6 Fen Zhang,2,3 Whitney Tang,3 Jessica Y L Ching,3 Risheng Zhao,2,3 Paul K S Chan,1,6 Joseph J Y Sung,2,3 Jun Yu, 2,3 Francis K L Chan, 1 Qian Cao,5,7 Jian-Qiu Sheng,4 Siew C Ng 1,2,3 ► Additional material is ABSTRact published online only. To view Objective The pathogenesis of UC relates to gut Significance of this study please visit the journal online microbiota dysbiosis. We postulate that alterations in the (http:// dx. doi. org/ 10. 1136/ What is already known on this subject? gutjnl- 2018- 318131). viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to ► Alterations in faecal bacteria and faecal virome For numbered affiliations see have been reported in patients with IBD. end of article. characterise the mucosal virome and their functions in health and UC. ► Patients with UC showed an expansion of Caudovirales bacteriophages and Caudovirales Correspondence to Design Deep metagenomics sequencing of virus-like Professor Siew C Ng, Medicine particle preparations and bacterial 16S rRNA sequencing species richness in the stool. and Therapeutics, The Chinese were performed on the rectal mucosa of 167 subjects What are the new findings? University of Hong Kong, Shatin, from three different geographical regions in China Hong Kong SAR, China; ► We demonstrated for the first time that UC siewchienng@ cuhk.
    [Show full text]
  • Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid- Received: 6 March 2019 Accepted: 17 June 2019 Producing E
    www.nature.com/scientificreports OPEN Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid- Received: 6 March 2019 Accepted: 17 June 2019 producing E. coli and Their Phages Published: xx xx xxxx George Tetz 1,2, Stuart M. Brown3, Yuhan Hao4,5 & Victor Tetz1 The etiopathogenesis of type 1 diabetes (T1D), a common autoimmune disorder, is not completely understood. Recent studies suggested the gut microbiome plays a role in T1D. We have used public longitudinal microbiome data from T1D patients to analyze amyloid-producing bacterial composition and found a signifcant association between initially high amyloid-producing Escherichia coli abundance, subsequent E. coli depletion prior to seroconversion, and T1D development. In children who presented seroconversion or developed T1D, we observed an increase in the E. coli phage/E. coli ratio prior to E. coli depletion, suggesting that the decrease in E. coli was due to prophage activation. Evaluation of the role of phages in amyloid release from E. coli bioflms in vitro suggested an indirect role of the bacterial phages in the modulation of host immunity. This study for the frst time suggests that amyloid-producing E. coli, their phages, and bacteria-derived amyloid might be involved in pro- diabetic pathway activation in children at risk for T1D. Type 1 diabetes (T1D) is an autoimmune disorder driven by T cell-mediated destruction of the insulin-secreting β-cells of the pancreatic islets that ofen manifests during childhood1. Tere are a number of factors associated with the development of T1D2–4. Te strongest susceptibility alleles for T1D encode certain human leukocyte antigens (HLAs), which play a central role in autoreactive T-cell activation in T1D pathogenesis5,6.
    [Show full text]
  • Archives of Virology
    Archives of Virology Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018) --Manuscript Draft-- Manuscript Number: Full Title: Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018) Article Type: Virology Division News: Virus Taxonomy/Nomenclature Keywords: virus taxonomy; virus phylogeny; virus nomenclature; International Committee on Taxonomy of Viruses; International Code of Virus Classification and Nomenclature Corresponding Author: Arcady Mushegian National Science Foundation McLean, Virginia UNITED STATES Corresponding Author Secondary Information: Corresponding Author's Institution: National Science Foundation Corresponding Author's Secondary Institution: First Author: Andrew M.Q. King First Author Secondary Information: Order of Authors: Andrew M.Q. King Elliot J Lefkowitz Arcady R Mushegian Michael J Adams Bas E Dutilh Alexander E Gorbalenya Balázs Harrach Robert L Harrison Sandra Junglen Nick J Knowles Andrew M Kropinski Mart Krupovic Jens H Kuhn Max Nibert Luisa Rubino Sead Sabanadzovic Hélène Sanfaçon Stuart G Siddell Peter Simmonds Arvind Varsani Francisco Murilo Zerbini Andrew J Davison Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Order of Authors Secondary Information: Funding Information: Medical Research Council Dr Andrew J Davison (MC_UU_12014/3) Nederlandse Organisatie voor
    [Show full text]
  • Evidence to Support Safe Return to Clinical Practice
    Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University July 31st, 2020 1 Contents Page Foreword 4 Background 5 Project goal and specific objectives 5 Methods used to identify and include relevant literature 6 Report structure 7 Report summary 7 Report results a) Which patients are at greater risk of the consequences of COVID-19 9 and so consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that dental 10 professionals should screen for prior to providing in-person oral health care? c) What evidence exists to support patient scheduling, waiting and 11 other non-treatment management measures for in-person oral health care? d) What evidence exists to support the use of various forms of 13 personal protective equipment (PPE) while providing in-person oral health care? e) What evidence exists to support the decontamination and re-use of 14 PPE? f) What evidence exists concerning the provision of aerosol- 14 generating procedures (AGP) as part of in-person oral health care? g) What
    [Show full text]