DOCSLIB.ORG

The Temperate Burkholderia Phage AP3 of the Peduovirinae Shows Efficient Antimicrobial Activity Against B. Cenocepacia of the IIIA Lineage

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Temperate Burkholderia Phage AP3 of the Peduovirinae Shows Efficient Antimicrobial Activity Against B. Cenocepacia of the IIIA Lineage Appl Microbiol Biotechnol DOI 10.1007/s00253-016-7924-7 APPLIED GENETICS AND MOLECULAR BIOTECHNOLOGY The temperate Burkholderia phage AP3 of the Peduovirinae shows efficient antimicrobial activity against B. cenocepacia of the IIIA lineage Bartosz Roszniowski1 & Agnieszka Latka 1 & Barbara Maciejewska1 & Dieter Vandenheuvel2 & Tomasz Olszak1 & Yves Briers2,3 & Giles S. Holt4 & Miguel A. Valvano5 & Rob Lavigne2 & Darren L. Smith4 & Zuzanna Drulis-Kawa1 Received: 8 July 2016 /Revised: 2 October 2016 /Accepted: 9 October 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract Burkholderia phage AP3 (vB_BceM_AP3) is a remaining infective particles after 24 h of treatment. AP3 ly- temperate virus of the Myoviridae and the Peduovirinae sub- sogeny can occur by stable genomic integration and by pseu- family (P2likevirus genus). This phage specifically infects do-lysogeny. The lysogenic bacterial mutants did not exhibit multidrug-resistant clinical Burkholderia cenocepacia lineage any significant changes in virulence compared to wild-type IIIA strains commonly isolated from cystic fibrosis patients. host strain when tested in the Galleria mellonella moth wax AP3 exhibits high pairwise nucleotide identity (61.7 %) to model. Moreover, AP3 treatment of larvae infected with Burkholderia phage KS5, specific to the same B. cenocepacia revealed a significant increase (P <0.0001) B. cenocepacia host, and has 46.7–49.5 % identity to phages in larvae survival in comparison to AP3-untreated infected infecting other species of Burkholderia. The lysis cassette of larvae. AP3 showed robust lytic activity, as evidenced by its these related phages has a similar organization (putative broad host range, the absence of increased virulence in lyso- antiholin, putative holin, endolysin, and spanins) and shows genic isolates, the lack of bacterial gene disruption condi- 29–98 % homology between specific lysis genes, in contrast tioned by bacterial tRNA downstream integration site, and to Enterobacteria phage P2, the hallmark phage of this genus. the absence of detected toxin sequences. These data suggest The AP3 and KS5 lysis genes have conserved locations and that the AP3 phage is a promising potent agent against bacte- high amino acid sequence similarity. The AP3 bacteriophage ria belonging to the most common B. cenocepacia IIIA line- particles remain infective up to 5 h at pH 4–10 and are stable at age strains. 60 °C for 30 min, but are sensitive to chloroform, with no Keywords Temperate phage . Peduovirinae . Burkholderia Electronic supplementary material The online version of this article cepacia lineage IIIA (doi:10.1007/s00253-016-7924-7) contains supplementary material, which is available to authorized users. * Zuzanna Drulis-Kawa Introduction [email protected] Gram-negative, non-fermentative bacilli of the Burkholderia 1 Institute of Genetics and Microbiology, University of Wroclaw, cepacia complex (BCC) are inherently difficult to eradicate Przybyszewskiego 63/77, 51-148 Wroclaw, Poland clinically. They are dangerous opportunistic pathogens that 2 Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg infect patients suffering from cystic fibrosis (CF). The BCC 21, box 2462, 3001 Leuven, Belgium includes 17 closely related bacterial species (B. cepacia, 3 Present address: Department of Applied Biosciences, Ghent Burkholderia multivorans, Burkholderia cenocepacia, University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium Burkholderia stabilis, Burkholderia vietnamiensis, 4 Applied Sciences, University of Northumbria, Ellison Building Burkholderia dolosa, Burkholderia ambifaria, Burkholderia EBD222, Newcastle upon Tyne NE1 8ST, UK anthina, Burkholderia pyrrocinia, Burkholderia ubonensis, 5 Center for Experimental Medicine, Queen’s University of Belfast, 97 Burkholderia latens, Burkholderia diffusa, Burkholderia Lisburn Rd., Belfast BT9 7BL, UK arboris, Burkholderia seminalis, Burkholderia metallica, Appl Microbiol Biotechnol Burkholderia contaminans,andBurkholderia lata), which biofilm formation, leading to significant decrease in the mor- can only be discriminated from each other using molecular tality of Pseudomonas-infected animals. The changes in bac- methods (Drevinek and Mahenthiralingam 2010; Medina- terial pathogenicity after phage integration into bacterial ge- Pascualetal.2012). The BCC bacteria survive for long pe- nome can be explained by host gene disruption, CRISPR/Cas riods in moist environments and can cause hospital outbreaks system interaction, or by mechanisms independent of the host especially in immunocompromised patients; they also con- background (Chung et al. 2012; Zegans et al. 2009;Cadyetal. taminate pharmaceutical products and water supplies 2012; Drulis-Kawa et al. 2015). (Gilligan et al. 2003). The most prevalent isolates in CF pa- To date, 37 Burkholderia specific phages have been depos- tients, B. multivorans and B. cenocepacia, are responsible for ited into GenBank (status on 28.06.2016), including members 85–97 % of infections (Drevinek and Mahenthiralingam of the Myoviridae (18), Siphoviridae (9), and Podoviridae 2010). B. cenocepacia also infects patients suffering from (10) families. The presence of a recombinase or integrase in chronic granulomatous disease (CGD; Bylund et al. 2005). the bacteriophage genome, indicating the temperate nature of Lung infection of CF patients by BCC leads to Bcepacia the phage (Gill and Young 2011), was confirmed for 22 of syndrome,^ an acute, necrotizing pneumonia leading to death these 37 sequenced genomes (phiE202, phi52237, KS14, (Isles et al. 1984). Based on recA gene polymorphisms, KL3, KS5, BEK, and φX216 from Myoviridae, B. cenocepacia isolates can be subdivided into four lineages. Peduovirinae,andP2likevirus;AH2,KL1,Bcep176, Lineages IIIA–D and IIIA/IIID are exclusively found in clin- Phi1026b, phiE125, and KS9 from Siphoviridae;and ical samples, IIIC occurs only in soil, and IIIB occurs in both BcepMigl, DC1, BcepC6B, BcepIL02, Bcep22 Bp-AMP1, environmental and clinical samples (Mahenthiralingam et al. Bp-AMP2, Bp-AMP3, and Bp-AMP4 from Podoviridae). 2000;Vandammeetal.2003; Manno et al. 2004). Also several other viruses including Enterobacteria phages: B. cenocepacia has multiple virulence factors, including P2, 186, PsP3, and Wφ; Yersinia phage L-413C; Salmonella cepacian exopolysaccharide (crucial for chronic infections), phages Fels-2 and SopEφ; Pseudomonas phage φCTX; adhesins, pili and flagella, biofilm, and type III and IV secre- Mannheimia phage φ-MhaA1_PHL101; and Ralstonia phage tion systems, recently reviewed in detail (Leitão et al. 2010; RSA1 belong to the P2likevirus genus (Lavigne et al. 2009). Casey and McClean 2015). The B. cenocepacia genome in- Even though these phages were classified as temperate, they cludes large, horizontally transferred genomic islands span- could be engineered as lytic mutants (Lynch et al. 2010r )o ning up to 9.3 % of the chromosome, which are considered provide a source for proteins (e.g., endolysins and to be important in adaptation to different environments depolymerases), which could potentially be used as enzyme- (Holden et al. 2009). based antibacterials. Here, we report a newly discovered Bacteriophages have been proposed as effective antibacte- B. cenocepacia IIIA-specific temperate phage, designated rial agents to eradicate bacterial pathogens (Hyman and AP3 (vB_BceM_AP3), and classified to the P2likevirus ge- Abedon 2010; Abedon 2011; Drulis-Kawa et al. 2012 and nus. This phage was characterized in terms of genome orga- 2015). Treatment with bacteriophages allows targeting patho- nization including lysis cassette, the integration site and lysog- gens that are resistant to conventional drugs without damaging eny event analysis, and the tail fiber protein amino acids com- the host’s natural flora. The efficacy of bacteriophages against position with the other P2-like phages and prophages found in CF pathogens has been shown in vivo using the Galleria host sequences. Furthermore, the efficacy of AP3 in the erad- mellonella insect model and various mouse pulmonary infec- ication of B. cenocepacia infection in moth larvae and the tion models (Seed and Dennis 2009; Carmody et al. 2010; emergence of resistant clones was studied. Lynch et al. 2010; Saussereau et al. 2014; Olszak et al. 2015;Danis-Włodarczyk et al. 2016). The synergistic effect of combining bacterial viruses with antibiotics may lead to higher production of phage progeny and increased phage ac- Materials and methods tivity, improving bacterial killing (Kamal and Dennis 2015). Phage-based treatment poses some risks and limitations; Phage isolation and propagation therefore, a principle requirement is phage precise characteri- zation not only in terms of biology, but also in genomic as- Phage AP3 was isolated from a natural wastewater treatment pects (Merril et al. 2003; Drulis-Kawa et al. 2012 and 2015). plant (irrigated fields) in Wroclaw (Poland) as previously de- There are reports that reinforce the idea of possible temperate scribed (Olszak et al. 2015). AP3 was isolated from and prop- phage application with approaches in using them for bacterial agated in the clinical isolate 7780 of B. cenocepacia IIIA virulence modification. The lysogenization process of temper- lineage (Table 1). The titer and plaque morphology were ate Pseudomonas phages DMS3, MP22, and D3112 caused assessed by the double-agar layer technique (Adams 1959). the inhibition in the expression of virulence factors, including
Load more

Recommended publications
  • First Description of a Temperate Bacteriophage (Vb Fhim KIRK) of Francisella Hispaniensis Strain 3523
    viruses Article First Description of a Temperate Bacteriophage (vB_FhiM_KIRK) of Francisella hispaniensis Strain 3523 Kristin Köppen 1,†, Grisna I. Prensa 1,†, Kerstin Rydzewski 1, Hana Tlapák 1, Gudrun Holland 2 and Klaus Heuner 1,* 1 Centre for Biological Threats and Special Pathogens, Cellular Interactions of Bacterial Pathogens, ZBS 2, Robert Koch Institute, 13353 Berlin, Germany; [email protected] (K.K.); [email protected] (G.I.P.); [email protected] (K.R.); [email protected] (H.T.) 2 Centre for Biological Threats and Special Pathogens, Advanced Light and Electron Microscopy, ZBS 4, Robert Koch Institute, D-13353 Berlin, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-30-18754-2226 † Both authors contributed equally to this work. Abstract: Here we present the characterization of a Francisella bacteriophage (vB_FhiM_KIRK) includ- ing the morphology, the genome sequence and the induction of the prophage. The prophage sequence (FhaGI-1) has previously been identified in F. hispaniensis strain 3523. UV radiation induced the prophage to assemble phage particles consisting of an icosahedral head (~52 nm in diameter), a tail of up to 97 nm in length and a mean width of 9 nm. The double stranded genome of vB_FhiM_KIRK contains 51 open reading frames and is 34,259 bp in length. The genotypic and phylogenetic analysis indicated that this phage seems to belong to the Myoviridae family of bacteriophages. Under the Citation: Köppen, K.; Prensa, G.I.; conditions tested here, host cell (Francisella hispaniensis 3523) lysis activity of KIRK was very low, and Rydzewski, K.; Tlapák, H.; Holland, the phage particles seem to be defective for infecting new bacterial cells.
    [Show full text]
  • Genomic Analysis and Relatedness of P2-Like Phages of the Burkholderia Cepacia Complex Karlene H Lynch1, Paul Stothard2, Jonathan J Dennis1*
    Lynch et al. BMC Genomics 2010, 11:599 http://www.biomedcentral.com/1471-2164/11/599 RESEARCH ARTICLE Open Access Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex Karlene H Lynch1, Paul Stothard2, Jonathan J Dennis1* Abstract Background: The Burkholderia cepacia complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ-CEP511). Results: KS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the Peduovirinae subfamily and the “P2-like viruses” genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 E+E’ translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins.
    [Show full text]
  • Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula
    fmicb-10-01014 May 10, 2019 Time: 14:46 # 1 ORIGINAL RESEARCH published: 14 May 2019 doi: 10.3389/fmicb.2019.01014 Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula Tomás Alarcón-Schumacher1,2†, Sergio Guajardo-Leiva1†, Josefa Antón3 and Beatriz Díez1,4* 1 Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile, 2 Max Planck Institute for Marine Microbiology, Bremen, Germany, 3 Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain, 4 Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile In Antarctic coastal waters where nutrient limitations are low, viruses are expected to play a major role in the regulation of bloom events. Despite this, research in viral identification and dynamics is scarce, with limited information available for the Southern Ocean (SO). This study presents an integrative-omics approach, comparing variation in the viral and microbial active communities on two contrasting sample conditions from Edited by: a diatom-dominated phytoplankton bloom occurring in Chile Bay in the West Antarctic David Velazquez, Autonomous University of Madrid, Peninsula (WAP) in the summer of 2014. The known viral community, initially dominated Spain by Myoviridae family (∼82% of the total assigned reads), changed to become dominated Reviewed by: by Phycodnaviridae (∼90%), while viral activity was predominantly driven by dsDNA Carole Anne Llewellyn, ∼ ∼ Swansea University, United Kingdom members of the Phycodnaviridae ( 50%) and diatom infecting ssRNA viruses ( 38%), Márcio Silva de Souza, becoming more significant as chlorophyll a increased. A genomic and phylogenetic Fundação Universidade Federal do characterization allowed the identification of a new viral lineage within the Myoviridae Rio Grande, Brazil family.
    [Show full text]
  • Exploration Des Communautés Virales Thermophiles Dans Les Écosystèmes
    présentée par THÈSE / UNIVERSITÉ DE BRETAGNE OCCIDENTALE Kaarle Joonas Parikka sous le sceau de l’Université européenne de Bretagne Préparée à l'Institut Universitaire pour obtenir le titre de Européen de la Mer, au sein du DOCTEUR DE L’UNIVERSITÉ DE BRETAGNE OCCIDENTALE Mention :Microbiologie Laboratoire de Microbiologie des École Doctorale des Sciences de la Mer Environnements Extrêmes Thèse soutenue le 28 mars 2013 devant le jury composé de : Exploration des communautés Hélène Montanié (Rapporteur) virales thermophiles dans Maître de Conférences, HDR, Université de La Rochelle les écosystèmes chauds des Michael DuBow (Rapporteur) Professeur, Université Paris-Sud 11 Terres australes et Stéphan Jacquet (Examinateur) antarctiques françaises Directeur de Recherche, INRA, UMR CARRTEL Thierry Bouvier (Examinateur) Chargé de Recherche CNRS, Université de Montpellier 2 Christine Paillard (Examinateur) Directrice de Recherche CNRS, Université de Bretagne Occidentale Marc Le Romancer (Directeur de thèse) Maître de Conférences, HDR, Université de Bretagne Occidentale Remerciements Cette thèse a été financée par le Ministère de l’Enseignement Supérieur et de la Recherche. Je voudrais remercier l’ancienne et la nouvelle direction du LM2E : Daniel Prieur, Anne Godfroy et Mohamed Jebbar (qui m’a lancé dans la génomique), de m’avoir accueilli au sein du laboratoire afin de pouvoir effectuer ce travail. Merci Daniel Prieur également d’avoir été mon directeur de thèse la première année de ma thèse. J’aimerais exprimer ma gratitude à Marc Le Romancer, qui m’a recruté du Plat Pays pour venir travailler sur un sujet de thèse très exotique, qui m’a permis de découvrir la virologie extrêmophile. Je lui suis reconnaissant également pour m’avoir pris avec lui à 13 000 Km de Brest pour échantillonner aux Terres australes et antarctiques françaises, la terre des « oubliés ».
    [Show full text]
  • Biocontrol of Foodborne Bacterial Pathogens Using
    BIOCONTROL OF FOODBORNE BACTERIAL PATHOGENS USING IMMOBILIZED BACTERIOPHAGES A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph by HANY EL-SAID MOHAMAD ANANY In partial fulfillment of requirements for the degree of Doctor of Philosophy August, 2010 ©HanyAnany, 2010 Library and Archives Bibliotheque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 OttawaONK1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-67847-3 Our file Notre reference ISBN: 978-0-494-67847-3 NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par I'lnternet, preter, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distribute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non­ support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in this et des droits moraux qui protege cette these. Ni thesis. Neither the thesis nor la these ni des extra its substantiels de celle-ci substantial extracts from it may be ne doivent etre imprimes ou autrement printed or otherwise reproduced reproduits sans son autorisation.
    [Show full text]
  • TESIS DOCTORAL Estudio Metagenómico De La Comunidad De
    TESIS DOCTORAL Estudio metagenómico de la comunidad de virus y de su interacción con la microbiota en la cavidad bucal humana Marcos Parras Moltó Madrid, 2019 Estudio metagenómico de la comunidad de virus y de su interacción con la microbiota en la cavidad bucal humana Memoria presentada por Marcos Parras Moltó para optar al título de Doctor por la Universidad Autónoma de Madrid Esta Tesis se ha realizado en el Centro de Biología Molecular Severo Ochoa bajo la supervisión del Tutor y Director Alberto López Bueno, en el Programa de Doctorado en Biociencias Moleculares (RD 99/2011) Universidad Autónoma de Madrid Facultad de Ciencias Departamento de Biología Molecular Centro de Biología Molecular Severo Ochoa (CBMSO) Madrid, 2019 El Dr. Alberto López Bueno, Profesor Contratado Doctor en el Departamento de Biología Molecular de la Universidad Autónoma de Madrid (UAM) e investigador en el Centro de Biología Molecular Severo Ochoa (CBMSO): CERTIFICA: Haber dirigido y supervisado la Tesis Doctoral titulada "Estudio metagenómico de la comunidad de virus y de su interacción con la microbiota en la cavidad bucal humana” realizada por D. Marcos Parras Moltó, en el Programa de Doctorado en Biociencias Moleculares de la Universidad Autónoma de Madrid, por lo que autoriza la presentación de la misma. Madrid, a 23 de Abril de 2019, Alberto López Bueno La presente tesis doctoral ha sido posible gracias a la concesión de una “Ayuda para Contratos Predoctorales para la Formación de Doctores” convocatoria de 2013 (BES-2013-064773) asociada al proyecto SAF2012-38421 del Ministerio de Economía y Competitividad. Durante esta tesis se realizó una estancia de dos meses en el laboratorio del Catedrático Francisco Rodríguez Valera, director de grupo de investigación: Evolutionary Genomics Group de la Universidad Miguel Hernández de Elche (San Juan de Alicante), gracias a una “Ayuda a la Movilidad Predoctoral para la Realización de Estancias Breves en Centros de I+D” convocatoria de 2015 (EEBB-I-16-11876) concedida por el Ministerio de Economía y Competitividad.
    [Show full text]
  • Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar De Huasco, Chile
    microorganisms Communication Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile Yoanna Eissler 1,* , Cristina Dorador 2,3 , Brandon Kieft 4 , Verónica Molina 5,6 and Martha Hengst 3,7 1 Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso 2360102, Chile 2 Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Avenida Universidad de Antofagasta s/n, Antofagasta 1240000, Chile; [email protected] 3 Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7), Santiago 8320000, Chile; [email protected] 4 Lab of Dr. Steven Hallam, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; [email protected] 5 Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Avenida Leopoldo Carvallo 270, Playa Ancha, Valparaíso 2340000, Chile; [email protected] 6 HUB Ambiental UPLA, Universidad de Playa Ancha, Avenida Leopoldo Carvallo 200, Playa Ancha, Valparaíso 2340000, Chile 7 Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Av Angamos 0610, Antofagasta 1270709, Chile * Correspondence: [email protected]; Tel.: +56-32-250-8063 Received: 24 June 2020; Accepted: 3 July 2020; Published: 20 July 2020 Abstract: Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis.
    [Show full text]
  • The Temperate Burkholderia Phage AP3 of the Peduovirinae Shows Efficient Antimicrobial Activity Against B. Cenocepacia of the II
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Queen's University Research Portal The temperate Burkholderia phage AP3 of the Peduovirinae shows efficient antimicrobial activity against B. cenocepacia of the IIIA lineage Roszniowski, B., Latka, A., Maciejewska, B., Vandenheuvel, D., Olszak, T., Briers, Y., ... Drulis-Kawa, Z. (2017). The temperate Burkholderia phage AP3 of the Peduovirinae shows efficient antimicrobial activity against B. cenocepacia of the IIIA lineage. Applied Microbiology and Biotechnology, 101(3), 1203–1216. DOI: 10.1007/s00253-016-7924-7 Published in: Applied Microbiology and Biotechnology Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2017 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws.
    [Show full text]
  • Bacteriophage Therapy for Application Against Staphylococcus Aureus Infection and Biofilm in Chronic Rhinosinusitis
    Bacteriophage therapy for application against Staphylococcus aureus infection and biofilm in chronic rhinosinusitis Amanda Jane Drilling Faculty of Health Sciences School of Medicine Discipline of Surgery March 2015 The enemy of my enemy is my friend i Table of Contents I. Abstract ....................................................................................................................................... v II. Declaration ................................................................................................................................ vii III. Acknowledgments ................................................................................................................ viii IV. Presentations and Awards Arising from this thesis ................................................................. x V. List of tables .............................................................................................................................. xii VI. List of Figures ...................................................................................................................... xiii VII. Abbreviations ......................................................................................................................... 1 1 Systematic review of the Literature ........................................................................................... 3 1.1 Rhinosinusitis ..................................................................................................................... 3 1.1.1 Acute and Chronic
    [Show full text]
  • Exploring the Caudovirales: Evaluation of Their Internal Classification and Potential Relationships with the Tectiviridae Juan S
    Exploring the Caudovirales: Evaluation of their Internal Classification and Potential Relationships with the Tectiviridae Juan S. Andrade-Martínez1,2, Alejandro Reyes1,2,3 1. Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia. 2. Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia. 3. Center for Genome Sciences and Systems Biology, Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO, 63108, USA. Abstract The Caudovirales are the most abundant dsDNA viruses, infecting both Bacteria and Archaea. Recently developed distance and network-based approaches have put into question the morphology-based classification of the three traditional Caudovirales families: Podoviridae, Siphoviridae, and Myoviridae, and suggested an evolutionary relationship between such order and the phage family Tectiviridae. In that context, the present work aimed to, using of clusters of viral domain orthologous groups (VDOGs) and k-mers, determine whether the current Caudovirales classification is evolutionarily reasonable and explore the possibility of a common ancestry between Caudovirales and Tectiviridae. For this, we employed over 4000 Caudovirales and 15 Tectiviridae complete genomes obtained from the NCBI Assembly Database. These entries were dereplicated at the genome and protein level, yielding a set of representative proteomes. The latter were screened through a Hidden Markov Model search against a viral domain orthologous groups database to determine which proteomes harbored which VDOGs. A k-mer search was also conducted to establish which k-mers with lengths between 6 and 15 were abundant in the clades of interest. The representative features, k-mers or VDOGs, of the clades were determined, and dendrograms constructed based on them using a Neighbor-joining approach.
    [Show full text]
  • The Genome and Proteome of Serratia Bacteriophage Η Which Forms
    Denyes et al. Virology Journal 2014, 11:6 http://www.virologyj.com/content/11/1/6 RESEARCH Open Access The genome and proteome of Serratia bacteriophage η which forms unstable lysogens Jenna M Denyes1,6, Peter J Krell1, Richard A Manderville2, Hans-Wolfgang Ackermann3, Yi-Min She4 and Andrew M Kropinski1,5* Abstract Background: Serratia marcescens phage η is a temperate unclassified member of the Siphoviridae which had been reported as containing hypermodified guanine residues. Methods: The DNA was characterized by enzymatic digestion followed by HPLC analysis of the nucleoside composition, and by DNA sequencing and proteomic analysis. Its ability to form stable lysogens and integrate was also investigated. Results: Enzymatic digestion and HPLC analysis revealed phage η DNA did not contain modified bases. The genome sequence of this virus, determined using pyrosequencing, is 42,724 nucleotides in length with a mol% GC of 49.9 and is circularly permuted. Sixty-nine putative CDSs were identified of which 19 encode novel proteins. While seven close genetic relatives were identified, they shared sequence similarity with only genes 40 to 69 of the phage η genome, while gp1 to gp39 shared no conserved relationship. The structural proteome, determined by SDS-PAGE and mass spectrometry, revealed seven unique proteins. This phage forms very unstable lysogens with its host S. marcescens. Keywords: Serratia marcescens, Phage evolution, Genome, Proteome, Bioinformatics, Lysogeny, Unstable lysogeny, Modified nucleosides, Siphoviridae Background for use in bacterial typing systems [9,10] or for the trans- Serratia marcescens is a Gram-negative opportunistic ductional mapping of the genome [11,12] and their biol- human pathogen belonging to the family Enterobacteria- ogy remains poorly understood [13].
    [Show full text]
  • A Roadmap for Genome-Based Phage Taxonomy
    viruses Communication A Roadmap for Genome-Based Phage Taxonomy Dann Turner 1 , Andrew M. Kropinski 2,3 and Evelien M. Adriaenssens 4,* 1 Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK; [email protected] 2 Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada; [email protected] 3 Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada 4 Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK * Correspondence: [email protected] Abstract: Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy. Keywords: phage taxonomy; phage classification; Caudovirales; Myoviridae; Podoviridae; Siphoviridae; demarcation criteria 1. An Ongoing Revolution in Phage Taxonomy Historically, phages have been classified according to their morphology, dating from Citation: Turner, D.; Kropinski, A.M.; the time before the existence of PCR, sequencing or many of the molecular methods we Adriaenssens, E.M. A Roadmap for know today [1–3]. For tailed phages, the formal taxonomy was derived from the pioneering Genome-Based Phage Taxonomy. classification work of David Bradley (Memorial University, Canada) who classified them Viruses 2021, 13, 506.
    [Show full text]