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4. Perspective on taxonomic classification of uncultivated viruses

Author

Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, and Sullivan, Matthew B

Published
2021
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5. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author

Turner, Dann, Shkoporov, Andrey N, Lood, Cedric, Millard, Andrew D, Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna, Kropinski, Andrew M., Barylski, Jakub, Brister, J. Rodney, Chanisvili, Nina, Edwards, Rob, Enault, Francois, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtboke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan M, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea I., Morozova, Vera, Nakavuma, Jesca, Reyes Munoz, Alejandro, Rumnieks, Janis, Sarkar, B L, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M., Molecular and Integrative Biosciences Research Programme, Molecular Principles of Viruses, and Molecular and Translational Virology

Subjects
11832 Microbiology and virology
Published
2023

6. Phage therapy to allow liver transplantation in a toddler infected by an extensively drug-resistant Pseudomonas aeruginosa

Author

UCL - SSS/IREC/PEDI - Pôle de Pédiatrie, UCL - SSS/IREC/CHEX - Pôle de chirgurgie expérimentale et transplantation, UCL - (SLuc) Service de gastro-entérologie et hépatologie pédiatrique, UCL - (SLuc) Service de pédiatrie générale, UCL - (SLuc) Service de chirurgie et transplantation abdominale, Van Nieuwenhuyse, Brieuc, van Der Linden, Dimitri, Chatzis, Olga, Lood, Cedric, Wagemans, Jeroen, Lavigne, Rob, de Magnee, Catherine, Sokal, Etienne, Rodriguez-Villalobos, Hector, Djebara, Sarah, Soentjens, Patrick, Pirnay, Jean-Paul, International Pediatric Transplant Association, UCL - SSS/IREC/PEDI - Pôle de Pédiatrie, UCL - SSS/IREC/CHEX - Pôle de chirgurgie expérimentale et transplantation, UCL - (SLuc) Service de gastro-entérologie et hépatologie pédiatrique, UCL - (SLuc) Service de pédiatrie générale, UCL - (SLuc) Service de chirurgie et transplantation abdominale, Van Nieuwenhuyse, Brieuc, van Der Linden, Dimitri, Chatzis, Olga, Lood, Cedric, Wagemans, Jeroen, Lavigne, Rob, de Magnee, Catherine, Sokal, Etienne, Rodriguez-Villalobos, Hector, Djebara, Sarah, Soentjens, Patrick, Pirnay, Jean-Paul, and International Pediatric Transplant Association

Abstract

Brieuc Van Nieuwenhuyse1, Dimitri Van der Linden1,2, Olga Chatzis2, Cédric Lood3,4, Jeroen Wagemans3, Rob Lavigne4, Catherine de Magnée5, Étienne Sokal1,6, Hector Rodriguez-Villalobos7, Sarah Djebara8, Maya Merabishvili9, Patrick Soentjens8, Jean-Paul Pirnay9. 1Institute of Experimental and Clinical Research's Pediatric department, UCLouvain, Brussels, Belgium; 2Pediatric Infectious Diseases, General Pediatrics Department, Cliniques universitaires Saint-Luc, Brussels, Belgium; 3Department of Biosystems, Laboratory of Gene Technology, KULeuven, Leuven, Belgium; 4Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KULeuven, Leuven, Belgium; 5Pediatric and Transplantation Surgery, Cliniques universitaires Saint-Luc, Brussels, Belgium; 6Pediatric Hepatology and Gastro-enterology, Cliniques universitaires Saint-Luc, Brussels, Belgium; 7Department of Microbiology, Cliniques universitaires Saint-Luc, Brussels, Belgium; 8Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium; 9Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium A 14-month old boy undergoes a first liver transplantation (LT) (Day 0), from an ABO-incompatible living donor. On D+20, we detect a fecal carriage of an extensively drug-resistant (XDR) Pseudomonas aeruginosa (Pa) strain. Besides intermediate susceptibility to aztreonam and colistin and susceptibility to gentamycin, the strain is resistant to all other antibiotics. On D+53, the child enters a severe septic state due to a bacteremia with the same Pa strain. New antibiogram suggests a resistance to colistin. Liver bilomas' drainage material is cultured and grows the same Pa strain. Admission to the pediatric intensive care unit and adjunction of intravenous (IV) aztreonam, gentamycin, and colistin led to no improvement on the microbiological or clinical levels during the next four days. By collaborating with Queen Astrid Military Hospital (Bru

Published
2022

7. Phage therapy to allow liver transplantation in a toddler infected by an extensively drug-resistant Pseudomonas aeruginosa

Author

Van Nieuwenhuyse, Brieuc, van Der Linden, Dimitri, Chatzis, Olga, Lood, Cedric, Wagemans, Jeroen, Lavigne, Rob, de Magnee, Catherine, Sokal, Etienne, Rodriguez-Villalobos, Hector, Djebara, Sarah, Soentjens, Patrick, Pirnay, Jean-Paul, International Pediatric Transplant Association, UCL - SSS/IREC/PEDI - Pôle de Pédiatrie, UCL - SSS/IREC/CHEX - Pôle de chirgurgie expérimentale et transplantation, UCL - (SLuc) Service de gastro-entérologie et hépatologie pédiatrique, UCL - (SLuc) Service de pédiatrie générale, and UCL - (SLuc) Service de chirurgie et transplantation abdominale

Abstract

Brieuc Van Nieuwenhuyse1, Dimitri Van der Linden1,2, Olga Chatzis2, Cédric Lood3,4, Jeroen Wagemans3, Rob Lavigne4, Catherine de Magnée5, Étienne Sokal1,6, Hector Rodriguez-Villalobos7, Sarah Djebara8, Maya Merabishvili9, Patrick Soentjens8, Jean-Paul Pirnay9. 1Institute of Experimental and Clinical Research's Pediatric department, UCLouvain, Brussels, Belgium; 2Pediatric Infectious Diseases, General Pediatrics Department, Cliniques universitaires Saint-Luc, Brussels, Belgium; 3Department of Biosystems, Laboratory of Gene Technology, KULeuven, Leuven, Belgium; 4Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KULeuven, Leuven, Belgium; 5Pediatric and Transplantation Surgery, Cliniques universitaires Saint-Luc, Brussels, Belgium; 6Pediatric Hepatology and Gastro-enterology, Cliniques universitaires Saint-Luc, Brussels, Belgium; 7Department of Microbiology, Cliniques universitaires Saint-Luc, Brussels, Belgium; 8Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium; 9Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium A 14-month old boy undergoes a first liver transplantation (LT) (Day 0), from an ABO-incompatible living donor. On D+20, we detect a fecal carriage of an extensively drug-resistant (XDR) Pseudomonas aeruginosa (Pa) strain. Besides intermediate susceptibility to aztreonam and colistin and susceptibility to gentamycin, the strain is resistant to all other antibiotics. On D+53, the child enters a severe septic state due to a bacteremia with the same Pa strain. New antibiogram suggests a resistance to colistin. Liver bilomas' drainage material is cultured and grows the same Pa strain. Admission to the pediatric intensive care unit and adjunction of intravenous (IV) aztreonam, gentamycin, and colistin led to no improvement on the microbiological or clinical levels during the next four days. By collaborating with Queen Astrid Military Hospital (Brussels, Belgium), we initiated phage therapy (PT) on D+57 in accordance to the Article 37 of the Declaration of Helsinki and with the patient's parents' consent. PT is the use of lytic bacteriophage viruses to achieve antibacterial effect. Phage cocktail BFC1 contains two anti-Pa phages (PNM and 14/1) and one anti-Staphylococcus aureus phage (ISP). BFC1 was administered in situ by instillations through biliary catheter during six days, and in IV for 86 days (72 days until 2nd LT, 14 days afterwards), the longest described duration for IV PT in a child. Previous antibiotic therapy was pursued all along. Intraoperative PT was performed during 2nd LT by bathing the peritoneal cavity in phage solution during the anhepatic phase. To further our understanding of the case, seven Pa isolates, both bloodborne and liver-borne, were sequenced. Serum samples obtained before, during, and after phage therapy were analyzed through double agar overlay method to search for phage immune neutralization (PIN). Phage-induced virulence tradeoffs (PIVT) assays were performed in a Galleria mellonella model. In vitro phage-antibiotic interactions were evaluated with OmniLog® system. PT initiation was followed by immediate (

Published
2022

8. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: Update of taxonomy changes in 2021

Author

Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, UCL - SST/ELI/ELIM - Applied Microbiology, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], University of the West of England [Bristol] (UWE Bristol), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), University of Melbourne, University of Helsinki, Flinders Accelerator for Microbiome Exploration [Adelaide, Australia], Utrecht University [Utrecht], U.S. Food and Drug Administration (FDA), Universidad de los Andes [Bogota] (UNIANDES), Ohio State University [Columbus] (OSU), Azabu University, Makerere University [Kampala, Ouganda] (MAK), Adam Mickiewicz University in Poznań (UAM), Montana State University (MSU), Wuhan University [China], Universidade Federal de Vicosa (UFV), National Academy of Sciences of Ukraine (NASU), University of Guelph, University of the Sunshine Coast (USC), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Indian Council of Medical Research [New Dehli] (ICMR), Beijing University of Chemical Technology, Chinese Academy of Sciences [Beijing] (CAS), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], University of the Western Cape, Latvian Biomedical Research and Study Centre [Rīga], Tokyo Institute of Technology [Tokyo] (TITECH), University of Jyväskylä (JYU), Cairo University, Polish Academy of Sciences (PAN), Portland State University [Portland] (PSU), University College Cork (UCC), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Copenhagen = Københavns Universitet (KU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), University of Novi Sad, Chungbuk National University, University of Oldenburg, Pontificia Universidad Católica de Chile (UC), University of Leicester, Ivane Javakhishvili Tbilisi State University (TSU), Quadram Institute, V.M. was supported by Russian Ministry of Education and Science Project No. 0245-2021-0008, H.M.O. was supported by University of Helsinki funding for FINStruct and Instruct-ERIC research infrastructure, R.A.E. was supported by the National Institute Of Diabetes And Digestive And Kidney Diseases of the National Institutes of Health under Award Number RC2DK116713, B.E.D. was supported by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI, M.B.S. was supported by National Science Foundation Advances in Biological Infrastructure award #1758974, M.Y. acknowledges funding by the Gordon and Betty Moore Foundation grant GBMF9195, S.D. was supported by National Natural Science Foundation of of China grant 32070032, C.L. is supported by the Fonds Wetenschappelijk Onderzoek (1S64718N), L.H. was funded by the Strategic Priority Research Program of the Chinese Academy of Sciences Award XDB42000000,National Natural Science Foundation of China (NSFC) grant 31970170, T.M. was supported by JSPS KAKENHI Grant Numbers 21H02100, 19H04827, 18K14372, and JST JPMJJR2005, and SUMITOMO Fund 200673, MJ is supported by Academy of Finland grants #336518 and #297049 and Jane and Aatos Erkko Foundation, R.K.A. is supported by the Egyptian Academy of Scientific Research and Technology (ASRT) project #3046 (JESOR), M.L. is supported by the statutory funds for the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, K.M.S. is supported by the US. National Science Foundation (MCB1929273 and MCB2025305), A.N.S. is supported by Wellcome Trust Research Career Development Fellowship (220646/Z/20/Z) and by European Research Council (ERC) grant under the European Union’s Horizon 2020 research and innovation programme (grant agreement 101001684), X.P. is supported by Novo Nordisk Foundation/Hallas-Møller Ascending Investigator Grant (grant number NNF17OC0031154) and the Danish Council for Independent Research/FNU (grant number DFF–0135-00402), S.K.R. was supported by the National Research Foundation of Korea (NRF) grants funded by the Ministry of Science, ICT & Future Planning (2021R1A2C3004015), C.M. acknowledges funding by the Deutsche Forschungsgemeinschaft within the Collaborative Research Center TRR51 Roseobacter (INST 184/170-1), M.M.P. acknowledges funding from the Academy of Finland (grant 331627) and the Sigrid Juselius Foundation, E.M.A. gratefully acknowledges funding by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), European Project: 101001684,ERC-2020-COG,PHAGENET(2021), Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University of the Western Cape (UWC), University of Copenhagen = Københavns Universitet (UCPH), Biotechnology and Biological Sciences Research Council (BBSRC), Molecular and Integrative Biosciences Research Programme, and Molecular and Translational Virology

Subjects
Archaeal Viruses, Societies, Scientific, virukset, Library science, Biology, bakteriofagit, Executive committee, 03 medical and health sciences, Virology Division News, Virology, viruses, Bacteriophages, 030304 developmental biology, Taxonomy, 11832 Microbiology and virology, 0303 health sciences, Science & Technology, Bacteria, 030306 microbiology, systematiikka (biologia), General Medicine, Archaea, virologia, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonomy (biology), Bacterial virus, Life Sciences & Biomedicine
Abstract

In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted). Supplementary Information The online version contains supplementary material available at 10.1007/s00705-021-05205-9.

Published
2021
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9. In Vitro Evaluation of the Therapeutic Potential of Phage VA7 against Enterotoxigenic Bacteroides fragilis Infection

Author

Bakuradze, Nata, primary, Merabishvili, Maya, additional, Makalatia, Khatuna, additional, Kakabadze, Elene, additional, Grdzelishvili, Nino, additional, Wagemans, Jeroen, additional, Lood, Cedric, additional, Chachua, Irakli, additional, Vaneechoutte, Mario, additional, Lavigne, Rob, additional, Pirnay, Jean-Paul, additional, Abiatari, Ivane, additional, and Chanishvili, Nina, additional

Published
2021
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10. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.

Published
2021

11. Analyses of the complete genome sequence of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of (un)stable plasmids

Author

Nielsen, Tue Kjærgaard, primary, Horemans, Benjamin, additional, Lood, Cedric, additional, T’Syen, Jeroen, additional, van Noort, Vera, additional, Lavigne, Rob, additional, Ellegaard-Jensen, Lea, additional, Hylling, Ole, additional, Aamand, Jens, additional, Springael, Dirk, additional, and Hansen, Lars Hestbjerg, additional

Published
2021
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