Page 26 - Read Online
P. 26

Page 20 of 21              O’Connell et al. Microbiome Res Rep 2023;2:21  https://dx.doi.org/10.20517/mrr.2023.17

               REFERENCES
               1.       Saxena S, Spaink HP, Forn-Cuní G. Drug resistance in nontuberculous mycobacteria: mechanisms and models. Biology 2021;10:96.
                   DOI  PubMed  PMC
               2.       Tarashi S, Siadat SD, Fateh A. Nontuberculous mycobacterial resistance to antibiotics and disinfectants: challenges still ahead. Biomed
                   Res Int 2022;2022:8168750.  DOI  PubMed  PMC
               3.       Field NL, McAloon CG, Gavey L, Mee JF. Mycobacterium avium subspecies paratuberculosis infection in cattle - a review in the
                   context of seasonal pasture-based dairy herds. Ir Vet J 2022;75:12.  DOI  PubMed  PMC
               4.       Allué-Guardia A, Saranathan R, Chan J, Torrelles JB. Mycobacteriophages as potential therapeutic agents against drug-resistant
                   tuberculosis. Int J Mol Sci 2021;22:735.  DOI  PubMed  PMC
               5.       Dedrick RM, Guerrero-Bustamante CA, Garlena RA, et al. Engineered bacteriophages for treatment of a patient with a disseminated
                   drug-resistant Mycobacterium abscessus. Nat Med 2019;25:730-3.  DOI  PubMed  PMC
               6.       Hatfull GF, Dedrick RM, Schooley RT. Phage Therapy for Antibiotic-resistant bacterial infections. Annu Rev Med 2022;73:197-211.
                   DOI  PubMed
               7.       Lawrence JG, Hatfull GF, Hendrix RW. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J
                   Bacteriol 2002;184:4891-905.  DOI  PubMed  PMC
               8.       Nelson D. Phage taxonomy: we agree to disagree. J Bacteriol 2004;186:7029-31.  DOI  PubMed  PMC
               9.       Adriaenssens E, Brister JR. How to name and classify your phage: an informal guide. Viruses 2017;9:70.  DOI  PubMed  PMC
               10.      Moraru C, Varsani A, Kropinski AM. VIRIDIC-A novel tool to calculate the intergenomic similarities of prokaryote-infecting Viruses.
                   Viruses 2020;12:1268.  DOI  PubMed  PMC
               11.      Adriaenssens EM. Phage diversity in the human gut microbiome: a taxonomist’s perspective. mSystems 2021;6:e0079921.  DOI
                   PubMed  PMC
               12.      Turner D, Kropinski AM, Adriaenssens EM. A roadmap for genome-based phage taxonomy. Viruses 2021;13:506.  DOI  PubMed
                   PMC
               13.      Sharma S, Datta S, Chatterjee S, et al. Isolation and characterization of a lytic bacteriophage against Pseudomonas aeruginosa. Sci Rep
                   2021;11:19393.  DOI  PubMed  PMC
               14.      Gorbalenya AE, Lauber C. Bioinformatics of virus taxonomy: foundations and tools for developing sequence-based hierarchical
                   classification. Curr Opin Virol 2022;52:48-56.  DOI  PubMed
               15.      Rodwell EV, Wenner N, Pulford CV, et al. Isolation and characterisation of bacteriophages with activity against invasive non-
                   typhoidal salmonella causing bloodstream infection in Malawi. Viruses 2021;13:478.  DOI  PubMed  PMC
               16.      Stanton CR, Rice DTF, Beer M, Batinovic S, Petrovski S. Isolation and characterisation of the bundooravirus genus and phylogenetic
                   investigation of the salasmaviridae bacteriophages. Viruses 2021;13:1557.  DOI  PubMed  PMC
               17.      Li J, Tian F, Hu Y, et al. Characterization and genomic analysis of BUCT549, a novel bacteriophage infecting vibrio alginolyticus with
                   flagella as receptor. Front Microbiol 2021;12:668319.  DOI  PubMed  PMC
               18.      Hatfull GF. Mycobacteriophages. Microbiol Spectr 2018:6.  DOI  PubMed  PMC
               19.      Hatfull GF. Mycobacteriophages: From Petri dish to patient. PLoS Pathog 2022;18:e1010602.  DOI  PubMed  PMC
               20.      Pope WH, Bowman CA, Russell DA, et al; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary
                   Science; Phage Hunters Integrating Research and Education; Mycobacterial Genetics Course. Whole genome comparison of a large
                   collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife 2015;4:e06416.  DOI  PubMed  PMC
               21.      Agren J, Sundström A, Håfström T, Segerman B. Gegenees: fragmented alignment of multiple genomes for determining phylogenomic
                   distances and genetic signatures unique for specified target groups. PLoS One 2012;7:e39107.  DOI  PubMed  PMC
               22.      Kyrkou I, Carstens AB, Ellegaard-Jensen L, et al. Isolation and characterisation of novel phages infecting Lactobacillus plantarum and
                   proposal of a new genus, “Silenusvirus”. Sci Rep 2020;10:8763.  DOI  PubMed  PMC
               23.      Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics
                   2017;33:3396-404.  DOI  PubMed  PMC
               24.      Mavrich TN, Hatfull GF. Bacteriophage evolution differs by host, lifestyle and genome. Nat Microbiol 2017;2:17112.  DOI  PubMed
                   PMC
               25.      Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. Phamerator: a bioinformatic tool for comparative
                   bacteriophage genomics. BMC Bioinformatics 2011;12:395.  DOI  PubMed  PMC
               26.      Jacobs-sera D, Marinelli LJ, Bowman C, et al; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary
                   Science (SEA-PHAGES) program. On the nature of mycobacteriophage diversity and host preference. Virology 2012;434:187-201.
                   DOI  PubMed  PMC
               27.      Grose JH, Casjens SR. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family
                   Enterobacteriaceae. Virology 2014;468-470:421-43.  DOI  PubMed  PMC
               28.      Demo S, Kapinos A, Bernardino A, et al. BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of
                   Arthrobacter phage Cluster FE. PLoS One 2021;16:e0248418.  DOI  PubMed  PMC
               29.      Mu A, Lawley TD. Bacteriophage discovery to advance biotechnology and biotherapeutics. Nat Rev Microbiol 2023;21:279.  DOI
                   PubMed
               30.      Crane A, Versoza CJ, Hua T, et al. Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages. G3
                   2021;11:jkab291.  DOI  PubMed  PMC
   21   22   23   24   25   26   27   28   29   30   31