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Characterization and in vitro testing of newly isolated lytic bacteriophages for the biocontrol of Pseudomonas aeruginosa

    Liliam K Harada

    PhageLab – Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil

    ,
    Erica C Silva

    PhageLab – Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil

    ,
    Fernando PN Rossi

    Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil

    ,
    Basilio Cieza

    Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA

    ,
    Thais J Oliveira

    PhageLab – Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil

    ,
    Carla Pereira

    Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal

    ,
    Geizecler Tomazetto

    Department of Engineering, Biological & Chemical Engineering Section (BCE), Aarhus University, Aarhus, Denmark

    ,
    Bianca B Silva

    PhageLab – Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil

    ,
    Fabio M Squina

    PhageLab – Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil

    ,
    Marta MDC Vila

    PhageLab – Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil

    ,
    João C Setubal

    Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil

    ,
    Taekjip Ha

    Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA

    ,
    Aline M da Silva

    Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil

    &
    Victor M Balcão

    *Author for correspondence: Tel.: +55 (15) 2101 7029;

    E-mail Address: victor.balcao@prof.uniso.br

    PhageLab – Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil

    Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal

    Published Online:https://doi.org/10.2217/fmb-2021-0027

    Aim: Two lytic phages were isolated using P. aeruginosa DSM19880 as host and fully characterized. Materials & methods: Phages were characterized physicochemically, biologically and genomically. Results & conclusion: Host range analysis revealed that the phages also infect some multidrug-resistant (MDR) P. aeruginosa clinical isolates. Increasing MOI from 1 to 1000 significantly increased phage efficiency and retarded bacteria regrowth, but phage ph0034 (reduction of 7.5 log CFU/ml) was more effective than phage ph0031 (reduction of 5.1 log CFU/ml) after 24 h. Both phages belong to Myoviridae family. Genome sequencing of phages ph0031 and ph0034 showed that they do not carry toxin, virulence, antibiotic resistance and integrase genes. The results obtained are highly relevant in the actual context of bacterial resistance to antibiotics.

    References

    • 1. Prestinaci F, Pezzotti P, Pantosti A. Antimicrobial resistance: a global multifaceted phenomenon. Pathog. Glob. Health 109(7), 309–318 (2015).
    • 2. Ferri M, Ranucci E, Romagnoli P, Giaccone V. Antimicrobial resistance: a global emerging threat to public health systems. Crit. Rev. Food Sci. Nutr. 57(13), 2857–2876 (2017).
    • 3. Naylor NR, Atun R, Zhu N et al. Estimating the burden of antimicrobial resistance: a systematic literature review. Antimicrob. Resist. Infect. Control 7, 58 (2018).
    • 4. Tacconelli E, Magrini N, Carmeli Y et al. Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics. World Health Organ. 1–7 (2017).
    • 5. Pires DP, Boas DV, Sillankorva S, Azeredo J. Phage therapy: a step forward in the treatment of Pseudomonas aeruginosa infections. J. Virol. 89, 7449–7566 (2015).
    • 6. CDC. Antibiotic resistance threats in the United States. GA, USA www.cdc.gov/drugresistance/pdf/threats–report/2019–ar–threats–report–508.pdf
    • 7. Kerr K, Senelling A. Pseudomonas aeruginosa: a formidable and ever-present adversary. J. Hosp. Infect. 73, 338–344 (2009).
    • 8. Pachori P, Gothalwal R, Gandhi P. Emergence of antibiotic resistance Pseudomonas aeruginosa in intensive care unit: a critical review. Genes Dis. 6(2), 109–119 (2019).
    • 9. Poole K. Outer membranes and efflux: the path to multidrug resistance in Gram-negative bacteria. Curr. Pharm. Biotechnol. 3, 77–98 (2002).
    • 10. Wagner V, Filiatrault M, Picardo K, Iglewski B, Cornelis P. Pseudomonas: genomics and molecular biology. Caister Academic Press, Norfolk, UK, (2008).
    • 11. Fajardo A, Martínez-Martín N, Mercadillo M et al. The neglected intrinsic resistome of bacterial pathogens. PLoS One. 3, e1619 (2008).
    • 12. Botelho J, Grosso F, Peixe L. Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist. Updat. 44, 26–47 (2019).
    • 13. Breidenstein EB, de la Fuente-Núñez C, Hancock RE. Pseudomonas aeruginosa: all roads lead to resistance. Trends Microbiol. 19, 419–426 (2011).
    • 14. Lopes A, Pereira C, Almeida A. Sequential combined effect of phages and antibiotics on the inactivation of E. coli. Microorganisms 6(125), 2–20 (2018).
    • 15. Dorotkiewicz–Jach A, Augustyniak D, Olszak T, Drulis-Kawa Z. Modern therapeutic approaches against Pseudomonas aeruginosa infections. Curr. Med. Chem. 22(14), 1642–1664 (2015).
    • 16. Chan BK, Abedon ST, Loc-Carrillo C. Phage cocktails and the future of phage therapy. Future Microbiol. 8(6), 769–783 (2013).
    • 17. Haq IU, Chaudhry WN, Akhtar MN, Andleeb S, Qadri I. Bacteriophages and their implications on future biotechnology: a review. Virol. J. 9(1), 2–8 (2012).
    • 18. Górski A, Międzybrodzki R, Węgrzyn G, Jończyk-Matysiak E, Borysowski J, Weber-Dąbrowska B. Phage therapy: current status and perspectives. Med. Res. Rev. 40(1), 459–463 (2020).
    • 19. Kortright KE, Chan BK, Koff JL, Turner PE. Phage therapy: a renewed approach to combat antibiotic-resistant bacteria. Cell Host Microbe 25(2), 219–232 (2019).
    • 20. Rios AC, Moutinho CG, Pinto FC et al. Alternatives to overcoming bacterial resistances: state-of-the-art. Microbiol. Res. 191, 51–80 (2016).
    • 21. Harada LK, Silva EC, Campos WF et al. Biotechnological applications of bacteriophages: state of the art. Microbiol. Res. 212–213, 38–58 (2018).
    • 22. Almeida A, Cunha Â, Gomes NCM, Alves E, Costa L, Faustino MAF. Phage therapy and photodynamic therapy: low environmental impact approaches to inactivate microorganisms in fish farming plants. Mar. Drugs 7(3), 268–313 (2009).
    • 23. Beeton ML, Alves DR, Enright MC, Jenkins ATA. Assessing phage therapy against Pseudomonas aeruginosa using a Galleria mellonella infection model. Int. J. Antimicrob. Agents 46(2), 196–200 (2015).
    • 24. Debarbieux L, Leduc D, Maura D et al. Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections. J. Infect. Dis. 201(7), 1096–1104 (2010).
    • 25. Forti F, Roach DR, Cafora M et al. Design of a broad-range bacteriophage cocktail that reduces Pseudomonas aeruginosa biofilms and treats acute infections in two animal models. Antimicrob. Agents Chemother. 62(6), e02573–17 (2018).
    • 26. Chegini Z, Khoshbayan A, Moghadam MT, Farahani I, Jazireian P, Shariati A. Bacteriophage therapy against Pseudomonas aeruginosa biofilms: a review. Ann. Clin. Microbiol. Antimicrob. 19, 45 (2020).
    • 27. Alvi IA, Asif M, Tabassum R, Aslam R, Abbas Z, Rehman SU. RLP, a bacteriophage of the family Podoviridae, rescues mice from bacteremia caused by multi-drug-resistant Pseudomonas aeruginosa. Arch. Virol. 165, 1289–1297 (2020).
    • 28. Ceyssens PJ, Lavigne R. Bacteriophages of Pseudomonas. Future Microbiol. 5(7), 1041–1055 (2010).
    • 29. Danis-Wlodarczyk K, Olszak T, Arabski M et al. Characterization of the newly isolated lytic bacteriophages KTN6 and KT28 and their efficacy against Pseudomonas aeruginosa biofilm. PLoS ONE 10(5), e0127603 (2015).
    • 30. Duplessis C, Biswas B, Hanisch B et al. Refractory Pseudomonas bacteremia in a 2-year-old sterilized by bacteriophage therapy. J. Pediatric Infect. Dis. Soc. 7, 253–256 (2017).
    • 31. Jault P, Leclerc T, Jennes S et al. Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial. Lancet Infect. Dis. 19, 35–45 (2019).
    • 32. Hyman P, Abedon ST. Bacteriophage host range and bacterial resistance. Adv. Appl. Microbiol. 70, 217–248 (2010).
    • 33. Chaturongakul S, Ounjai P. Phage–host interplay: examples from tailed phages and Gram-negative bacterial pathogens. Front. Microbiol. 5, 442 (2014).
    • 34. Adams MH. Bacteriophages. Adams MH (Ed.). Interscience Publishers, Inc., London, UK, 592 (1959).
    • 35. Rios AC, Vila MMDC, Lima R et al. Structural and functional stabilization of bacteriophage particles within the aqueous core of a W/O/W multiple emulsion: a potential biotherapeutic system for the inhalational treatment of bacterial pneumonia. Process Biochem. 64(September 2017), 177–192 (2018).
    • 36. Silva EC, Oliveira TJ, Moreli FC, Harada LK, Vila MMDC, Balcão VM. Newly isolated lytic bacteriophages for Staphylococcus intermedius, structurally and functionally stabilized in a hydroxyethylcellulose gel containing choline geranate: potential for transdermal permeation in veterinary phage therapy. Res. Vet. Sci. 135, 42–58 (2021).
    • 37. Scherrer P. Bestimmung der Größe und der inneren Struktur von Kolloidteilchen mittels Röntgenstrahlen. Nachrichten von der Gesellschaft der Wissenschaften zu Göttingen. 26(98–100), (1918).
    • 38. Pereira C, Moreirinha C, Lewicka M et al. Bacteriophages with potential to inactivate Salmonella typhimurium: Use of single phage suspensions and phage cocktails. Virus Res. 220, 179–192 (2016).
    • 39. Pinheiro LAM, Pereira C, Barreal ME, Gallego PP, Balcão VM, Almeida A. Use of phage ϕ6 to inactivate Pseudomonas syringae pv. actinidiae in kiwifruit plants: in vitro and ex vivo experiments. Appl. Microbiol. Biotechnol. 104(3), 1319–1330 (2020).
    • 40. Melo LDR, Sillankorva S, Ackermann H–W, Kropinski AM, Azeredo J, Cerca N. Isolation and characterization of a new Staphylococcus epidermidis broad-spectrum bacteriophage. J. Gen. Virol. 95, 506–515 (2014).
    • 41. Pinheiro LAM, Pereira C, Frazão C, Balcão VM, Almeida A. Efficiency of phage ϕ6 for biocontrol of Pseudomonas syringae pv. syringae: an in vitro preliminary study. Microorganisms 7(9), 286 (2019).
    • 42. Pinheiro LAM, Pereira C, Barreal ME, Gallego PP, Balcão VM, Almeida A. Use of phage ϕ6 to inactivate Pseudomonas syringae pv. actinidiae in kiwifruit plants: in vitro and ex vivo experiments. Appl. Microbiol. Biotechnol. 104(3), 1319–1330 (2019).
    • 43. Stuer-Lauridsen B, Janzen T, Schnabl J, Johansen E. Identification of the host determinant of two prolate-headed phages infecting Lactococcus lactis. Virology 309(1), 10–17 (2003).
    • 44. Shao Y, Wang I-N. Bacteriophage adsorption rate and optimal lysis time. Genetics 180(1), 471–482 (2008).
    • 45. Santos SB, Carvalho C, Azeredo J, Ferreira EC. Population dynamics of a Salmonella lytic phage and its host: implications of the host bacterial growth rate in modelling. PLoS ONE 9(7), e102507 (2014).
    • 46. García R, Latz S, Romero J, Higuera G, García K, Bastías R. Bacteriophage production models: an overview. Front. Microbiol. 10(June), 1–7 (2019).
    • 47. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17), i884–i890 (2018).
    • 48. Bankevich A, Nurk S, Antipov D et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455–477 (2012).
    • 49. Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 7(9), e42304 (2012).
    • 50. Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics 29(21), 2669–2677 (2013).
    • 51. Hunt M, Gall A, Ong SH et al. IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics 31(14), 2374–2376 (2015).
    • 52. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8), 1072–1075 (2013).
    • 53. Wences AH, Schatz MC. Metassembler: merging and optimizing de novo genome assemblies. Genome Biol. 16, 207 (2015).
    • 54. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
    • 55. Zhou CLE, Kimbrel J, Edwards R, McNair K, Souza BA, Malfatti S. MultiPhATE2: code for functional annotation and comparison of bacteriophage genomes. doi: https://doi.org/10.1101/2020.10.05.324566 bioRxiv (2020).
    • 56. Grazziotin AL, Koonin EV, Kristensen DM. Prokaryotic virus orthologous groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 45(D1), D491–D498 (2017).
    • 57. Brister JR, Ako-adjei D, Bao Y, Blinkova O. NCBI viral genomes resource. Nucleic Acids Res. 43(D1), D571–D577 (2015).
    • 58. Overbeek R, Olson R, Pusch GD et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 42(D1), D206–D214 (2014).
    • 59. Bolduc B, Jang HB, Doulcier G, You Z-Q, Roux S, Sullivan MB. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect archaea and bacteria. PeerJ. 5, e3243 (2017).
    • 60. Li W, Godzik A. CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13), 1658–1659 (2006).
    • 61. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Br. Bioinform. 20(4), 1160–1166 (2019).
    • 62. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26(7), 1641–1650 (2009).
    • 63. Zhou T, Yang L, Lu Y et al. DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res. 41, W56–W62 (2013).
    • 64. Pires DP, Oliveira H, Melo LDR, Sillankorva S, Azeredo J. Bacteriophage-encoded depolymerases: their diversity and biotechnological applications. Appl. Microbiol. Biotechnol. 100(5), 2141–2151 (2016).
    • 65. Oliveira H, São-José C, Azeredo J. Phage-derived peptidoglycan degrading enzymes: challenges and future prospects for in vivo therapy. Viruses 10(6), 292 (2018).
    • 66. Hyman P. Phages for phage therapy: isolation, characterization and host range breadth. Pharmaceuticals 12, 35 (2019).
    • 67. Mbonyiryivuze A, Omollo I, Ngom BD et al. Natural dye sensitizer for Grätzel cells: Sepia melanin. Phys. Mater. Chem. 3(1), 1–6 (2015).
    • 68. Pereira C, Moreirinha C, Lewicka M et al. Characterization and in vitro evaluation of new bacteriophages for the biocontrol of Escherichia coli. Virus Res. 227, 171–182 (2017).
    • 69. Hawkins C, Harper D, Burch D, Anggard E, Soothill J. Topical treatment of Pseudomonas aeruginosa otitis of dogs with a bacteriophage mixture: a before/after clinical trial. Vet. Microbiol. 146, 309–313 (2010).
    • 70. Meaden S, Koskella B. Exploring the risks of phage application in the environment. Front. Microbiol. 4, 358 (2013).
    • 71. Abedon ST. Lysis from without. Bacteriophage 1(1), 46–49 (2011).
    • 72. Ross A, Ward S, Hyman P. More is better: selecting for broad host range bacteriophages. Front. Microbiol. 7, 1352 (2016).
    • 73. Kutter E. Phage host range and efficiency of plating. In: Bacteriophage: Methods and protocols. Clokie MRKropinski AM (Ed.). Humana Press, 141–149 (2009).
    • 74. Seed KD. Battling phages: how bacteria defend against viral attack. PLOS Pathog. 11, e1004847 (2015).
    • 75. Speyer JF, Khairallah LH. Crystalline T4 bacteriophage. J. Mol. Biol. 76(3), 415–417 (1973).
    • 76. Fischer C, Yoichi M, Unno H, Tanji Y. The coexistence of Escherichia coli serotype O157:H7 and its specific bacteriophage in continuous culture. FEMS Microbiol. Lett. 241, 171–177 (2004).
    • 77. Cao Z, Zhang J, Niu YD et al. Isolation and characterization of a “phiKMV–like” bacteriophage and its therapeutic effect on mink hemorrhagic pneumonia. PLoS One 10(1), e0116571 (2015).
    • 78. Abedon S, Culler RR. Optimizing bacteriophage plaque fecundity. J. Theor. Biol. 249, 582–592 (2007).
    • 79. Mateus L, Costa L, Silva YJ, Pereira C, Cunha A, Almeida A. Efficiency of phage cocktails in the inactivation of Vibrio in aquaculture. Aquaculture 424–425, 167–173 (2014).
    • 80. Bull JJ, Gill JJ. The habits of highly effective phages: population dynamics as a framework for identifying therapeutic phages. Front. Microbiol. 5, 1–12 (2014).
    • 81. Drulis–Kawa Z, Majkowska–Skrobek G, Maciejewska B, Delattre A–S, Lavigne R. Learning from bacteriophages – advantages and limitations of phage and phage-encoded protein applications. Curr. Protein Pept. Sci. 13(8), 699–722 (2012).
    • 82. Jin J, Li ZJ, Wang S-W et al. Isolation and characterization of ZZ1, a novel lytic phage that infects Acinetobacter baumannii clinical isolates. BMC Microbiol. 12, 156 (2012).
    • 83. Ceyssens P-J. Isolation and characterization of lytic bacteriophages infecting Pseudomonas aeruginosa. ISBN 978–90–8826–123–7 (2009).
    • 84. Hyman P, Abedon ST. Practical methods for determining phage growth parameters. In: Bacteriophages: methods and protocols, volume 1: isolation, characterization, and interactions. Clokie MRJKropinski AM (Eds). Humana Press, 175–202 (2009).
    • 85. Moldovan R, Chapman-McQuiston E, Wu XL. On kinetics of phage adsorption. Biophys. J. 93(1), 303–315 (2007).
    • 86. Storms ZJ, Sauvageau D. Modeling tailed bacteriophage adsorption: insight into mechanisms. Virology 485, 355–362 (2015).
    • 87. Rakhuba DV, Kolomiets EI, Szwajcer Dey E, Novik GI. Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Polish J. Microbiol. 59(3), 145–155 (2010).
    • 88. Lindberg HM, McKean KA, Wang I–N. Phage fitness may help predict phage therapy efficacy. Bacteriophage 4(4), e964081 (2014).
    • 89. Shephard J, McQuillan AJ, Bremer PJ. Mechanisms of cation exchange by Pseudomonas aeruginosa PAO1 and PAO1 wbpL, a strain with a truncated lipopolysaccharide. Appl. Environ. Microbiol. 74(22), 6980–6986 (2008).
    • 90. Marcus IM, Herzberg M, Walker SL, Freger V. Pseudomonas aeruginosa attachment on QCM-D sensors: the role of cell and surface hydrophobicities. Langmuir 28(15), 6396–6402 (2012).
    • 91. Esteban PP, Jenkins ATA, Arnot TC. Elucidation of the mechanisms of action of bacteriophage K/nano-emulsion formulations against S. aureus via measurement of particle size and zeta potential. Colloids Surfaces B Biointerfaces 139, 87–94 (2016).
    • 92. Kőnig-Péter A, Kilár F, Pernyeszi T. Copper(II) biosorption characteristics of lyophilized and thermally treated Pseudomonas cells. Environ. Eng. Manag. J. 18(2), 455–464 (2019).
    • 93. Choi N, Bae Y, Lee S. Cell surface properties and biofilm formation of pathogenic bacteria. Food Sci. Biotechnol. 24, 2257–2264 (2015).
    • 94. Zemb O, Manefield M, Thomas F, Jacquet S. Phage adsorption to bacteria in the light of the electrostatics: a case study using E. coli, T2 and flow cytometry. J. Virol. Methods 189(2), 283–289 (2013).
    • 95. Glasser CA, Vila MMDC, Pereira JC et al. Development of a water-in-oil-in-water multiple emulsion system integrating biomimetic aqueous-core lipid nanodroplets for protein entity stabilization. Part II: process and product characterization. Drug Dev. Ind. Pharm. 42(12), 1990–2000 (2016).
    • 96. Katayama K, Nomura H, Ogata H, Eitoku T. Diffusion coefficients for nanoparticles under flow and stop–flow conditions. Phys. Chem. Chem. Phys. 11, 10494–10499 (2009).
    • 97. Derjaguin BV, Churaev NV, Muller VM. The Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of stability of lyophobic colloids. In: Surface Forces Springer, MA, USA, 293–310 (1987).
    • 98. Wang H, Newby B-MZ. Applicability of the extended Derjaguin-Landau-Verwey-Overbeek theory on the adsorption of bovine serum albumin on solid surfaces. Biointerphases. 9(4), 041006–1–041006–8 (2014).
    • 99. ChiHsin H, ChongYi L, JongKang L, ChanShing L. Control of the eel (Anguilla japonica) pathogens, Aeromonas hydrophila and Edwardsiella tarda, by bacteriophages. J. Fish. Soc. Taiwan. 27(1), 21–31 (2000).
    • 100. Pasharawipas T, Manopvisetcharean J, Flegel T. Phage treatment of Vibrio harveyi: a general concept of protection against bacterial infection. Res. J. Microbiol. 6(6), 560–567 (2011).
    • 101. Prasad Y, Arpana, Kumar D, Sharma A. Lytic bacteriophages specific to flavobacterium columnare rescue catfish, Clarias batrachus (Linn.) from columnaris disease. J Env. Biol. 32(2), 161–168 (2011).
    • 102. Pereira C, Moreirinha C, Lewicka M et al. Characterization and in vitro evaluation of new bacteriophages for the biocontrol of Escherichia coli. Virus Res. 227, 171–182 (2017).
    • 103. Duarte J, Pereira C, Moreirinha C et al. New insights on phage efficacy to control Aeromonas salmonicida in aquaculture systems: an in vitro preliminary study. Aquaculture. 495(January), 970–982 (2018).
    • 104. Costa P, Pereira C, Gomes A, Almeida A. Efficiency of single phage suspensions and phage cocktail in the inactivation of Escherichia coli and Salmonella typhimurium: an in vitro preliminary study. Microorganisms 7(4), 94 (2019).
    • 105. Ceyssens P–J, Miroshnikov K, Mattheus W et al. Comparative analysis of the widespread andconserved PB1-like viruses infecting Pseudomonas aeruginosa. Environ. Microbiol. 11(11), 2874–2883 (2009).
    • 106. Cui X, You J, Sun L et al. Characterization of Pseudomonas aeruginosa phage C11 and identification of host genes required for Virion maturation. Sci. Rep. 6(39130), 1–14 (2016).
    • 107. Henry M, Lavigne R, Debarbieux L. Predicting in vivo efficacy of therapeutic bacteriophages used to treat pulmonary infections. Antimicrob. Agents Chemother. 57(12), 5961–5968 (2013).
    • 108. Henry M, Bobay L-M, Chevallereau A, Saussereau E, Ceyssens P-J, Debarbieux L. The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of Pseudomonas-infecting Myoviridae. PLoS ONE 10(1), e0117163 (2015).
    • 109. Basu A, Bobrovnikov DG, Qureshi Z et al. Measuring DNA mechanics on the genome scale. Nature 589, 462–467 (2020).
    • 110. Basu A, Bobrovnikov DG, Cieza B, Qureshi Z, Ha T. Deciphering the mechanical code of genome and epigenome. bioRxiv. doi:https://doi.org/10.1101/2020.08.22.262352 (2020).
    • 111. Wu Q, Zhou W, Wang J, Yan H. Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences. J. Theor. Biol. 284(1), 92–98 (2011).
    • 112. Harteis S, Schneider S. Making the bend: DNA tertiary structure and protein–DNA interactions. Int. J. Mol. Sci. 15(7), 12335–12363 (2014).
    • 113. Mrázek J. Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression. J. Bacteriol. 192(14), 3763–3772 (2010).
    • 114. Yella VR, Bhimsaria D, Ghoshdastidar D, Rodríguez-Martínez JA, Ansari AZ, Bansal M. Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif. Nucleic Acids Res. 46(22), 11883–11897 (2018).
    • 115. Jursa J, Kypr J. Propeller-twisted adenine-thymine and guanine-cytosine base pairs tend to buckle and stagger in opposite directions. Gen. Physiol. Biophys. 10, 373–381 (1991).
    • 116. Skewes AD, Welch RD. A Markovian analysis of bacterial genome sequence constraints. PeerJ. 1, e127 (2013).