Kortright, K. E., Chan, B. K., Koff, J. L. & Turner, P. E. Phage therapy: a renewed approach to combat antibiotic-resistant bacteria. Cell Host Microbe 25, 219–232 (2019).

Article  CAS  PubMed  Google Scholar 

Pires, D. P., Cleto, S., Sillankorva, S., Azeredo, J. & Lu, T. K. Genetically engineered phages: a review of advances over the last decade. Microbiol. Mol. Biol. Rev. 80, 523–543 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doss, J., Culbertson, K., Hahn, D., Camacho, J. & Barekzi, N. A review of phage therapy against bacterial pathogens of aquatic and terrestrial organisms.Viruses 9, 50 (2017).

Article  PubMed Central  Google Scholar 

Nobrega, F. L., Costa, A. R., Kluskens, L. D. & Azeredo, J. Revisiting phage therapy: new applications for old resources. Trends Microbiol. 23, 185–191 (2015).

Article  CAS  PubMed  Google Scholar 

Łusiak-Szelachowska, M. et al. Phage neutralization by sera of patients receiving phage therapy. Viral Immunol. 27, 295–304 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Weber-Dąbrowska, B. et al. Bacteriophage procurement for therapeutic purposes. Front. Microbiol. 7, 1177 (2016).

PubMed  PubMed Central  Google Scholar 

Lu, T. K. & Koeris, M. S. The next generation of bacteriophage therapy. Curr. Opin. Microbiol. 14, 524–531 (2011).

Article  PubMed  Google Scholar 

Lenneman, B. R., Fernbach, J., Loessner, M. J., Lu, T. K. & Kilcher, S. Enhancing phage therapy through synthetic biology and genome engineering. Curr. Opin. Biotechnol. 68, 151–159 (2021).

Article  CAS  PubMed  Google Scholar 

Ando, H., Lemire, S., Pires, D. P. & Lu, T. K. Engineering modular viral scaffolds for targeted bacterial population editing. Cell Syst. 1, 187–196 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mahichi, F., Synnott, A. J., Yamamichi, K., Osada, T. & Tanji, Y. Site-specific recombination of T2 phage using IP008 long tail fiber genes provides a targeted method for expanding host range while retaining lytic activity. FEMS Microbiol. Lett. 295, 211–217 (2009).

Article  CAS  PubMed  Google Scholar 

Matsuda, T. et al. Lysis-deficient bacteriophage therapy decreases endotoxin and inflammatory mediator release and improves survival in a murine peritonitis model. Surgery 137, 639–646 (2005).

Article  PubMed  Google Scholar 

Monteiro, R., Pires, D. P., Costa, A. R. & Azeredo, J. Phage therapy: going temperate? Trends Microbiol. 27, 368–378 (2019).

Article  CAS  PubMed  Google Scholar 

Kilcher, S. & Loessner, M. J. Engineering bacteriophages as versatile biologics. Trends Microbiol. 27, 355–367 (2019).

Article  CAS  PubMed  Google Scholar 

Marinelli, L. J., Hatfull, G. F. & Piuri, M. Recombineering: a powerful tool for modification of bacteriophage genomes. Bacteriophage 2, 5–14 (2012).

Article  PubMed  PubMed Central  Google Scholar 

Deveau, H., Garneau, J. E. & Moineau, S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu. Rev. Microbiol. 64, 475–493 (2010).

Article  CAS  PubMed  Google Scholar 

Hille, F. et al. The Biology of CRISPR–Cas: backward and forward. Cell 172, 1239–1259 (2018).

Article  CAS  PubMed  Google Scholar 

Mayo-Muñoz, D. et al. Anti-CRISPR-based and CRISPR-based genome editing of Sulfolobus islandicus rod-shaped virus 2.Viruses 10, 695 (2018).

Article  PubMed Central  Google Scholar 

Samson, J. E., Magadan, A. H., Sabri, M. & Moineau, S. Revenge of the phages: defeating bacterial defences. Nat. Rev. Microbiol. 11, 675–687 (2013).

Article  CAS  PubMed  Google Scholar 

Malone, L. M., Birkholz, N. & Fineran, P. C. Conquering CRISPR: how phages overcome bacterial adaptive immunity. Curr. Opin. Biotechnol. 68, 30–36 (2021).

Article  CAS  PubMed  Google Scholar 

Mendoza, S. D. et al. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature 577, 244–248 (2020).

Article  CAS  PubMed  Google Scholar 

Malone, L. M. et al. A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nat. Microbiol. 5, 48–55 (2020).

Article  CAS  PubMed  Google Scholar 

Guan, J. & Bondy-Denomy, J.Intracellular organization by jumbo bacteriophages.J. Bacteriol. 203, e00362-20 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Abudayyeh, O. O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Meeske, A. J., Nakandakari-Higa, S. & Marraffini, L. A. Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature 570, 241–245 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Meeske, A. J. et al. A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR–Cas immunity. Science 369, 54–59 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

East-Seletsky, A. et al. Two distinct RNase activities of CRISPR–C2c2 enable guide-RNA processing and RNA detection. Nature 538, 270–273 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Meeske, A. J. & Marraffini, L. A. RNA guide complementarity prevents self-targeting in type VI CRISPR systems. Mol. Cell 71, 791–801.e3 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

M Iyer, L., Anantharaman, V., Krishnan, A., Maxwell Burroughs, A. & Aravind, L. Jumbo phages: a comparative genomic overview of core functions and adaptions for biological conflicts.Viruses 13, 63 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Al-Shayeb, B. et al. Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aylett, C. H. S., Izoré, T., Amos, L. A. & Löwe, J. Structure of the tubulin/FtsZ-like protein TubZ from Pseudomonas bacteriophage ΦKZ. J. Mol. Biol. 425, 2164–2173 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chaikeeratisak, V. et al. The phage nucleus and tubulin spindle are conserved among large Pseudomonas phages. Cell Rep. 20, 1563–1571 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chaikeeratisak, V. et al. Viral capsid trafficking along treadmilling tubulin filaments in bacteria. Cell 177, 1771–1780.e12 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kraemer, J. A. et al. A phage tubulin assembles dynamic filaments by an atypical mechanism to center viral DNA within the host cell. Cell 149, 1488–1499 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chaikeeratisak, V. et al. Assembly of a nucleus-like structure during viral replication in bacteria. Science 355, 194–197 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu, W., Thomas, J. A., Cheng, N., Black, L. W. & Steven, A. C. Bubblegrams reveal the inner body of bacteriophage ΦKZ. Science 335, 182 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thomas, J. A. et al. Extensive proteolysis of head and inner body proteins by a morphogenetic protease in the giant Pseudomonas aeruginosa phage ΦKZ. Mol. Microbiol. 84, 324–339 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chan, B. K. et al. Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci. Rep. 6, 26717 (2016).

Article  CAS