Żaczek, M., Weber-Dąbrowska, B., Międzybrodzki, R., Łusiak-Szelachowska, M. & Górski, A. Phage therapy in Poland—a centennial journey to the first ethically approved treatment facility in Europe. Front. Microbiol. 11, 1056 (2020).
Google Scholar
Antimicrobial Resistance CollaboratorsGlobal burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).
Google Scholar
O’Neill, J. Tackling drug-resistant infections globally: final report and recommendations. In The Review on Antimicrobial Resistance. (Government of the United Kingdom, 2016).
Chan, B. K., Stanley, G., Modak, M., Koff, J. L. & Turner, P. E. Bacteriophage therapy for infections in CF. Pediatr. Pulmonol. 56, S4–S9 (2021).
Google Scholar
Schooley, R. T. et al. Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob. Agents Chemother. 61, e00954-17 (2017).
Google Scholar
Strathdee, S. A., Hatfull, G. F., Mutalik, V. K. & Schooley, R. T. Phage therapy: from biological mechanisms to future directions. Cell 186, 17–31 (2023).
Google Scholar
Gencay, Y. E. et al. Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice. Nat. Biotechnol. 42, 265–274 (2024).
Google Scholar
Dedrick, R. M. et al. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat. Med. 25, 730–733 (2019).
Google Scholar
Mahler, M., Costa, A. R., van Beljouw, S. P. B., Fineran, P. C. & Brouns, S. J. J.Approaches for bacteriophage genome engineering. Trends Biotechnol. 41, 669–685 (2023).
Google Scholar
Kiro, R., Shitrit, D. & Qimron, U. Efficient engineering of a bacteriophage genome using the type I-E CRISPR–Cas system. RNA Biol. 11, 42–44 (2014).
Google Scholar
Box, A. M., McGuffie, M. J., O’Hara, B. J. & Seed, K. D. Functional analysis of bacteriophage immunity through a type I-E CRISPR–Cas system in Vibrio cholerae and its application in bacteriophage genome engineering. J. Bacteriol. 198, 578–590 (2016).
Google Scholar
Bari, S. M. N., Walker, F. C., Cater, K., Aslan, B. & Hatoum-Aslan, A. Strategies for editing virulent staphylococcal phages using CRISPR–Cas10. ACS Synth. Biol. 6, 2316–2325 (2017).
Google Scholar
Ramirez-Chamorro, L., Boulanger, P. & Rossier, O. Strategies for bacteriophage T5 mutagenesis: expanding the toolbox for phage genome engineering. Front. Microbiol. 12, 667332 (2021).
Google Scholar
Adler, B. A. et al. Broad-spectrum CRISPR–Cas13a enables efficient phage genome editing. Nat. Microbiol. 7, 1967–1979 (2022).
Google Scholar
Strotskaya, A. et al. The action of Escherichia coli CRISPR–Cas system on lytic bacteriophages with different lifestyles and development strategies. Nucleic Acids Res. 45, 1946–1957 (2017).
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).
Google Scholar
Nozaki, S. Rapid and accurate assembly of large DNA assisted by in vitro packaging of bacteriophage. ACS Synth. Biol. 11, 4113–4122 (2022).
Google Scholar
Emslander, Q. et al. Cell-free production of personalized therapeutic phages targeting multidrug-resistant bacteria. Cell Chem. Biol. 29, 1434–1445 (2022).
Google Scholar
Farzadfard, F. & Lu, T. K. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science 346, 1256272 (2014).
Google Scholar
Schubert, M. G. et al. High-throughput functional variant screens via in vivo production of single-stranded DNA. Proc. Natl Acad. Sci. USA 118, e2018181118 (2021).
Google Scholar
Simon, A. J., Morrow, B. R. & Ellington, A. D. Retroelement-based genome editing and evolution. ACS Synth. Biol. 7, 2600–2611 (2018).
Google Scholar
Lopez, S. C., Crawford, K. D., Lear, S. K., Bhattarai-Kline, S. & Shipman, S. L. Precise genome editing across kingdoms of life using retron-derived DNA. Nat. Chem. Biol. 18, 199–206 (2022).
Google Scholar
Bobonis, J. et al. Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems. Nature 609, 144–150 (2022).
Google Scholar
Millman, A. et al. Bacterial retrons function in anti-phage defense. Cell 183, 1551–1561 (2020).
Google Scholar
Palka, C., Fishman, C. B., Bhattarai-Kline, S., Myers, S. A. & Shipman, S. L. Retron reverse transcriptase termination and phage defense are dependent on host RNase H1. Nucleic Acids Res. 50, 3490–3504 (2022).
Google Scholar
Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084 (2020).
Google Scholar
Mosberg, J. A., Lajoie, M. J. & Church, G. M. Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics 186, 791–799 (2010).
Google Scholar
Nyerges, Á. et al. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species. Proc. Natl Acad. Sci. USA 113, 2502–2507 (2016).
Google Scholar
Wannier, T. M. et al. Improved bacterial recombineering by parallelized protein discovery. Proc. Natl Acad. Sci. USA 117, 13689–13698 (2020).
Google Scholar
Nyerges, Á. et al. Conditional DNA repair mutants enable highly precise genome engineering. Nucleic Acids Res. 42, e62 (2014).
Google Scholar
Bhattarai-Kline, S. et al. Recording gene expression order in DNA by CRISPR addition of retron barcodes. Nature 608, 217–225 (2022).
Google Scholar
Aronshtam, A. & Marinus, M. G. Dominant negative mutator mutations in the mutL gene of Escherichia coli. Nucleic Acids Res. 24, 2498–2504 (1996).
Google Scholar
Ellis, H. M., Yu, D., DiTizio, T. & Court, D. L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl Acad. Sci. USA 98, 6742–6746 (2001).
Google Scholar
Weigele, P. & Raleigh, E. A. Biosynthesis and function of modified bases in bacteria and their viruses. Chem. Rev. 116, 12655–12687 (2016).
Google Scholar
Bryson, A. L. et al. Covalent modification of bacteriophage T4 DNA inhibits CRISPR–Cas9. mBio 6, e00648 (2015).
Google Scholar
Fleischman, R. A., Cambell, J. L. & Richardson, C. C. Modification and restriction of T-even bacteriophages. In vitro degradation of deoxyribonucleic acid containing 5-hydroxymethylctosine. J. Biol. Chem. 251, 1561–1570 (1976).
Google Scholar
Weigel, C. & Seitz, H. Bacteriophage replication modules. FEMS Microbiol. Rev. 30, 321–381 (2006).
Google Scholar
Wolfson, J., Dressler, D. & Magazin, M. Bacteriophage T7 DNA replication: a linear replicating intermediate (gradient centrifugation–electron microscopy–E. coli–DNA partial denaturation). Proc. Natl Acad. Sci. USA 69, 499–504 (1972).
Google Scholar
Bourguignon, G. J., Sweeney, T. K. & Delius, H. Multiple origins and circular structures in replicating T5 bacteriophage DNA. J. Virol. 18, 245–259 (1976).
Google Scholar
Hochschild, A. & Lewis, M. The bacteriophage lambda CI protein finds an asymmetric solution. Curr. Opin. Struct. Biol. 19, 79–86 (2009).
Google Scholar
Tal, A., Arbel-Goren, R., Costantino, N., Court, D. L. & Stavans, J. Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo. Proc. Natl Acad. Sci. USA 111, 7308–7312 (2014).
Google Scholar
Filsinger, G. T. et al. Characterizing the portability of phage-encoded homologous recombination proteins. Nat. Chem. Biol. 17, 394–402 (2021).
Google Scholar
Hernandez, A. J. & Richardson, C. C. Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein. Semin. Cell Dev. Biol. 86, 92–101 (2019).
Google Scholar
Werten, S. Identification of the ssDNA-binding protein of bacteriophage T5: implications for T5 replication. Bacteriophage 3, e27304 (2013).
Google Scholar
Maffei, E. et al. Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection. PLoS Biol. 19, e3001424 (2021).
Google Scholar
Marinelli, L. J. et al. BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes. PLoS ONE 3, e3957 (2008).
Google Scholar
Mosberg, J. A., Gregg, C. J., Lajoie, M. J., Wang, H. H. & Church, G. M. Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases. PLoS ONE 7, e44638 (2012).
Google Scholar
Huss, P., Meger, A., Leander, M., Nishikawa, K. & Raman, S.Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning. eLife 10, e63775 (2021).
Google Scholar
Parson, K. A. & Snustad, D. P. Host DNA degradation after infection of Escherichia coli with bacteriophage T4: dependence of the alternate pathway of degradation which occurs in the absence of both T4 endonuclease II and nuclear disruption on T4 endonuclease IV. J. Virol. 15, 221–224 (1975).
Google Scholar
Warner, H. R., Drong, R. F. & Berget, S. M. Early events after infection of Escherichia coli by bacteriophage T5. Induction of a 5′-nucleotidase activity and excretion of free bases. J. Virol. 15, 273–280 (1975).
Google Scholar
Dunne, M. et al. Reprogramming bacteriophage host range through structure-guided design of chimeric receptor binding proteins. Cell Rep. 29, 1336–1350 (2019).
Google Scholar
Yehl, K. et al. Engineering phage host-range and suppressing bacterial resistance through phage tail fiber mutagenesis. Cell 179, 459–469 (2019).
Google Scholar
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).
Google Scholar
Jeong, H., Kim, H. J. & Lee, S. J.Complete genome sequence of Escherichia coli strain BL21. Genome Announc. 3, e00134-15 (2015).
Google Scholar
Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
Google Scholar
Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).
Google Scholar
Fortier, L. C. & Moineau, S. Phage production and maintenance of stocks, including expected stock lifetimes. Methods Mol. Biol. 501, 203–219 (2009).
Google Scholar
Kropinski, A. M., Mazzocco, A., Waddell, T. E., Lingohr, E. & Johnson, R. P. Enumeration of bacteriophages by double agar overlay plaque assay. Methods Mol. Biol. 501, 69–76 (2009).
Google Scholar
Rajagopala, S. V., Casjens, S. & Uetz, P. The protein interaction map of bacteriophage lambda. BMC Microbiol. 11, 213 (2011).
Google Scholar
Epp, C., Pearson, M. L. & Enquist, L. Downstream regulation of int gene expression by the b2 region in phage lambda. Gene 13, 327–337 (1981).
Google Scholar
Mazzocco, A., Waddell, T. E., Lingohr, E. & Johnson, R. P. Enumeration of bacteriophages using the small drop plaque assay system. Methods Mol. Biol. 501, 81–85 (2009).
Google Scholar