| [1] |
Mendelson M, Lewnard JA, Sharland M, Cook A, Pouwels KB, et al. 2024. Ensuring progress on sustainable access to effective antibiotics at the 2024 UN General Assembly: a target-based approach. |
| [2] |
Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, et al. 2022. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. |
| [3] |
Naghavi M, Vollset SE, Ikuta KS, Swetschinski LR, Gray AP, et al. 2024. Global burden of bacterial antimicrobial resistance 1990−2021: a systematic analysis with forecasts to 2050. |
| [4] |
WHO. 2024. WHO Bacterial Priority Pathogens List, 2024: bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance. https://iris.who.int/server/api/core/bitstreams/1a41ef7e-dd24-4ce6-a9a6-1573562e7f37/content |
| [5] |
Leitner L, McCallin S. 2024. Guiding phage therapy with genomic surveillance. |
| [6] |
Kviatcovsky D, Valdés-Mas R, Federici S, Elinav E. 2023. Phage therapy in noncommunicable diseases. |
| [7] |
Hampton HG, Watson BNJ, Fineran PC. 2020. The arms race between bacteria and their phage foes. |
| [8] |
Taglialegna A. 2024. A never-ending defence fight. |
| [9] |
Tesson F, Hervé A, Mordret E, Touchon M, D’Humières C, et al. 2022. Systematic and quantitative view of the antiviral arsenal of prokaryotes. |
| [10] |
Beavogui A, Lacroix A, Wiart N, Poulain J, Delmont TO, et al. 2024. The defensome of complex bacterial communities. |
| [11] |
Yirmiya E, Leavitt A, Lu A, Ragucci AE, Avraham C, et al. 2024. Phages overcome bacterial immunity via diverse anti-defence proteins. |
| [12] |
Li X, Bao N, Yan Z, Yuan XZ, Wang SG, et al. 2023. Degradation of antibiotic resistance genes by VADER with CRISPR-cas immunity. |
| [13] |
Li FY, Tan XE, Shimamori Y, Kiga K, Veeranarayanan S, et al. 2024. Phagemid-based capsid system for CRISPR-Cas13a antimicrobials targeting methicillin-resistant Staphylococcus aureus. |
| [14] |
Kawaguchi T, Watanabe S, Liu Y, Aiba Y, Tan XE, et al. 2025. Gene-specific reversal of carbapenem- resistant Pseudomonas aeruginosa via phage-delivered CRISPR-Cas13a. |
| [15] |
Cheng ZH, Luo XY, Liu DF, Han J, Wang HD, et al. 2024. Optimized antibiotic resistance genes monitoring scenarios promote sustainability of urban water cycle. |
| [16] |
Ghatbale P, Blanc A, Sue A, Leonard J, Bates M, et al. 2025. Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates. |
| [17] |
Subedi D, Gordillo Altamirano F, Deehan R, Perera A, Patwa R, et al. 2025. Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections. |
| [18] |
Millman A, Melamed S, Leavitt A, Doron S, Bernheim A, et al. 2022. An expanded arsenal of immune systems that protect bacteria from phages. |
| [19] |
Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, et al. 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. |
| [20] |
Wang M, Liu G, Liu M, Tai C, Deng Z, et al. 2024. ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria. |
| [21] |
Kieffer N, Hipólito A, Ortiz-Miravalles L, Blanco P, Delobelle T, et al. 2025. Mobile integrons encode phage defense systems. |
| [22] |
Zhang J, Lu T, Song Y, da Rocha UN, Liu J, et al. 2024. Viral communities contribute more to the lysis of antibiotic-resistant bacteria than the transduction of antibiotic resistance genes in anaerobic digestion revealed by metagenomics. |
| [23] |
Yan X, Xin Y, Zhu L, Tang Q, Chen M, et al. 2025. Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater. |
| [24] |
Nishijima S, Fullam A, Schmidt TSB, Kuhn M, Bork P. 2026. VIRE: a metagenome-derived, planetary-scale virome resource with environmental context. |
| [25] |
Kleiner M, Bushnell B, Sanderson KE, Hooper LV, Duerkop BA. 2020. Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities. |
| [26] |
Chevallereau A, Pons BJ, van Houte S, Westra ER. 2022. Interactions between bacterial and phage communities in natural environments. |
| [27] |
Shkoporov AN, Turkington CJ, Hill C. 2022. Mutualistic interplay between bacteriophages and bacteria in the human gut. |
| [28] |
Luo XQ, Wang P, Li JL, Ahmad M, Duan L, et al. 2022. Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts. |
| [29] |
Jansson JK, Wu R. 2023. Soil viral diversity, ecology and climate change. |
| [30] |
Graham EB, Camargo AP, Wu R, Neches RY, Nolan M, et al. 2024. A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. |
| [31] |
Zhong ZP, Du J, Köstlbacher S, Pjevac P, Orlić S, et al. 2024. Viral potential to modulate microbial methane metabolism varies by habitat. |
| [32] |
Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, et al. 2020. DRAM for distilling microbial metabolism to automate the curation of microbiome function. |
| [33] |
Dougherty PE, Bernard C, Carstens AB, Bumunang E, Gerovac M, et al. 2026. Persistent virulent phages exist across bacterial isolates. |
| [34] |
Marantos A, Mitarai N, Sneppen K. 2022. From kill the winner to eliminate the winner in open phage-bacteria systems. |
| [35] |
Tang X, Fan C, Zeng G, Zhong L, Li C, et al. 2022. Phage-host interactions: the neglected part of biological wastewater treatment. |
| [36] |
Correa AMS, Howard-Varona C, Coy SR, Buchan A, Sullivan MB, et al. 2021. Revisiting the rules of life for viruses of microorganisms. |
| [37] |
Chen X, Weinbauer MG, Jiao N, Zhang R. 2021. Revisiting marine lytic and lysogenic virus-host interactions: Kill-the-Winner and Piggyback-the-Winner. |
| [38] |
Ma B, Wang Y, Zhao K, Stirling E, Lv X, et al. 2024. Biogeographic patterns and drivers of soil viromes. |
| [39] |
Luong T, Salabarria AC, Edwards RA, Roach DR. 2020. Standardized bacteriophage purification for personalized phage therapy. |