Al-Anany, A. M., Fatima, R., & Hynes, A. P. (2021). Temperate phage-antibiotic synergy eradicates bacteria through depletion of lysogens. Cell Reports, 35, 109172.

Article  CAS  PubMed  Google Scholar 

Al-Anany, A. M., Fatima, R., Nair, G., Mayol, J. T., & Hynes, A. P. (2024). Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny. Mbio, 15, e0050424.

Article  PubMed  Google Scholar 

Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A. V., Cheng, A. A., Liu, S., et al. (2020). CARD 2020: ANTIBIOTIC resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research, 48, D517–D525.

CAS  PubMed  Google Scholar 

Berry, J., Summer, E. J., Struck, D. K., & Young, R. (2008). The final step in the phage infection cycle: The Rz and Rz1 lysis proteins link the inner and outer membranes. Molecular Microbiology, 70, 341–351.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolduc, B., Jang, H. B., Doulcier, G., You, Z. Q., Roux, S., & Sullivan, M. B. (2017). vConTACT: An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ, 5, e3243.

Article  PubMed  PubMed Central  Google Scholar 

Boyd, E. F. (2012). Bacteriophage-encoded bacterial virulence factors and phage-pathogenicity island interactions. Advances in Virus Research, 82, 91–118.

Article  CAS  PubMed  Google Scholar 

Boyd, E. F., & Brüssow, H. (2002). Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends in Microbiology, 10, 521–529.

Article  CAS  PubMed  Google Scholar 

Brown, J., Pirrung, M., & McCue, L. A. (2017). FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics, 33, 3137–3139.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bylund, J., Campsall, P., Ma, R., Conway, B., & Speert, D. (2005). Burkholderia cenocepacia induces neutrophil necrosis in chronic granulomatous disease. The Journal of Immunology, 174, 3562–3569.

Article  CAS  PubMed  Google Scholar 

Chan, P. P., & Lowe, T. M. (2019). tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods in Molecular Biology, 1962, 1–14.

Article  CAS  PubMed  Google Scholar 

Chaudhary, N., Maurya, R. K., Singh, D., Mohan, B., & Taneja, N. (2022). Genome analysis and antibiofilm activity of phage 590B against multidrug-resistant and extensively drug-resistant uropathogenic Escherichia coli isolates. India. Pathogens, 11, 1448.

Article  CAS  PubMed  Google Scholar 

Chen, L., Yang, J., Yu, J., Yao, Z., Sun, L., Shen, Y., & Jin, Q. (2005). VFDB: A reference database for bacterial virulence factors. Nucleic Acids Research, 33, D325–D328.

Article  CAS  PubMed  Google Scholar 

Chen, Y., Li, X., Song, J., Yang, D., Liu, W., Chen, H., Wu, B., & Qian, P. (2019). Isolation and characterization of a novel temperate bacteriophage from gut-associated Escherichia within black soldier fly larvae. Archives of Virology, 164, 2277–2284.

Article  CAS  PubMed  Google Scholar 

Chen, Y., Yang, L., Yang, D., Song, J., Wang, C., Sun, E., Gu, C., Chen, H., Tong, Y., Tao, P., et al. (2020). Specific integration of temperate phage decreases the pathogenicity of host bacteria. Frontiers in Cellular and Infection Microbiology, 10, 14.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cho, J. H., Kwon, J. G., O’Sullivan, D. J., Ryu, S., & Lee, J. H. (2021). Development of an endolysin enzyme and its cell wall-binding domain protein and their applications for biocontrol and rapid detection of Clostridium perfringens in food. Food Chemistry, 345, 128562.

Article  CAS  PubMed  Google Scholar 

Chung, I. Y., Sim, N., & Cho, Y. H. (2012). Antibacterial efficacy of temperate phage-mediated inhibition of bacterial group motilities. Antimicrobial Agents and Chemotherapy, 56, 5612–5617.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clokie, M. R., Millard, A. D., Letarov, A. V., & Heaphy, S. (2011). Phages in Nature. Bacteriophage, 1, 31–45.

Article  PubMed  Google Scholar 

Conway, B., Venu, V., & Speert, D. (2002). Biofilm formation and acyl homoserine lactone production in the Burkholderia cepacia complex. Journal of Bacteriology, 184, 5678–5685.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Courtney, J., Dunbar, K., McDowell, A., Moore, J., Warke, T., Stevenson, M., & Elborn, J. (2004). Clinical outcome of Burkholderia cepacia complex infection in cystic fibrosis adults. Journal of Cystic Fibrosis, 3, 93–98.

Article  CAS  PubMed  Google Scholar 

Darling, A. E., Mau, B., & Perna, N. T. (2010). progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE, 5, e11147.

Article  PubMed  PubMed Central  Google Scholar 

Davies, E., Winstanley, C., Fothergill, J., & James, C. (2016). The role of temperate bacteriophages in bacterial infection. FEMS Microbiology Letters, 363, fnw015.

Davis, R., & Brown, P. D. (2016). Multiple antibiotic resistance index, fitness and virulence potential in respiratory Pseudomonas aeruginosa from Jamaica. Journal of Medical Microbiology, 65, 261–271.

Article  CAS  PubMed  Google Scholar 

Davis, J. J., Wattam, A. R., Aziz, R. K., Brettin, T., Butler, R., Butler, R. M., Chlenski, P., Conrad, N., Dickerman, A., Dietrich, E. M., et al. (2020). The PATRIC Bioinformatics Resource Center: Expanding data and analysis capabilities. Nucleic Acids Research, 48, D606–D612.

CAS  PubMed  Google Scholar 

Davis, C. M., Ruest, M. K., Cole, J. H., & Dennis, J. J. (2022). The isolation and characterization of a broad host range Bcep22-like Podovirus JC1. Viruses, 14, 938.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Depoorter, E., Bull, M., Peeters, C., Coenye, T., Vandamme, P., & Mahenthiralingam, E. (2016). Burkholderia: An update on taxonomy and biotechnological potential as antibiotic producers. Applied Microbiology and Biotechnology, 100, 5215–5229.

Article  CAS  PubMed  Google Scholar 

Desai, M., Bühler, T., Weller, P. H., & Brown, M. R. (1998). Increasing resistance of planktonic and biofilm cultures of Burkholderia cepacia to ciprofloxacin and ceftazidime during exponential growth. Journal of Antimicrobial Chemotherapy, 42, 153–160.

Article  CAS  PubMed  Google Scholar 

El Chakhtoura, G., Saade, E., Wilson, B., Perez, F., Papp-Wallace, K., & Bonomo, R. (2017). A 17-year nationwide study of Burkholderia cepacia complex bloodstream infections among patients in the United States Veterans Health Administration. Clinical Infectious Diseases, 65, 1327–1334.

Article  PubMed Central  Google Scholar 

Eram, S., Behzadian Nejad, Q., Khatami, G., & Nafissi, N. (2004). Detection of Burkholderia cepacia complex in patients with cystic fibrosis. Tanaffos Tanaffos, 3, 47–52.

Google Scholar 

Eriksson, H., Maciejewska, B., Latka, A., Majkowska-Skrobek, G., Hellstrand, M., Melefors, Ö., Wang, J.-T., Kropinski, A. M., Drulis-Kawa, Z., & Nilsson, A. S. (2015). A suggested new bacteriophage genus, “Kp34likevirus”, within the Autographivirinae subfamily of Podoviridae. Viruses, 7, 1804–1822.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gordillo Altamirano, F. L., & Barr, J. J. (2019). Phage therapy in the postantibiotic era. Clinical Microbiology Reviews, 32, e00066-e118.

Article  PubMed  PubMed Central  Google Scholar 

Groth, A. C., & Calos, M. P. (2004). Phage integrases: Biology and applications. Journal of Molecular Biology, 335, 667–678.

Article  CAS  PubMed  Google Scholar 

Gurevich, A., & Saveliev, V. (2013). QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 29, 1072–1075.