Список литературы
- Jajere S.M. A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance. Vet World. 2019;12(4):504-521. doi: 10.14202/vetworld.2019.504-521
- El-Saadony M.T., Salem H.M., El-Tahan A.M., Abd El-Mageed T.A., Soliman S.M., Khafaga A.F., Swelum A.A., Ahmed A.E., Alshammari F.A., Abd El-Hack M.E. The control of poultry salmonellosis using organic agents: an updated overview. Poult Sci. 2022;101(4):101716. doi: 10.1016/j.psj.2022.101716
- Rozhnova S.Sh., Kuleshov K.V., Pavlova A.S., Guseva A.N., Kozhakhmetova T.A., Akulova N.K., Podkolzin A.T. Heterogeneity of Salmonella isolates obtained from various sources in Russia 2010–2019. Epidemiology and infectious diseases. 2020;25(1):26-34 (in Russ). doi: 10.17816/EID35184
- Edwards R.A., Olsen G.J., Maloy S.R. Comparative genomics of closely related salmonellae. Trends Microbiol. 2002;10(2):94-99. doi: 10.1016/S0966-842X(01)02293-4
- Owen S.V., Wenner N., Dulberger C.L., Rodwell E.V., Bowers-Barnard A., Quinones-Olvera N., Rigden D.J., Rubin E.J., Garner E.C., Baym M., Hinton J.C.D. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021;29(11):1620-1633.e8. doi: 10.1016/j.chom.2021.09.002
- Wahl A., Battesti A., Ansaldi M. Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host? Mol. Microbiol. 2019;111(2):303-316. doi: 10.1111/mmi.14167
- Trofeit L., Sattler E., Künz J., Hilbert F. Salmonella Prophages, Their Propagation, Host Specificity and Antimicrobial Resistance Gene Transduction. Antibiotics (Basel). 2023;12(3):595. doi: 10.3390/antibiotics12030595
- Goh S. Phage Transduction. Methods Mol Biol. 2016;1476:177-185. doi: 10.1007/978-1-4939-6361-4_13
- Hille F., Richter H., Wong S.P., Bratovič M., Ressel S., Charpentier E. The Biology of CRISPR-Cas: Backward and Forward. Cell. 2018;172(6):1239-1259. doi: 10.1016/j.cell.2017.11.032
- Makarova K.S., Wolf Y.I., Iranzo J., Shmakov S.A., Alkhnbashi O.S., Brouns S.J.J., Charpentier E., Cheng D., Haft D.H., Horvath P., et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 2020;18(2):67-83. doi: 10.1038/s41579-019-0299-x
- Pourcel C., Touchon M., Villeriot N., Vernadet J.P., Couvin D., Toffano-Nioche C., Vergnaud G. CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. Nucleic Acids Res. 2020;48(D1):D535-D544. doi: 10.1093/nar/gkz915
- Shakya M., Ahmed S.A., Davenport K.W., Flynn M.C., Lo C., Chain PS.G. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Sci Rep. 2020;10(1723). doi: 10.1038/s41598-020-58356-1
- Minh B.Q., Schmidt H.A., Chernomor O., Schrempf D., Woodhams M.D., Haeseler A., Lanfear R. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution. 2020;37(5):1530-1534. doi: 10.1093/molbev/msaa015
- Hoang D.T., Chernomor O., Haeseler A., Minh B.Q., Vinh L.S. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution. 2018;35(2):518-522. doi: 10.1093/molbev/msx28
- Letunic I., Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Research. 2024;52(W1):W78-W82. doi: 10.1093/nar/gkae268
- BLAST® Command Line Applications User Manual. Bethesda: NCBI. 2008. https://www.ncbi.nlm.nih.gov/books/NBK279690/ (accessed 24.11.2024).
- Alonge M., Lebeigle L., Kirsche M., Jenike K., Ou S., Aganezov S., Wang X., Lippman Z.B., Schatz M.C., Soyk S. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 2022;23(258). doi: 10.1186/s13059-022-02823-7
- Seemann T. Prokka: Rapid Prokaryotic Genome Annotation. Bioinformatics. 2014;30(14):2068-2069. doi: 10.1093/bioinformatics/btu153
- Gan R., Zhou F., Si Y., Yang H., Chen C., Ren C., Wu J., Zhang F. DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation. Front. Genet. 2022;13:885048. doi: 10.3389/fgene.2022.885048
- Canty A., Ripley B.D., Brazzale A.R. boot: Bootstrap R (S-Plus) Functions. 2024. https://cran.r-project.org/web/packages/boot/index.html (accessed 24.11.2024).
- He L., St John James M., Radovcic M., Ivancic-Bace I., Bolt E.L. Cas3 Protein-A Review of a Multi-Tasking Machine. Genes (Basel). 2020;11(2):208. doi: 10.3390/genes11020208
- Tay M., Liu S., Yuan Y.A. Crystal structure of Thermobifida fusca Cse1 reveals target DNA binding site. Protein Sci. 2015;24(2):236-245. doi: 10.1002/pro.2609
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