Русская версия English version   
Том 18   Выпуск 2   Год 2023
Мирошниченко Л.А.1, Арефьева Н.А.2,3, Джиоев Ю.П.2, Гусев В.Д.1, Борисенко А.Ю.2, Эрдынеев С.В.2, Букин Ю.С.4,5

Структура повторов в геномах сальмонелл

Математическая биология и биоинформатика. 2023;18(2):602-620.

doi: 10.17537/2023.18.602.

Список литературы

  1. Popoff M.Y., Bockemüh J., Brenner F.W. Supplement 1998 (no. 42) to the Kauffmann-White scheme. Res. Microbiol. 2000;151(1):63–65. doi: 10.1016/S0923-2508(00)00126-1
  2. Brenner F.W., Villar R.G., Angulo F.J., Tauxe R., Swaminathan B. Salmonella nomenclature. Clin. Microbiol. 2000;38(7):2465–2467. doi: 10.1128/JCM.38.7.2465-2467.2000
  3. Knodler L.A., Elfenbein J.R. Salmonella enterica. Trends Microbiol. 2019;27(11):964–965. doi: 10.1016/j.tim.2019.05.002
  4. Braden Ch.R. Salmonella enterica serotype Enteritidis and eggs: a national epidemic in the United States. Clin. Infect. Dis. 2006;43(4):512–517. doi: 10.1086/505973
  5. Alali W.Q., Thakur S., Berghaus R.D., Martin M.P., Gebreyes W.A. Prevalence and distribution of Salmonella in organic and conventional broiler poultry farms. Foodborne Pathog. Dis. 2010;7(11):1363–1371. doi: 10.1089/fpd.2010.0566
  6. Johnson R., Mylona E., Frankel G. Typhoidal Salmonella: Distinctive virulence factors and pathogenesis. Cell Microbiol. 2018;20(9):e12939. doi: 10.1111/cmi.12939
  7. Crump J.A., Luby S.P., Mintz E.D. The global burden of typhoid fever. Bull. World Health Organ. 2004;82(5):346–353.
  8. Buckle G.C., Walker C.L., Black R.E. Typhoid fever and paratyphoid fever: Systematic review to estimate global morbidity and mortality for 2010. J. Glob. Health. 2012;2(1):010401. doi: 10.7189/jogh.02.010401
  9. Chen J., Long J.E., Vannice K., Shewchuk T., Kumar S., Duncan S.A., Zaidi A.K.M. Taking on Typhoid: Eliminating Typhoid Fever as a Global Health Problem. Open Forum Infect Dis. 2023;10(1):S74–S81. doi: 10.1093/ofid/ofad055
  10. Aljeldah M.M. Antimicrobial Resistance and Its Spread Is a Global Threat. Antibiotics. 2022;11(8):1082. doi: 10.3390/antibiotics11081082
  11. Chang Y.-J., Chen C.-L., Yang H.-P., Chiu C.-H. Prevalence, Serotypes, and Antimicrobial Resistance Patterns of Non–Typhoid Salmonella in Food in Northern Taiwan. Pathogens. 2022;11(6):705. doi: 10.3390/pathogens11060705
  12. Salam M.A., Al-Amin M.Y., Salam M.T., Pawar J.S., Akhter N., Rabaan A.A., Alqumber M.A.A. Antimicrobial Resistance: A Growing Serious Threat for Global Public Health. Healthcare. 2023;11(13):1946. doi: 10.3390/healthcare11131946
  13. O’Neill J. Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations / the Review on Antimicrobial Resistance chaired by Jim O'Neill. 2014. https://wellcomecollection.org/works/rdpck35v (accessed 21.12.2023).
  14. Wagenlehner F.M.E., Dittmar F. Global Burden of Bacterial Antimicrobial Resistance in 2019: A Systematic Analysis. Eur. Urol. 2022;82(6):658. doi: 10.1016/j.eururo.2022.08.023
  15. Adebisi Y.A., Alaran A.J., Okereke M., Oke G.I., Amos O.A., Olaoye O.C., Oladunjoye I., Olanrewaju A.Y., Ukor N.A., Lucero-Prisno D.E. COVID-19 and Antimicrobial Resistance: A Review. Infect. Dis. (Auckl). 2021;14. doi: 10.1177/11786337211033870
  16. Lewis K. The science of antibiotic discovery. Cell. 2020;181(1):29–45. doi: 10.1016/j.cell.2020.02.056
  17. Dheman N., Mahoney N., Cox E.M., Farley J.J., Amini T., Lanthier M.L. An Analysis of Antibacterial Drug Development Trends in the United States, 1980–2019. Clin. Infect. Dis. 2021;73(11):e4444–e4450. doi: 10.1093/cid/ciaa859
  18. Luong T., Salabarria A.C., Roach D.R. Phage Therapy in the Resistance Era: Where Do We Stand and Where Are We Going? Clin. Ther. 2020;42(9):1659–1680. doi: 10.1016/j.clinthera.2020.07.014
  19. Hatfull G.F., Dedrick R.M., Schooley R.T. Phage Therapy for Antibiotic–Resistant Bacterial Infections. Annu Rev Med. 2022;73:197–211. doi: 10.1146/annurev-med-080219-122208
  20. Biswas A., Gagnon J.N., Brouns S.J.J., Fineran P.C., Brown C.M. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol. 2013;10(5):817–827. doi: 10.4161/rna.24046
  21. Barrangou R., Marraffini L.A. CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol. Cell. 2014;54(2):234–244. doi: 10.1016/j.molcel.2014.03.011
  22. Nazarov P.A. Alternatives to antibiotics: phage lytic enzymes and phage therapy. Bulletin of RSMU. 2018;1:5–15 (in Russ.). doi: 10.24075/vrgmu.2018.002
  23. Royer S., Morais A.P., da Fonseca Batistão D.W. Phage therapy as strategy to face post-antibiotic era: a guide to beginners and experts. Arch. Microbiol. 2021;203(4):1271–1279. doi: 10.1007/s00203-020-02167-5
  24. Nale J.Y., Ahmed B., Haigh R., Shan J., Phothaworn P., Thiennimitr P., Garcia A., AbuOun M., Anjum M.F., Korbsrisate S., Galyov E.E., Malik D.J., Clokie M.R.J. Activity of a Bacteriophage Cocktail to Control Salmonella Growth Ex Vivo in Avian, Porcine, and Human Epithelial Cell Cultures. Phage (New Rochelle). 2023;4(1):11–25. doi: 10.1089/phage.2023.0001
  25. Miroshnichenko L.A., Gusev V.D. Complete spectra of periodicities in the problems of differentiation of closely related bacterial genomes. J. Phys.: Conf. Ser. 2021;1715:012026. doi: 10.1088/1742-6596/1715/1/012026
  26. Gusev V.D., Miroshnichenko L.A., Titkova T.N., Dzhioev Y.P., Kozlova I.V., Paramonov A.I. Structured RNA Markers for Genotyping of Tick-Borne Encephalitis Virus. Mathematical Biology and Bioinformatics. 2018;13(1):13–37 (in Russ.). doi: 10.17537/2018.13.13
  27. Dimovski K., Cao H., Wijburg O.L., Strugnell R.A., Mantena R.K., Whipp M., Hogg G,. Holt K.E. Analysis of Salmonella enterica serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons. J. Bacteriol. 2014;196(16):3036–3044. doi: 10.1128/JB.01820-14
  28. Kjeldsen M.K., Torpdahl M., Pedersen K., Nielsen E.M. Development and comparison of a generic multiple-locus variable-number tandem repeat analysis with pulsed-field gel electrophoresis for typing of Salmonella enterica subsp. enterica. J. Appl. Microbiol. 2015;119(6):1707–1717. doi: 10.1111/jam.12965
  29. Kolmogorov A.N. Three approaches to the definition of the concept “quantity of information”. Probl. Peredachi Inf. 1965;1(1):3–11.(in Russ.).
  30. Gusev V.D., Miroshnichenko L.A. The complexity of DNA sequences. Different approaches and definitions. Mathematical Biology and Bioinformatics. 2020;15(2):313–337 (in Russ.). doi: 10.17537/2020.15.313
  31. Gusev V.D., Nemytikova L.A., Chuzhanova N.A. On the complexity measures of genetic sequences. Bioinformatics. 1999;15(12):994–999. doi: 10.1093/bioinformatics/15.12.994
  32. Lempel A., Ziv J. On the complexity of finite sequences. IEEE Trans. Inform. Theory. 1976;IT-22(1):75–81. doi: 10.1109/TIT.1976.1055501
  33. Gusev V.D., Miroshnichenko L.A., Chuzhanova N.A. Information Science & Computing. Classification, Forecasting, Data Mining. 2009;8:117–123. (International Book Series).
  34. Sneath P.H.A., Sokal R.R. Numerical Taxonomy. San Francisco: Freeman, 1973.
  35. Kumar S., Stecher G., Li M., Knyaz C., Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution. 2018;35:1547–1549. doi: 10.1093/molbev/msy096
  36. Saitou N., Nei M. The neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987;4:406–425.
  37. Hauth AM, Joseph DA. Beyond tandem repeats: complex pattern structures and distant regions of similarity. Bioinformatics. 2002;18(1):S31–37. doi: 10.1093/bioinformatics/18.suppl_1.S31
  38. Kushwaha S.K., Bhavesh N.L.S., Abdella B., Lahiri C., Marathe S.A. The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella. Sci Rep. 2020;10(1):21156. doi: 10.1038/s41598-020-77890-6
Содержание Оригинальная статья
Мат. биол. и биоинф.
2023;18(2):602-620
doi: 10.17537/2023.18.602
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы

 

  Copyright ИМПБ РАН © 2005-2024