9. Lee I., Chalita M., Ha S. M., Na S. I., Yoon S. H., Chun J. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences // International Journal of Systematic and Evolutionary microbiology. 2017. Vol. 67, no. 6. P 2053-2057.
10. Parks D. H., Imelfort M., Skennerton C. T., Hugenholtz P, Tyson G W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes // Genome Research. 2015. Vol. 25, no. 7. P 1043-1055.
11. Gurevich A., Saveliev V, Vyahhi N., Tesler G QUAST: quality assessment tool for genome assemblies // Bioinformatics. 2013. Vol. 29, no. 8. P. 1072-1075.
12. Tabacchioni S., Ferri L., Manno G, Mentasti M., Cocchi P, Campana S., Ravenni N., Taccetti G, Dalmastri C., Chiarini L., Bevivino A., Fani R. Use of the gyrB gene to discriminate among species of the Burkholderia cepacia complex // FEMS Microbiology Letters. 2008. Vol. 281, no. 2. P 175-182.
13. Cystic Fibrosis Foundation 2019 report. URL: https://www.cff.org/Research/Researcher-Resources/PatientRegistry/2019-Cystic-Fibrosis-Foundation-Patient-Registry-Snapshot.
14. European Cystic Fibrosis Society Patient Registry Annual Data report 2018. URL: https://www. ecfs.eu/sites/default/files/general -content-files/working-groups/ecfs-patientregistry/ECFSPR_Report_2018_v1.4.pdf.
15. Воронина О. Л., Чернуха М. Ю., Шагинян И. А., Кунда М. С., Аветисян Л. Р, Орлова А. А., Лунин В. Г., Авакян Л. В., Капранов Н. И., Амелина Е. Л., Чучалин А. Г, Гинцбург А. Л. Характеристика генотипов штаммов Burkholderia cepacia complex, выделенных от больных в стационарах Российской Федерации // Молекулярная генетика, микробиология и вирусология. 2013. № 2. С. 22-30.
16. Кондратенко О. В. Гетерогенность популяции штаммов рода Burkholderia, выделенных от пациентов с муковисцидозом в Российской Федерации // Иммунопатология, аллергология, инфектология. 2019. № 3. С. 71-74.
17. Cipolla L., Rocca F., Martinez C., Aguerre L., Barrios R., Prieto M. Prevalence of Burkholderiacepacia complex species in cystic fibrosis patients in Argentina during the period 2011-2015 // Enfermedades infecciosas y microbiologia clinica (English Edition). 2018. Vol. 36, no. 7. P 431-434.
18. Kenna D. T. D., Lilley D., Coward A., Martin K., Perry C., Pike R., Hill R., Turton J. F. Prevalence of Burkholderia species, including members of Burkholderia cepacia complex, among UK cystic and non-cystic fibrosis patients // Journal of Medical Microbiology. 2017. Vol. 66, no. 4. P. 490-501.
19. Silva I. N., Santos P M., Santos M. R., Zlosnik J. E., Speert D. P, Buskirk S. W., Bruger E. L., Waters C. M., Cooper V S., Moreira L. M. Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection // mSystems. 2016. Vol. 1, no. 3. e00029-16.
20. Domingues S., da Silva G. J., Nielsen K. M. Integrons: Vehicles and pathways for horizontal dissemination in bacteria // Mobile Genetic Elements. 2012. Vol. 2, no. 5. P. 211-223.
21. Heuer H., Binh C. T., Jechalke S., Kopmann C., Zimmerling U., Krogerrecklenfort E., Ledger T., Gonzalez B., Top E., Smalla K. IncP-1e Plasmids are Important Vectors of Antibiotic Resistance Genes in Agricultural Systems: Diversification Driven by Class 1 Integron Gene Cassettes // Frontiers in Microbiology. 2012. Vol. 3. P 2.
References
1. Jones A. M., Dodd M. E., Govan J. R., Barcus V, Doherty C. J., Morris J., Webb A. K. Burkholderia cenocepacia and Burkholderia multivorans: influence on survival in cystic fibrosis. Thorax. 2004; 59 (11): 948-951.
2. Nash E. F., Thomas A., Whitmill R., Rashid R., Barker B., Rayner R. J., Whitehouse J. L., Honeybourne D. “Cepacia syndrome” associated with Burkholderia cepacia (genomovar I) infection in an adolescent with cystic fibrosis. Pediatric pulmonology. 2011; 46 (5): 512-514.
3. Lynch J. P Burkholderia cepacia complex: impact on the cystic fibrosis lung lesion. In Seminars in respiratory and critical care medicine. 2009; 30 (5): 596-610.
4. Whiteford M. L., Wilkinson J. D., McColl J. H., Conlon F. M., Michie J. R., Evans T. J., Paton J. Y. Outcome of Burkholderia (Pseudomonas) cepacia colonisation in children with cystic fibrosis following a hospital outbreak: Thorax. 1995. № 50 (11): 1194-1198.
5. Drevinek P, Mahenthiralingam E. Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence. Clinical Microbiology and Infection. 2010; 16 (7): 821-830.
6. Russian Association for patients with cystic fibrosis. URL: https://mukoviscidoz.org/doc/registr/site_Registre_2019.pdf. (In Russ.).
7. Bankevich A. Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., Lesin V. M., Nikolenko S. I., Pham S., Prjibelski A. D., Pyshkin A. V., Sirotkin A. V., Vyahhi N., Tesler G, Alekseyev M. A., Pevzner P A. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology. 2012; 19 (5): 455-477.
8. Lee I., Chalita M., Ha S.M., Na S. I., Yoon S. H., Chun J. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. International Journal of Systematic and Evolutionary microbiology. 2017; 67 (6): 2053-2057.
9. Parks D. H., Imelfort M., Skennerton C. T., Hugenholtz P., Tyson G W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research. 2015; 25 (7): 1043-1055.
10. Gurevich A., Saveliev V., Vyahhi N., Tesler G QUAST: quality assessment tool for genome assemblies // Bioinformatics. 2013; 29 (8): 1072-1075.
11. Tabacchioni S., Ferri L., Manno G., Mentasti M., Cocchi P., Campana S., Ravenni N., Taccetti G, Dalmastri C., Chiarini L., Bevivino A., Fani R. Use of the gyrB gene to discriminate among species of the Burkholderia cepacia complex. FEMS Microbiology Letters. 2008; 281 (2): 175-182.
12. Cystic Fibrosis Foundation 2019 report. URL: https://www.cff.org/Research/Researcher-Resources/PatientRegistry/2019-Cystic-Fibrosis-Foundation-Patient-Registry-Snapshot.
13. European Cystic Fibrosis Society Patient Registry Annual Data report 2018. URL: https://www.ecfs.eu/sites/default/files/general-content-files/working-groups/ecfs-patientregistry/ECFSPR_Report_2018_v1.4.pdf
14. Voronina O. L., Chernukha M. Y., Shaginyan I. A., Kunda M. S., Avetisyan L. R., Orlova A. A., Lunin V G, Avakyan L. V, Kapranov N. I., Amelina E. L., Chuchalin A. G Gintsburg A. L. Characterization of genotypes for Burkholderia cepacia complex strains isolated from patients in hospitals of the Russian Federation. Molekulyarnaya genetika, mikrobiologiya i virusologiya = Molecular Genetics, Microbiology and Virology. 2013; (2): 22-30. (In Russ.)
15. Kondratenko O. V Heterogeneity of Burkholderia strains isolated from patients with cystic fibrosis in Russian Federation. Immunopatologiya, allergologiya, infektologiya = Immunopathology, Allergology, Infectology. 2019; (3): 71-74. (In Russ.).
16. Cipolla L.,Rocca F., Martinez C., Aguerre L., Barrios R., Prieto M. Prevalence of Burkholderia cepacia complex species in cystic fibrosis patients in Argentina during the period 2011-2015. Enfermedades infecciosas y microbiologia clinica (English Edition). 2018; 36 (7): 431-434.
17. Kenna D. T. D., Lilley D., Coward A., Martin K., Perry C., Pike R., Hill R., Turton J. F. Prevalence of Burkholderia species, including members of Burkholderia cepacia complex, among UK cystic and non-cystic fibrosis patients. Journal of Medical Microbiology. 2017; 66 (4): 490-501.
18. Silva I. N., Santos P M., Santos M. R., Zlosnik J. E., Speert D. P, Buskirk S. W., Bruger E. L., Waters C. M., Cooper V S., Moreira L. M. Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection. mSystems. 2016; 1 (3): e00029-16.
19. Domingues S., da Silva G J., Nielsen K. M. Integrons: Vehicles and pathways for horizontal dissemination in bacteria. Mobile Genetic Elements. 2012; 2 (5): 211-223.
20. Heuer H., Binh C. T., Jechalke S., Kopmann C., Zimmerling U., Krogerrecklenfort E., Ledger T., Gonzalez B., Top E., Smalla K. IncP-1e Plasmids are Important Vectors of Antibiotic Resistance Genes in Agricultural Systems: Diversification Driven by Class 1 Integron Gene Cassettes. Frontiers in Microbiology. 2012; 3: 2.