Clonal groups of uropatogenic escherichia coli isolated in the russian federation in 2004–2019

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Abstract

Objective. Identification and characteristics of clonal groups of E. coli isolated from patients with urinary tract infections in the Russian Federation in 2004–2019.

Materials and methods. E. coli strains (n = 303) isolated in 2004–2019 from urine samples of patients with urological diagnoses. The microbiological, molecular genetic and bioinformatic methods for assessing resistance and virulence, as well as molecular genetic methods for identifying phylogenetic groups, O-groups and sequence types were used in the study.

Results. The widespread distribution of uropathogenic strains of the O25-B2-ST131 clonal group in Russia has been shown; in addition, O2-B2-ST141, O89-A-ST744, O4/O6-B2-ST127, B1-ST58, D-ST69, O2/O6-B2-ST73, A-CC10 and O75-B2-CC14clonal groups have been identified.

Conclusion. Assessing the distribution of clonal groups of uropathogenic strains in Russia allows to assess the epidemic situation, predict its development in the future, and also determine the optimal directions of therapy.

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About the authors

Pavel V. Slukin

State Scientific Center for Applied Microbiology and Biotechnology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Author for correspondence.
Email: xopgi@yandex.ru
ORCID iD: 0000-0002-4976-0145

Researcher, Department of Molecular Microbiology

Russian Federation, Obolensk, Moscow Region

Nadezhda K. Fursova

State Scientific Center for Applied Microbiology and Biotechnology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: n-fursova@yandex.ru
ORCID iD: 0000-0001-6053-2621

Cand. Biol. Sci., Leading Researcher, Department of Molecular Microbiology

Russian Federation, Obolensk, Moscow Region

Eduard A. Svetoch

State Scientific Center for Applied Microbiology and Biotechnology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: svetoch@obolensk.org
ORCID iD: 0000-0002-3185-1954

DVSc, Professor, Chief Researcher, Department of Molecular Microbiology

Russian Federation, Obolensk, Moscow Region

Tamara S. Perepanova

N.A. Lopatkin Scientific Research Institute of Urology and Interventional Radiology – Branch of the National Medical Research Radiological Center, Ministry of Health of Russia

Email: perepanova2003@mail.ru

МD, Professor, Head, Group of Infectious and Inflammatory Diseases and Clinical Pharmacology

Russian Federation, Moscow

Marina G. Ershova

Infectious Clinical Hospital № 1

Email: mary.erschowa2013@yandex.ru
ORCID iD: 0000-0003-4691-648X

Head, Microbiological Laboratory

Russian Federation, Yaroslavl

Elena D. Poletaeva

Infectious Clinical Hospital № 1

Email: mary.erschowa2013@yandex.ru
ORCID iD: 0000-0002-7074-6989

Bacteriologist

Russian Federation, Yaroslavl

Aleksandr N. Kruglov

Moscow Multidisciplinary Clinical Center «Kommunarka» of the Moscow Healthcare Department

Email: kruglov_a_n@mail.ru
ORCID iD: 0000-0001-6849-0008

Cand. Biol. Sci., Senior Researcher, Head, Laboratory of Clinical Microbiology

Russian Federation, Moscow

Tatyana V. Priputnevich

Academician V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Ministry of Health of Russia

Email: t_priputnevich@oparina4.ru
ORCID iD: 0000-0002-4126-9730

Professor, Corresponding Member of the Russian Academy of Sciences, МD, Director

Russian Federation, Moscow

References

  1. Кузнецова М.В., Проворова С.В., Кубарев О.Г., Юдин Д.П., Каримова Н.В., Баяндина Н.В. и др. Сравнительная характеристика штаммов уропатогенной Escherichia coli, выделенных в условиях поликлиники и стационара. Урология 2018; (6): 37–44. doi: 10.18565/urology.2018.6.37-44
  2. Kuznetsova M.V., Provorova S.V., Kubarev O.G., Yudin D.S., Karimova N.V., Bajandina N.V. et al. [Comparative characteristics of uropathogenic Escherichia coli strains, allocated in polyclinic and stationary conditions]. Urologiia 2018; (6): 37–44. (In Russ.). doi: 10.18565/urology.2018.6.37-44
  3. Javed S., Mirani Z.A., Pirzada Z.A. Phylogenetic group B2 expressed significant biofilm formation among drug resistant uropathogenic Escherichia coli. Libyan J. Med. 2021; 16(1): 1845444. doi: 10.1080/19932820.2020.1845444
  4. Zhong Z.X., Cui Z.H., Li X.J., Tang T., Zheng Z.J., Ni W.N. et al. Nitrofurantoin combined with amikacin: a promising alternative strategy for combating MDR uropathogenic Escherichia coli. Front Cell Infect. Microbiol. 2020; (10): 608547. doi: 10.3389/fcimb.2020.608547
  5. Magiorakos A.P., Srinivasan A., Carey R.B., Carmeli Y., Falagas M.E., Giske C.G. et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin. Microbiol. Infect. 2012; 18(3): 268–81. doi: 10.1111/j.1469-0691.2011.03570.x
  6. Naziri Z., Derakhshandeh A., Soltani Borchaloee A., Poormaleknia M., Azimzadeh N. Treatment failure in urinary tract infections: a warning witness for virulent multi-drug resistant ESBL-producing Escherichia coli. Infect. Drug. Resist. 2020; 13: 1839–50. doi: 10.2147/IDR.S256131
  7. Manges A.R., Johnson J.R. Reservoirs of extraintestinal pathogenic Escherichia coli. Microbiol. Spectr. 2015; 3(5): 10.1128/microbiolspec.UTI-0006-2012. doi: 10.1128/microbiolspec.UTI-0006-2012
  8. Flament-Simon S.C., Toro M., García V., Blanco J.E., Blanco M., Alonso M.P. et al. Molecular characteristics of extraintestinal pathogenic E. coli (ExPEC), uropathogenic E. coli (UPEC), and multidrug resistant E. coli isolated from healthy dogs in Spain. Whole Genome Sequencing of Canine ST372 Isolates and Comparison with Human Isolates Causing Extraintestinal Infections. Microorganisms 2020; 8(11): 1712. doi: 10.3390/microorganisms8111712
  9. Nüesch-Inderbinen M.T., Baschera M., Zurfluh K., Hächler H., Nüesch H., Stephan R. Clonal diversity, virulence potential and antimicrobial resistance of Escherichia coli causing community acquired urinary tract infection in Switzerland. Front. Microbiol. 2017; (8): 2334. doi: 10.3389/fmicb.2017.02334
  10. Hojabri Z., Mirmohammadkhani M., Darabi N., Arab M., Pajand O. Characterization of antibiotic-susceptibility patterns and virulence genes of five major sequence types of Escherichia coli isolates cultured from extraintestinal specimens: a 1-year surveillance study from Iran. Infect. Drug. Resist. 2019; (12): 893–903. doi: 10.2147/IDR.S199759
  11. Shahbazi R., Salmanzadeh-Ahrabi S., Aslani M.M., Alebouyeh M., Falahi J., Nikbin V.S. The genotypic and phenotypic characteristics contributing to high virulence and antibiotics resistance in Escherichia coli O25-B2-ST131 in comparison to non-O25-B2-ST131. BMC Pediatr. 2023; 23(1): 59. doi: 10.1186/s12887-023-03866-w
  12. Kuzina E.S., Astashkin E.I., Lev A.I., Ageeva E.N., Kartsev N.N., Svetoch E.A. et al. Class 1 and 2 Integrons in Hospital Strains of Gram-Negative Bacteria Isolated in Moscow and in Regions of the Russian Federation. Molecular Genetics, Microbiology and Virology 2019; 34(1): 16–24. doi: 10.3103/S0891416819010051
  13. Казанцев А.В., Осина Н.А., Глинская Т.О., Кошелева О.Н., Максимов Ю.В., Девдариани З.Л. и др. Факторы вирулентности и филогенетическая характеристика уропатогенных штаммов Escherichia coli, выделенных на территории г. Саратова. Проблемы особо опасных инфекций; 2019: (4): 56–60. doi: 10.21055/0370-1069-2019-4-56-60
  14. Kazantsev A.V., Osina N.A., Glinskaya T.O., Kosheleva O.N., Maksimov Yu.V., Devdariani Z.L. et al. [Virulence factors and phylogenetic characteristics of uropathogenic Eschericihia coli strains isolated in Saratov]. Problems of Particularly Dangerous Infections; 2019: (4): 56–60. (In Russ.) doi: 10.21055/0370-1069-2019-4-56-60
  15. Iguchi A., Iyoda S., Seto K., Morita-Ishihara T., Scheutz F., Ohnishi M. Pathogenic E. coli working group in Japan. Escherichia coli O-genotyping PCR: a comprehensive and practical platform for molecular O serogrouping. J. Clin. Microbiol. 2015; 53(8): 2427–32. doi: 10.1128/JCM.00321-15
  16. Clermont O., Christenson J.K., Denamur E., Gordon D.M. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol. Rep. 2013; 5(1): 58–65. doi: 10.1111/1758-2229.12019
  17. Alikhan N.F., Zhou Z., Sergeant M.J., Achtman M. A genomic overview of the population structure of Salmonella. PLoS Genet. 2018; 14(4): e1007261. doi: 10.1371/journal.pgen.1007261
  18. Ny S., Edquist P., Dumpis U., Gröndahl-Yli-Hannuksela K., Hermes J., Kling A.M. et al. Аntimicrobial resistance of Escherichia coli isolates from outpatient urinary tract infections in women in six European countries including Russia. J. Glob. Antimicrob. Resist. 2019; 17: 25–34. doi: 10.1016/j.jgar.2018.11.004
  19. Platell J.L., Trott D.J., Johnson J.R., Heisig P., Heisig A., Clabots C.R. et al. Prominence of an O75 clonal group (clonal complex 14) among non-ST131 fluoroquinolone-resistant Escherichia coli causing extraintestinal infections in humans and dogs in Australia. Antimicrob. Agents Chemother. 2012; 56(7): 3898–904. doi: 10.1128/AAC.06120-11
  20. Gati N.S., Middendorf-Bauchart B., Bletz S., Dobrindt U., Mellmann A. Origin and evolution of hybrid shiga toxin-producing and uropathogenic Escherichia coli strains of sequence type 141. J. Clin. Microbiol. 2019; 58(1): e01309–19. doi: 10.1128/JCM.01309-19
  21. Reid C.J., Blau K., Jechalke S., Smalla K., Djordjevic S.P. Whole genome sequencing of Escherichia coli from store-bought produce. Front Microbiol. 2020; 10: 3050. doi: 10.3389/fmicb.2019.03050
  22. Halaji M., Shahidi S., Ataei B., Atapour A., Feizi A., Havaei S.A. Molecular epidemiology of blaCTX-M gene-producing uropathogenic Escherichia coli among Iranian kidney transplant patients: clonal dissemination of CC131 and CC10. Ann. Clin. Microbiol. Antimicrob. 2021; 20(1): 65. doi: 10.1186/s12941-021-00470-7
  23. Riley L.W. Pandemic lineages of extraintestinal pathogenic Escherichia coli. Clin. Microbiol. Infect. 2014; 20(5): 380–90. doi: 10.1111/1469-0691.12646
  24. Kubelová M., Koláčková I., Gelbíčová T., Florianová M., Kalová A., Karpíšková R. Virulence properties of mcr-1-positive Escherichia coli isolated from retail poultry meat. Microorganisms 2021; 9(2): 308. doi: 10.3390/microorganisms9020308

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2. Figure. Representation of Е. coli collection strains (n = 303), resistant to antimicrobial drugs (а), carrying antibiotic resistance genes (b) and pathogenicity factor genes (с) АМР - ampicillin, АМС - amoxicillin/clavulanate, СТХ- cefotaxime, CIP - ciproftoxacin, LVX- levoftoxacin, GEN - gentamicin, AMI - amikacin, FOS - fosfomycin, NIT - nitrofurantoin, СТХ-М - blaстх-м gene, ТЕМ - blaTEM gene, ОХА - blaОХА-48 gene

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