The phylogenomic analysis of Salmonella enterica enterica serovar Enteritidis isolates associated with sporadic and group morbidity in Russia
- 作者: Kuleshov K.V.1, Pavlova A.S.1, Egorova A.E.1, Guseva A.N.1, Krutova N.E.1, Akulova N.K.1, Bikmetova K.R.1, Parkina N.V.1, Mikhaylova Y.V.1, Veselova O.A.1, Podkolzin A.T.1, Akimkin V.G.1
-
隶属关系:
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
- 期: 卷 13, 编号 2 (2023)
- 页面: 76-82
- 栏目: Articles
- URL: https://journals.eco-vector.com/2226-6976/article/view/554167
- DOI: https://doi.org/10.18565/epidem.2023.13.2.76–82
- ID: 554167
如何引用文章
开放存取
##reader.subscriptionAccessGranted##
详细
Objective. To assess the genetic diversity of Salmonella enterica subsp. enterica serovar Enteritidis isolates circulating in Russia, which were obtained in cases of group and sporadic morbidity, using genome-wide sequencing data.
Subjects and methods. Genome-wide sequencing and a phylogenetic analysis of 460 S. Enteritidis isolates obtained during the work of the Reference Center for Monitoring Salmonellosis were carried out.
Results. The findings made it possible to describe the population structure of Russian S. Enteritidis isolates and to understand their phylogenetic position in the context of global pathogen diversity, to assess the concordance of epidemiological data with genetic clustering data and to show the spatial and temporal features of clustering the isolates belonging to epidemiologically unrelated cases of group morbidity.
Conclusion. The results of the study create prerequisites for the formation of a unified national laboratory and information system for monitoring S. Enteritidis and investigating the epidemic foci of group morbidity with salmonellosis.
全文:
作者简介
Konstantin Kuleshov
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
编辑信件的主要联系方式.
Email: konstantinkul@gmail.com
ORCID iD: 0000-0002-5238-7900
Cand. Biol. Sci., Senior Researcher, Laboratory of Molecular Diagnostics and Epidemiology of Intestinal Infections
俄罗斯联邦, MoscowAnastasia Pavlova
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: nasty-pavlov@yandex.ru
ORCID iD: 0000-0003-4619-9337
Junior Researcher, Laboratory of Molecular Diagnostics and Epidemiology of Intestinal Infections
俄罗斯联邦, MoscowAnna Egorova
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: bioanna1995@gmail.com
ORCID iD: 0000-0003-0486-1353
Researcher, Laboratory for the Molecular Mechanisms of Antibiotic Resistance
俄罗斯联邦, MoscowAnna Guseva
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: anguseva@cmd.su
ORCID iD: 0000-0001-7028-0253
Junior Researcher, Laboratory of Molecular Diagnostics and Epidemiology of Intestinal Infections
俄罗斯联邦, MoscowNatalia Krutova
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: nkrutova@cmd.su
ORCID iD: 0000-0003-2925-5376
Junior Researcher, Laboratory of Molecular Diagnostics and Epidemiology of Intestinal Infections
俄罗斯联邦, MoscowNadezhda Akulova
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: akulova.n@gmail.com
ORCID iD: 0000-0003-0208-7165
Senior Researcher, Laboratory of Molecular Diagnostics and Epidemiology of Intestinal Infections
俄罗斯联邦, MoscowKristina Bikmetova
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: c.bicmetowa@yandex.ru
ORCID iD: 0000-0003-3368-7833
Junior Researcher, Laboratory of Molecular Diagnostics and Epidemiology of Intestinal Infections
俄罗斯联邦, MoscowNatalia Parkina
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: parkina@cmd.su
ORCID iD: 0000-0003-3948-1385
Researcher, Laboratory of Molecular Diagnostics and Epidemiology of Intestinal Infections
俄罗斯联邦, MoscowYulia Mikhaylova
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: mihailova@cmd.su
ORCID iD: 0000-0002-5646-538X
Head of Laboratory of Molecular Mechanisms of Antibiotic Resistance
俄罗斯联邦, MoscowOlga Veselova
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: sapienscri@gmail.com
ORCID iD: 0000-0002-5041-4370
Researcher, Laboratory of Molecular Diagnostics and Epidemiology of Intestinal Infections
俄罗斯联邦, MoscowAlexandr Podkolzin
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: apodkolzin@pcr.ru
ORCID iD: 0000-0002-0044-3341
MD, Deputy Director in Epidemiology
俄罗斯联邦, MoscowVasiliy Akimkin
Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being
Email: vgakimkin@yandex.ru
ORCID iD: 0000-0003-4228-9044
Academician of the Russian Academy of Sciences; MD, Professor, Director
俄罗斯联邦, Moscow参考
- Li Y.J., Yang Y.F., Zhou Y.J., Zhang R.H., Liu C.W., Liu H. et al. Estimating the burden of foodborne gastroenteritis due to nontyphoidal Salmonella enterica, Shigella and Vibrio parahaemolyticus in China. PLoS One 2022; (11): e0277203. doi: 10.1371/journal.pone.0277203
- Majowicz S.E., Musto J., Scallan E., Angulo F.J., Kirk M., O’Brien S.J. et al. The global burden of nontyphoidal Salmonella gastroenteritis. Clin. Infect. Dis. 2010 50(6): 882–9. doi: 10.1086/650733
- Braden C.R. Salmonella enterica serotype Enteritidis and eggs: a national epidemic in the United States. Clin. Infect. Dis. 2006; 43(4): 512–7. doi: 10.1086/505973
- Kuleshov K.V., Pavlova A.S., Shedko E.D., Mikhaylova Y.V., Margos G., Hepner S. et al. Mobile Colistin Resistance Genetic Determinants of Non-Typhoid Salmonella enterica Isolates from Russia. Microorganisms 2021; 9(12): 2515. doi: 10.3390/microorganisms9122515
- Li S., He Y., Mann D.A., Deng X. Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks. Nat. Commun. 2021; 12(1): 5109. doi: 10.1038/s41467-021-25319-7
- Rodrigue D.C., Tauxe R.V., Rowe B. International increase in Salmonella Enteritidis: a new pandemic? Epidemiol. Infect. 1990; (1): 21–7. doi: 10.1017/s0950268800047609
- Wright A.P., Richardson L., Mahon B.E., Rothenberg R., Cole D.J. The rise and decline in Salmonella enterica serovar Enteritidis outbreaks attributed to egg-containing foods in the United States, 1973-2009. Epidemiol. Infect. 2016; 144(4): 810–9. doi: 10.1017/S0950268815001867
- Pijnacker R., Dallman T.J., Tijsma A.S.L., Hawkins G., Larkin L., Kotila S.M. et al. An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study. Lancet Infect Dis. 2019; 9(7): 778–86. doi: 10.1016/S1473-3099(19)30047-7
- Allard M.W., Luo Y., Strain E., Pettengill J., Timme R., Wang C. et al. On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004. PLoS One 2013; 8(1): e55254. doi: 10.1371/journal.pone.0055254
- Botteldoorn N., van Coillie E., Goris J., Werbrouck H., Piessens V., Godard C. et al. Limited genetic diversity and gene expression differences between egg- and non-egg-related Salmonella Enteritidis strains. Zoonoses Public Health. 2010; 57(5): 345–57. doi: 10.1111/j.1863-2378.2008.01216.x
- Ribot E.M., Fair M.A., Gautom R., Cameron D.N., Hunter S.B., Swaminathan B. et al. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for Pulse Net. Foodborne Pathog Dis. 2006; 3(1): 59–67. doi: 10.1089/fpd.2006.3.59
- Prjibelski A., Antipov D., Meleshko D., Lapidus A., Korobeynikov A. Using SPAdes De Novo Assembler. Curr. Protoc. Bioinformatics 2020; 70(1): e102. doi: 10.1002/cpbi.102
- Robertson J., Yoshida C., Kruczkiewicz P., Nadon C., Nichani A., Taboada E.N. et al. Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR). Microb. Genom. 2018; 4(2): e000151. doi: 10.1099/mgen.0.000151
- Croucher N.J., Page A.J., Connor T.R., Delaney A.J., Keane J.A., Bentley S.D. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015; 43(3): e15. doi: 10.1093/nar/gku1196
- Tonkin-Hill G., Lees J.A., Bentley S.D., Frost S.D.W., Corander J. Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Res. 2019; 47(11): 5539–49. doi: 10.1093/nar/gkz361
- Chattaway M.A., Dallman T.J., Larkin L., Nair S., McCormick J., Mikhail A. et al. The Transformation of Reference Microbiology Methods and Surveillance for Salmonella with the Use of Whole Genome Sequencing in England and Wales. Front Public Health 2019; (7): 317. doi: 10.3389/fpubh.2019.00317
补充文件
