Comparative Molecular-Genetic Analysis of Francisella tularensis Strains Isolated in the Rostov Region in 2020 and Genome Sequences of the Strains Collected in Various Regions of the World
Six cultures of tularemia microbe from fallen and captured live animals were isolated during epizootiological monitoring in the steppe focus in the south-east of the Rostov Region in 2020 against the background of extensive epizootics in the populations of the common vole Microtus arvalis obscurus a...
Published in: | Problems of Particularly Dangerous Infections |
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Federal Government Health Institution, Russian Research Anti-Plague Institute “Microbe”
2023
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Online Access: | https://doi.org/10.21055/0370-1069-2023-3-59-65 https://doaj.org/article/fc07d148f91e4ef7854892541878672d |
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ftdoajarticles:oai:doaj.org/article:fc07d148f91e4ef7854892541878672d 2024-09-15T18:02:50+00:00 Comparative Molecular-Genetic Analysis of Francisella tularensis Strains Isolated in the Rostov Region in 2020 and Genome Sequences of the Strains Collected in Various Regions of the World A. S. Vodop’yanov R. V. Pisanov S. O. Vodop’yanov M. V. Tsimbalistova N. L. Pichurina V. M. Sorokin N. V. Pavlovich A. K. Noskov 2023-10-01T00:00:00Z https://doi.org/10.21055/0370-1069-2023-3-59-65 https://doaj.org/article/fc07d148f91e4ef7854892541878672d RU rus Federal Government Health Institution, Russian Research Anti-Plague Institute “Microbe” https://journal.microbe.ru/jour/article/view/1855 https://doaj.org/toc/0370-1069 https://doaj.org/toc/2658-719X 0370-1069 2658-719X doi:10.21055/0370-1069-2023-3-59-65 https://doaj.org/article/fc07d148f91e4ef7854892541878672d Проблемы особо опасных инфекций, Vol 0, Iss 3, Pp 59-65 (2023) francisella tularensis indel whole-genome sequencing pcr genotyping snp Infectious and parasitic diseases RC109-216 article 2023 ftdoajarticles https://doi.org/10.21055/0370-1069-2023-3-59-65 2024-08-05T17:49:00Z Six cultures of tularemia microbe from fallen and captured live animals were isolated during epizootiological monitoring in the steppe focus in the south-east of the Rostov Region in 2020 against the background of extensive epizootics in the populations of the common vole Microtus arvalis obscurus and the public vole Microtus socialis.The aim of the work was to develop an SNP-typing scheme and to conduct a comparative study of the phylogenetic relations between Francisella tularensis strains isolated in the Rostov Region (2020) and strains from other regions.Materials and methods. Genome-wide sequencing was performed on the MiSeq Illumina platform. The author’s software GeneExpert, PrimerM and VirtualPCR, written in the Java programming language, were used for the analysis.Results and discussion. The strains of tularemia agent, isolated on the territory of the Rostov Region in 2020, can be allocated to two different clusters. It is established that two strains of tularemia pathogen (F0884 and F0889) isolated in Turkey are genetically close to some isolates circulating in the Rostov Region. A unique INDEL marker characteristic of this group of strains has been identified. The comparison of our proposed typing scheme with the scheme of “canonical” SNPs has showed a fairly good consistency and convergence of results within large clusters, meanwhile using a set of 6626 SNPs allows for differentiating the strains within one canSNP type. It is revealed that the vaccine strain has a common canSNP type with clinical and natural strains. A set of SNP markers has been selected for comparative analysis. A new INDEL marker that enables intraspecific typing of F. tularensis has been discovered and the possibility of its application in vitro and in silico has been comfirmed. Article in Journal/Newspaper Common vole Microtus arvalis Directory of Open Access Journals: DOAJ Articles Problems of Particularly Dangerous Infections 3 59 65 |
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Directory of Open Access Journals: DOAJ Articles |
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Russian |
topic |
francisella tularensis indel whole-genome sequencing pcr genotyping snp Infectious and parasitic diseases RC109-216 |
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francisella tularensis indel whole-genome sequencing pcr genotyping snp Infectious and parasitic diseases RC109-216 A. S. Vodop’yanov R. V. Pisanov S. O. Vodop’yanov M. V. Tsimbalistova N. L. Pichurina V. M. Sorokin N. V. Pavlovich A. K. Noskov Comparative Molecular-Genetic Analysis of Francisella tularensis Strains Isolated in the Rostov Region in 2020 and Genome Sequences of the Strains Collected in Various Regions of the World |
topic_facet |
francisella tularensis indel whole-genome sequencing pcr genotyping snp Infectious and parasitic diseases RC109-216 |
description |
Six cultures of tularemia microbe from fallen and captured live animals were isolated during epizootiological monitoring in the steppe focus in the south-east of the Rostov Region in 2020 against the background of extensive epizootics in the populations of the common vole Microtus arvalis obscurus and the public vole Microtus socialis.The aim of the work was to develop an SNP-typing scheme and to conduct a comparative study of the phylogenetic relations between Francisella tularensis strains isolated in the Rostov Region (2020) and strains from other regions.Materials and methods. Genome-wide sequencing was performed on the MiSeq Illumina platform. The author’s software GeneExpert, PrimerM and VirtualPCR, written in the Java programming language, were used for the analysis.Results and discussion. The strains of tularemia agent, isolated on the territory of the Rostov Region in 2020, can be allocated to two different clusters. It is established that two strains of tularemia pathogen (F0884 and F0889) isolated in Turkey are genetically close to some isolates circulating in the Rostov Region. A unique INDEL marker characteristic of this group of strains has been identified. The comparison of our proposed typing scheme with the scheme of “canonical” SNPs has showed a fairly good consistency and convergence of results within large clusters, meanwhile using a set of 6626 SNPs allows for differentiating the strains within one canSNP type. It is revealed that the vaccine strain has a common canSNP type with clinical and natural strains. A set of SNP markers has been selected for comparative analysis. A new INDEL marker that enables intraspecific typing of F. tularensis has been discovered and the possibility of its application in vitro and in silico has been comfirmed. |
format |
Article in Journal/Newspaper |
author |
A. S. Vodop’yanov R. V. Pisanov S. O. Vodop’yanov M. V. Tsimbalistova N. L. Pichurina V. M. Sorokin N. V. Pavlovich A. K. Noskov |
author_facet |
A. S. Vodop’yanov R. V. Pisanov S. O. Vodop’yanov M. V. Tsimbalistova N. L. Pichurina V. M. Sorokin N. V. Pavlovich A. K. Noskov |
author_sort |
A. S. Vodop’yanov |
title |
Comparative Molecular-Genetic Analysis of Francisella tularensis Strains Isolated in the Rostov Region in 2020 and Genome Sequences of the Strains Collected in Various Regions of the World |
title_short |
Comparative Molecular-Genetic Analysis of Francisella tularensis Strains Isolated in the Rostov Region in 2020 and Genome Sequences of the Strains Collected in Various Regions of the World |
title_full |
Comparative Molecular-Genetic Analysis of Francisella tularensis Strains Isolated in the Rostov Region in 2020 and Genome Sequences of the Strains Collected in Various Regions of the World |
title_fullStr |
Comparative Molecular-Genetic Analysis of Francisella tularensis Strains Isolated in the Rostov Region in 2020 and Genome Sequences of the Strains Collected in Various Regions of the World |
title_full_unstemmed |
Comparative Molecular-Genetic Analysis of Francisella tularensis Strains Isolated in the Rostov Region in 2020 and Genome Sequences of the Strains Collected in Various Regions of the World |
title_sort |
comparative molecular-genetic analysis of francisella tularensis strains isolated in the rostov region in 2020 and genome sequences of the strains collected in various regions of the world |
publisher |
Federal Government Health Institution, Russian Research Anti-Plague Institute “Microbe” |
publishDate |
2023 |
url |
https://doi.org/10.21055/0370-1069-2023-3-59-65 https://doaj.org/article/fc07d148f91e4ef7854892541878672d |
genre |
Common vole Microtus arvalis |
genre_facet |
Common vole Microtus arvalis |
op_source |
Проблемы особо опасных инфекций, Vol 0, Iss 3, Pp 59-65 (2023) |
op_relation |
https://journal.microbe.ru/jour/article/view/1855 https://doaj.org/toc/0370-1069 https://doaj.org/toc/2658-719X 0370-1069 2658-719X doi:10.21055/0370-1069-2023-3-59-65 https://doaj.org/article/fc07d148f91e4ef7854892541878672d |
op_doi |
https://doi.org/10.21055/0370-1069-2023-3-59-65 |
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Problems of Particularly Dangerous Infections |
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