GENOMOSYSTEMATICS OF RICKETTSIAE

The definition of the term genome was given by the German botanist G. Winkler almost one hundred years ago in 1920. A genome definition for bacterial (rickettsia) with a single chromosome was recently presented from the perspective of information theory, biology and bioinformatics as the informat...

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Autores principales:	S. N. Shpynov, N. N. Pozdnichenko, A. S. Gumenyuk, A. A. Skiba
Formato:	article
Lenguaje:	RU
Publicado:	Sankt-Peterburg : NIIÈM imeni Pastera 2018
Materias:	rickettsiae rickettsioses systematics ecology epidemiology virulence genome formal order analysis genomosystematics Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/4e729103167246acbc4444bc88d907b3
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spelling	oai:doaj.org-article:4e729103167246acbc4444bc88d907b32021-11-22T07:09:49ZGENOMOSYSTEMATICS OF RICKETTSIAE2220-76192313-739810.15789/2220-7619-2018-2-107-118https://doaj.org/article/4e729103167246acbc4444bc88d907b32018-09-01T00:00:00Zhttps://www.iimmun.ru/iimm/article/view/728https://doaj.org/toc/2220-7619https://doaj.org/toc/2313-7398The definition of the term genome was given by the German botanist G. Winkler almost one hundred years ago in 1920. A genome definition for bacterial (rickettsia) with a single chromosome was recently presented from the perspective of information theory, biology and bioinformatics as the information chain of nucleotides. The systematics of rickettsiae (obligate intracellular microorganisms) is based on a limited number of phenotypic characters. Classifications built on the analysis of genes, fragments of genomes and their concatenations cause discussion. Application of the Formal Order Analysis (FOA, http://foarlab.org) in the study of complete genomes allowed to submit the systematics of representatives of the family Rickettsiaceae. This approach confirmed the existence of typhus group (TG), spotted fever group (SFG), and an «ancestral» group within the genus Rickettsia, and allowed the isolation of the Rickettsia felis group within this genus, located between the «ancestral» group and the SFG and the R. akari group on the border between the SFG group and the genus Orientia. The development of the tools of FOA — «Map of Genes» and «Matrix of Similarity» — helped to conduct an in-depth study of the complete genomes of rickettsia, taking into account the characteristics of their genes and noncoding sequences. Application of these instruments, with the help of the obtained classification, confirmed the notion of ecological features of rickettsia, the structure of nosological forms and the epidemiological patterns of rickettsiosis, and made it possible to assess the virulence of the strains of the two most pathogenic species of rickettsia, R. prowazekii and R. rickettsia. In this work, for the first time, a holistic, consistent and multidimensional observation of a set of closely related bacteria (a family of bacteria) and the manifestations associated with them was carried out. The basis of the developed and herein described systematic approach to the study of bacteria is a new mathematical model — the arrangement of nucleotides in a complete genome and its sensitive unambiguous numerical characteristics. A new methodological approach named genomosystematics and based on mathematical modeling of complete genomes of rickettsiae (bacteria) using FOA. Classification of rickettsiae and rickettsioses obtained with the help of this approach corresponds to ecological, epidemiological and etiological principles. Application of the genomosystematics can serve the goals and objectives of preventive medicine. The publication completes a series of scientific works presenting the methodology of an integrated approach based on the application of mathematical analysis tools in the study of objects and laws of natural science disciplines of biological and medical profile.S. N. ShpynovN. N. PozdnichenkoA. S. GumenyukA. A. SkibaSankt-Peterburg : NIIÈM imeni Pasteraarticlerickettsiaerickettsiosessystematicsecologyepidemiologyvirulencegenomeformal order analysisgenomosystematicsInfectious and parasitic diseasesRC109-216RUInfekciâ i Immunitet, Vol 8, Iss 2, Pp 107-118 (2018)
institution	DOAJ
collection	DOAJ
language	RU
topic	rickettsiae rickettsioses systematics ecology epidemiology virulence genome formal order analysis genomosystematics Infectious and parasitic diseases RC109-216
spellingShingle	rickettsiae rickettsioses systematics ecology epidemiology virulence genome formal order analysis genomosystematics Infectious and parasitic diseases RC109-216 S. N. Shpynov N. N. Pozdnichenko A. S. Gumenyuk A. A. Skiba GENOMOSYSTEMATICS OF RICKETTSIAE
description	The definition of the term genome was given by the German botanist G. Winkler almost one hundred years ago in 1920. A genome definition for bacterial (rickettsia) with a single chromosome was recently presented from the perspective of information theory, biology and bioinformatics as the information chain of nucleotides. The systematics of rickettsiae (obligate intracellular microorganisms) is based on a limited number of phenotypic characters. Classifications built on the analysis of genes, fragments of genomes and their concatenations cause discussion. Application of the Formal Order Analysis (FOA, http://foarlab.org) in the study of complete genomes allowed to submit the systematics of representatives of the family Rickettsiaceae. This approach confirmed the existence of typhus group (TG), spotted fever group (SFG), and an «ancestral» group within the genus Rickettsia, and allowed the isolation of the Rickettsia felis group within this genus, located between the «ancestral» group and the SFG and the R. akari group on the border between the SFG group and the genus Orientia. The development of the tools of FOA — «Map of Genes» and «Matrix of Similarity» — helped to conduct an in-depth study of the complete genomes of rickettsia, taking into account the characteristics of their genes and noncoding sequences. Application of these instruments, with the help of the obtained classification, confirmed the notion of ecological features of rickettsia, the structure of nosological forms and the epidemiological patterns of rickettsiosis, and made it possible to assess the virulence of the strains of the two most pathogenic species of rickettsia, R. prowazekii and R. rickettsia. In this work, for the first time, a holistic, consistent and multidimensional observation of a set of closely related bacteria (a family of bacteria) and the manifestations associated with them was carried out. The basis of the developed and herein described systematic approach to the study of bacteria is a new mathematical model — the arrangement of nucleotides in a complete genome and its sensitive unambiguous numerical characteristics. A new methodological approach named genomosystematics and based on mathematical modeling of complete genomes of rickettsiae (bacteria) using FOA. Classification of rickettsiae and rickettsioses obtained with the help of this approach corresponds to ecological, epidemiological and etiological principles. Application of the genomosystematics can serve the goals and objectives of preventive medicine. The publication completes a series of scientific works presenting the methodology of an integrated approach based on the application of mathematical analysis tools in the study of objects and laws of natural science disciplines of biological and medical profile.
format	article
author	S. N. Shpynov N. N. Pozdnichenko A. S. Gumenyuk A. A. Skiba
author_facet	S. N. Shpynov N. N. Pozdnichenko A. S. Gumenyuk A. A. Skiba
author_sort	S. N. Shpynov
title	GENOMOSYSTEMATICS OF RICKETTSIAE
title_short	GENOMOSYSTEMATICS OF RICKETTSIAE
title_full	GENOMOSYSTEMATICS OF RICKETTSIAE
title_fullStr	GENOMOSYSTEMATICS OF RICKETTSIAE
title_full_unstemmed	GENOMOSYSTEMATICS OF RICKETTSIAE
title_sort	genomosystematics of rickettsiae
publisher	Sankt-Peterburg : NIIÈM imeni Pastera
publishDate	2018
url	https://doaj.org/article/4e729103167246acbc4444bc88d907b3
work_keys_str_mv	AT snshpynov genomosystematicsofrickettsiae AT nnpozdnichenko genomosystematicsofrickettsiae AT asgumenyuk genomosystematicsofrickettsiae AT aaskiba genomosystematicsofrickettsiae
_version_	1718417975971676160

GENOMOSYSTEMATICS OF RICKETTSIAE

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