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Abstract
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.
Highlights
Исторически на основании фенотипических характеристик представители рода Rickettsia были классифицированы на группы: I) клещевой пятнистой лихорадки (КПЛ); II) сыпного тифа (СТ) и III) группу кустарникового тифа (КТ), с единственным представителем — R. tsutsugamushi [40, 59]
Механизм передачи возбудителя при риккетсиозах группы КПЛ и лихорадке цуцугамуши осуществляется путем инокуляции во время кровососания членистоногого и является трансмиссивным с инокуляционным путем заражения, фактор передачи — слюна клеща
Authors: Shpynov S.N., PhD, MD (Medicine), Head of Laboratory of Ecology of Rickettsie, N.F. Gamaleya Federal Center of Epidemiology and Microbiology, Moscow, Russian Federation; Pozdnichenko N.N., Senior Lecturer, Informatics and Computer Engineering Department, Omsk State Technical University, Omsk, Russian Federation; Gumenyuk A.S., PhD (Engineering Sciences), Associate Professor, Informatics and Computer Engineering Department, Omsk State Technical University, Omsk, Russian Federation; Skiba A.A., Software Developer, Informatics and Computer Engineering Department, Omsk State Technical University, Omsk, Russian Federation
Summary
Недавно было представлено определение генома для бактерий (риккетсий) с одной хромосомой с позиции теории информации, биологии и биоинформатики как информационной цепи нуклеотидов. Классификации, построенные при анализе генов, фрагментов геномов и их конкатенаций вызывают дискуссии. Применение разработанного аппарата формального анализа строя (http://foarlab.org) при изучении полноразмерных геномов позволило представить систематику риккетсий и Orientia tsutsugamushi из семейства Rickettsiaceae. Разработка инструментов формального анализа строя — «Карта генов» и «Матрица сходства» — помогла провести углубленное изучение полноразмерных геномов риккетсий с учетом характеристик их генов и некодирующих последовательностей. Применение данных инструментов позволило подтвердить с помощью полученной классификации представление об экологических особенностях риккетсий, структуре нозологических форм и эпидемиологических закономерностях риккетсиозов, а также оценить вирулентность штаммов двух наиболее патогенных видов риккетсий — R. prowazekii и R. rickettsii. Предложенный методологический подход назван «геномосистематика» и основывается на математическом моделировании полноразмерных геномов риккетсий (бактерий) с помощью средств формального анализа строя.
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