GENOMOSYSTEMATICS OF RICKETTSIAE

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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.

About the authors

S. N. Shpynov

N.F. Gamaleya National Research Center of Epidemiology and Microbiology

Author for correspondence.
Email: stan63@inbox.ru

PhD, MD (Medicine), Head of Laboratory of Ecology of Rickettsie

123098, Russian Federation, Moscow, Gamaleya str., 18

Phone/fax: +7 (499) 193-61-85 (office)

Russian Federation

N. N. Pozdnichenko

Omsk State Technical University

Email: fake@neicon.ru

Senior Lecturer, Informatics and Computer Engineering Department

Russian Federation

A. S. Gumenyuk

Omsk State Technical University

Email: fake@neicon.ru

PhD (Engineering Sciences), Associate Professor, Informatics and Computer Engineering Department

Russian Federation

A. A. Skiba

Omsk State Technical University

Email: fake@neicon.ru

Software Developer, Informatics and Computer Engineering Department

 

Russian Federation

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