New approaches in the systematics of rickettsiae

Abstract

The development of a formal order analysis (FOA) allowed constructing a classification of 49 genomes of Rickettsiaceae family representatives. Recently FOA has been extended with new tools—‘Map of genes,’ ‘Matrix of similarity’ and ‘Locality-sensitive hashing’—for a more in-depth study of the structure of rickettsial genomes. The new classification confirmed and supplemented the previously constructed one by determining the position of Rickettsia africae str. ESF-5, R. heilongjiangensis 054, R. monacensis str. IrR/Munich, R. montanensis str. OSU 85-930, R. raoultii str. Khabarovsk, R. rhipicephali str. 3-7-female6-CWPP and Rickettsiales bacterium str. Ac37b. The ‘Map of genes’ demonstrated the complete genomes and their components in a graphical form. The ‘Matrix of similarity’ was applied for an in-depth classification to a subtaxonomic category of the strain within the species R. rickettsii (11 strains) and R. prowazekii (ten strains). The ‘Matrix of similarity’ determines the degree of homology of complete genomes by pairwise comparison of their components and identification of those being identical and similar in the arrangement of nucleotides. A new genomosystematics approach is proposed for the study of complete genomes and their components through the development and application of FOA tools. Its applications include the development of principles for the classification of microorganisms, based on the analysis of complete genomes and their annotations. This approach may help in the taxonomic classification and characterization of some Candidatus Rickettsia spp. that are found in large numbers in arthropods worldwide.

Molecular epidemiology and phylogeny of spotted fever group Rickettsia in camels ( Camelus dromedarius ) and their infesting ticks from Tunisia

“…Spotted fever Rickettsiosis is a group of the oldest known vector‐borne disease, caused by obligate intracellular Gram‐negative bacteria belonging to Rickettsia genus (Shpynov, Fournier, Pozdnichenko, Gumenuk, & Skiba, ). These microorganisms, identified in humans and animals, are widely distributed worldwide (Parola et al, ).…”

Genomosystematics of Rickettsiae

“…В данной работе представлена верификация классификации прокариот из семейства Rickettsiaceae [49,50], построенная на основании сравнения показателей одной характеристики строя -средней удаленности нуклеотидов в полноразмерных геномах, с учетом таксономии их хозяев -членистоногих (Arthropoda), классификации вызываемых ими нозологических форм и особенностей механизма передачи этиологических агентов при эпидемиологических проявлениях (рис. ).…”

“…Полученная классификация продемонстрировала значительную дивергенцию родов Rickettsia и Orientia в семействе Rickettsiaceae (рис.) [49] По оси абсцисс расположены геномы риккетсий, а по оси ординат -характеристика средней удаленности. В р -вшивый риккетсиоз; Г р -гамазовый (клещевой) риккетсиоз; К л -краснотелковая (клещевая) лихорадка.…”

Molecular detection of Rickettsia in fleas from micromammals in Chile

“…Currently, 32 species are recognized (http://www.bacterio.net/-allnamesmr.html), and there are many strains that have not yet been characterized, while subspecies and uncultivated species are classi ed as Candidatus [4]. Recently, using new classi cation methods based on formal order analysis (FOA), which considers whole-genome sequencing analysis, two groups are recognized within the Rickettsia genus: the major typhus group (MTG) and major spotted fever group (MSFG).…”

“…The MTG is divided into the typhus group (TG) and ancestral group (AG) and is transmitted by insects. MSFG includes the R. felis group, R. akari group, and "classical" spotted fever group that includes several species transmitted by mites and hard ticks, of which the most important are R. rickettsi and R. conorii, that cause Rocky Mountain spotted fever and Mediterranean spotted fever, respectively [4]. Since Rickettsia research has focused on species that affect humans, other species have received less attention [5].…”