Bakterii roda Aerococcus chasto associirovany s infekciyami mochevyvodyashchih putej i krovotoka u cheloveka. SHtamm Aerococcus sp. 1KP-2016, vydelennyj iz lejkocitarnogo sloya krovi, obladal posledovatel'nost'yu 16S rRNK, sovpadayushchej na 98,7% i menee s ranee opisannymi predstavitelyami dannogo roda. Cel'yu raboty bylo provesti polnogenomnoe sekvenirovanie Aerococcus 1KP-2016 s posleduyushchej filogeneticheskoj rekonstrukciej. Pokazano, chto Aerococcus 1KP-2016 yavlyaetsya predstavitelem novogo vida roda Aerococcus, naibolee blizkogo k Aerococcus viridans i Aerococcus urinaeequi. Genomnaya posledovatel'nost', imeyushchaya dlinu 2,042 mln p.n. i GC-sostav 38,5%, deponirovana v DBJ/EMBL/GenBank pod identifikatorom NEEY00000000.

Aerococcus genus bacteria are often associated with human urinary tract and bloodstream infections. The Aerococcus sp. 1KP-2016 strain isolated from the buffy coat had the 16S rRNA sequence that was a 98.7% (and less) match with the previously described members of this genus. The purpose of this study was to perform whole genome sequencing of Aerococcus 1KP-2016 followed by phylogenetic reconstruction. We have shown that Aerococcus 1KP-2016 belongs to the new species of the Aerococcus genus that is closest to Aerococcus viridans and Aerococcus urinaeequi. The genomic sequence, which consists of 2.042 million bps with GC content at 38.5%, was deposited in the DBJ/EMBL/GenBank under identifier NEEY00000000.

In 2018, a few sequencing studies were published revealing the existence of two monophyletic clusters within the C. diphtheriae species, meaning that this species can be divided into two subspecies: C. diphtheriae subsp. diphtheriae and C. diphtheriae subsp. lausannense. The objective of our study was to describe the genotype and the phenotype of 2 nontoxigenic C. diphtheriae strains isolated in Russia in 2017–2018, which were classified by us as C. diphtheriae subsp. lausannense based on the aggregated data yielded by a variety of techniques, including microbiological and molecular genetic techniques, as well as a bioinformatic search for subspecies-specific genes in the publicly available genomes of C. diphtheriae. The isolated strains had morphological and biochemical characteristics of C. diphtheriae. The strains were assigned to the MLST type ST199 included in the clonal complex associated with subsp. lausannense. PCR revealed that both analyzed strains of C. diphtheriae subsp. lausannense carried the ptsI gene encoding phosphoenolpyruvate-protein phosphotransferase and did not carry the narG gene encoding the synthesis of nitrate reductase subunits, whereas the strains of C. diphtheriae subsp. diphtheriae had the narG gene and did not have ptsI. We experimentally proved the ability of lausannense strains to ferment N-acetylglucosamine. Our findings expand the knowledge of the biological diversity of C. diphtheriae and indicate the need for estimating the spread of these microorganisms in Russia, as well as their pathogenic potential.

В 2018 г. на основании полногеномных данных появились публикации о наличии двух монофилетических кластеров внутри вида C. diphtheriae, что позволяет дифференцировать этот вид на два подвида: C. diphtheriae subsp. diphtheriae и C. diphtheriae subsp. lausannense. Целью работы было описать генотип и фенотип двух нетоксигенных штаммов C. diphtheriae, выделенных в 2017–2018 гг. с профилактической целью, которые на основании совокупности результатов множества методов могут быть отнесены к C. diphtheriae subsp. lausannense. В исследовании использовали микробиологические и молекулярно-генетические методы, а также биоинформатический поиск подвид-специфичных генов в публично доступных геномах C. diphtheriae. Выделенные штаммы имели характерные для C. diphtheriae морфо-культуральные свойства и биохимическую характеристику. В МЛСТ штаммы принадлежали к сиквенс-типу ST199, входящему в клональный комплекс, ассоциированный с subsp. lausannense. С использованием ПЦР были показаны наличие ptsI (гена, кодирующего фосфоенолпируват-белок фосфотрансферазы) и отсутствие narG (гена, кодирующего синтез субъединиц нитратредуктазы) у двух исследуемых штаммов C. diphtheriae subsp. lausannense и противоположная картина — у штаммов C. diphtheriae subsp. diphtheriae. Была экспериментально подтверждена способность выделенных штаммов подвида lausannense сбраживать N-aцетилглюкозамин. Полученные результаты расширяют представления о биологическом разнообразии вида C. diphtheriae и свидетельствуют о необходимости дальнейших исследований по оценке распространенности этих микроорганизмов и изучению их патогенного потенциала.

Purpose: whooping cough diagnostics by molecular-genetic methods.Materials and methods. Under observation there were 4930 people during the period from 2012 to 2015. All samples were received in 8 schools of Moscow and the Moscow region: in 3 schools had been found children with whooping cough, in other 5 schools – only children with prolonged cough. Whooping cough diagnosis had been given earlier by bacteriological and serological methods. 430 clinical samples were studied by 2 methods: PCR with fluorescent hybridized detection of amplified products and isothermal amplification.Results. In three of eight schools whooping cough cases at 7 children at the age of 7, 9, 11 and 15 years were revealed earlier. The diagnosis of whooping cough at them was confirmed by means of bacteriological and serological methods. 33 positive DNA samples (7.7%) are revealed. DNA-positive samples are allocated from 18 pupils and 15 employees of schools. In two schools where earlier infection sources were established, 15 DNA-positive samples from which in three cases clinical manifestations were observed are revealed. In those schools where it wasn’t earlier established a source of an infection and examinations conducted it is long the coughing children, 18 DNA-positive samples are revealed, and in two cases clinical manifestations in the form of cough were observed.Conclusion. Performed research confirmed high efectiveness of molecular-genetic methods during pertussis infection foci examination in schools for infection source identification also amongst long coughing children.

Relevance. Despite more than 50 years of successful experience with pertussis immunization, pertussis remains an important public health problem. WHO estimated 16 million people worldwide are infected per year, a significant number of whom are children under 1 year of age. In the last 10 years a significant increase in the incidence of whooping cough has been observed in many countries with a high immunization coverage level. In Russia, specific prevention of whooping cough, is held since 1959. Specific prevention of whooping cough has led to considerable improvement of an epidemiological situation and has shown its social and economic importance for maintenance of sanitary and epidemiologic wellbeing on this infection in Russia. Goal. Study the structure of population B. pertussis circulating in Russia in dynamics of whooping cough epidemic process. Materials and methods Studied 573 B. pertussis strains allocated from patients with whooping cough in 1948 - 2015 used multilocus sequence typing (MAST). Isolates divided in five groups: 1948 - 1969 - 37 strains, isolated in the vaccination period and the first ten years of mass childhood immunization; 1970 - 1989 - 63 strains; 1990 - 2005 - 203 strains (from G.N. Gabrichevsky Institute of Epidemiology and Microbiology collection); 2006 - 2012 - 185 strains; 2013 - 2015 - 85 strains. Genotyping of strains was carried out according to the scheme MAST2 on the basis of a sequence of fragments of genes of ptxP-fim3-prn. Results of sequencing-typing were computed in the CromasLite program, identification of alleles and sequencing types carried out on EMBL/GenBank. Results. Formation of population of B.pertussis strains during more than 50 years went on the way of consecutive change of vaccinal genotype strains with strains of new nonvaccinal genotypes. Conclusions. Modern population of the causative agent of whooping cough is presented by the strains of genotype 322 and 329 possessing high virulence and causing heavier clinical course of disease.

Relevance. Despite more than 50 years of successful experience with pertussis immunization, pertussis remains an important public health problem. WHO estimated 16 million people worldwide are infected per year, a significant number of whom are children under 1 year of age. In the last 10 years a significant increase in the incidence of whooping cough has been observed in many countries with a high immunization coverage level. In Russia, specific prevention of whooping cough, is held since 1959. Specific prevention of whooping cough has led to considerable improvement of an epidemiological situation and has shown its social and economic importance for maintenance of sanitary and epidemiologic wellbeing on this infection in Russia. Goal. Study the structure of population B. pertussis circulating in Russia in dynamics of whooping cough epidemic process. Materials and methods Studied 573 B. pertussis strains allocated from patients with whooping cough in 1948 - 2015 used multilocus sequence typing (MAST). Isolates divided in five groups: 1948 - 1969 - 37 strains, isolated in the vaccination period and the first ten years of mass childhood immunization; 1970 - 1989 - 63 strains; 1990 - 2005 - 203 strains (from G.N. Gabrichevsky Institute of Epidemiology and Microbiology collection); 2006 - 2012 - 185 strains; 2013 - 2015 - 85 strains. Genotyping of strains was carried out according to the scheme MAST2 on the basis of a sequence of fragments of genes of ptxP-fim3-prn. Results of sequencing-typing were computed in the CromasLite program, identification of alleles and sequencing types carried out on EMBL/GenBank. Results. Formation of population of B.pertussis strains during more than 50 years went on the way of consecutive change of vaccinal genotype strains with strains of new nonvaccinal genotypes. Conclusions. Modern population of the causative agent of whooping cough is presented by the strains of genotype 322 and 329 possessing high virulence and causing heavier clinical course of disease.

178 strains of B. pertussis isolated from infected individuals in various regions of Russia from 1948 to 2012 have been studied for their susceptibility to six antibacterial preparations. It has been shown, that B. pertussis strains isolated from 1948 to 1989 were predominantly sensitive to erythromycin. In the following years a gradual decrease in susceptibility of circulating strains of B. pertussis to this antibiotic was registered with the emergence of strains with intermediate susceptibility in 22% of cases from 1990 to 2005 (MIC 0,060 mcg/mL), up to 59,3% in the last six years (MIC 0,125 mcg/mL). As for azithromycin, high susceptibility of strains of B. pertussis to this preparation was shown throughout the entire duration of the survey. However, the rate of incidence of intermediate strains reached 14% among those strains isolated from 1990 to 2005, and is now at 32%. Thus, after several decades of active use of antibiotics pertussis underwent a series of transformations resulting in a decrease in susceptibility of B. pertussis strains to erythromycin and azithromycin.

Qualitative and quantitative composition of enteric bifidoflora was studied in a group of 13 mother–infant pairs. Pure cultures of Bifidobacterium strains were isolated from feces and their species were identified by PCR with species-specific primers or by partial sequencing of 16S rDNA. The strains were compared by REP-PCR. The most incident Bifidobacterium species in mothers were B. longum and B. adolescentis. The infants were mainly colonized by B. bifdum and B. longum. The mother and her baby were colonized by the same Bifidobacterium species in 9 of 13 cases. In 5 (38.5%) of these cases, these pairs of strains were identical by their REP-PCR profiles. These strains belonged to B. longum in one case, B. bifidum in 3 cases, and B. adolescentis in 1 case. Our results support the hypothesis on early colonization of infants with maternal bifidobacterium strains.