Vol 97, No 5 (2020)

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Distribution of SARS-CоV-2 seroprevalence among residents of the Tyumen Region during the COVID-19 epidemic period. Journal of microbiology, epidemiology and immunobiology

Popova A.Y., Ezhlova E.B., Melnikova A.A., Stepanova T.F., Sharukho G.V., Letyushev A.N., Folmer A.Y., Shepotkova A.A., Lyalina L.V., Smirnov V.S., Stepanova K.B., Panina T.A., Sidorenko O.N., Ivanova N.A., Smirnova S.S., Malchenko I.N., Okhotnikova E.V., Stakhova E.G., Totolian A.A.


Introduction. In late 2019 - early 2020, an outbreak of infection caused by a novel strain of beta coronavirus SARS-CoV-2 was reported. The World Health Organization defined the disease as coronavirus disease 2019 (COVID-19). In the Tyumen Region, the first case of COVID-19 was diagnosed on 31/1/2020. The source of infection was a female student who came from Jinan, Shandong province (China). The number and rate of cases were steadily increasing from the 16th week through 28th week in 2020. The highest rate was 36.87 cases per 100 thousand people. Afterwards, the cumulative incidence kept increasing gradually, but not as quickly.

The purpose of the seroepidemiological study was to measure the level and to identify the structure of herd immunity against the SARS-CoV-2 virus among the population of the Tyumen Region during the rapid spread of the COVID-19 outbreak.

Materials and methods. Volunteers for participation in the study were selected through questionnaire surveys and random sampling. The exclusion criterion was an active COVID-19 infection at the time of the survey. A total of 2,758 individuals were tested for SARS-CoV-2 specific antibodies. The age of the surveyed volunteers ranged from 1 year to 70 years and older.

Results of the study. During the active phase of the COVID-19 incidence, the population of the Tyumen Region showed moderate (24.5%) seroprevalence of SARS-CoV-2. At the same time, the tests revealed a high (97.8%) rate of asymptomatic infection cases in seropositive individuals who had never been diagnosed with COVID-19 and did not have history of positive PCR test results or acute respiratory infection symptoms on the day of testing. The maximum level of herd immunity was identified in children aged 1-6 years (34.7%), which was significantly higher compared to the average level of seroprevalence in the entire cohort. In recovered COVID-19 patients, antibodies were detected in 68.2%. In individuals with positive PCR test results, antibodies were detected in 64%. Conclusion. The results of the assessment of the level of herd immunity against the SARS-CoV-2 virus are crucial for prediction of the development trend of the epidemic and for planning specific and non-specific COVID-19 prevention measures.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):392-400
pages 392-400 views

Features of changes in spectra of fatty acids of the bacteria of the Enterobacteriaceae family in the process of forming stable (dormant) cell forms

Andryukov B.G., Somova L.M., Lyapun I.N., Bynina M.P., Matosova E.V.


Introduction. With the advent of the paradigm of heterogeneity of the bacterial population, attention has been drawn to the phenotype of dormant cells, the active generation of which occurs when adverse environmental conditions of microorganisms appear. These cells are characterized by metabolic and reproductive dormancy, as well as antibiotic resistance. However, upon the occurrence of favorable living conditions, they are able to germinate again and cause an exacerbation of infectious diseases. In recent years, a threatening decrease in the effectiveness of antimicrobial therapy and an increase in the incidence of persistent, chronic and hospital infections have been associated with these phenotypes of pathogenic bacteria. Given the key role of fatty acid (FA) in the adaptation of bacteria, the aim of this study was to identify the specific features of changes in the fatty acid composition of gram-negative bacteria from the Enterobacteriaceae family during their long-term storage under extreme conditions and the formation of dormant (uncultured) subpopulations of cell forms.

Materials and methods. Static cultures of following reference strains were used in the study: Yersinia pseudotuberculosis, Salmonella enterica Typhimurium, and Escherichia coli, stored under vaseline oil at 4-8°С for 5-10 years. Dormant cell forms were obtained by removing the oil layer and collecting the microbial mass. The ultrastructural features of the dormant cell forms were confirmed by transmission electron microscopy. The viability of dormant cells was assessed by a molecular genetic method. The lack of reproductive activity of dormant forms was checked by repeated inoculations on LB broth, Endo and Serov media and incubation at 4-6°C, 22-24°C, and 37°С. Methyl esters of total FAs were obtained according to the procedure approved by the European Committee for Standardization and recommended by the Sherlock MIS protocol. Analysis of fatty acid methyl esters was carried out by gas chromatography in combination with mass spectrometry. After preliminary homogenization of the bacterial masses, lipids were extracted, and FA spectra were obtained by electron impact at 70 eV

Results. It was demonstrated that phenotypic uncultured generation of dormant cells is formed under extreme conditions (low temperature, nutrient deficiency, hypoxia) in populations of E. coli, Y. pseudotuberculosis and S. Typhimurium. A comparative analysis of changes in the fatty acid spectrum in the dormant phenotype revealed certain features compared to vegetative cells associated with a decrease in the unsaturation index and the dominance of long-chain saturated FAs (C14-C18).

Conclusion. The biological significance of the observed transformations is apparently associated with the special role of these FA fractions in the reversible formation of dormant (uncultivated) cell phenotype and as an alternative source of carbohydrates in a metabolically inactive state, as well as their subsequent reversal to vegetative cells upon favorable living conditions.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):401-412
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Sensitivity of Bordetella pertussis biofilms to polyvalent pertussis serum Eugene M. Zaytsev

Zaуtsev E.M., Вritsina M.V., Ozeretskovskaya M.N., Mertsalova N.U., Bazhanova I.G.


Aim. Study of the sensitivity of Bordetella pertussis biofilms to polyvalent pertussis serum.

Materials and methods. The intensity of biofilm formation by strains of B. pertussis in round-bottomed polystyrene 96-well plates in the presence of polyvalent pertussis serum was estimated by staining with 0.1% gentian-violet solution. The serum titer was estimated as a highest dilution, which suppressed the growth of biofilm cultures.

Results. Serum titers that completely suppressed the formation of biofilms by the studied strains ranged from  : 1,000 to 1 : 20,000. Vaccine strain No. 475a (serotype 1.2.3) was characterized by the highest sensitivity to serum, the titer of which was 1 : 20,000. Vaccine strain No. 305 (serotype 1.2.0) and strains isolated from whooping cough patients in the period from 2001 to 2010: No. 287 (serotype 1.0.3), No. 178 (serotype 1.2.0), No. 317 (serotype 1.2.3) were sensitive to serum in the titers 1 : 1,000-1 : 2,000. Vaccine strain No. 703 (serotype 1.0.3) was resistant to all serum dilutions studied. When sowing supernatants from wells with biofilms on a dense nutrient medium, the growth of colonies typical for B. pertussis was observed. Similar results were obtained when seeding the supernatants of the cultures from the wells with no biofilm.

Conclusion. These data indicate that B. pertussis strains are heterogeneous in sensitivity to pertussis serum. The growth of colonies typical for B. pertussis when culture supernatants are sown on a dense nutrient medium, in the absence of biofilms in the wells, indicates that the biofilm formation is suppressed by inhibiting the adhesion of microbial cells on the substrate, and not due to the bactericidal action of the serum.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):413-417
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Colonization activity of Candida clinical isolates and their antibiotic sensitivity

Akhapkina I.G., Glushakova A.M., Rodionova E.N., Kachalkin A.V.


Background. The development of fungal infections is associated with immunocompromising of a macroorganism.

Aim. To study the colonization activity and resistance of Candida yeast strains isolated from clinical specimens in 2014 and 2019 in Moscow.

Materials and methods. Antibiotic sensitivity of 75 strains of the following yeast species was determined by disc-diffuse method: C. albicans, C. parapsilosis, C. glabrata, C. krusei (Pichia kudriavzevii), C. intermedia, C. tropicalis, C. lusitaniae (Clavispora lusitaniae), C. guilliermondii (Meyerozyma guilliermondii). In 2014, 34 strains were isolated in people with hypersensitivity history (27 — from the skin, 7 — from the oral mucosa). In 2019, 41 strains were isolated from the vaginal mucosa in people with cancer. Discs with fluconazole (40 pg), nystatin (80 pg), clotrimazole (10 pg), itraconazole (10 pg), amphotericin B (40 pg) were used.

Results. Among strains isolated in 2014, colonization activity was detected, in descending order, in C. albicans (23.53%), C. tropicalis (20.59%), C. guilliermondii (20.59%); C. parapsilosis (17.65%), C. glabrata (17.65%); in 2019 — C. parapsilosis (21.95%), C. albicans (17.07%), C. tropicalis (12.19%), C. guilliermondii (12.19%), C. krusei (9.76%), C. glabrata (9.76%), C. lusitaniae (9.76%), C. intermedia (7.32%). The yeasts isolated in 2014 were resistant to all antimicotics except 16.67% strains of C. glabrata (fluconazole) and 14.28% strains of C. tropicalis (nystatin). 11.11% C. parapsilosis and 40% C. tropicalis isolated in 2019 were sensitive to all antimicotics; 71.43% C. albicans, 50% C. glabrata, 20% C. guilliermondii were resistant to fluconazole; 28.57% C. albicans were resistant to nystatin, clotrimazole, intraconazole, amphotericin B; 25% C. glabrata resistant to amphotericin В; C. krusei — were resistant to clotrimazole (100%), fluconazole and nystatin (50%), itraconazole и amphotericin B (25%); C. lusitaniae resistant to fluconazole and nystatin (100%), clotrimazole and amphotericin B (75%), itraconazole (50%).

Conclusion. The range of detected species has expanded over five years in the Moscow region due to C. krusei, C. lusitaniae and C. intermedia (26.86% of candidiasis in 2019). Moreover, yeast fungi isolated in 2019 have a high number of resistant strains, compared to fungi isolated in 2014.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):418-423
pages 418-423 views

In vitro study of the effect of Bifidobacterium bifidum probiotic strain DNA on the cell concentration and colonization properties of intestinal microsymbionts

Zakharova Y.V., Sukhikh A.S., Levanova L.A., Plotnikova E.Y.


Aim. To estimate in vitro the effect of DNA isolated from the probiotic strain Bifidobacterium bifidum 791 on the cell concentration and adhesive properties of fecal isolates of bifidobacteria and opportunistic microorganisms of different species.

Materials and methods. DNA was isolated from the probiotic strain Bifidobacterium bifidum 791. Biomass containing bifidobacteria was washed from the nutrient medium. The suspension of bacteria in the buffer solution was subjected to ultrasonic disintegration with a frequency of 40 kHz three times for 30 minutes, followed by centrifugation. The supernatants were combined and purified chromatographically on CL-4B Sepharose. B. breve, B. bifidum, B. infantis, Staphylococcus aureus, Escherichia coli lac-, Enterococcus faecalis, and Candida albicans were used as test cultures, isolated from the intestines of conditionally healthy adults. 

Results. The nucleic acid solution with a concentration of 3.54 |jg/ml did not affect the cell number of bifidobacteria (p = 0.61). The DNA content in the solution of 14.15-21.23 jg/ml increased the titers of B. bifidum and B. breve by 2 lg CFU/ml compared to the control (p = 0.01), but did not affect the titers of S. aureus, E. coli lac-, E. faecalis, C. albicans (p = 0.73). The DNA solution stimulated the self-aggregation of bifidobacteria in 1.5-2.0 times. The ability to autoaggregate under the influence of bifidobacterial DNA in S. aureus, E. faecalis, C. albicans did not change, in E. coli lacincreased 2.3 times (p = 0.05).

Conclusion. A DNA solution of the probiotic strain B. bifidum 791 with a content 14.15-21.23 jg/ml stimulates the reproduction and autoaggregation of fecal B. breve, B. bifidum.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):424-430
pages 424-430 views

SARS, SARS again, and MERS. Review of animal models of human respiratory syndromes caused by coronavirus infections

Nagornykh A.M., Tyumentsev A.I., Tyumentseva M.A., Akimkin V.G.


Since the beginning of the 21th century, major outbreaks of human respiratory syndromes caused by coronavirus infections have caused more than million deaths on the planet. Despite the fact that the first wave of the coronavirus infection took place back in 2002, even now there is not any adequate animal model that would meet the needs of the scientific community for reproducing the pathogenesis, clinical manifestations, immunogenicity, development and testing of preventive and therapeutic compounds specific to Severe Acute Respiratory Syndrome, Middle East Respiratory Syndrome, and Coronavirus Disease 2019 (COVID-19).

The purpose of the study is to provide relevant information on known animal models of human respiratory syndromes caused by coronavirus infections and to focus the reader's attention on their adequacy, which consists in the most accurate imitation of clinical signs and pathomorphological changes.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):431-444
pages 431-444 views


The status of herd immunity to measles in Russia: A systematic review and meta-analysis of epidemiological studies

Nozdracheva A.V., Semenenko T.A.


Introduction. The comprehensive assessment of the herd immunity to measles in Russia can be challenging, as Russian subject-related studies tend to focus on seroprevalence in various cohorts of different sizes. The systematic review and subsequent meta-analysis of different research findings increase the total number of observations and statistical significance of the studies, thus enhancing the reliability of conclusions.

The purpose of the study is to assess the status of herd immunity to measles in Russia by analyzing the findings of studies published by Russian researchers. 

Materials and methods. The conducted systematic review and meta-analysis covered 13 Russian studies (the total number of the examined was 15,353, from birth to 79 years of age) published in 2011-2020 and addressing the assessment of herd immunity to measles in population of different regions in Russia.

Results. It was found that the principal approach in all the studies was assessment of herd immunity through examination of adult people, including healthcare workers, with no regard for their vaccination history. The proportion of seronegative cases among young people (18-30 years) — 27.3% (95% CI 25.7-27.3%) and among children under 17 — 38.3% (95% CI 35.8-40.8%), who were born after the two-time vaccination had been included in the National Immunization Calendar, was larger than in older age groups — 19.8% (95% CI 17.8¬21.8%). The level of herd immunity among healthcare workers representing a decreed group — 84.5% (95% CI 83.7-85.3%) was higher than that of relatively healthy population — 75.4% (95% CI 74.1-76.6%), which can be explained by stricter vaccination requirements.

Conclusion. The high proportion of seronegative cases among children and young adults of under 30 years of age is a risk factor associated with measles spread among the population and can be seen as the result of insufficient vaccination coverage.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):445-457
pages 445-457 views

The role of microbiota in the regulation of homeostasis in the human body during infection

Bukharin O.V., Perunova N.B.


The review considers the regulatory capabilities of the human microbiota to preserve human health. The problem is not new, but it has expanded with the inclusion of new “findings” since the time of I.I. Mechnikov, a staunch supporter of the useful (protective) function of the normal flora.

The study of the integration of human metabolism and microbes inhabiting human body revealed the participation of microbial metabolites — “signaling molecules” — in providing the homeostasis of the host. Particular attention 

is paid to the metabolic products aromatic amino acids as regulators of the physiological functions of humans and microbes. “Signal” molecules regulate the microbial “quorum”, the immune system (its cellular and humoral components). Opiates, hormonal peptides, in particular, natriuretic hormone, hypothalamic nonapeptides (oxytocin and vasopressin), which have both a direct antimicrobial and an indirect effect in the host's body, are not ignored. Researchers are also showing interest in the products of adipose tissue — “adipokines” (in particular, leptin), which turned out to be a multipurpose regulator showing a pro-inflammatory nature.

The category of “signaling” molecules also includes cytokines that interact with gram-positive bacteria, which is actively discussed in the literature.

In the evaluation of the material presented on various models of infections, a general pattern is observed: under the conditions of symbiosis, a “single regulatory environment” is formed, in which a variety of connections from immediate (direct) interactions are noted, i.e. the destruction of “signaling” molecules, induction of physiological functions due to the presence of similar receptors with ligands and, finally, modification of “signaling” molecules, i.e. expansion of the spectrum of action. The combination of this variety of integration mechanisms in this “single regulatory environment” (microorganism-host) probably leads to the formation of homeostasis, i.e. dynamic balance of the “signaling” systems of the microbiota and humans in the conditions of associative symbiosis, where an infection is its model system.

This concept fits well our method of intermicrobial recognition of friend-foe in the dominant-associate pair and the described triangle: microbiota-hypothalamic-pituitary neurosecretion-oxytocin, organically constituting the gut-brain axis.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):458-467
pages 458-467 views

Neutrophil extracellular traps in the fight against biofilm-forming microorganisms: hunters or prey?

Dolgushin I.I., Mezentseva E.A.


The review presents up-to-date data on the relationships between neutrophil extracellular traps (NETs) and biofilm-forming microorganisms P aeruginosa, S. aureus, Candida spp. obtained in vitro and in vivo studies. Up to 80% of human microbial infections are associated with biofilm-forming microorganisms. The formation of highly specialized biofilm communities is one of the main strategies for the survival of bacteria and fungi, significantly increasing their tolerance to aggressive and stressful environmental conditions, chemotherapeutic drugs, and immune system factors, contributing to their persistence and chronicity of the infectious process. The formation of NETs in the process of NETosis is one of the biological mechanisms used by neutrophils in protection against pathogens. Chemoattractants of biofilm origin, as well as those secreted by epithelial and immunocompetent cells, attract and activate migrating neutrophils. However, given that bacteria form fairly large cell clusters and aggregates in biofilms, the process of phagocytosis is sometimes difficult or impossible. Under these conditions, it is logical to assume that the importance of NETs in anti-biofilm immunity increases. However, due to the components of the extracellular biofilm matrix (e.g., Psl exopolysaccharide P aeruginosa), quorum sensing (QS) molecules (e.g., LasR QS system P aeruginosa), enzymes (e.g., LasA protease and LasB elastase P. aeruginosa), toxins (e.g., Panton-Valentine leukocidin and AB Y-hemolysin S. aureus) and probably other factors yet to be studied, the microorganisms in biofilms are able to influence the signaling systems involved in NETosis, the intensity of the formation of NETs, the sequestration and killing mechanisms in them, sometimes subordinating and using NETs components for their own purposes.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):468-481
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Atypicity of Vibrio cholerae O1 strains based on agglutability

Levchenko D.A., Arhangelskaya I.V., Kruglikov V.D., Podoinitsina O.A.


The review analyzes literature data on the phenotypic variability of Vibrio cholerae of the O1 serogroup. Three types of polysaccharide structures are distinguished in the cholera pathogen: lipopolysaccharide, or O-antigen, capsular polysaccharide and exopolysaccharide. The rugous form of V. cholerae strains is able to synthesize exopolysaccharide which is highly resistant to antimicrobials, and to form wrinkled colonies that can be agglutinated with cholera sera in various combinations. Serological classification of V. cholerae is based on the specificity of the lipopolysaccharide. V. cholerae of serogroups O1 and O139 causes cholera epidemics, although strains from non-O1/non-O139 serogroups with the main virulence factors are known. Upon transition from the Sto the R-form, lipopolysaccharide loses the O-polysaccharide, and the central region begins to fulfill the function of somatic antigen, exhibiting R-specificity. The serological differences in the strains of V. cholerae are based on a change in the regulation or structural organization of genes encoding the biosynthesis of O-antigen (rfb). From 1988 to 2019, 168 strains of V. cholerae that are atypical for agglutinability and were isolated from the R variant were isolated from environmental objects in the territory of the former USSR and subjects of the Russian Federation; the genetic organization of these strains has not been fully studied. The evolutionary relationships of atypical strains of cholera vibrios isolated from environmental objects in Siberia and the Far East are determined on the basis of a comparative analysis of housekeeping genes. The analysis of the results of basic and applied research indicates that the problem of variability in agglutinability of V. cholerae strains isolated from humans and from environmental objects remains relevant at the current stage of development of the seventh cholera pandemic. The atypicality of strains of V. cholerae O1 on this basis is considered in aspects of the environmental conditions of their existence and the conditionality of phenotypic manifestations by molecular biological determination.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):482-491
pages 482-491 views


Causes and consequences of delayed vaccination against pertussis infection in the Russian Federation

Lomonosova A.V.


Introduction. One of the reasons for the increase of pertussis in the Russian Federation on the background of the widespread coverage of prophylactic vaccinations of more than 95% is a large number of unreasonable medical recusals and parental refusals and, as a result, untimely prophylactic vaccinations against pertussis infection.

Materials and methods. We analyzed 5101 emergency notifications for pertussis in children under 17 years of age in Moscow in 2012-2017 and 300 child development histories for children under 14 years of age in two clinics in Moscow. A сase-сontrol study was conducted to assess the relationship between pertussis and the presence of deviations in the immunization schedule.

Results. It was found that the level of timely immunization against pertussis did not exceed 5%. Medical (20%) and parental refusals (45%) prevail among the reasons for delayed vaccination. In the structure of medical exemption, the main causes are perinatal encephalopathy, congenital heart defects, intestinal dysbiosis, allergic diseases, anemia and some chronic diseases.

Discussion. The main principle for the formation of a full protective immunity from pertussis infection is the mandatory administration of a full primary course of vaccination against pertussis, with the completion of three vaccinations at the age of 10-12 months and mandatory control over the timely receipt of a booster dose no later than the child reaches two years of age. In addition, it is necessary to introduce additional booster doses of pertussis vaccine at the age of 6-7 years, 12-14 years, vaccination of adults every 10 years, as well as consider the introduction of vaccination of expectant mothers in each pregnancy at 27-36 weeks, vaccination for medical personnel and employees who provide child care services.

Journal of microbiology, epidemiology and immunobiology. 2020;97(5):492-502
pages 492-502 views


Review of the monograph by Boris A. Shenderov, Alexander V. Sinitsa, Mikhail M. Zakharchenko, Christine Lang «Metabiotics. Present State, Challenges and Perspectives» (Springer Nature Switzeland AG, 2020)

Suvorov A.N.


Journal of microbiology, epidemiology and immunobiology. 2020;97(5):503-504
pages 503-504 views

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