Vol 8, No 2 (2018)

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.

This review was to aimed to access the prevalence of HIV recombinant forms in Russia and countries of the CIS, which have  close social and economic ties. We conducted a search in Russian  Science Citation Index and PubMed for a depth of 8 years. We  included 22 articles, which contained the results of 35 independent  cross-sectional studies, in our review. Meta-analysis of HIV  recombinant forms prevalence was conducted in Open Meta-analyst  with the use of Der Simonian & Laird method, arcsin transformation  and correction factor for zero values. Subgroup analysis was used  along with meta-regression (by date of collection). Pooled prevalence of HIV recombinant forms was 21.3% (95% CI 16.2–26.5) and was  highly heterogeneous. Blood samples from 3,494 HIV patients living  in various regions of the Russian Federation and CIS countries —  Belarus, Kazakhstan, Kyrgyzstan, Uzbekistan, Tajikistan, Armenia,  Georgia — were examined. Among subtypes of HIV-1, the main  share was occupied by subtype A — 75.6% (n = 2643), subtype B —  5.5% (n = 193), C — 0.8% (n = 31), G — 0.2% (n = 7), F —  0.14% (n = 5). Among the recombinant forms (n = 616), the  fraction of CRF02_ AG was 39.6% (n = 244), CRF02_AG/A was  32.9% (n = 203), CRF63_02A1 was 15.9% (n = 98), CRF03_AB —  5.2% (n = 32), CRF06_cpx — 2.1% (n = 13). Unique recombinant  forms were 2.7% (n = 17), including URF63_A1 (2.5%). In Russia, the highest prevalence of recombinant forms of HIV-1 was  registered in the Siberian Federal District (33.2% (95% CI 12.2– 54.1), the lowest in the Northwest Federal District — 1.6% (95% CI  0.9–2.3). In the CIS countries, the highest prevalence of  recombinant forms of HIV-1 is found in a subgroup of the Central  Asian republics — Uzbekistan, Tajikistan, Kyrgyzstan, Kazakhstan —  51.7% (95% CI 38.5–64.9). The significant upward trend was shown with a meta-regression. Our review is the first such research in  Russia and thus is of significant interest, but the result should be  applied with caution due to high risk of publication bias as well as significant heterogeneity of our results.

Chemoattractants monocyte protein-1 (MCP-1) is a low molecular weight cytokine, secreted by many cells of the body. The synthesis  of MCP-1 can induce the lipopolysaccharides of bacteria, a range of  cytokines. It is believed that MCP-1 regulates the migration and  infiltration of tissue by monocytes, T-lymphocytes memory, natural  killer cells, is involved in differentiation of naive T-helper cells. There  is evidence oncogenic and antitumor activity of MCP-1 at different stages of tumor progression. The aim of this work was the  determination and comparison of serum level of MCP-1 by infection  with Helicobacter (H.) pylori in precancerous conditions and gastric cancer.

Material and methods. Surveyed with the informed consent 204  patients with precancerous diseases of the stomach, 40 patients with gastric cancer and 40 healthy volunteers. Patients at  esophagogastroduodenoscopy conducted the fence of material for  target biopsy for histological and microbiological studies. Blood on  the immunoassay climbed in the morning on an empty stomach from the cubital vein in a volume of 5 ml in a vial without preserving  agent, the serum was separated by centrifugation for 10 minutes. By ELISA in the serum of patients determined the level of MCP-1, titer of total antibodies to the cytotoxin-associated protein of H. pylori. The obtained data statistically processed.

Results. The amount of MCP-1 in serum of the patients significantly  exceeded the data of healthy individuals in all groups of comparison. Values of MCP-1 during exacerbation of gastric ulcer  was higher than patients with exacerbation of chronic not atrophic  and focal atrophic gastritis. The concentration of MCP-1 > 280 pg/ml was detected in 17.6% of patients with pre-cancerous conditions of the stomach. When ulceration process there was a strong direct correlation of the severity of its course and the number of MCP-1 in  serum. Serum level of MCP-1 in 5.0% of patients with gastric cancer was at the upper limit of normal values, and 77.5% of  patients exceeded it. Indicator in gastric cancer significantly prevailed over the values in precancerous conditions, was correlated with the tumor stage. The level of MCP-1 in serum of  the examined healthy volunteers, patients with exacerbation of  chronic gastritis, gastric ulcer disease, polyposis, gastric cancer was  correlated with the titers of total antibodies to the cytotoxin-associated protein of H. pylori.

Conclusion. Determination of serum level of MCP-1 in precancerous conditions and gastric cancer is diagnostically valuable. Comparison  of indicator values with the titers of total antibodies to the cytotoxin- associated protein of H. pylori prognostically significant, as it allows  to assess the intensity of the induction signal to production of a  cytokine.

The Сomamonas genus, described in 1985, included one species — Сomamonas terrigena. At present, the Сomamonas genus includes  21 species. The ability of Comamonas to survive in environmental  objects (samples of water, soil and plants), including hospital  environment and medical equipment, allows them to be considered  as opportunistic microorganisms. The purpose of the research was to study the biological properties and antimicrobial susceptibility of  Сomamonas kerstersii strains isolated from fecal samples of healthy  people living in Saint Petersburg (Russian Federation) and the  Republic of Guinea. The study was carried out in the laboratory of  enteric infections of the St. Petersburg Pasteur Institute. 1532 fecal  samples were obtained from residents of St. Petersburg and 46  samples from residents of the Republic of Guinea. The generic and  species identification of the isolated microorganisms was carried out  using routine biochemical tests, the NEFERM test24 commercial test  system (MIKROLATEST, Erba Rus, Russia) and Vitek 2 Compact  (BioMerieux). The difficult for identification microorganisms were  studied by MALDI-TOF mass spectrometry, on a “Microflex LRF”  mass-spectrometer. Antimicrobial susceptibility was determined by  the gradient method with MICEvaluator™ (OXOID, UK) on Müller– Hinton agar (Russia). In the intestine microbiota of 1532 St.  Petersburg residents among the opportunistic microorganisms two  strains of С. kerstersii were isolated (0.13%). In a survey of 46  residents of the Republic of Guinea in 8 cases (17.4%) С. kerstersii  were isolated. The identification of C. kerstersii strains using various  methods and biochemical tests has shown different results: routine  biochemical tests allowed the strains to be assigned to the group of  non-fermenting gram-negative bacteria; NEFERM test24 kit identified all strains as С. testosteroni; VITEC 2 referred all strains to С.  testosteroni; using mass spectrometry with a coincidence ratio of  2.19–2.33, all strains were identified as С. kerstersii. It should be  taken into account that the С. kerstersii bacteria cannot be identified by the tests of NEFERM test24 kit and the GN VITEC 2 card, since  only the С. testosteroni is represented in the databases of both  methods. The taxonomic base of mass spectrometry includes  reference spectra of five species of Сomamonas from 21 known  ones, including С. kerstersii. Strains isolated from the inhabitants of  the Republic of Guinea were unsusceptible to at least one tested  antibiotic: ciprofloxacin (4 strains), tetracycline (5 strains) and  trimethoprim/sulfamethoxazole (5 strains), almost all strains being simultaneously unsusceptible to several antibio tics: ciprofloxacin  and trimethoprim/sulfamethoxazole (2 strains), tetracycline and  trimethoprim/sulfamethoxazole (2 strains), ciprofloxacin and  tetracycline (1 strain). One strain was unsusceptible to ciprofloxacin, tetracycline, and trimethoprim/sulfamethoxazole.

The phenotypic properties of the M. tuberculosis strains obtained from patients with pulmonary or extra-pulmonary tuberculosis are  determined by a complex set of factors: the genetic characteristics  of the pathogen, its ability to adapt in vivo and in vitro, the influence of the host’s immune system and chemotherapy. The growth rate as  the phenotypic property is the most accessible for the study of the  host-pathogen relationships at the level of host/strain population  interactions. The aim of the study is to assess in vitro of the growth  rate of M. tuberculosis strains isolated from patients with pulmonary  and extra-pulmonary tuberculosis: untreated and treated (with  surgical and non-surgical treatment) and also sensitive and resistant isolates in comparison with the reference strain H37Rv. To estimate  the growth rate of 116 clinical isolates we have used the modified  method originally developed by von Groll and co-authors: to get the  bacteria growth curve the fluorescence intensity of growing strains  (with indicator resazurin) has been measured daily for 8 days in 96- well plate. The growth rate is determined as the slope of the growth  curve. The mean values of the growth rate have been calculated in  the following groups of patients: 1 — untreated patients with  pulmonary tuberculosis (PT), respiratory material; 2 — non-surgical  treated PT patients, respiratory material; 3 — surgical treated PT  patients (mainly with chronic and hyperchronic process), respiratory  material; 4 — patients like in 3rd group, surgical material; 5 — bone  and joint tuberculosis (BJT), surgical material. In addition, groups of  sensitive and resistant strains have been examined, but there are no  significant differences in growth rates. It has been obtained that  the growth rate of strains isolated from the PT patients is higher than in BJT patients: it can be explained less favorable  conditions for the pathogen vegetation in the BJT. In the case of a  closed tuberculous lesion where the pathogen transmission to  another host is impossible, then the selection of strains with the  property to survive in the tissues of the osteoarticular system is  impossible too, therefor it should be observed only an adaptation of  the pathogen strain population to the individual host. The growth  rate of isolates from untreated PT patients is higher than that of the  treated ones. Comparison of the growth parameters of only MDR  strains 1–5 groups to eliminate the influence of the  sensitivity/resistance has resulted in the same conclusions. We  suggest that the decrease in the growth rate of strains from the  treated PT patients is in not only result of the treatment, but also is  conditioned by adaptation of the pathogen to its external  environment, which is the internal environment of the  macroorganism. To confirm this assumption, the bacterial load of  1,083 diagnostic specimens grouped in a similar manner has been  estimated, taking into account only MDR/XDR strains. In the group  of treated patients the frequency of high bacterial load (CFU ≥ 100)  reached 52.5–63.8% that shows the conserved fitness of bacteria in  such patients. The mean values of the growth rate of the strain  H37Rv non-adapted to the macroorganism (due to numerous  passages on artificial media) are higher than in all groups of clinical  strains. Thus, heterogeneity of phenotypic properties of M.  tuberculosis clinical strains on the basis of growth rate has been  obtained. The growth rate of M. tuberculosis clinical strains is  depended on the tuberculosis localization (PT, BJT) and on the joint  effect of patient treatment and pathogen adaptation to the host. 

Influenza is an acute respiratory viral infection, which represents an important health problem. Every year, influenza causes epidemics  and pandemics, leading to increase in morbidity and mortality in all  regions of the globe. Due to the segmental organization of the  genome and low accuracy of its replication, the influenza virus is  capable of escaping the host’s immune response (antigenic drift), as  well as the selection of drug-resistant variants. This calls for  constant monitoring of the sensitivity of viral isolates to antiviral  drugs and the development of new etiotropic antiviral agents that  have alternative targets and mechanisms of activity. The purpose of  this study was to characterize the new aminobenzimidazole  derivatives as protective agents in lethal influenza infection in white  mice. The efficacy of the compounds was assessed by their ability to  reduce specific mortality of animals in the course of lethal influenza  pneumonia caused by the influenza A/Puerto Rico/8/34 (H1N1)  irus, increase the life duration of animals, and normalize the  morphological structure of lung tissue comparing to the placebo  group. For all the compounds studied, a decrease in the specific  mortality of animals (from 20 to 60%) has been shown. The  reference drug (oseltamivir phosphate) reduced the mortality of  mice by 80%. The benzimidazole derivative 2519 demonstrated the  highest indices of protective activity, its use reduced the mortality of  animals by 60% and increased their mean day of death by 1.6 days in comparison with the control group. Morphological analysis showed that the activity of derivative 2519 was manifested in the  normalization of the morphological structure of lung tissue in the  course of influenza pneumonia. On day 5 after infection, the cells of  the bronchial epithelium looked intact, in contrast to destroyed cells  with numerous viral inclusions in control animals. The foci of  inflammation themselves occupied a smaller area compared to the  control. At the same time, there was no correlation between the  previously obtained data on the virus-inhibiting effect of these  compounds in vitro and the data obtained in animals. This suggests  that despite the presence of direct antiviral activity detected  previously in in vitro experiments, the protective properties of the  studied aminobenzimidazoles on animals are caused, in addition to  the etiotropic effect, by other pathogenetic factors. In conclusion,  amino derivatives of benzimidazole should be considered as  compounds that are promising for further development and  introduction as an anti-influenza agents. 

The protective role of macrophages closely related to the production of bactericidal molecules, in which nitrogen monoxide (NO) play an  important role. Arginine serves as a substrate for inducible NO  synthase (iNOS) in course of NO production. Expression and activity  of iNOS are regulated by the availability of the substrate (arginine)  in the intercellular space. The bacterial enzyme arginine deiminase  also uses arginine as a substrate, causing its deficiency for host  cells. The aim of this study was to confirm the possible role of  arginine deiminase from S. pyogenes in inhibiting NO synthesis by  macrophages. For this purpose, a comparative study was made of  the effect on the synthesis of NO by macrophages of the products of  destruction of two strains: the initial S. pyogenes M49-16 and the  isogenic mutant S. pyogenes M49-16 delArcA with the inactivated  arginine deiminase gene (arcA). It has been shown that the ability of S. pyogenes M49-16 to inhibit production of NO by macrophages  depends on its arginine deiminase activity because the isogenous mutant of S. pyogenes M49-16 delArcA with the  inactivated gene arcA has lost its ability to inhibit NO synthesis. This allows us to consider the effects of S. pyogenes M49-16 as  effects of arginine deiminase. An analysis of the inhibitory mechanisms of the enzyme showed that suppression of NO synthesis was not associated with the effect of destruction products  of S. pyogenes M49-16 on the viability of macrophages. According to data of flow cytometry, incubation of cells in the presence of S.  pyogenes destruction products of the original and mutant strains did  not affect the level of iNOS expression, i.e. did not alter synthesis or  stability of this enzyme. At the same time, the decrease in NO  production under the influence of the original S. pyogenes strain  M49-16 correlated with a decrease in the content of arginine in the  culture medium. When exogenous arginine to the culture medium  was added, the effect of the original strain of the suppression of NO  production was declined. This confirms that the depletion of arginine  is the main mechanism of the inhibitory effect of arginine deiminase  on the production of NO by macrophages. The deficiency of NO  production in the course of streptococcal infection can lead to a  weakening of bactericidal activity of macrophages and to a decrease  in the effectiveness of antimicrobial protection.

Tick-borne infections are the most common group of zooanthroponotic diseases in the Northern Hemisphere. For the  Baltic Sea region and Fennoscandia, the dominant infectious pathologies transmitted by ticks are tick-borne borreliosis and tick- borne encephalitis. The presence of vast forested areas, actively  visited by people in St. Petersburg and the Leningrad region,  contributes to a rather high level of encroachment on the flares and  intelligence of the borreliosis and tick-borne encephalitis among the  population of these regions. The relatively dangerous pathogens that can be transmitted with the tick bite are also of particular danger:  Anaplasma sp., Ehrlichia sp., Coxiella burnetii, Rickettsia sp. In this  work, detection was performed using molecular genetic methods of  TBE virus, B. burgdorferi sensu lato and Rickettsia sp. in engorged  ticksple, as well as questing ticks collected from vegetation. The established levels of infection of TBE on infected ticks, levels of infection by pathogenic Borrelia of questing and engorgeded ticks  were approximately equal. Rickettsia was not found in the ticks. The  conducted analysis of the pathogens prevalence in comparison with  the data of russian and foreign authors. Monitoring the prevalence of tick-borne pathogens is an important issue in the prevention of tick- borne infections in the North-Western Russia. 

Detection of the measles virus (MV) specific IgM antibodies in blood serum of patients is considered to be the main standard for the  laboratory confirmation of measles diagnosis, the test being  acknowledged by WHO. As it was demonstrated earlier the specific  IgM antibodies as the marker of the acute MV infection were  detected in 97.2–100% of blood serum samples from patients using  the ELISA test-systems of the “capture” format (Microimmun Ltd.  and Vector Best). In case when the ELISA test-system of the  “indirect” format (Siemens, Germany) was used only 63.9% of these sera turned to be IgM positive. And on the contrary using the  “indirect” format ELISA test-system Euroimmun, Germany, for  detection of the MV specific IgM the false positive results were  obtained.

The aim of the study was the comparative evaluation of  the different format ELISA test-systems used for the detection of the  MV specific IgM antibodies in blood sera of patients and healthy  adults collected in different geographic zones.

Materials and  methods. In total 108 serum specimens collected in 2015–2017 were studied: from healthy adult Guineans, residents of the Republic of Guinea (RG); patients aged 1–70 with the initial  “infectious mononucleosis”, “infectious cytomegalovirus” and  “rubella” diagnosis and taken from the bank of sera in the  Subnational Measles/Rubella laboratory, StP Measles/Rubella RC in  NWFR. The MV specific IgM antibodies were detected using the commercial ELISA test-systems “VectoMeasles-IgM” (Vector-Best,  Russia) (“capture” format) and “Anti-Measles Virus ELISA IgM (NP)”  (Euroimmun Medizinische Labordiagnostik AG, Germany) («indirect»  format). The specific Epshtein-Barr Virus (EBV) IgM and IgG  antibodies were detected with the commercial ELISA test-systems «DS-ELISA-anti-EBV-VCA-M», «DS-ELISA-anti-EBV-EA-G» and «DS-ELISA-anti-EBV-NA-G» (“Diagnostic Systems”, Russia).

Results and discussion. The MV specific IgM antibodies were not revealed in the total of 108 blood serum samples from the healthy adults and patients, residents of the Russia and of the RG, with the “capture”  format “VectoMeasles-IgM” ELISA test-system. The absence of the  acute MV infection was also confirmed by the high measles immunity  level (i.e. IgG MV antibodies titers) as well as by detection of the IgG antibodies of high avidity. At the same time in 6  of 108 total sera (5.5%) IgM MV antibodies were detected with the «indirect» format ELISA test system Euroimmun, Germany. In these 6 sera the EBV specific antibodies were also evidenced. The results  obtained demonstrate the nonspecific reaction due to the possible  reactivity with anti-EBV antibodies. Besides this the different  percentage of the false positive reactions in sera from healthy  adults, residents of the RG and residents of Russia was determined  — 8.5±4.0% and 3.2±2.2% correspondently. Thus the preliminary  results, and to get the final results for general conclusions increase  of the total amount of the clinical specimens under studying is of extremely importance.