Epidemiological significance of microbiote monitoring of arctic settlements along the Northern Sea Route

Monitoring of polar ecosystems is one of the most important areas of research in the use of Arctic territories in economic activities. An important place in such work is occupied by biomedical research aimed at identifying the risks of the occurrence of foci of infectious diseases in the areas of polar settlements.The purpose: to develop an algorithm for microbiological monitoring in the Arctic region.Materials and methods: classical bacteriological, mycological research, molecular-genetic, MALDI-TOF mass spectrometric analysis, phenotypic methods for determining antibiotic resistance, methods of mathematical data processing.Results and their discussion. The paper considers the scientific and methodological principles and the main stages of microbiota monitoring in the areas of polar settlements. The results of the study of samples from several territories along the Northern Sea Route are presented. The main habitats where potentially dangerous microorganisms should be detected are indicated. The role of anthropogenic invasion in the formation of Arctic microbiocenoses is noted. The trends of increasing the number and diversity of pathogenic microorganisms, both in the natural biocenoses of the Arctic and in the areas of polar settlements, are discussed. The necessity of microbiological monitoring as an integral part of epidemiological monitoring in the areas of Arctic settlements along the Northern Sea Route is substantiated.

Determination of diphtheria risk indicators based on the study of antidiphtheria immunity in the population of Dnipropetrovsk region

Background. Vaccination is the most effective part of primary prevention. Serological monitoring of infectious diseases covered by national immunization programs is very important as it provides up-to-date information on the burden of the infection and the immunological status of the population. The study was aimed to present an analysis of epidemiological monitoring of the protection against diphtheria of the population, to show the generalized epidemiological situation regarding diphtheria, and to determine the risk of diphtheria among the population of Dnipropetrovsk region. Materials and methods. Epidemiological analysis of diphtheria immunity (2017–2019) was performed based on the results of enzyme-linked immunosorbent assay of IgG antibodies levels against diphtheria toxin in 271 residents of Dnipropetrovsk region. Results. Analysis of the results revealed that only 30.6 % (n = 83) of the population have levels of antitoxic antibodies of 1.0 IU/ml or more, which provides sufficient protection against diphtheria in the next 5–7 years of life. At that time, the majority of the population (69.4 %) needs immediate one-time booster vaccination (n = 134; 49.5 %) or immediate basic vaccination (n = 54; 19.9 %) due to low levels of antitoxic diphtheria antibodies. In the age group 8–15 years, 65.9 % (n = 62) of patients require immediate basic or booster vaccination, which indicates that children of this age do not have basic immunological protection due to violations of the vaccination schedule or its absence. In the group aged 27 years and older, 79.1 % (n = 72) of the subjects do not have protective levels of anti-diphtheria antibodies, which indicates a lack of actual protection against diphtheria. Conclusions. The results indicate insufficient protection of the population against diphtheria. In this regard, the development of strategic measures for mass immunoprophylaxis of diphtheria both in children and adults is relevant. The country should conduct regular epidemiological monitoring, which would study the population’s immunity against diphtheria and other controlled infections, and draw up a long-term strategic and tactical plan to address shortcomings in the work of mass immunoprophylaxis of the population.

Pneumococcal Serotype Identification by Capsular Sequence Typing (CST): A Modified Novel Approach for Serotyping Directly in Clinical Samples

As almost 60–70% of Invasive Pneumococcal Disease (IPD) is identified by nonculture methods in Greece, serotyping is of high importance for the better monitoring of pneumococcal serotypes due to the availability of conjugate vaccines. The aim of the study was the modification and direct application of the Capsular Sequence Typing (CST) assay in clinical samples in order to serotype Streptococcus pneumoniae culture-negative, Polymerase Chain Reaction (PCR_-positive samples, followed by CST group specific single-tube PCR assays. A two-step PCR modified assay was applied on a total of 306 samples (such as CSF, blood, pleural and middle ear fluids, isolates) obtained from 283 patients with IPD. The overall performance permits a rapid, accurate and cost-effective method for nonculture pneumococcal serotyping. As the management of IPD is closely related to the continuous monitoring of pneumococcal serotypes, the proposed approach proved to be a valuable tool for the typing and epidemiological monitoring of S. pneumoniae, for the evaluation of the overall impact of vaccination programs in the era of pneumococcal conjugate vaccines, in order to initiate the appropriate vaccination strategy.

Epidemiological monitoring of avian influenza in the Republic of Crimea in 2019–2020

The paper presents results of avian influenza epidemiological monitoring in the Republic of Crimea in 2019–2020. The attention was focused on the study of water basins of the Azov and Black Seas, the Sivash Lagoon and freshwater lakes in the Feodosia Urban Okrug, Leninsky, Sovetsky, Nizhnegorsky, Chernomorsky and Saksky Raions to detect the avian influenza virus circulation. Examination of the above mentioned areas showed that some freshwater reservoirs became shallow and dry, and aquatic vegetation degraded. The natural biotope analysis conducted in 2019 and 2020 showed a decreased number of semiaquatic wild birds. The pathological material was sampled from semiaquatic and migratory wild birds, as well as from poultry kept in poultry farms and backyards. The collected samples were tested using real-time RT-PCR. In 2019, the AIV type A (H9) genome was detected in one fecal sample taken from wild birds near Kuchuk-Adzhigol Lake in Feodosia Urban Okrug. The AIV type A (H5) genome was detected in 2020 during laboratory testing of pathological material taken from the remains of a mute swan within the shoreline of a freshwater lake near the Ermakovo settlement of the Dzhankoysky Raion. The genetic analysis was performed in the FGBI “ARRIAH” (Vladimir), and the N8 subtype neuraminidase of the influenza virus isolate was determined. The comparative genetic analysis of 258 bp nucleic acid sequences of the AIV H gene fragment showed that the identified isolate belongs to the Asian genetic lineage of highly pathogenic AIV subtype H5 (clade 2.3.4.4) associated with the epidemic spread in Asia, Europe, the Middle East and Africa in 2016–2020.

Epidemiology of Collective Food poisoning in Tlemcen- Western Algeria: A retrospective analysis of data from 2011-2020

Food poisoning is a serious public health problem in the world that needs to be addressed as early as possible. However, mitigation efforts can be possi-ble only when data and information resulting from the implementation of monitoring or continuous surveillance are available. Here we report a study that was conducted taking into account all the data of poisoning report sheets, filled in by the doctor in charge of the case or, failing that, by the nurse, coming from health facilities (in sixteen regions in Tlemcen) were in-cluded in the analysis. For data processing, we have used some descriptive tools such as the frequencies and the lethality rates. The description of the sample concerned the characteristics of the poisoned population (year, gen-der, age, origin, hospitalisation, etc.) and the characteristics related to the suspected food. The survey showed a concentration of family focus, espe-cially in urban areas. Meats, Chickens and cream filled bakery food were the three most important incriminated foods and most of the infections in the outbreaks were related to fecal coliform, Clostridium and Staphylococcus. Some of the factors identified to contribute to food poisoning were lack of self-hygiene by food handlers and poor water and environmental supplies, poor preservation of food, the consumption of inadequately cooked or thawed meat or chicken, cross-contamination of food from infected food handlers, as well as the lack of awareness and information transmission and the lack of health infrastructures and means of communications. The present study highlights the needs for creating adequate infrastructure related to hygiene, regular epidemiological monitoring and increasing the awareness level of the residents.

Study of the Level and Structure of Population Immunity to SARS-CoV2 in the Population of the Republic of Tatarstan during the Second Peak of the Spread of COVID-19

Background. The COVID-19 pandemic has become a serious challenge for all of humanity due to the rapid global spread, high frequency of severe forms, increased mortality and required the development of new approaches to managing epidemiological processes. Serological studies are the most important tool for monitoring the infectious process, identifying risk groups, assessing the effect of vaccines used and epidemiological projections.Purpose. Conducting serological monitoring in relation to the modern transferred new coronavirus infection determining the level and structure of population immunity to SARS-CoV-2 in the population of the Republic of Tatarstan; maintaining the period of spread of COVID-19 from August to December 2020.Materials and methods. The study involved 41 444 residents of the Republic of Tatarstan, who filled out questionnaires that included clinical, anamnestic data and an epidemiological history in relation to COVID-19, who were tested for the presence of common antibodies (IgG, IgA and IgM) to the SARS coronavirus. CoV-2 by the method of enhanced chemiluminescence on the VITROS 3600 analyzer using the VITROS Anti-SARS-CoV-2 Total Reagent Pack test systems.Statistical processing was carried out by methods of variation statistics and correlation analysis according to the Pearson method using MS Excel and WinPepi.Results. Seropositivity to SARSCoV-2 in the population of the Republic of Tatarstan averaged 35.8 ± 0.235%. An increase in the level of seropositive persons was noted from 29.95 ± 0.674% in August to 68 ± 9.33% in December. The highest proportion of seropositive individuals was found in was found in the group of the able-bodied population aged 18–59 years. The average geometric titer of antibodies was 4.2 (4.09–4.31), among seropositive – 89.29 (88.13–90.46). In the social and professional structure of the population, the largest proportion of seropositive individuals was found in was found among production workers 40.35 ± 2.177, creative professions – 40 ± 9.798; health care 35.24 ± 0.389; 34.26 ± 1.218 unemployed and 33.06 ± 2.479 civil servants. Among the residents of the Republic of Tatarstan, seropositive to the SARS-CoV-2 virus, the proportion of asymptomatic forms of infection was 82.59 ± 0.446%.Сonclusions. There is a positive dynamics of seropositivity among the population of the Republic of Tatarstan. The results of sero-epidemiological monitoring can be used to predict the epidemiological situation, plan measures for specific and non-specific prophylaxis of COVID19.

Seroprevalence, prevalence, and genomic surveillance: monitoring the initial phases of the SARS-CoV-2 pandemic in Betim, Brazil

The Covid-19 pandemic has created an unprecedented need for epidemiological monitoring using diverse strategies. We conducted a project combining prevalence, seroprevalence, and genomic surveillance approaches to describe the initial pandemic stages in Betim City, Brazil. We collected 3239 subjects in a population-based age-, sex- and neighborhood-stratified, household, prospective; cross-sectional study divided into three surveys 21 days apart sampling the same geographical area. In the first survey, overall prevalence (participants positive in serological or molecular tests) reached 0.46% (90% CI 0.12% - 0.80%), followed by 2.69% (90% CI 1.88% - 3.49%) in the second survey and 6.67% (90% CI 5.42% - 7.92%) in the third. The underreporting reached 11, 19.6, and 20.4 times in each survey, respectively. We observed increased odds to test positive in females compared to males (OR 1.88 95% CI 1.25 - 2.82), while the single best predictor for positivity was ageusia/ anosmia (OR 8.12, 95% CI 4.72 - 13.98). Thirty-five SARS-CoV-2 genomes were sequenced, of which 18 were classified as lineage B.1.1.28, while 17 were B.1.1.33. Multiple independent viral introductions were observed. Integration of multiple epidemiological strategies was able to describe Covid-19 dispersion in the city adequately. Presented results have helped local government authorities to guide pandemic management.

Prevalence dynamics of uropatogens and antimicrobial resistance determinants in children's significant bacteriuria in 2017 and 2019: a monocenter study

Urinary tract infections are the second most common infections in children with spreading of antimicrobial resistance among uropathogens currently poses a high epidemiological threat.Purpose. Analysis of species prevalence and the presence of genetic determinants of antibiotic resistance.Materials and methods. In the study 215 midstream urine samples were retrospectively analyzed. Samples were obtained during 2017 and 2019 from patients aged 4 weeks to 17 years at the National Medical Research Center for Children's Health Federal State Autonomous Institution of the Ministry of Health of the Russian Federation.Results. Species of pathogen were identified in 93 samples, while the bacterial composition of other samples was classified as «intestinal flora» (n = 17), «coccus flora» (n = 16) or «mixed flora» (n = 89). The most common types of uropathogens in monopathogenic infections in 2017 and 2019 were Escherichia coli (37.5% and 29.2%, respectively). Among infections caused by multiple pathogens, the most common etiological agents were Pseudomonas aeruginosa and Staphylococcus spp. Among all studied samples, 31.9% contained CTX-M-like genes, 5% VIM genes, 1.8% NDM genes, and 3.0% — OXA-48-like genes, and 5.6% of samples contained two and more genetic determinants associated with resistance, with the most prevalent gene combination being the combination of CTX-M- and OXA-48-like genes. In 69 samples with identified species of uropathogens, resistance profile to antimicrobial, determined by microbiological methods, correlated with detected resistance genetic determinants.Conclusion. Authors suggest that introduction of testing for the presence of genes associated with antibacterial resistance to general clinical practice would not only provide an opportunity to conduct epidemiological monitoring of the genetic determinants of antibiotic resistance, but also provide an opportunity to select the correct timely treatment of childhood bacteriuria caused by antibiotic-resistant infectious agents.

Complete Genome Sequences of Enterovirus D68 Clade A and D Strains in the Philippines

Complete genome sequences were determined for 4 clade A and 12 clade D enterovirus D68 strains detected in nasopharyngeal swabs from children with acute respiratory illness in the Philippines. These sequence data will be useful for future epidemiological monitoring, including watching for viral evolution.

The Evolving Faces of the SARS-CoV-2 Genome

Surveillance of the evolving SARS-COV-2 genome combined with epidemiological monitoring and emerging vaccination became paramount tasks to control the pandemic which is rapidly changing in time and space. Genomic surveillance must combine generation and sharing sequence data with appropriate bioinformatics monitoring and analysis methods. We applied molecular portrayal using self-organizing maps machine learning (SOM portrayal) to characterize the diversity of the virus genomes, their mutual relatedness and development since the beginning of the pandemic. The genetic landscape obtained visualizes the relevant mutations in a lineage-specific fashion and provides developmental paths in genetic state space from early lineages towards the variants of concern alpha, beta, gamma and delta. The different genes of the virus have specific footprints in the landscape reflecting their biological impact. SOM portrayal provides a novel option for ‘bioinformatics surveillance’ of the pandemic, with strong odds regarding visualization, intuitive perception and ‘personalization’ of the mutational patterns of the virus genomes.