Dynamics of SARS-CoV-2 lineages in children and adults in 2021 and 2022.

Purpose: We aimed to describe SARS-CoV-2 lineages and diversity in children and adults in Estonia and similarity to travel-related cases and neighbouring countries.

Methods: SARS-CoV-2 sequences in 2021-2022 from a nationwide study were included. The proportion of predominant lineages in Estonian regions and among travel-related cases was described by multinomial logistic regression.

Prevalence of chronic hepatitis C infection in the general population: results from a national survey, Estonia, July to December 2022.

IntroductionObtaining epidemiological data on chronic hepatitis C virus (HCV) infection is essential to monitor progress towards the hepatitis C elimination targets.AimWe aimed to estimate the prevalence of chronic HCV and the seroprevalence of HCV in the adult general population in Estonia.MethodsThis cross-sectional study, conducted between 12 July and 6 December 2022, included anonymised residual sera collected prospectively from patients 18 years and older visiting a general practitioner in all counties of Estonia.

SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic.

Background: The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022.

Age-specific and genotype-specific carcinogenic human papillomavirus prevalence in a country with a high cervical cancer burden: results of a cross-sectional study in Estonia.

Objectives: To describe age-specific and type-specific carcinogenic human papillomavirus (HPV) prevalence prior to large-scale effect of HPV vaccines in Estonia and to analyse the risk factors associated with carcinogenic HPV.

Design: Cross-sectional study using self-administered questionnaire and self-collected vaginal swabs for detection of HPV infection.

Setting: Estonian Biobank database.

Protective antibodies and T cell responses to Omicron variant after the booster dose of BNT162b2 vaccine.

The high number of mutations in the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes its immune escape. We report a longitudinal analysis of 111 vaccinated individuals for their antibody levels up to 6 months after the third dose of the BNT162b2 vaccine. After the third dose, the antibody levels decline but less than after the second dose.

Long-Term Elevated Inflammatory Protein Levels in Asymptomatic SARS-CoV-2 Infected Individuals.

The clinical features of SARS-CoV-2 infection range from asymptomatic to severe disease with life-threatening complications. Understanding the persistence of immune responses in asymptomatic individuals merit special attention because of their importance in controlling the spread of the infections. We here studied the antibody and T cell responses, and a wide range of inflammation markers, in 56 SARS-CoV-2 antibody-positive individuals, identified by a population screen after the first wave of SARS-CoV-2 infection.

Seroprevalence and levels of IgG antibodies after COVID-19 infection or vaccination.

Background: In a country-wide seroprevalence study of COVID-19 in Estonia, we aimed to determine the seroprevalence and the dynamics of IgG against SARS-CoV-2 after vaccination or positive PCR-test.

Methods: Leftover blood samples were selected between 8 February and 25 March 2021, by SYNLAB Estonia from all counties and age groups (0-9, 10-19, 20-59, 60-69, 70-79 and 80-100 years) proportionally to the whole Estonian population and tested for IgG against SARS-CoV-2 spike protein receptor-binding domain (anti-S-RBD IgG) using Abbott SARS-CoV-2 IgG II Quant assay. Antibody levels after positive PCR-test or vaccination were described by exponential increase-decrease models.

Dynamics of antibody response to BNT162b2 vaccine after six months: a longitudinal prospective study.

Background: SARS-CoV-2 mRNA vaccines have proven high efficacy, however, limited data exists on the duration of immune responses and their relation to age and side effects.

Methods: We studied the antibody and memory T cell responses after the two-dose BNT162b2 vaccine in 122 volunteers up to 6 months and correlated the findings with age and side effects.

Findings: We found a robust antibody response to Spike protein after the second dose.

Prevalence of SARS-CoV-2 IgG antibodies and their association with clinical symptoms of COVID-19 in Estonia (KoroSero-EST-1 study).

Purpose: In Estonia, during the first wave of COVID-19 total number of cases confirmed by PCR was 13.3/10,000, similar in most regions, including capital Tallinn, but in the hotspot of Estonian epidemic, an island Saaremaa, the cumulative incidence was 166.1/10,000.

Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data.

SARS-CoV-2 antibody tests are available in various formats, detecting different viral target proteins and antibody subclasses. The specificity and sensitivity of SARS-CoV-2 antibody tests are known to vary and very few studies have addressed the performance of these tests in COVID-19 patient groups at different time points. We here compared the sensitivity and specificity of seven commercial (SNIBE, Epitope, Euroimmun, Roche, Abbott, DiaSorin, Biosensor) and two in-house LIPS assays (LIPS N and LIPS S-RBD) IgG/total Ab tests in serum samples from 97 COVID-19 patients and 100 controls, and correlated the results with the patients' clinical data and the time-point the test was performed.

Application of Molecular Methods for Carbapenemase Detection.

This study has evaluated the correlation between different carbapenemases detection methods on carbapenem non-susceptible strains from Northern and Eastern Europe; 31 institutions in 9 countries participated in the research project, namely Finland, Estonia, Latvia, Lithuania, Russia, St. Petersburg, Poland, Belarus, Ukraine, and Georgia. During the research program, a total of 5,001 clinical isolates were screened for any carbapenem non-susceptibility by the disk diffusion method, Vitek 2 or Phoenix system following the EUCAST guideline on detection of resistance mechanisms, version 1.

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.

Background: Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees.

Results: A tool named StrainSeeker was developed that constructs a list of specific -mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1-2 min.

A combination of the probiotic and prebiotic product can prevent the germination of Clostridium difficile spores and infection.

Clostridium difficile infection (CDI) is one of the most prevalent healthcare associated infections in hospitals and nursing homes. Different approaches are used for prevention of CDI. Absence of intestinal lactobacilli and bifidobacteria has been associated with C.

Differences in extended-spectrum beta-lactamase producing Escherichia coli virulence factor genes in the Baltic Sea region.

The aim of this study was to compare the prevalence of different virulence factor (VF) genes in extended-spectrum beta-lactamase (ESBL) producing Escherichia coli strains isolated from the Baltic Sea region. A total of 432 strains of phenotypically ESBL positive E. coli were collected from 20 institutions located in Estonia, Latvia, Lithuania, and the region of St.

Detection of carbapenemase-producing enterobacteriaceae in the baltic countries and st. Petersburg area.

The spread of carbapenemase-producing Enterobacteriaceae is a global problem; however, no exact data on the epidemiology of carbapenemase in the Baltic countries and St. Petersburg area is available. We aimed to evaluate the epidemiology of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Baltic States and St.

Five-year prospective surveillance of nosocomial bloodstream infections in an Estonian paediatric intensive care unit.

Background: Few studies provide rates of nosocomial bloodstream infections (BSIs) in mixed neonatal and paediatric intensive care units (PICUs).

Aim: To determine the rate, pathogens and outcome of BSIs in an Estonian PICU.

Methods: Data were collected prospectively from 1st January 2004 to 31st December 2008 in the PICU of Tartu University Hospital.

Prolonged outbreak of Serratia marcescens in Tartu University Hospital: a case-control study.

Background: The aim of our study was to investigate and control an outbreak and identify risk factors for colonization and infection with Serratia marcescens in two departments in Tartu University Hospital.

Methods: The retrospective case-control study was conducted from July 2005 to December 2006. Molecular typing by pulsed field gel electrophoresis was used to confirm the relatedness of Serratia marcescens strains.

Quantification of Clostridium difficile in antibiotic-associated-diarrhea patients.

Comparing culture- and non-culture-based methods for quantifying Clostridium difficile in antibiotic-associated-diarrhea patients, we found that the real-time PCR method correlated well with quantitative culture and was more sensitive. A positive association between the population levels of C. difficile and the presence of its toxins was found.

Intestinal lactoflora in Estonian and Norwegian patients with antibiotic associated diarrhea.

The disruption of intestinal microbiota is an important risk factor for the development of Clostridium difficile caused antibiotic associated diarrhea (AAD). The role of intestinal lactoflora in protection against C. difficile is unclear.

Protective effect by Bacillus smithii TBMI12 spores of Salmonella serotype enteritidis in mice.

Avoiding food-borne diseases by competitive exclusion agents is a proactive strategy. In the current paper, we report the use of Bacillus smithii TBMI12 spores as potential competitive exclusion agents. One group of mice was predosed for three successive days with 10(8) colony forming units of B.

Periodontal disease in mothers indicates risk in their children.

Introduction: It is well established that severe periodontitis clusters in families, but there are no data about the relationship between mothers with chronic periodontitis and their children's periodontal status.

Objective: To evaluate a risk for periodontal diseases in children of periodontally diseased and healthy mothers.

Methods: Four study groups were included: (I) 20 female patients with untreated generalized severe chronic periodontitis, (II) their children (34), (III) 13 periodontally healthy mothers and (IV) their children (13).

The occurrence of antimicrobial resistance and class 1 integrons among commensal Escherichia coli isolates from infants and elderly persons.

Background: The aim of our study was to compare the presence of the intI1 gene and its associations with the antibiotic resistance of commensal Escherichia coli strains in children with/without previous antibiotic treatments and elderly hospitalized/healthy individuals.

Methods: One-hundred-and-fifteen intestinal E. coli strains were analyzed: 30 strains from 10 antibiotic-naive infants; 27 from 9 antibiotic-treated outpatient infants; 30 from 9 healthy elderly volunteers; and 28 from 9 hospitalized elderly patients.

Evaluation of ID-PaGIA syphilis antibody test.

Background: Laboratory diagnosis of syphilis is usually accomplished by serology. There are currently a large number of different commercial treponemal tests available that vary in format, sensitivity and specificity.

Aim: To evaluate the ID-PaGIA Syphilis Antibody Test as an alternative to other specific treponemal tests for primary screening or confirmation of diagnosis.