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Background: Peritonsillar abscess (PTA) is a severe deep neck space infection with an insufficiently characterized bacterial etiology. We aimed to reveal the bacteria associated with PTA applying next generation sequencing (NGS). Tonsil biopsies and pus samples of 91 PTA patients were analysed applying NGS method., Results: Over 400 genera and 800 species belonging to 34 phyla were revealed. The most abundant species in both sample types were Streptococcus pyogenes, Fusobacterium necrophorum and Fusobacterium nucleatum. When present, S. pyogenes was normally a predominant species, although it was recovered as a minor population in some samples dominated by F. nucleatum and occasionally F. necrophorum. S. pyogenes and F. necrophorum were the predominant species (> 10% in a community) in 28 (31%) pus samples, while F. nucleatum in 21 (23%) and S. anginosus in 8 (9%) pus samples. We observed no substantial differences between the microbial findings in pus and tonsil biopsies., Conclusions: The most probable causative agents of PTA according to our NGS-study include Streptococcus pyogenes, Fusobacterium necrophorum and Fusobacterium nucleatum. Some other streptococci (S. anginosus) and anaerobes (Prevotella, Porphyromonas) may contribute to the infection as well. Pus of the peritonsillar abscess is more representative specimen for microbiological examination than the tonsillar tissue. Our results are important in the context of optimizing the handling of the PTA patients., (© 2023. The Author(s).)

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. The booster dose remarkably increases the serum ability to block wild-type or Omicron variant spike protein's receptor-binding domain (RBD) interaction with the angiotensin-converting enzyme 2 (ACE2) receptor, and these protective antibodies persist 3 months later. Three months after the booster dose, memory CD4 + and CD8 + T cells to the wild-type and Omicron variant are detectable in the majority of vaccinated individuals. Our data show that the third dose restores the high levels of blocking antibodies and enhances T cell responses to Omicron., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

The composition of centenarians' gut microbiota has consistently been used as a model for healthy aging studies. However, there is an incomplete understanding of how childhood living conditions and eating habits affect the development and composition of gastrointestinal microbiota in centenarians with good cognitive functions. We compared the gut microbiota as well as the living and eating habits of the oldest-old group and the young people group. The richness and diversity of microbiota and the abundance of hereditary and environmental microbes were higher in people with longevity than young people. People with longevity ate more potatoes and cereal products. In their childhood, they had more exposure to farm animals and did not have sewers compared with young people. Young people's gut microbiota contained more butyrate-producing bacteria and bacteria that characterized an animal-based Western diet. These results expand our understanding of the effects of childhood environment and diet on the development and stability of the microbiota in people with longevity., Competing Interests: Author MV was employed by company BioCC OÜ. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Sepp, Smidt, Rööp, Štšepetova, Kõljalg, Mikelsaar, Soidla, Ainsaar, Kolk, Vallas, Jaagura and Mändar.)

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. However, the antibody levels declined at 12 weeks and 6 months post-vaccination, indicating a waning of the immune response over time. At 6 months after the second dose, the Spike antibody levels were similar to the levels in persons vaccinated with one dose or in COVID-19 convalescent individuals. The antibodies efficiently blocked ACE2 receptor binding to SARS-CoV-2 Spike protein of five variants of concern at one week but this was decreased at three months. 87% of individuals developed Spike-specific memory T cell responses, which were lower in individuals with increased proportions of immunosenescent CD8 + TEMRA cells. We found antibody response to correlate negatively with age and positively with the total score of vaccination side effects., Interpretation: The mRNA vaccine induces a strong antibody response to SARS-CoV-2 and five VOCs at 1 week post-vaccination that decreases thereafter. T cell responses, although detectable in the majority, were lower in individuals with higher T cell immunosenescence. The deterioration of vaccine response suggests the need to monitor for the potential booster vaccination., Competing Interests: The authors have nothing to disclose., (© 2021 The Authors.)

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. We found a remarkable variation in the sensitivity of antibody tests with the following performance: LIPS N (91.8%), Epitope (85.6%), Abbott and in-house LIPS S-RBD (both 84.5%), Roche (83.5%), Euroimmun (82.5%), DiaSorin (81.4%), SNIBE (70.1%), and Biosensor (64.9%). The overall agreement between the tests was between 71-95%, whereas the specificity of all tests was within 98-100%. The correlation with patients' clinical symptoms score ranged from strongest in LIPS N (ρ = 0.41; p<0.001) to nonsignificant in LIPS S-RBD. Furthermore, the time of testing since symptom onset had an impact on the sensitivity of some tests. Our study highlights the importance to consider clinical symptoms, time of testing, and using more than one viral antigen in SARS-CoV-2 antibody testing. Our results suggest that some antibody tests are more sensitive for the detection of antibodies in early stage and asymptomatic patients, which may explain the contradictory results of previous studies and should be taken into consideration in clinical practice and epidemiological studies., Competing Interests: The authors have read the journal's policy and have the following competing interests: PN, KH, JH, IE are employees of SYNLAB Estonia. There are no patents, products in development or marketed products associated with this research to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Extended-spectrum beta-lactamases (ESBL) and AmpC producing- Escherichia coli have spread worldwide, but data about ESBL-producing- E. coli in the Northern and Eastern regions of Europe is scant. The aim of this study has been to describe the phenotypical and molecular epidemiology of different ESBL/AmpC/Carbapenemases genes in E. coli strains isolated from the Baltic States (Estonia, Latvia, and Lithuania), Norway and St. Petersburg (Russia), and to determine the predominant multilocus sequence type and single nucleotide polymorphisms diversity of E. coli isolates deduced by whole genome sequencing (WGS). A total of 10,780 clinical E. coli strains were screened for reduced sensitivity to third-generation cephalosporins. They were collected from 21 hospitals located in Estonia, Latvia, Lithuania, Norway and St. Petersburg during a 5 month period in 2012. The overall prevalence of ESBL/AmpC strains was 4.7% by phenotypical test and 3.9% by sequencing. We found more strains with the ESBL/AmpC phenotype and genotype in St. Petersburg and Latvia than other countries. Of phenotypic E. coli strains, 85% contained confirmed ESBL genes (including bla CTX-M , bla TEM- 29 , bla TEM- 71 ), AmpC genes ( bla CMY- 59 , bla ACT- 12 / - 15 / - 20 , bla ESC- 6 , bla FEC- 1 , bla DHA- 1 ), or carbapenemase genes ( bla NDM- 1 ). bla CTX-M- 1 , bla CTX-M - 14 and bla CTX-M- 15 were found in all countries, but bla CTX-M- 15 prevalence was higher in Latvia than in St. Petersburg (Russia), Estonia, Norway and Lithuania. The dominating AmpC genes were bla CMY- 59 in the Baltic States and Norway, and bla DHA- 1 in St. Petersburg. E. coli strains belonged to 83 different sequence types, of which the most prevalent was ST131 (40%). In conclusion, we generally found low ESBL/AmpC/Carbapenemase prevalence in E. coli strains isolated in Northern/Eastern Europe. However, several inter-country differences in distribution of particular genes and multilocus sequence types were found., (Copyright © 2019 Sepp, Andreson, Balode, Bilozor, Brauer, Egorova, Huik, Ivanova, Kaftyreva, Kõljalg, Kõressaar, Makarova, Miciuleviciene, Pai, Remm, Rööp and Naaber.)

This study has evaluated the correlation between different carbapenemases detection methods on carbapenem non-susceptible Klebsiella pneumoniae 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 K. pneumoniae 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 1.0. Strains isolated from outpatients and hospitalized patients from April 2015 to June 2015 were included. All types of samples (blood, pus, urine, etc.) excluding fecal screening or fecal colonization samples have been represented. In total, 171 carbapenemase screening-positive K. pneumoniae isolates (3.42%) were found and characterized. Several methods were used for detection of carbapenemases production, including Luminex assay (PCR and hybridization), whole genome sequencing, MALDI-TOF based Imipenem degradation assay, and immunochromatography testing. Minimal inhibitory concentration determination for Meropenem by agar-based gradient method was also used. Finally, 83 K. pneumoniae strains were carbapenemase negative by all confirmation methods (49.4% of all screening-positive ones), 74 - positive by three methods (44.0%), 8 - positive by two methods (4.8%) and 3 - positive by only one method (1.8%). The sensitivity of the tests was 96.3% for Whole genome sequencing and MALDI-TOF assay (both three undetected cases), and 95.1% for Luminex-Carba (4 undetected cases). The most commonly detected carbapenemases were NDM ( n = 54) and OXA-48 ( n = 26), followed by KPC-2, VIM-5, and OXA-72 (one case of each). Our results showed that different types of carbapenemases can be detected in the countries involved in the project. The sensitivity of our methods for carbapenemase detection (including screening as a first step and further confirmation tests) was >95%, but we would recommend using different methods to increase the sensitivity of detection and make it more precise.

Baltic herring ( Clupea harengus membras ) is a total spawner with a group-synchronous ovarian organization. Age polymodality in total spawners is considered an important factor in assuring that a strong population is sustainable under an intensive harvesting regime and different climatic conditions. In the present study, we investigated the seasonal and inter-annual variation in spawner age structure and the effect of preceding winter thermal conditions on the start of the herring spawning and larvae retention period. Herring spawning season in the Gulf of Riga starts up to six weeks later after colder winters compared to milder winters. Significantly older individuals dominated at the beginning of the spawning season, and thus herring mean age gradually decreased towards the end of the spawning season from 1999-2015. On an annual scale, this pattern was obvious after cold winters, while after mild winters the pattern did not continue, indicating a more homogenous maturation cycle and spawning period, despite the age and size of the herring population in mild winters. Further, herring condition factor was studied in relation to age and spawning season following different winter thermal conditions. Young, 2- and 3- year old first-spawning herring experienced significantly lower conditions after cold winters compared to older ages, indicating an age-dependent effect of preceding winter on herring maturation cycle, condition and spawning time., Competing Interests: The authors declare there are no competing interests.

Very few studies have analyzed how the composition of mother's microbiota affects the development of infant's gut and oral microbiota during the first months of life. Here, microbiota present in the mothers' gut, vagina, breast milk, oral cavity, and mammary areola were compared with the gut and oral microbiota of their infants over the first six months following birth. Samples were collected from the aforementioned body sites from seven mothers and nine infants at three different time points over a 6-month period. Each sample was analyzed with 16S rRNA gene sequencing. The gut microbiota of the infants harbored distinct microbial communities that had low similarity with the various maternal microbiota communities. In contrast, the oral microbiota of the infants exhibited high similarity with the microbiota of the mothers' breast milk, mammary areola and mouth. These results demonstrate that constant contact between microbial communities increases their similarity. A majority of the operational taxonomic units in infant gut and oral microbiota were also shared with the mothers' gut and oral communities, respectively. The disparity between the similarity and the proportion of the OTUs shared between infants' and mothers' gut microbiota might be related to lower diversity and therefore competition in infants' gut microbiota.

Objective: The first aim of this study was to compare the microbiota of different locations (pus, tonsillar fossa, blood) in peritonsillar abscess (PTA) patients in order to optimize the sampling scheme. The second aim was to estimate the occurrence of tonsillitis episodes and macroscopic oropharyngeal signs characteristic of recurrent tonsillitis in PTA patients., Methods: The study group consisted of 22 consecutive patients with PTA undergoing bilateral tonsillectomy. The PTA was punctured; pus and tonsillar fossa biopsy samples and the peripheral blood cultures were collected. The index of tonsillitis was calculated by multiplying the number of tonsillitis episodes per year by the morbidity period in years. Macroscopic oropharyngeal signs were evaluated and they were as follows: tonsillar sclerosis, obstruction of the tonsillar crypts, scar tissue on tonsils, cryptic debris, and lymphatic tissue aggregates., Results: The cultures of the pus were positive in 16 out of 22 patients and the cultures of the tonsillar fossa samples were positive in all cases. In total, 62 different organisms were found from tonsillar fossa, pus, and blood samples, which belonged to 5 different phyla and 18 different families.In the tonsillar fossa, the most frequent bacteria found were Streptococcus spp. In pus samples, the most frequently found bacteria were Streptococcus spp. and bacteria from the Streptococcus milleri group., Conclusion: PTA patients had mixed anaerobic and aerobic microbiota both in the tissue of the tonsillar fossa and the pus of the peritonsillar space. We demonstrated that the tonsillar fossa specimen is a better material for microbiological analyses, because it reveals more bacteria per culture. PTA patients usually have a low number of tonsillitis episodes in their previous history, but a relatively high number of macroscopic oropharyngeal signs, indicating the sclerotic process in palatal tonsils.

The complex ecosystem of the gastrointestinal tract involves tight interrelations among host cells, diet, and billions of microbes, both beneficial and opportunistic pathogens. In spite of advanced genomic, metagenomic, and metabonomic approaches, knowledge is still quite limited regarding the biodiversity of beneficial microbiota, including Lactobacillus spp., and its impact on the main biomarkers of general health. In this paper, Lactobacillus biodiversity is demonstrated through its taxonomy, function, and host-microbial interactions. Its prevalence, composition, abundance, intertwined metabolic properties, and relation to host age, genotype, and socioeconomic factors are reviewed based on the literature and original research experience. The species richness, e.g., the biodiversity of gut microbiota, provides the host with a variety of metabolically active species and strains that predict their response for different health conditions and extrinsic interventions. Metabolically active and safe Lactobacillus species and specific strains with particular functional properties increase the biodiversity of the whole intestinal microbiota. The elaborated principles for effective application of probiotics are discussed, aimed at regulating the composition of microbiota simultaneously with blood and urine biomarkers at the borderline of normality. This approach targets the impact of probiotic strains to maintenance of health with anti-infectious, cardiovascular, and metabolic support.

We aimed at evaluating the association between intestinal Lactobacillus sp. composition and their metabolic activity with the host metabolism in adult and elderly individuals. Faecal and plasma metabolites were measured and correlated to the Lactobacillus species distribution in healthy Estonian cohorts of adult (n = 16; < 48 y) and elderly (n = 33; > 65 y). Total cholesterol, LDL, C-reactive protein and glycated hemoglobin were statistically higher in elderly, while platelets, white blood cells and urinary creatinine were higher in adults. Aging was associated with the presence of L. paracasei and L. plantarum and the absence of L. salivarius and L. helveticus. High levels of intestinal Lactobacillus sp. were positively associated with increased concentrations of faecal short chain fatty acids, lactate and essential amino acids. In adults, high red blood cell distribution width was positively associated with presence of L. helveticus and absence of L. ruminis. L. helveticus was correlated to lactate and butyrate in faecal waters. This indicates a strong relationship between the composition of the gut Lactobacillus sp. and host metabolism. Our results confirm that aging is associated with modulations of blood biomarkers and intestinal Lactobacillus species composition. We identified specific Lactobacillus contributions to gut metabolic environment and related those to blood biomarkers. Such associations may prove useful to decipher the biological mechanisms underlying host-gut microbial metabolic interactions in an ageing population.

Although gut microbiota has been studied relatively extensively in the context of allergic diseases, there have been several contradictions between these studies. By applying high-throughput sequencing, we aimed to analyze the differences in gut microbiota between atopic and healthy children at 5 and 12 years of age. 51 stool samples were collected from 14 atopic and 15 healthy children and analyzed with 454 pyrosequencing of the 16S rRNA gene. At the ages of 5 and 12 years, Bacteroides, Prevotella, and Dialister dominated gut microbiota in both atopic and healthy groups of children. Children in the atopic group had lower abundance and prevalence of Akkermansia in gut microbiota than their healthy counterparts. Thus, the composition of gut microbiota does not seem to be significantly different between atopic and healthy children, but lower abundance and prevalence of Akkermansia indicate that this bacterium may accompany or play a role in IgE-mediated atopic diseases.

Background: Some dominant bacterial divisions of the intestines have been linked to metabolic diseases such as overweight and diabetes., Objective: A pilot study aimed to evaluate the relations between the culturable intestinal bacteria with body mass index (BMI) and some principal cellular and metabolic markers of blood in people older than 65., Design: Altogether 38 generally healthy elderly people were recruited: ambulatory (n=19) and orthopedic surgery (n=19). Questionnaires on general health, anthropometric measurements, routine clinical and laboratory data, and quantitative composition of cultivable gut microbiota were performed., Results: Blood glucose level was positively correlated with BMI (r=0.402; p=0.014). Higher blood glucose level had negative correlation with relative share of intestinal anaerobic bacteria such as bacteroides (r=-0.434; p=0.0076) and gram-positive anaerobic cocci (r=-0.364; p=0.027). In contrast, the relative share of bifidobacteria (r=0.383; p=0.019) and staphylococci (r=0.433; p=0.008) was positively correlated to blood glucose level. In elderly people, a higher blood glucose concentration was predicted by the reduction of the anaerobes' proportion (adj. sex, age, and BMI R(2)=0.192, p=0.028) and that of Bacteroides sp. (adj. R(2)=0.309, p=0.016)., Conclusion: A tight interplay between increased BMI, level of blood glucose, and the reduced proportion of cultivable bacteroides is taking place in the gut microbiota of elderly people.

The aim of our study was to characterize the phylogenetic groups of Escherichia coli, antibiotic resistance, and containment of class 1 integrons in the first attack of pyelonephritis and in subsequent recurrences in young children. Altogether, 89 urine E. coli isolates from 41 children with urinary tract infection (UTI) were studied for prevalence and persistence of phylogenetic groups by pulsed-field gel electrophoresis (PFGE), antibacterial resistance by minimal inhibitory concentrations (MIC) and class 1 integrons by PCR. Phylogenetic group B2 was most common (57%), followed by D (20%), A (18%) and B1 (5%). Overall resistance to betalactams was 61%, trimethoprim-sulfamethoxazole 28%, and was not associated with phylogenetic groups. According to PFGE, the same clonal strain persisted in 77% of patients. The persistence was detected most often in phylogenetic group B2 (70%). Phylogenetic group B2 more often contained class 1 integrons than group A. Integron positive strains had higher MIC values of cefuroxime, cefotaxime, and gentamicin. In conclusion, phylogenetic group B2 was the most common cause of the first episode of pyelonephritis, as well as in case of the persistence of the same strain and contained frequently class 1 integrons in childhood recurrent UTI. An overall frequent betalactam resistance was equally distributed among phylogenetic groups., (© 2013 APMIS. Published by John Wiley & Sons Ltd.)

Objective: An increasing number of studies that are using high-throughput molecular methods are rapidly extending our knowledge of gut microbial colonization in preterm infants whose immaturity and requirement for extensive treatment may result in altered colonization process. We aimed to describe the profile of gut microbiota in 50 extremely low birth weight (<1200 g) critically ill infants at three different time points during the first two months of life by using 16S rRNA gene specific sequencing.  , Patients and Methods: Stool samples were collected at the age of one week, one month and two months. Bacterial community profiling was done using universal amplification of 16S rRNA gene and 454 pyrosequencing., Results: The diversity of gut microbiota in preterm neonates in the first week of life was low but increased significantly over two months. The gut microbiota was dominated by facultative anaerobic bacteria (Staphylococcus spp. and Enterobacteriaceae) and lacked colonization with bacteria known to provide resistance against pathogens (Bacteroides, Bifidobacterium, and Lactobacillus) throughout the study. Colonization of Escherichia coli and uncultured Veillionella was positively correlated with maturity. Infants born to mothers with chorioamnionitis had significantly higher bacterial diversity than those without., Conclusions: High prevalence and abundance of potentially pathogenic Enterobacteriaceae and Staphylococcaceae with low prevalence and abundance of colonization resistance providing taxa bifidobacteria, Bacteroides and lactobacilli may lead to high infection risk via microbial translocation from the gut. Additionally, our data suggest that maternal chorioamnionitis may have an effect on the diversity of infants' gut microbiota; however, the mechanisms involved remain to be elucidated.

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. Petersburg in Russia from January to May 2012 and analyzed for phylogenetic group and prevalence of 23 VF genes. The strains were collected from clinical material (urine, blood, wound, and respiratory tract). Bacterial isolates were compared according to phylogenetic group, clinical material, and geographical origin. Most of the VF genes were concentrated within phylogenetic group B2 and/or D. When comparing strains isolated from different countries, it was found that strains originating from Estonia and Latvia belonged mainly to group B2 and strains from Lithuania and Russia mainly to groups B2 and D. The P-fimbrial adhesin gene papEF was more prevalent in Russian strains, colicin gene cvaC in Lithuanian strains, and capsular gene kpsMTII in Latvian strains; serum resistant gene traT was less prevalent in Estonian strains. The regional differences of VF genes remained statistically significant after taking into account the phylogenetic distribution in the countries.

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. Petersburg, Russia, and to compare the different methods for carbapenemase detection. From January to May 2012, all K. pneumoniae (n = 1983) and E. coli (n = 7774) clinical isolates from 20 institutions in Estonia, Latvia, Lithuania, and St. Petersburg, Russia were screened for carbapenem susceptibility. The IMP, VIM, GIM, NDM, KPC, and OXA-48 genes were detected using real-time PCR and the ability to hydrolyze ertapenem was determined using MALDI-TOF MS. Seventy-seven strains were found to be carbapenem nonsusceptible. From these, 15 K. pneumoniae strains hydrolyzed ertapenem and carried the bla NDM gene. All of these strains carried integron 1 and most carried integron 3 as well as genes of the CTX-M-1 group. No carbapenemase-producing E. coli or K. pneumoniae strains were found in Estonia, Latvia, or Lithuania; however, NDM-positive K. pneumoniae was present in the hospital in St. Petersburg, Russia. A MALDI-TOF MS-based assay is a suitable and cost-effective method for the initial confirmation of carbapenemase production.

The intestinal microbiota is essential to the maturation and homeostasis of the immune system. Immunoblot assays were used to establish the prevalence of serum IgG, IgM, and IgA antibodies specific for Bifidobacterium adolescentis, Bifidobacterium longum, and Lactobacillus rhamnosus GG proteins in young children presenting with or without type 1 diabetes (T1D). We demonstrated that children between the ages of 6 and 12 months had a substantial increase in the frequency of IgG antibodies specific for L. rhamnosus GG proteins. We measured IgG, IgM, and IgA class antibody reactivity against B. adolescentis DSM 20083, B. adolescentis DSM 20086, and B. longum DSM 20088 proteins demonstrating significantly higher IgA responses against B. adolescentis DSM 20083 strain proteins in children who developed islet autoimmunity and T1D later in life. B. adolescentis strains showed more IgM type antibodies in children who developed T1D later in life, but the difference was not statistically significant. B. longum proteins were recognized by IgG and IgA antibodies to a higher extent compared to other bacteria studied. These results confirm that differences in immune reactivity against some commensal strains in young children may represent a different risk factor for developing T1D.

Coagulase-negative staphylococci (CoNS) are the leading cause of late-onset sepsis (LOS) in neonates. Increasing resistance of CoNS to beta-lactams and aminoglycosides has led to widespread use of vancomycin, which in turn may lead to resistance to vancomycin. Thus, combination therapy of LOS has been advocated. We aimed to determine the interaction of oxacillin and gentamicin against CoNS. In 2005, 34 isolates of oxacillin- and gentamicin-resistant CoNS were obtained from blood samples of neonates with LOS. Combination effect was tested using the checkerboard method, E-test with the other antibiotic incorporated in the medium (E-test-1) and two E-test strips placed in a cross-formation (E-test-2). Of 34 isolates 61.8%, 53% and 73.5% revealed synergy or an additive effect when tested by the checkerboard method, E-test-1 and E-test-2, respectively. Results of all three tests were concordant for six (17.6%) isolates, four showing synergy, and two indifference. Our in vitro results support that combination therapy with penicillinase-resistant penicillin and aminoglycoside can be an alternative to vancomycin., (© 2013 APMIS. Published by John Wiley & Sons Ltd.)

Background: The gut microbiota has been shown to affect both fat storage and energy harvesting, suggesting that it plays a direct role in the development of obesity. The aim of this study was to investigate whether intestinal colonization by particular species/groups of the intestinal microbiota is related to body weight values in Estonian preschool children born in different years during the entire 1990s., Methods: Body weight, height, body mass index (BMI), and quantitative composition of cultivable gut microbiota (staphylococci, enterococci, streptococci, enterobacteria, lactobacilli, anaerobic gram-positive cocci, bifidobacteria, eubacteria, bacteroides, clostridia, and candida) were studied in 51 healthy 5-year-old children (40 were born between 1993 and 94 and 11 were born between 1996 and 97)., Results: At the age of 5 years, median weight was 19.5 kg and median BMI was 15.3 kg/m(2). Significantly higher BMI (p=0.006) was found in 5-year-old children born in late versus early 1990s during the development of socioeconomic situation of Estonia (2% rise in gross domestic product). The counts of the different gut bacteria did not show any association with weight and BMI in the 5-year-old children. However, the BMI values were in positive correlation with a relative share of anaerobic gram-positive bacteria, for example, bifidobacteria when adjusted for sex and year of birth (adj R(2)=0.459, p=0.026) and eubacteria (adj R(2)=0.484, p=0.014) in the community of cultured intestinal microbiota. The relative share of bacteroides showed a negative correlation with the childrens' weight (adj R(2)=- 0.481, p=0.015)., Conclusion: The body weight indices of preschool children of the general population are associated with the proportion of anaerobic intestinal microbiota and can be predicted by sex and particular socioeconomic situation from birth to 5 years of age.

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. Fecal samples (n = 74) from AAD patients were investigated for C. difficile and lactobacilli by culture and real-time PCR. Lactobacilli were identified by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and sequencing of 16S rRNA. In C. difficile negative cases we found somewhat higher counts of intestinal Lactobacilli (5.02 vs. 2.15 CFU log(10)/g; p = 0.053) by culture and more frequently Lactobacillus plantarum (33.3% vs. 9.4%; p = 0.03) as compared with positive ones. Results of total counts of lactobacilli comparing Estonian and Norwegian samples were conflicting by culture and PCR. We found higher colonization of Norwegian AAD patients with L. plantarum (21% vs. 5%, p = 0.053) and Estonians with Lactobacillus gasseri (19% vs. 2%, p = 0.023). Particular lactobacilli (e.g. L. plantarum) may have a role in protection against C. difficile, whereas the meaning of total counts of lactobacilli remains questionable. In different persons and nations, different lactobacilli species may have a protective role against C. difficile., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Background: There are no comparative data on the impact of different empiric antibiotic regimens on early bowel colonization as well as on clinical efficacy in extremely low-birthweight (ELBW) neonates at risk of early onset sepsis (EOS)., Methods: A subgroup analysis was carried out of ELBW neonates recruited into a two-center, prospective, cluster randomized study comparing ampicillin and penicillin both combined with gentamicin, within the first 72 h of life. A composite primary end-point (need for change of antibiotics within 72 h and/or 7 day all-cause mortality) and the rate and duration of colonization by opportunistic aerobic microorganisms were assessed using hierarchical models corrected for study center and period., Results: In the ampicillin (n= 36) and penicillin (n= 39) groups change of antibiotics, 7 day mortality and the composite end-point occurred at similar rates. Neonatal intensive care unit mortality for infants with gestational age <26 weeks was lower in the ampicillin group. Ampicillin treatment was associated with a higher colonization rate by Klebsiella pneumoniae, including ampicillin-resistant strains., Conclusion: Preliminary data indicate an urgent need for adequately powered studies of early antibiotic therapy in the subpopulation of ELBW neonates at risk of EOS., (© 2011 The Authors. Pediatrics International © 2011 Japan Pediatric Society.)

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.

Aim: To characterize dynamics of mucosal colonization of neonates by common aerobic Gram negative species and Candida spp. and to identify independent perinatal, neonatal, and environmental factors influencing the colonization process., Study Design: The nasopharyngeal (n=1145) and rectal (n=1242) swabs were collected on admission and thereafter twice a week in neonates with risk factors of early onset sepsis (n=276) admitted within the first 72 h of life. The association between colonization by different microbes and a total of 22 predefined risk factors was assessed using univariate and multiple logistic regression analyses., Results: Throughout the study about half of the patients had rectal (55.8%) or nasopharyngeal colonization (42.8%) with common Gram-negative microorganisms. Colonization dynamics and risk factors were in general similar for a given bacterial species in both mucosal sites; nonfermentative microbes more often found in nasopharyngeal swabs and Enterobacteriaceae in rectal swabs. All organisms except Escherichia coli were influenced by the duration of intensive care unit stay but other risk factors were species specific, perhaps reflecting their mode of acquisition. While colonization by E. coli and Candida albicans was associated with perinatal factors like term birth, vaginal delivery, and breast milk feeding; colonization by Klebsiella pneumoniae, Enteribacter cloacae, Acinetobacter spp. and non-albicans Candida spp. were mostly determined by hospital environment (treatment unit and period, artificial interventions and their duration) and gestation age ≤ 28 weeks., Conclusions: The knowledge of risk factor profiles may permit the development of strategies to prevent heavy colonization and subsequent invasive disease in high risk infants., (Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.)

The present study aimed at assessing the counts and species distribution of intestinal lactobacilli and exploring if the data are associated with BMI and blood glucose level in healthy adults and elderly persons. The BMI (P < 0·01), the level of fasting blood glucose (P < 0·001) and the total counts of lactobacilli (P < 0·01 by bacteriology; P < 0·001 by real-time PCR) were higher in the elderly. The number of species in adults was lower (P < 0·05), who were more often colonised with Lactobacillus acidophilus (P = 0·031) and L. helveticus (P < 0·001). In contrast, L. plantarum (P = 0·035), L. paracasei (P < 0·001) and L. reuteri (P = 0·031) were more prevalent in the elderly. L. rhamnosus was detected in adults (P < 0·001), but not in any elderly person. BMI was associated with counts of lactobacilli, adjusted for age and sex (P = 0·008). The higher BMI in both groups of persons was associated with the presence of obligate homofermentative lactobacilli and L. sakei, both adjusted for age and sex. Plasma glucose values were positively correlated with BMI and negatively correlated with colonisation with L. paracasei (P = 0·0238) in adults and on the borderline with L. fermentum (P = 0·052) in the elderly. Thus, the species-specific PCR analysis of Lactobacillus sp. combined with viable plating data indicates substantial age-related structural differences in the intestinal lactobacilli communities. The higher counts of intestinal Lactobacillus sp. are associated with higher BMI and blood glucose content, while their specific fermentative groups and species of lactobacilli appear at different glucose levels both in adults and in the elderly.

Two common chronic childhood diseases-celiac disease (CD) and type 1 diabetes (T1D)-result from complex pathological mechanisms where genetic susceptibility, environmental exposure, alterations in intestinal permeability and immune responses play central roles. In this study, we investigated whether these characteristics were universal for CD independently of T1D association. For this purpose, we studied 36 children with normal small-bowel mucosa and 26 children with active CD, including 12 patients with T1D. In samples from the small-bowel mucosa, we detected the lowest expression of tight junction protein 1 (TJP1) mRNA in CD patients with T1D, indicating an increase in intestinal permeability. Furthermore, these samples displayed the highest expression of forkhead box P3 (FoxP3) mRNA, a marker for regulatory T cells, as compared with other patient groups. At the same time, serum levels of IgA antibodies specific for the CD-related antigens deamidated gliadin and tissue transglutaminase (tTG) were the highest in CD patients with T1D. In contrast, no significant differences were found in IgA or IgG antibodies specific for bovine beta-lactoglobulin or Bifidobacterium adolescentis DSM 20083-derived proteins. There were also no differences in the transamidating activity of serum autoantibodies between patients and control individuals. Our results show that patients with T1D and newly detected CD exhibit severely altered intestinal permeability, strong local immune activation and increased immunoregulatory mechanisms in the small bowel. Further study is required to determine whether these extreme changes in this CD subgroup are due to some specific environmental factors (virus infections), unknown genetic effects or autoimmune reactions to antigenic targets in intracellular tight junctions.

Immune responses to lactobacilli have been so far insufficiently investigated in patients with autoimmune diseases. We used whole-cell lysate of an indigenous Lactobacillus acidophilus strain isolated from an Estonian child to study serum IgG antibodies in children groups with type 1 diabetes [insulin dependent diabetes mellitus (IDDM)] (n = 21, age 4-18 yr) and with acute coeliac disease (CD) (n = 20, age 0.6-15 yr) and to compare the results with the controls (n = 24, age 2-17 yr). We found that our developed 1-D immunoblot assay readily enables to reveal antibodies against 28 L. acidophilus antigenic proteins in patients' and controls' sera. As verified by immunoproteomics analysis with 2-D and LC ESI-MS/MS the antigens of L. acidophilus were mainly common cytoplasmic proteins GroEL (HSP60), enolase, transcription factor EF-Ts and EF-Tu. However, in addition we identified formyl-CoA transferase being target for antibodies in every tested IDDM patients' serum. We have characterized for the first time the antigenic profile of L. acidophilus whole-cell lysate using sera from children with IDDM, CD, and controls. The different prevalence of reactions against tested antigens in patients and controls sera may indicate significant differences in immune system and commensal bacteria cross-talk in these groups.

The higher counts or particular groups (Firmicutes/Bacteroidetes) of intestinal microbiota are related to host metabolic reactions, supporting a balance of human ecosystem. We further explored whether intestinal lactobacilli were associated with some principal cellular and metabolic markers of blood in 38 healthy >65-year-old persons. The questionnaire, routine clinical and laboratory data of blood indices as much as the oxidized low-density lipoprotein (ox-LDL) and baseline diene conjugates in low-density lipoprotein (BDC-LDL) of blood sera were explored. The PCR-based intestinal Lactobacillus sp. composition and counts of cultivable lactobacilli (LAB) were tested. The facultative heterofermentative lactobacilli (Lactobacillus casei and Lactobacillus paracasei) were the most frequent (89 and 97%, respectively) species found, while Lactobacillus acidophilus, Lactobacillus plantarum and Lactobacillus reuteri were present in almost half of the elderly persons. The number of species simultaneously colonizing the individuals ranged from 1 to 7 (median 4). In elderly consuming probiotics the LAB counts were significantly higher than in these not consuming (median 7.8, range 4.2-10.8 vs. median 6.3, range 3.3-9.7 log cfu/g; p=0.005), adjusted (OR=1.71, CI95 1.04-2.82; p=0.035) for age and body mass index (BMI). The colonization by L. acidophilus was negatively related (r=-0.367, p=0.0275) to L. reuteri, staying significant after adjusting for age, sex and BMI (OR=0.16, CI95 0.04-0.73; p=0.018). However, the blood glucose concentration showed a tendency for a negative correlation for colonization with Lactobacillus fermentum (r=-0.309, p=0.062) adjusted for BMI (Adj. R(2)=0.181; p=0.013) but not for age and sex. The higher white blood cells (WBC) count was positively related (r=0.434, p=0.007) to presence of Lactobacillus reuteri adjusted for age, sex and BMI (Adj. R(2)=0.193, p=0.027). The lower values of ox-LDL were predicted by higher counts of cultivable lactobacilli adjusted by sex, age and BMI (r = -0.389, p = 0.016; Adj. R(2)=0.184 p=0.029). In conclusion, the pilot study of elderly persons shows that the intestinal lactobacilli are tightly associated with WBC count, blood glucose and content of ox-LDL which all serve as risk markers in pathogenesis of inflammation, metabolic syndrome and cardiovascular disease (CVD)., (2010 Elsevier Ltd. All rights reserved.)

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. The MIC values of ampicillin, cefuroxime, cefotaxime, gentamicin, ciprofloxacin, and sulfamethoxazole were measured by E-test and IntI1 was detected by PCR., Results: Out of the 115 strains, 56 (49%) carried class 1 integron genes. Comparing persons without medical interventions, we found in antibiotic-naive children a significantly higher frequency of integron-bearing strains and MIC values than in healthy elderly persons (53% versus 17%; p < 0.01). Evaluating medical interventions, we found a higher resistance and frequency of integrons in strains from hospitalized elderly persons compared with non-hospitalized ones. Children treated with antibiotics had strains with higher MIC values (when compared with antibiotic-naive ones), but the integron-bearing in strains was similar. In most cases, the differences in resistance between the groups (integron-positive and negative strains separately) were higher than the differences between integron-positive and negative strains within the groups., Conclusion: The prevalence of integrons in commensal E. coli strains in persons without previous medical intervention depended on age. The resistance of integron-carrying and non-carrying strains is more dependent on influencing factors (hospitalization and antibiotic administration) in particular groups than merely the presence or absence of integrons.

We assessed the clonality of consecutive Escherichia coli isolates during the course of recurrent urinary tract infections (RUTI) in childhood in order to compare clonality with phenotypic antibiotic resistance patterns, the presence of integrons, and the presence of the sul1, sul2, and sul3 genes. Altogether, 78 urinary E. coli isolates from 27 children, who experienced recurrences during a 1-year follow-up after the first attack of acute pyelonephritis, were investigated. The MICs of sulfamethoxazole, trimethoprim-sulfamethoxazole (SXT), ampicillin, cefuroxime, cefotaxime, and gentamicin and the presence or absence of the intI gene for class 1 integrons and the sulfamethoxazole resistance-encoding genes sul1, sul2, and sul3 were determined. All E. coli strains were genotyped by pulsed-field gel electrophoresis. There were no significant differences in the prevalences of resistance to beta-lactams and SXT between initial and consecutive E. coli isolates (41 versus 45% and 41 versus 29%, respectively). However, the E. coli strains obtained after SXT administration more frequently carried two or more sul genes than the nonexposed strains (9/21 [43%] versus 11/57 [19%], respectively; P = 0.044). In 78% of the patients, the recurrence of unique clonal E. coli strains alone or combined with individual strains was detected. Phenotypic resistance and the occurrence of sul genes were more stable in clonal strains than in individual strains (odds ratios, 8.7 [95% confidence interval {95% CI}, 1.8 to 40.8] and 4.4 [95% CI, 1.1 to 17.7], respectively). Thus, in children with RUTIs, the majority of E. coli strains from consecutive episodes are unique persisting clones, with rare increases in the initially high antimicrobial resistance, the presence of sul genes, and the presence of integrons.

The composition of intestinal microbiota and the Bifidobacterium group community in 20 allergic and 20 nonallergic 5-year-old children was visualized by PCR-denaturing gradient gel electrophoresis (DGGE). The number of dominant bands in the DGGE profiles was smaller in allergic children than in nonallergic children (P<0.001). Allergic children mainly formed a single group upon cluster analysis, whereas nonallergic children were divided between four different groups. In allergic children the Bifidobacterium adolescentis species prevailed, and in nonallergic children the Bifidobacterium catenulatum/pseudocatenulatum prevailed (P=0.01 and P=0.01, respectively). The less diverse composition of intestinal microbiota and prevalence of particular species of Bifidobacterium were characteristic of allergic children even at the age of 5 years.

A total of 560 invasive and 1062 non-invasive isolates were collected. The antimicrobial susceptibility of invasive versus non-invasive Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae isolates were evaluated using the E-tests. The equal domination of Gram-negative among both invasive and non-invasive pathogens was estimated in our study if contaminants were excluded. The emergence trend of Gram-positive microbes especially of coagulase negative staphylococci may be proved only after application of exclusive algorithms. Due to similar susceptibility, the data of non-invasive Gram-negative pathogens can be useful to predict resistance of invasive ones. Also, the surveillance of invasive pathogens provides useful information about the general susceptibility of pathogens.

The aim of the present study was to evaluate the needs for surveillance of invasive Gram-negative pathogens in Estonia. The antimicrobial susceptibility data of invasive isolates of Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella spp, Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae and enterococci were collected in accordance with EARSS (European Antimicrobial Resistance Surveillance System) protocols. Despite the higher rate of Gram positive pathogens, their resistance to antimicrobials was low in contrast to the elevated resistance established for Gram negative pathogens. The higher resistance to antimicrobials was particularly associated with A. baumannii and P. aeruginosa. Also, the proportion of extended spectrum betalactamase (ESBL)-producing strains was 23% among Klebsiella spp. and 3.6% among E. coli. The inclusion of invasive Gram negative pathogens in antimicrobial resistance surveillance provides useful information concerning local pathogen susceptibility, as well as for the empirical treatment of suspected infections.

This prospective cohort study was performed from April to December 2003 for the purpose of collecting a maximum of 50 non-duplicate isolates of Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae from each of 4 ICUs to determine minimum inhibitory concentrations. The most prevalent species were Enterobacteriaceae (13%), K. pneumoniae and A. baumannii (both 12%). 60% of A. baumannii strains were susceptible to ampicillin/sulbactam and cefepime, 95% to meropenem and imipenem, and 75% to amikacin. 79% of P. aeruginosa strains were piperacillin/tazobactam, 58% ceftazidime, 81% meropenem, 72% imipenem, 69% ciprofloxacin and 97% amikacin susceptible. The susceptibility of K. pneumoniae to meropenem and imipenem was 99%, to ciprofloxacin was 91% and to amikacin was 98%. Gram-negative bacteria (especially K. pneumoniae and A. baumannii) were prevalent in our ICUs compared to other European studies. Carbapenem susceptibility of Estonian strains was higher, but P. aeruginosa sensitivity to ceftazidime was lower, compared to other EU countries.

Helicobacter pylori (H. pylori) often play an important role in the pathogenesis of gastritis, peptic ulcer, and probably also gastric cancer. Reactive oxygen species (ROS) produced by this bacterium may be one of the crucial factors whereby oxidative stress can play a role in the pathogenesis of ulcer disease. The aim of this study was to assess ROS activity and glutathione redox status, a principal cellular redox sensor, in H. pylori-associated indomethacin-induced gastric ulcers in rats. Gastric lesion was produced by intragastric administration of indomethacin (7 mg/kg) for three days followed by administration of H. pylori suspension (density 10(9) colony forming units). Animals receiving indomethacin only or followed by administration of H. pylori suspension were sacrificed after 11 and 18 days. ROS activity was assessed by the level of lipid peroxidation (LPO) and the glutathione redox status by the ratio between oxidized and reduced glutathione (GSSG/GSH). Indomethacin did not significantly increase the level of LPO and the GSSG/GSH ratio. When H. pylori suspension was given together with indomethacin the LPO was increased both on days 11 and 18 and GSSG/GSH on day 18. H. pylori, thus, substantially increases glutathione redox ratio and lipid peroxidation in gastric mucosa, which may play an important role in the pathological mechanisms of this bacterium. The findings support the idea that dietary antioxidants could be beneficial in combination therapy for eradication of H. pylori.

Diagnostic significance of quantitative measurement of muscle acetylcholine receptor (AChR) antibodies by ELISA in patients with myasthenia was shown. Blood serum analysis of 111 patients (30 in dynamics for various treatment types) was carried out. The most essential elevation of antibodies quantity was observed in patients with generalized myasthenia type. After thymectomy it was significantly reduced. Quantitative antibodies measurement by interaction with AChR domen in ELISA is supposed to be used as additional diagnostic method of autoimmune myasthenia.

Acethylcholine receptor (AChR) antibodies in patients with myasthenia were studied for the first time in Russia with radioimmuno-assay application. Seronegative result (antibody titer lower than 0.2 nmol/l) was obtained for 33% of the patients and seropositive one (antibody titer higher than 0.2 nmol/l)--for 67%. AChR antibodies level varied from 1.9 to 115.0 nmol/l. The AChR antibodies were found more frequently and in higher titers in women than in men. Correlation analysis revealed strong correlation between AChR antibodies level and severity of myasthenia.