Вчені України — лауреати міжнародних премій і нагород

Рецензія на книгу: Абліцов В.Г. «Вчені України — лауреати міжнародних премій і нагород» (Серія «Наука України у світовому інформаційному просторі». Вип. 4) Київ: Академперіодика, 2011. — 192 с

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data

Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics. With the premise that accumulation of putative resistance-conferring SNPs, potentially in combination with specific resistance genes, precedes full resistance, we retrogressively surveyed the hotspot loci and quantified the number of SNPs and/or genes, which if accumulated would confer full resistance to an otherwise susceptible strain. We name this approach the € distance to resistance'. It can be used to identify the creep towards complete antibiotics resistance in bacteria using genome sequencing. This approach serves as a basis for the development of future sequencing-based methods for predicting resistance profiles of bacterial strains in hospital microbiology and public health settings

Identification of conditionally essential genes for Streptococcus suis infection in pigs

Streptococcus suis is a Gram-positive bacterium and zoonotic pathogen that causes meningitis and sepsis in pigs and humans. The aim of this study was to identify genes required for S. suis infection. We created Tn-Seq libraries in a virulent S. suis strain 10, which was used to inoculate pigs in an intrathecal experimental infection. Comparative analysis of the relative abundance of mutants recovered from different sites of infection (blood, cerebrospinal fluid, and meninges of the brain) identified 361 conditionally essential genes, i.e. required for infection, which is about 18% of the genome. The conditionally essential genes were primarily involved in metabolic and transport processes, regulation, ribosomal structure and biogenesis, transcription, and cell wall membrane and envelope biogenesis, stress defenses, and immune evasion. Directed mutants were created in a set of 10 genes of different genetic ontologies and their role was determined in ex vivo models. Mutants showed different levels of sensitivity to survival in whole blood, serum, cerebrospinal fluid, thermic shock, and stress conditions, as compared to the wild type. Additionally, the role of three selected mutants was validated in co-infection experiments in which pigs were infected with both wild type and isogenic mutant strains. The genetic determinants of infection identified in this work contribute to novel insights in S. suis pathogenesis and could serve as targets for novel vaccines or antimicrobial drugs

Sex differences in clinical presentation and risk stratification in the emergency department: an observational multicenter cohort study

Objective: The aim of this study was to investigate whether sex differences exist in disease presentations, disease severity and (case-mix adjusted) outcomes in the Emergency Department (ED).Methods: Observational multicenter cohort study using the Netherlands Emergency Department Evaluation Database (NEED), including patients >= 18 years of three Dutch EDs. Multivariable logistic regression was used to study the associations between sex and outcome measures in-hospital mortality and Intensive Care Unit/Medium Care Unit (ICU/MCU) admission in ED patients and in subgroups triage categories and presenting complaints.Results: Of 148,825 patients, 72,554 (48.8%) were females. Patient characteristics at ED presentation and diagnoses (such as pneumonia, cerebral infarction, and fractures) were comparable between sexes at ED presentation. In-hospital mortality was 2.2% in males and 1.7% in females. ICU/MCU admission was 4.7% in males and 3.1% in females. Males had higher unadjusted (OR 1.34(1.25-1.45)) and adjusted (AOR 1.34(1.24-1.46)) risks for mortality, and unadjusted (OR 1.54(1.46-1.63)) and adjusted (AOR 1.46(1.37-1.56)) risks for ICU/MCU admission. Males had higher adjusted mortality and ICU/MCU admission for all triage categories, and with almost all presenting complaints except for headache.Conclusions: Although patient characteristics at ED presentation for both sexes are comparable, males are at higher unadjusted and adjusted risk for adverse outcomes. Males have higher risks in all triage categories and with almost all presenting complaints. Future studies should investigate reasons for higher risk in male ED patients

From microbial gene essentiality to novel antimicrobial drug targets

Background: Bacterial respiratory tract infections, mainly caused by Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are among the leading causes of global mortality and morbidity. Increased resistance of these pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials. Result: Here, we report a proof of concept study for the reliable identification of potential drug targets in these human respiratory pathogens by combining high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics. Approximately 20% of all genes in these three species were essential for growth and viability, including 128 essential and conserved genes, part of 47 metabolic pathways. By comparing these essential genes to the human genome, and a database of genes from commensal human gut microbiota, we identified and excluded potential drug targets in respiratory tract pathogens that will have off-target effects in the host, or disrupt the natural host microbiota. We propose 249 potential drug targets, 67 of which are targets for 75 FDA-approved antimicrobials and 35 other researched small molecule inhibitors. Two out of four selected novel targets were experimentally validated, proofing the concept. Conclusion: Here we have pioneered an attempt in systematically combining the power of high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics to discover potential drug targets at genome-scale. By circumventing the time-consuming and expensive laboratory screens traditionally used to select potential drug targets, our approach provides an attractive alternative that could accelerate the much needed discovery of novel antimicrobials

IgM Augments Complement Bactericidal Activity with Serum from a Patient with a Novel CD79a Mutation

Antibody replacement therapy for patients with antibody deficiencies contains only IgG. As a result, concurrent IgM and IgA deficiency present in a large proportion of antibody deficient patients persists. Especially patients with IgM deficiency remain at risk for recurrent infections of the gastrointestinal and respiratory tract. The lack of IgM in the current IgG replacement therapy is likely to contribute to the persistence of these mucosal infections because this antibody class is especially important for complement activation on the mucosal surface. We evaluated whether supplementation with IgM increased serum bactericidal capacity in vitro. Serum was collected from a patient with agammaglobulinemia and supplemented with purified serum IgM to normal levels. Antibody and complement deposition on the bacterial surface was determined by multi-color flow cytometry. Bacterial survival in serum was determined by colony-forming unit counts. We present a patient previously diagnosed with agammaglobulinemia due to CD79A (Igα) deficiency revealing a novel pathogenic insertion variant in the CD79a gene (NM_001783.3:c.353_354insT). Despite IgG replacement therapy and antibiotic prophylaxis, this patient developed a Campylobacter jejuni spondylodiscitis of lumbar vertebrae L4–L5. We found that serum IgM significantly contributes to complement activation on the bacterial surface of C. jejuni. Furthermore, supplementation of serum IgM augmented serum bactericidal activity significantly. In conclusion, supplementation of intravenous IgG replacement therapy with IgM may potentially offer greater protection against bacterial infections, also in the context of increasing antibiotic resistance

The association between systolic blood pressure and heart rate in emergency department patients: a multicenter cohort study

BackgroundGuidelines and textbooks assert that tachycardia is an early and reliable sign of hypotension, and an increased heart rate (HR) is believed to be an early warning sign for the development of shock, although this response may change by aging, pain, and stress.ObjectiveTo assess the unadjusted and adjusted associations between systolic blood pressure (SBP) and HR in emergency department (ED) patients of different age categories (18–50 years; 50–80 years; > 80 years).MethodsA multicenter cohort study using the Netherlands Emergency department Evaluation Database (NEED) including all ED patients ≥ 18 years from three hospitals in whom HR and SBP were registered at arrival to the ED. Findings were validated in a Danish cohort including ED patients. In addition, a separate cohort was used including ED patients with a suspected infection who were hospitalized from whom measurement of SBP and HR were available prior to, during, and after ED treatment. Associations between SBP and HR were visualized and quantified with scatterplots and regression coefficients (95% confidence interval [CI]).ResultsA total of 81,750 ED patients were included from the NEED, and a total of 2358 patients with a suspected infection. No associations were found between SBP and HR in any age category (18–50 years: −0.03 beats/min/10 mm Hg, 95% CI −0.13–0.07, 51–80 years: −0.43 beats/min/10 mm Hg, 95% CI −0.38 to −0.50, > 80 years: −0.61 beats/min/10 mm Hg, 95% CI −0.53 to −0.71), nor in different subgroups of ED patient. No increase in HR existed with a decreasing SBP during ED treatment in ED patients with a suspected infection.ConclusionNo association between SBP and HR existed in ED patients of any age category, nor in ED patients who were hospitalized with a suspected infection, even during and after ED treatment. Emergency physicians may be misled by traditional concepts about HR disturbances because tachycardia may be absent in hypotension.Development and application of statistical models for medical scientific researc

Development of endotoxin tolerance does not influence the response to a challenge with the mucosal live-attenuated influenza vaccine in humans in vivo

Introduction: The effects of bacterial infections on the response to subsequent viral infections are largely unknown. This is important to elucidate to increase insight into the pathophysiology of bacterial and viral co-infections, and to assess whether bacterial infections may influence the course of viral infections. Methods: Healthy male subjects received either bacterial endotoxin [Escherichia coli-derived lipopolysaccharide (LPS), 2 ng/kg, n = 15] or placebo (n = 15) intravenously, followed by intranasal Fluenz (live-attenuated influenza vaccine) 1 week later. Results: LPS administration resulted in increased plasma cytokine levels and development of endotoxin tolerance in vivo and ex vivo, illustrated by attenuated cytokine production upon rechallenge with LPS. Following Fluenz administration, infectivity for the Fluenz A/B strains was similar between the LPS-Fluenz and placebo-Fluenz groups (13/15 subjects in both groups). Also, the Fluenz-induced increase in temperature and IL-6, G-CSF and IP-10 concentrations in nasal wash were similar between both groups. Conclusion: While endotoxemia profoundly attenuates the immune response upon a second LPS challenge, it does not influence the Fluenz-induced immune response. These results suggest immune suppression after bacterial infection does not alter the response to a subsequent viral infection

Prognostic biomarker soluble ST2 exhibits diurnal variation in chronic heart failure patients

Aim: Soluble suppression of tumorigenicity-2 (sST2) is a strong prognostic biomarker in heart failure. The emerging understanding of circadian biology in cardiovascular disease may lead to novel applications in prognosis and diagnosis and may provide insight into mechanistic aspects of the disease–biomarker interaction. So far, it is unknown whether sST2 exhibits a diurnal rhythm. Repeated measurements of sST2 may aid in clinical decision making. The goal of this study was to investigate whether sST2 exhibits diurnal variation in patients with heart failure with reduced ejection fraction (HFrEF) and in control subjects, thereby enhancing its diagnostic and prognostic values. Methods and results: The study comprised 32 subjects: 16 HFrEF patients and 16 controls. Blood was collected at seven subsequent time points during a 24 h time period. sST2, N-terminal pro-B-type natriuretic peptide (NT-proBNP), melatonin, and cortisol were measured from serum. Peak values of sST2 clustered at daytime (modal value: 5 p.m.) in 87.6% of all subjects (81.3% of patients, P = 0.021; 93.8% of controls, P = 0.001), and minimum concentrations at night-time (modal value: 5 a.m.) in 84.4% (87.5% of patients, P = 0.004 81.3% of controls, P = 0.021). A cosinor analysis of mean normalized sST2 values revealed significant cosine shaped 24 h oscillations of patients (P = 0.026) and controls (P = 0.037). NT-proBNP in contrast did not show a diurnal rhythm, while melatonin and cortisol patterns were intact in all subjects. Conclusions: sST2 exhibits a diurnal rhythm with lower values in the morning than in the late afternoon. This new insight could lead to refinement of its diagnostic and prognostic values through specified and consistent sampling times with repeated measurements. For example, by measuring sST2 during the afternoon, when levels are at their highest, false negatives on prognosis prediction could be avoided

The application of X-ray micro Computed Tomography imaging for tracing particle movement in soil

Despite significant advances in recent years in the application of sensing and imaging technologies to the study of the hydraulic behaviour of soils, our understanding of how solutes and particulate matter move through soil is still limited and often based on idealised soil structures. The aim of this work was to use an appropriate proxy material, in this case (Decabromodiphenyl ether (DBDE)), to represent 1–2 μm sized chemical particles, frequently used in agricultural practices, in order to trace their spatial and temporal movement through a soil column. X-ray Computed Tomography (CT) was employed to map the 3D pore geometry and facilitate visualization of the concentration distribution of the highly X-ray attenuating proxy material as it was applied and subsequently leached through the soil over a 5 hour period. Simultaneously the soil eluate was collected from the bottom of each column and the concentration of proxy material measured using gas chromatography to compare with the imaged data. The method developed for visualizing the tracer material in 3D at the pore-scale was successful. The results demonstrated that the tracer material initially moved rapidly through the upper portion of the soil but subsequently became immobile, despite repeated elution with water as confirmed by imagery. Similar concentrations to those applied to the soil surface were not recorded at any point in time towards the bottom of the soil column. By visualizing the DBDE distribution in 3D it was possible to correlate the highest concentrations of the tracer material with the location of the smaller size pores (i.e. mesopores). Dynamic X-ray CT imaging of tracer materials has considerable potential as a proxy for the visualization of particulate agricultural chemicals that will assist with understanding how their transport behaviour varies both spatially and temporally