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| 31. |
- Backhaus, Erik, et al.
(author)
-
Antimicrobial susceptibility of invasive pneumococcal isolates from a region in south-west Sweden 1998-2001.
- 2007
-
In: Scandinavian journal of infectious diseases. - : Informa UK Limited. - 0036-5548 .- 1651-1980. ; 39:1, s. 19-27
-
Journal article (peer-reviewed)abstract
- Invasive disease caused by antibiotic resistant pneumococci is a worldwide problem. All invasive pneumococcal strains in an area of south-west Sweden with 1.7 million inhabitants were collected prospectively during 1998-2001. Minimum inhibitory concentrations (MICs) were determined by E-test and correlated to serotypes and clinical characteristics. Of 827 strains, 744 (90%) were susceptible (S) to all agents tested and 83 (10%) were indeterminate (I) or resistant (R) to at least 1 agent. 22 isolates (2.7%) were I to penicillin (MIC >0.06 to < or = 1.0 mg/l), but none were R (MIC >1.0 mg/l). Numbers and proportions of decreased susceptibility against other agents tested were as follows: erythromycin R: 30 (3.6%), clindamycin R: 6 (0.7%), tetracycline R: 16 (1.9%), moxifloxacin R: 1 (0.1%), cotrimoxazole I: 17 (2%) and R: 31(4%). Non-susceptibility to at least 1 agent was not correlated with age, clinical manifestation, underlying diseases and outcome. The serotype distribution differed between non-susceptible and susceptible strains. The serotypes in the 7-valent pneumococcal conjugate vaccine covered 42% of all infections and 73% of those caused by non-susceptible strains. In conclusion, the impact of antibiotic resistance in invasive pneumococcal disease remains limited in south-west Sweden.
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| 32. |
- Backhaus, Erik, et al.
(author)
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Epidemiology of invasive pneumococcal infections: manifestations, incidence and case fatality rate correlated to age, gender and risk factors
- 2016
-
In: Bmc Infectious Diseases. - : Springer Science and Business Media LLC. - 1471-2334. ; 16
-
Journal article (peer-reviewed)abstract
- Background: Incidence, manifestations and case-fatality rate (CFR) of invasive pneumococcal disease (IPD) vary with age and comorbidities. New vaccines, changing age distribution, prolonged survival among immunocompromised patients and improved sepsis management have created a need for an update of basic facts to inform vaccine recommendations. Methods: Age, gender and comorbidities were related to manifestations and death for 2977 consecutive patients with IPD in a Swedish region with 1.5 million inhabitants during 13 years before introduction of pneumococcal conjugate vaccines (PCV) in the infant vaccination program. These data were related to population statistics and prevalence of several comorbidities, and compared with two previous studies giving a total follow-up of 45 years in the same area. Results: The annual incidence was 15/100,000 for any IPD and 1.1/100,000 for meningitis; highest among elderly followed by children < 2 years. It was 2238/100,000 among myeloma patients, followed by chronic lymphatic leukemia, hemodialysis and lung cancer, but not elevated among asthma patients. CFR was 10 % among all patients, varying from 3 % below 18 years to 22 %>= 80 years. During 45 years, the IPD incidence increased threefold and CFR dropped from 20 to 10 %. Meningitis incidence remained stable (1.1/100,000/year) but CFR dropped from 33 to 13 %. IPD-specific mortality decreased among children < 2 years from 3.1 to 0.46/100,000/year but tripled among those >= 65 years. Conclusions: IPD incidence and CFR vary widely between age and risk groups and over time even without general infant vaccination. Knowledge about specific epidemiological characteristics is important for informing and evaluating vaccination policies.
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| 33. |
- Backhaus, Erik
(author)
-
Invasive Pneumococcal Infections
- 2011
-
Doctoral thesis (other academic/artistic)abstract
- Streptococcus pneumoniae is a major cause of disease, ranging from uncomplicated respiratory infections to severe invasive pneumococcal disease (IPD), including bacteraemic pneumonia, septicaemia with unknown focus and meningitis. Case fatality rate (CFR) remains high and antibiotic resistance is increasing globally. S. pneumoniae is surrounded by a polysaccharide capsule that can be divided into more than 90 immunologically different serotypes. Vaccination may reduce morbidity and mortality due to IPD. Two vaccine types exist: pneumococcal polysaccharide vaccine (PPV-23) and pneumococcal conjugate vaccines (PCV-7, 10, 13). The former contains 23 serotypes, but does not work in small children, whereas the latter also protects children below two years of age, but includes only 7, 10 and 13 serotypes, respectively. The aim was to explore the epidemiology of IPD before the introduction of PCV-7 in the Swedish childhood vaccination programme, in January 2009: serotype distribution, antimicrobial susceptibility and potential vaccine coverage among isolates causing IPD; mortality, case fatality rate and incidence of different IPD manifestations related to age and risk groups; the impact of serotype and genotype on manifestations and outcome; and finally, long-term changes in the epidemiology during 45 years. Consecutive isolates and clinical data from 836 adults and children with IPD were collected in the Västra Götaland region (VGR) and Halland during 1998-2001. Serotype and antibiotic susceptibility were tested. Clonal complex (CC) was determined for these isolates together with 424 IPD isolates from adults and children in Stockholm using pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Clinical data for all 2977 IPD episodes in VGR during 1996-2008 were retrieved from hospital notes. Prevalence data for predisposing factors were included from patient registries and recent publications. Of 836 strains, 42%, 70%, 75% and 94% belonged to serotypes included in PCV-7, -10, -13 and PPV- 23, respectively. Decreased susceptibility was uncommon, and largely confined to certain clones and serotypes, especially those included in PCV-7. Serotypes 1 and 7F were most common; they infected younger patients with less underlying disease and caused lower CFR than other serotypes, whereas 19A caused higher CFR. Clonal distribution differed between adults and children. CC306 (all serotype 1), caused lower CFR among adults than six other CCs. The relation between serotype and CC was complicated; clinical characteristics differed between some CCs within the same serotype and between some serotypes within the same CC; it was often difficult to determine whether these differences were related to serotype, CC or both. The annual incidence of IPD was 15/100,000 and varied largely with age and underlying disease. It was highest at extremes of age and in patients with myeloma (2238/100,000), followed by chronic lymphatic leukemia, haemodialysis, lung cancer, HIV, rheumatic diseases, chronic obstructive pulmonary disease and diabetes mellitus. In contrast, it was not elevated among asthma patients. When compared with data from previous studies during 45 years, the incidence increased threefold and the CFR dropped from 20 to 10% for all IPD, whereas the incidence remained stable (1.1/100,000/year) and the CFR dropped from 33 to 13% for meningitis. In conclusion, incidence and CFR have changed considerably over time and vary widely between different age and risk groups. CFR is also influenced by serotype and genotype. These factors have to be considered during planning and evaluation of vaccination against pneumococci.
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| 34. |
- Brack, Werner, et al.
(author)
-
The SOLUTIONS project : Challenges and responses for present and future emerging pollutants in land and water resources management
- 2015
-
In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 503, s. 22-31
-
Journal article (peer-reviewed)abstract
- SOLUTIONS (2013 to 2018) is a European Union Seventh Framework Programme Project (EU-FP7). The project aims to deliver a conceptual framework to support the evidence-based development of environmental policies with regard to water quality. SOLUTIONS will develop the tools for the identification, prioritisation and assessment of those water contaminants that may pose a risk to ecosystems and human health. To this end, a new generation of chemical and effect-based monitoring tools is developed and integrated with a full set of exposure, effect and risk assessment models. SOLUTIONS attempts to address legacy, present and future contamination by integrating monitoring and modelling based approaches with scenarios on future developments in society, economy and technology and thus in contamination. The project follows a solutions-oriented approach by addressing major problems of water and chemicals management and by assessing abatement options. SOLUTIONS takes advantage of the access to the infrastructure necessary to investigate the large basins of the Danube and Rhine as well as relevant Mediterranean basins as case studies, and puts major efforts on stakeholder dialogue and support. Particularly, the EU Water Framework Directive (WFD) Common Implementation Strategy (CIS) working groups, International River Commissions, and water works associations are directly supported. with consistent guidance for the early detection, identification, prioritisation, and abatement of chemicals in the water cycle. SOLUTIONS will give a specific emphasis on concepts and tools for the impact and risk assessment of complex mixtures of emerging pollutants, their metabolites and transformation products. Analytical and effect-based screening tools will be applied together with ecological assessment tools for the identification of toxicants and their impacts. The SOLUTIONS approach is expected to provide transparent and evidence-based candidates or River Basin Specific Pollutants in the case study basins and to assist future review of priority pollutants under the WFD as well as potential abatement options.
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| 35. |
- Browall, Sarah, et al.
(author)
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Clinical manifestations of invasive pneumococcal disease by vaccine and non-vaccine types
- 2014
-
In: European Respiratory Journal. - : European Respiratory Society. - 0903-1936 .- 1399-3003. ; 44:6, s. 1646-1657
-
Journal article (peer-reviewed)abstract
- Pneumococcal conjugated vaccines (PCVs) have shown protection against invasive pneumococcal disease by vaccine serotypes, but an increase in non-vaccine serotype disease has been observed. Type-specific effects on clinical manifestation need to be explored.Clinical data from 2096 adults and 192 children with invasive pneumococcal disease were correlated to pneumococcal molecular serotypes. Invasive disease potential for pneumococcal serotypes were calculated using 165 invasive and 550 carriage isolates from children.The invasive disease potential was lower for non-PCV13 compared to vaccine-type strains. Patients infected with non-PCV13 strains had more underlying diseases, were less likely to have pneumonia and, in adults, tended to have a higher mortality. Furthermore, patients infected with pneumococci belonging to clonal serotypes only expressing non-PCV13 capsules had a higher risk for septicaemia and mortality.PCV vaccination will probably lead to a decrease in invasive pneumococcal disease but an alteration in the clinical manifestation of invasive pneumococcal disease. Genetic lineages causing invasive pneumococcal disease in adults often express non-vaccine serotypes, which can expand after vaccination with an increased risk of infection in patients with underlying diseases.
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| 36. |
- Buongermino Pereira, Mariana, 1982, et al.
(author)
-
A comprehensive survey of integron-associated genes present in metagenomes
- 2020
-
In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
-
Journal article (peer-reviewed)abstract
- BackgroundIntegrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging.ResultsHere, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants.ConclusionsOur results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.
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| 37. |
- Corcoll, Natàlia, 1981, et al.
(author)
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Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing
- 2017
-
In: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968 .- 0378-1097. ; 364:14
-
Journal article (peer-reviewed)abstract
- High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterization of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol® Reagent (PlantDNAzol) and the Fast DNATM SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77 - 130 μg g wet wt-1). Lower amounts of DNA were obtained (
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| 38. |
- Eriksson, Martin, 1970, et al.
(author)
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Triclosan changes community composition and selects for specific bacterial taxa in marine periphyton biofilms in low nanomolar concentrations
- 2020
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In: Ecotoxicology. - : Springer Science and Business Media LLC. - 0963-9292 .- 1573-3017. ; 29:7, s. 1083-1094
-
Journal article (peer-reviewed)abstract
- The antibacterial agent Triclosan (TCS) is a ubiquitous environmental contaminant due to its widespread use. Sensitivity to TCS varies substantially among eu- and pro-karyotic species and its risk for the marine environment remains to be better elucidated. In particular, the effects that TCS causes on marine microbial communities are largely unknown. In this study we therefore used 16S amplicon rDNA sequencing to investigate TCS effects on the bacterial composition in marine periphyton communities that developed under long-term exposure to different TCS concentrations. Exposure to TCS resulted in clear changes in bacterial composition already at concentrations of 1 to 3.16 nM. We conclude that TCS affects the structure of the bacterial part of periphyton communities at concentrations that actually occur in the marine environment. Sensitive taxa, whose abundance decreased significantly with increasing TCS concentrations, include the Rhodobiaceae and Rhodobacteraceae families of Alphaproteobacteria, and unidentified members of the Candidate division Parcubacteria. Tolerant taxa, whose abundance increased significantly with higher TCS concentrations, include the families Erythrobacteraceae (Alphaproteobacteria), Flavobacteriaceae (Bacteroidetes), Bdellovibrionaceae (Deltaproteobacteria), several families of Gammaproteobacteria, and members of the Candidate phylum Gracilibacteria. Our results demonstrate the variability of TCS sensitivity among bacteria, and that TCS can change marine bacterial composition at concentrations that have been detected in the marine environment.
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| 39. |
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| 40. |
- Gustavsson, Mikael, 1983, et al.
(author)
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Estimating the release of chemical substances from consumer products, textiles and pharmaceuticals to wastewater
- 2022
-
In: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 287
-
Journal article (peer-reviewed)abstract
- Chemical emissions from households originate from a wide range of sources and results in highly diverse mixtures. This makes traditional monitoring based on analytical chemistry challenging, especially for compounds that appear in low concentrations. We therefore developed a method for predicting emissions of chemicals from households into wastewater, relying on consumption patterns from multiple data sources. The method was then used to predict the emissions of chemical preparations, chemicals leaching from textiles and prescription pharmaceuticals in Sweden. In total we predicted emissions of 2007 chemicals with a combined emission of 62,659 tonnes per year - or 18 g/person and day. Of the emitted chemicals, 2.0% (w/w) were either classified as hazardous to the environment or were both persistent and mobile. We also show that chemical emissions come from a wide range of uses and that the total emission of any individual chemical is determined primarily by its use pattern, not by the total amount used. This emphasizes the need for continuous updates and additional knowledge generation both on emission factors and excretion rates as well as a need for improved reporting on the intended use of individual chemicals. Finally, we scrutinize the model and its uncertainty and suggest areas that need improvement to increase the accuracy of future emission modelling. We conclude that emission modelling can help guide environmental monitoring and provide input into management strategies aimed at reducing the environmental effect caused by hazardous chemicals.
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| 41. |
- Gustavsson, Mikael, 1983, et al.
(author)
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Risk assessment of chemicals and their mixtures are hindered by scarcity and inconsistencies between different environmental exposure limits
- 2023
-
In: Environmental Research. - : Elsevier BV. - 0013-9351 .- 1096-0953. ; 225
-
Journal article (peer-reviewed)abstract
- In chemical risk assessment, measured or modelled environmental concentrations are compared to environ-mental exposure limits (EELs), such as Predicted No Effect Concentrations (PNECs) or hazardous concentrations for 5% of species (HC05s) derived from species sensitivity distributions (SSDs). However, for many chemicals the EELs include large uncertainties or, in the worst case, the necessary data for their estimation are completely missing. This makes the assessment of chemical risks and any subsequent implementation of management strategies challenging. In this study we analyzed the uncertainty of EELs and its impact on chemical risk assessment. First, we compared three individual EEL datasets, two primarily based on experimental data and one based on computational predictions. The comparison demonstrates large disagreements between EEL data sources, with experimentally derived EELs differing by more than seven orders of magnitude. In a case-study, based on the predicted emissions of 2005 chemicals, we showed that these uncertainties lead to significantly different risk assessment outcomes, including large differences in the magnitude of the total risk, risk driver identification, and the ranking of use categories as risk contributors. We also show that the large data-gaps in EEL datasets cannot be covered by commonly used computational approaches (QSARs). We conclude that an expanded framework for interpreting risk characterization outcomes is needed. We also argue that the large data -gaps present in ecotoxicological data need to be addressed in order to achieve the European zero pollution vision as the growing emphasis on ambient exposures will further increase the demand for accurate and well -established EELs.
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| 42. |
- Gustavsson, Mikael, et al.
(author)
-
Transformers enable accurate prediction of acute and chronic chemical toxicity in aquatic organisms
- 2024
-
In: Sciences Advances. ; 10:10
-
Journal article (peer-reviewed)abstract
- Environmental hazard assessments are reliant on toxicity data that cover multiple organism groups. Generating experimental toxicity data is, however, resource-intensive and time-consuming. Computational methods are fast and cost-efficient alternatives, but the low accuracy and narrow applicability domains have made their adaptation slow. Here, we present a AI-based model for predicting chemical toxicity. The model uses transformers to capture toxicity-specific features directly from the chemical structures and deep neural networks to predict effect concentrations. The model showed high predictive performance for all tested organism groups—algae, aquatic invertebrates and fish—and has, in comparison to commonly used QSAR methods, a larger applicability domain and a considerably lower error. When the model was trained on data with multiple effect concentrations (EC50/EC10), the performance was further improved. We conclude that deep learning and transformers have the potential to markedly advance computational prediction of chemical toxicity.
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| 43. |
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| 44. |
- Lönnermark, Elisabeth, 1965, et al.
(author)
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Effects of Probiotic Intake and Gender on Nontyphoid Salmonella Infection
- 2015
-
In: Journal of Clinical Gastroenterology. - 0192-0790 .- 1539-2031. ; 49:2, s. 116-123
-
Journal article (peer-reviewed)abstract
- The goal of the study was to examine if intake of Lactobacillus plantarum can accelerate clearance of nontyphoid Salmonella and reduce infection-related symptoms.
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| 45. |
- Molander, Viktor, 1985, et al.
(author)
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Invasive pneumococcal infections in Vellore, India: clinical characteristics and distribution of serotypes.
- 2013
-
In: BMC infectious diseases. - : Springer Science and Business Media LLC. - 1471-2334. ; 13:532
-
Journal article (peer-reviewed)abstract
- Streptococcus pneumoniae infection is a serious problem worldwide and the case fatality rate remains high. The aim of this study was to analyze the distribution of pneumococcal serotypes causing invasive pneumococcal disease (IPD), to survey the potential coverage of present and future vaccines, and to investigate differences between serotypes and groups of serotypes with regard to manifestation, case fatality rate, age, and other risk factors.
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| 46. |
- Nolskog, Peter, et al.
(author)
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STI with Mycoplasma genitalium : More common than Chlamydia trachomatis in patients attending youth clinics in Sweden
- 2019
-
In: European Journal of Clinical Microbiology and Infectious Diseases. - : Springer. - 0934-9723 .- 1435-4373. ; 38:1, s. 81-86
-
Journal article (peer-reviewed)abstract
- The prevalence of Chlamydia trachomatis in Sweden is well known, whereas the prevalence of Mycoplasma genitalium is less well documented. Youth clinics offer free contraception advice, sexually transmitted infection (STI) testing and/or contact tracing for the age group 15–25 years. The main objective of this study was to determine the prevalence of STIs, the presence of symptoms and the role of contact tracing. From July 2013 to March 2014, 1001 persons, 509 women and 492 men, were included in this study of six youth clinics in the Region of Västra Götaland. Symptoms were registered and whether the patient was tested because of contract tracing. Collection of urine samples, testing, treatment and disease registration were performed according to clinical routines. Urine samples were analysed for C. trachomatis/N. gonorrhoeae on the Cobas 4800 system (Roche). M. genitalium was analysed by lab-developed PCR. Genital infection was present in 16.8%. The prevalence of M. genitalium was higher than for C. trachomatis (9.6% and 7.1%). Men with symptoms have a significantly higher relative risk for infection with M. genitalium or C. trachomatis compared to asymptomatic men, while there is no increase for women. Contact tracing is important since positive outcome has a high relative risk for both infections. The prevalence of M. genitalium was higher than C. trachomatis in this study population. Initial testing for both C. trachomatis and M. genitalium should at least be considered for young men presenting with symptoms of genital infection. In finding positive cases, contact tracing is of great importance. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.
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| 47. |
- Svedberg, Patrik, et al.
(author)
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Dataset on aquatic ecotoxicity predictions of 2697 chemicals, using three quantitative structure-activity relationship platforms
- 2023
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In: Data in Brief. - 2352-3409. ; 51
-
Journal article (peer-reviewed)abstract
- Empirical and in silico data on the aquatic ecotoxicology of 2697 organic chemicals were collected in order to compile a dataset for assessing the predictive power of current Quantitative Structure Activity Relationship (QSAR) models and software platforms. This document presents the dataset and the data pipeline for its creation. Empirical data were collected from the US EPA ECOTOX Knowledgebase (ECOTOX) and the EFSA (European Food Safety Authority) report “Completion of data entry of pesticide ecotoxicology Tier 1 study endpoints in a XML schema – database”. Only data for OECD recommended algae, daphnia and fish species were retained. QSAR toxicity predictions were calculated for each chemical and each of six endpoints using ECOSAR, VEGA and the Toxicity Estimation Software Tool (T.E.S.T.) platforms. Finally, the dataset was amended with SMILES, InChIKey, pKa and logP collected from webchem and PubChem.
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| 48. |
- Aad, G., et al.
(author)
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- 2014
-
In: Physical Review C (Nuclear Physics). - 0556-2813 .- 1089-490X. ; 90:4
-
Journal article (peer-reviewed)
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| 49. |
- Aad, G., et al.
(author)
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- 2013
-
Journal article (peer-reviewed)
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| 50. |
- Aad, G., et al.
(author)
-
- 2013
-
In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 15
-
Journal article (peer-reviewed)
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