| 1. |
- Barrio, Isabel C., et al.
(författare)
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Background invertebrate herbivory on dwarf birch (Betula glandulosa-nana complex) increases with temperature and precipitation across the tundra biome
- 2017
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Ingår i: Polar Biology. - : Springer. - 0722-4060 .- 1432-2056. ; 40:11, s. 2265-2278
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Tidskriftsartikel (refereegranskat)abstract
- Chronic, low intensity herbivory by invertebrates, termed background herbivory, has been understudied in tundra, yet its impacts are likely to increase in a warmer Arctic. The magnitude of these changes is however hard to predict as we know little about the drivers of current levels of invertebrate herbivory in tundra. We assessed the intensity of invertebrate herbivory on a common tundra plant, the dwarf birch (Betula glandulosa-nana complex), and investigated its relationship to latitude and climate across the tundra biome. Leaf damage by defoliating, mining and gall-forming invertebrates was measured in samples collected from 192 sites at 56 locations. Our results indicate that invertebrate herbivory is nearly ubiquitous across the tundra biome but occurs at low intensity. On average, invertebrates damaged 11.2% of the leaves and removed 1.4% of total leaf area. The damage was mainly caused by external leaf feeders, and most damaged leaves were only slightly affected (12% leaf area lost). Foliar damage was consistently positively correlated with mid-summer (July) temperature and, to a lesser extent, precipitation in the year of data collection, irrespective of latitude. Our models predict that, on average, foliar losses to invertebrates on dwarf birch are likely to increase by 6-7% over the current levels with a 1 degrees C increase in summer temperatures. Our results show that invertebrate herbivory on dwarf birch is small in magnitude but given its prevalence and dependence on climatic variables, background invertebrate herbivory should be included in predictions of climate change impacts on tundra ecosystems.
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| 2. |
- Barrio, Isabel C., et al.
(författare)
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Publisher Correction to : Background invertebrate herbivory on dwarf birch (Betula glandulosa-nana complex) increases with temperature and precipitation across the tundra biome (vol 40, pg 2265, 2017)
- 2018
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Ingår i: Polar Biology. - : Springer. - 0722-4060 .- 1432-2056. ; 41:8, s. 1653-1654
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Tidskriftsartikel (refereegranskat)abstract
- The above mentioned article was originally scheduled for publication in the special issue on Ecology of Tundra Arthropods with guest editors Toke T. Hoye . Lauren E. Culler. Erroneously, the article was published in Polar Biology, Volume 40, Issue 11, November, 2017. The publisher sincerely apologizes to the guest editors and the authors for the inconvenience caused.
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| 3. |
- Beecham, Ashley H, et al.
(författare)
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Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
- 2013
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:11, s. 1353-60
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Tidskriftsartikel (refereegranskat)abstract
- Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
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| 4. |
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| 5. |
- Andersson, Martin, et al.
(författare)
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Seasonal variations in use and outcome of rapid antigen detection tests and cultures in pharyngotonsillitis : a register study in primary care
- 2021
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Ingår i: BMC Infectious Diseases. - : BioMed Central. - 1471-2334. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Diagnosis and treatment of pharyngotonsillitis are commonly focused on group A streptococci (GAS), although the disease is often associated with other pathogens. While the incidence of pharyngotonsillitis is known to vary with season, seasonal variations in the prevalence of potential pathogens are sparsely explored. The aim of this study was to explore any seasonal variations in the use and outcome of rapid antigen detection tests (RADTs) for GAS and throat cultures among patients diagnosed with pharyngotonsillitis in primary care.METHODS: We retrieved and combined retrospective data from the electronic medical record system and the laboratory information system in Kronoberg County, Sweden. Primary care visits resulting in a diagnosis of tonsillitis or pharyngitis were included, covering the period 2013-2016. The monthly rate of visits was measured, along with the use and outcome of RADTs for GAS and throat cultures obtained on the date of diagnosis. The variations between calendar months were then analysed.RESULTS: We found variations between calendar months, not only in the mean rate of visits resulting in a diagnosis of pharyngotonsillitis (p < 0.001), but in the mean proportion of RADTs being positive for GAS among the diagnosed (p < 0.001), and in the mean proportion of visits associated with a throat culture (p < 0.001). A lower mean rate of visits in August and September coincided with a lower proportion of RADTs being positive for GAS among them, which correlated with a higher proportion of visits associated with a throat culture.CONCLUSIONS: This study suggests that the role of GAS in pharyngotonsillitis in Sweden is less prominent in August and September than during the rest of the year.
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| 6. |
- Lindén, Elin, et al.
(författare)
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Circum-Arctic distribution of chemical anti-herbivore compounds suggests biome-wide trade-off in defence strategies in Arctic shrubs
- 2022
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Ingår i: Ecography. - : John Wiley & Sons. - 0906-7590 .- 1600-0587. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top–down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic chemical defence and leaf digestibility in resinous (Betula glandulosa, B. nana ssp. exilis) and non-resinous (B. nana ssp. nana, B. pumila) shrub birches to see how they vary among and within taxa and functional groups. Using liquid chromatography–mass spectrometry (LC–MS) metabolomic analyses and in vitro leaf digestibility via incubation in cattle rumen fluid, we analysed defence composition and leaf digestibility in 128 samples from 44 tundra locations.We found biogeographical patterns in anti-herbivore defence where mean leaf triterpene concentrations and twig resin gland density were greater in resinous taxa and mean concentrations of condensing tannins were greater in non-resinous taxa. This indicates a biome-wide trade-off between triterpene- or tannin-dominated defences. However, we also found variations in chemical defence composition and resin gland density both within and among functional groups (resinous/non-resinous) and taxa, suggesting these categorisations only partly predict chemical herbivore defence. Complex tannins were the only defence compounds negatively related to in vitro digestibility, identifying this previously neglected tannin group as having a potential key role in birch anti-herbivore defence.We conclude that circum-Arctic variation in birch anti-herbivore defence can be partly derived from biogeographical distributions of birch taxa, although our detailed mapping of plant defence provides more information on this variation and can be used for better predictions of herbivore effects on Arctic vegetation.
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| 7. |
- Suzuki, Chikako, et al.
(författare)
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Impact of the first tumor response at eight weeks on overall survival in metastatic breast cancer patients treated with first-line combination chemotherapy
- 2013
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Ingår i: Medical Oncology. - : Humana Press. - 1357-0560 .- 1559-131X. ; 30:1
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this was to determine whether the change of size observed at the first response evaluation after initiation of first-line combination chemotherapy correlates with overall survival (OS) in patients with metastatic breast cancer (MBC). The change in size of tumors derived from measurements according to Response Evaluation Criteria In Solid Tumors (RECIST) at the first evaluation on computed tomography (CT) was obtained from a multicenter, randomized phase III trial ("TEX trial," n = 287) comparing treatment with a combination of epirubicin and paclitaxel alone or with capecitabine (TEX). Cox regression and Kaplan-Meier analyses were performed to evaluate the correlations between the first change in tumor size, response according to RECIST and OS. Data from CT evaluations of 233 patients were available. Appearance of new lesions or progression of non-target lesions (new/non-target) indicated short OS by univariable regression analysis (HR 3.76, 95 % CI 1.90-7.42, p andlt; 0.001). A decrease by andgt;30 % at this early time point was prognostic favorable (HR 0.69, 95 % CI 0.49-0.98, p = 0.04) and not significantly less than the best overall response according to RECIST. After adjustment for previous adjuvant treatment and the treatment given within the frame of the randomized trial, OS was still significantly shorter in patients with new/non-target lesions after a median 8 weeks of treatment (HR 4.41, 95 % CI 2.74-7.11, p andlt; 0.001). Disease progression at the first evaluation correlates with OS in patients with MBC treated with first-line combination chemotherapy. The main reason for early disease progression was the appearance of new lesions or progression of non-target lesions. These patients had poor OS even though more lines of treatment were available. Thus, these factors should be focused on in the response evaluations besides tumor size changes.
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| 8. |
- Andersson, Madelen, et al.
(författare)
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Outbreak of a beta-lactam resistant non-typeable Haemophilus influenzae sequence type 14 associated with severe clinical outcomes
- 2015
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Ingår i: BMC Infectious Diseases. - : BioMed Central. - 1471-2334. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: During October 2011 several residents and staff members at a long-term care facility (LTCF) for elderly fell ill with respiratory symptoms. Several of the residents required hospitalization and one died. Non-typeable Haemophilus influenzae (NTHi) was identified as the causative pathogen. Methods: A descriptive analysis of the outbreak and countermeasures was performed. For each identified bacterial isolate implied in the outbreak, standard laboratory resistance testing was performed, as well as molecular typing and phylogenetic analysis. Results: The identified H. influenzae was beta-lactamase negative but had strikingly high MIC-values of ampicillin, cefuroxime and cefotaxime. All isolates displayed the same mutation in the ftsI gene encoding penicillin-binding protein (PBP) 3, and all but one were identified as sequence type 14 by Multilocus Sequence Typing (MLST). In total 15 individuals in connection to the LTCF; 8 residents, 6 staff members and one partner to a staff member were colonized with the strain. Conclusion: This report illustrates the existence of non-typeable H. influenzae with high virulence, and furthermore emphasizes the importance of continuous surveillance of possible outbreaks in health care facilities and prompt measures when outbreaks occur.
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| 9. |
- Asayama, Shinichiro, et al.
(författare)
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Three institutional pathways to envision the future of the IPCC
- 2023
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Ingår i: Nature Climate Change. - : Nature Portfolio. - 1758-678X .- 1758-6798. ; 13:9, s. 877-880
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Tidskriftsartikel (refereegranskat)abstract
- The IPCC has been successful at building its scientific authority, but it will require institutional reform for staying relevant to new and changing political contexts. Exploring a range of alternative future pathways for the IPCC can help guide crucial decisions about redefining its purpose.
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| 10. |
- Bengtsson, Stina, et al.
(författare)
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Sequence types and plasmid carriage of uropathogenic Escherichia coli devoid of phenotypically detectable resistance
- 2012
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Ingår i: Journal of Antimicrobial Chemotherapy. - : Oxford University Press (OUP). - 0305-7453 .- 1460-2091. ; 67:1, s. 69-73
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Tidskriftsartikel (refereegranskat)abstract
- Objectives Plasmids play a major role in the dissemination of antibiotic resistance, and several studies have shown the association between specific resistance mechanisms and certain plasmid types and/or Escherichia coli lineages. This study describes the distribution of plasmids, replicon types, sequence types (STs) and ST complexes (STCs) of E. coli devoid of phenotypic resistance to 24 antibiotics. Methods Eighty E. coli isolates from urinary tract infections from four European countries were selected because of their lack of phenotypically detectable antibiotic resistance. The isolates were characterized to the phylogenetic group level using PCR and to ST by multilocus sequence typing. Plasmid carriage was assessed using S1 nuclease PFGE profiling and PCR-based replicon typing. Results Plasmids were detected in only 38/80 (47%) of the isolates; one (n = 18), two (n = 14), three (n = 5) and four (n = 1) plasmids. Six different replicon types were identified, the most common being a combination of IncFII and IncFIB. Most isolates belonged to phylogenetic group B2 and STC73 (n = 20), STC95 (n = 7) and ST420 (n = 6). A high proportion of STC73 isolates (75%) was devoid of plasmids. No association could be found between specific STs and replicon type. Conclusions A large proportion of E. coli strains phenotypically devoid of antibiotic resistance were plasmid naive. Those isolates that harboured plasmids displayed replicon types similar to those of resistant isolates, but the distributions of STs and STCs were different. This may indicate chromosomally encoded mechanisms important for the stabilization of plasmids harbouring antibiotic resistance.
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| 11. |
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| 12. |
- Björk, Helena, et al.
(författare)
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Tonsillar colonisation of Fusobacterium necrophorum in patients subjected to tonsillectomy
- 2015
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Ingår i: BMC Infectious Diseases. - London, United Kingdom : BioMed Central. - 1471-2334. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Fusobacterium necrophorum is a well-known cause of Lemirre's disease and accumulating evidence support its pathogenic role in peritonsillar abscess while its role in recurrent and chronic tonsillitis is uncertain. The objective of this study was to assess the prevalence of oropharyngeal colonisation with F. necrophorum and Beta-haemolytic streptococci in a cohort of patients scheduled for tonsillectomy due to recurrent or persistent throat pain, and to evaluate the dynamics of colonisation with repeated sampling during a follow-up time of 6 to 8 months. Methods: Fifty-seven (57) patients aged 15-52 years scheduled for tonsillectomy due to chronic/recurrent tonsillitis or recurrent peritonsillar abscess were included. Throat swabs for the detection of F. necrophorum and Beta-haemolytic streptococci and clinical data was collected at inclusion, at the time of surgery and 6 to 8 months after surgery. Statistical analysis was performed using the Chi-square, Fisher's exact and Mc Nemar tests. Results: Fusobacterium necrophorum was found in 28, 30 and 16 % of the patients at inclusion, surgery and follow up respectively. The corresponding results for beta-haemolytic streptococci were 5, 9 and 5 %. Patients colonised with F. necrophorum at follow-up, after tonsillectomy, were equally relieved from their previous throat pain as non-colonised patients. Looking at individual patients, the culture results for F. necrophorum varied over time, indicating a transient colonisation. Conclusion: Fusobacterium necrophorum was frequently found in throat cultures in this cohort of patients with recurrent or chronic throat pain leading to tonsillectomy. Colonisation was equally frequent in the asymptomatic cohort post-tonsillectomy, indicating that F. necrophorum is not alone causative of the symptoms. In an individual perspective, colonisation with F. necrophorum was transient over time.
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| 13. |
- Brolund, Alma, et al.
(författare)
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Molecular Characterisation of Trimethoprim Resistance in Escherichia coli and Klebsiella pneumoniae during a 2 year intervention on Trimethoprim use
- 2010
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:2, s. e9233-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Trimethoprim resistance is increasing in Enterobacteriaceae. In 2004-2006 an intervention on trimethoprim use was conducted in Kronoberg County, Sweden, resulting in 85% reduction in trimethoprim prescriptions. We investigated the distribution of dihydrofolate reductase (dfr)-genes and integrons in Escherichia coli and Klebsiella pneumoniae and the effect of the intervention on this distribution. METHODOLOGY/PRINCIPAL FINDINGS: Consecutively isolated E. coli (n = 320) and K. pneumoniae (n = 54) isolates phenotypically resistant to trimethoprim were studied. All were investigated for the presence of dfrA1, dfrA5, dfrA7, dfrA8, dfrA12, dfrA14, dfrA17 and integrons class I and II. Isolates negative for the seven dfr-genes (n = 12) were also screened for dfr2d, dfrA3, dfrA9, dfrA10, dfrA24 and dfrA26. These genes accounted for 96% of trimethoprim resistance in E. coli and 69% in K. pneumoniae. The most prevalent was dfrA1 in both species. This was followed by dfrA17 in E. coli which was only found in one K. pneumoniae isolate. Class I and II Integrons were more common in E. coli (85%) than in K. pneumoniae (57%). The distribution of dfr-genes did not change during the course of the 2-year intervention. CONCLUSIONS/SIGNIFICANCE: The differences observed between the studied species in terms of dfr-gene and integron prevalence indicated a low rate of dfr-gene transfer between these two species and highlighted the possible role of narrow host range plasmids in the spread of trimethoprim resistance. The stability of dfr-genes, despite large changes in the selective pressure, indirectly suggests a low fitness cost of dfr-gene carriage.
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| 14. |
- Campillay Lagos, Amaya, 1989-, et al.
(författare)
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Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches
- 2022
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003-2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0-5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.
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| 15. |
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| 16. |
- Fagerström, Anna, 1980-, et al.
(författare)
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Comparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters
- 2019
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Ingår i: PLOS ONE. - : PLOS. - 1932-6203. ; 14:11
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Tidskriftsartikel (refereegranskat)abstract
- Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli have been reported in natural environments, and may be released through wastewater. In this study, the genetic relationship between ESBL-producing E. coli collected from patient urine samples (n = 45, both hospitalized patients and out-patients) and from environmental water (n = 82, from five locations), during the same time period, was investigated. Three independent water samples were collected from the municipal wastewater treatment plant, both incoming water and treated effluent water; the receiving river and lake; and a bird sanctuary near the lake, on two different occasions. The water was filtered and cultured on selective chromID ESBL agar plates in order to detect and isolate ESBL-producing E. coli. Illumina whole genome sequencing was performed on all bacterial isolates (n = 127). Phylogenetic group B2 was more common among the clinical isolates than the environmental isolates (44.4% vs. 17.1%, p < 0.01) due to a significantly higher prevalence of sequence type (ST) 131 (33.3% vs. 13.4%, p < 0.01). ST131 was, however, one of the most prevalent STs among the environmental isolates. There was no significant difference in diversity between the clinical isolates (DI 0.872 (0.790-0.953)) and the environmental isolates (DI 0.947 (0.920-0.969)). The distribution of ESBL genes was similar: blaCTX-M-15 dominated, followed by blaCTX-M-14 and blaCTX-M-27 in both the clinical (60.0%, 8.9%, and 6.7%) and the environmental isolates (62.2%, 12.2%, and 8.5%). Core genome multi-locus sequence typing showed that five environmental isolates, from incoming wastewater, treated wastewater, Svartån river and Hjälmaren lake, were indistinguishable or closely related (≤10 allele differences) to clinical isolates. Isolates of ST131, serotype O25:H4 and fimtype H30, from the environment were as closely related to the clinical isolates as the isolates from different patients were. This study confirms that ESBL-producing E. coli are common in the aquatic environment even in low-endemic regions and suggests that wastewater discharge is an important route for the release of ESBL-producing E. coli into the aquatic environment.
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| 17. |
- Fagerström, Anna, 1980-
(författare)
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Long-term molecular epidemiology of extended-spectrum β-lactamase producing Escherichia coli in a low-endemic setting
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Escherichia coli is a commensal inhabitant in the gastro-intestinal tract of humans and animals but it is also the most common bacterial species causing urinary tract infection, which ranges in severity from distal cystitis to urosepsis and septic shock. During the past decades, the prevalence of antibiotic resistant E. coli has increased worldwide. Extended-spectrum β-lactamases (ESBL) causes resistance to β-lactam antibiotics, the most widely used class of antibiotics. The genes encoding ESBL, bla, are usually carried on conjugative plasmids, which can be transferred between different bacterial lineages and different species. These plasmids frequently also carry resistance genes to additional antibiotic classes, and ESBL-producing E. coli are therefore often multidrug-resistant. The aim of this thesis was to describe the long-term molecular epidemiology of ESBL-producing E. coli in Örebro County during the time when they first started to emerge. In addition, potential transmission to the environment was investigated by performing a comparative analysis on ESBL-producing E. coli isolated from patients and from the aquatic environment in Örebro city. In general, the E. coli population was genetically diverse, but the pandemic lineage ST131, first identified in 2004, appears to have been responsible for the dramatic increase of CTX-M-15-producing E.coli observed during the late 2000s. CTX-M-15 was the most prevalent ESBL-type followed by CTX-M-14 and these genes were mainly found on plasmids belonging to the IncF or IncI1 families. Continuous horizontal transmission of IncI1 ST31 and ST37 plasmids between diverse E. coli lineages have also contributed to the dissemination of blaCTX-M-15 in Örebro County. Extended spectrum β-lactamase-producing E. coli were found to be common in the aquatic environment in Örebro city and E. coli lineages genetically similar to those causing infections in humans were present in environmental waters indicating that transmission of ESBL-producing E. colifrom humans to the aquatic environment likely has occurred.
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| 18. |
- Finné, Martin, et al.
(författare)
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Can XRF scanning of speleothems be used as a non-destructive method to identify paleoflood events in caves?
- 2015
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Ingår i: International Journal of Speleology. - 0392-6672 .- 1827-806X. ; 44:1, s. 17-23
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a novel, quick and non-destructive method for tracing flood events in caves through the analysis of a stalagmite thick section with an XRF core scanner. The analyzed stalagmite has multiple horizons of fine sediments from past flood events intercalated with areas of cleaner calcite. Flood events detected from the elemental XRF core scanning data show good agreement with the position of flood horizons identified in petrographic thin sections. The geochemical composition of the individual flood layers shows that in certain cases the clay horizons had a distinct geochemical fingerprint suggesting that it may be possible to distinguish individual flood layers based on their geochemistry. This presents the possibility for using flood events as marker horizons to chronologically tie different speleothems in a cave to each other.
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| 19. |
- Finné, Martin, et al.
(författare)
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Climate in the eastern Mediterranean, and adjacent regions, during the past 6000 years - A review
- 2011
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Ingår i: Journal of Archaeological Science. - : Elsevier BV. - 0305-4403 .- 1095-9238. ; 38:12, s. 3153-3173
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Forskningsöversikt (refereegranskat)abstract
- The eastern Mediterranean, with its long archaeological and historical records, provides a unique opportunity to study human responses to climate variability. We review paleoclimate data and reconstructions from the region with a focus on the last 6000 years. We aim to provide an up-to-date source of information on climate variability and to outline present limitations and future opportunities. The review work is threefold: (1) literature review, (2) spatial and temporal analysis of proxy records, and (3) statistical estimation of uncertainties in present paleoclimate reconstructions (temperature, C). On a regional scale the review reveals a wetter situation from 6000 to 5400 yrs BP (note: all ages in this paper are in calibrated years before present (i.e. before 1950), abbreviated yrs BP, unless otherwise stated). This is followed by a less wet period leading up to one of fully-developed aridity from c. 4600 yrs BP. There is a need for more high-resolution paleoclimate records, in order to (i) better understand regional patterns and trends versus local climate variability and to (ii) fill the gap of data from some regions, such as the Near East, Greece and Egypt. Further, we evaluate the regional occurrence of a proposed widespread climate event at 4200 yrs BP. This proposed climate anomaly has been used to explain profound changes in human societies at different locations in the region around this time. We suggest that although aridity was widespread around 4200 yrs BP in the eastern Mediterranean region, there is not enough evidence to support the notion of a climate event with rapidly drying conditions in this region.
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| 20. |
- Finné, Martin, 1981-
(författare)
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Climate in the eastern Mediterranean during the Holocene and beyond – A Peloponnesian perspective
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis contributes increased knowledge about climate variability during the late Quaternary in the eastern Mediterranean. Results from a paleoclimate review reveal that regional wetter conditions from 6000 to 5400 years BP were replaced by a less wet period from 5400 to 4600 years BP and to fully arid conditions around 4600 years BP. The data available, however, show that there is not enough evidence to support the notion of a widespread climate event with rapidly drying conditions in the region around 4200 years ago. The review further highlights the lack of paleoclimate data from the archaeologically rich Peloponnese Peninsula. This gap is addressed in this thesis by the provision of new paleoclimate records from the Peloponnese. One stalagmite from Kapsia Cave and two stalagmites from Glyfada Cave were dated and analyzed for stable oxygen (δ18O) and carbon (δ13C) isotopes. The Glyfada record covers a period from ~78 ka to ~37 ka and shows that the climate in this region responded rapidly to changes in temperatures over Greenland. During Greenland stadial (interstadial) conditions colder (warmer) and drier (wetter) conditions are reflected by depleted (enriched) δ13C-values in the speleothems. The Kapsia record covers a period from ~2900 to ~1100 years BP. A comparison between the modern stalagmite top isotopes and meteorological data shows that a main control on stalagmite δ18O is wet season precipitation amount. The δ18O record from Kapsia indicates cyclical humidity changes of close to 500 years, with rapid shifts toward wetter conditions followed by slowly developing aridity. Superimposed on this signal is a centennial signal of precipitation variability. A second speleothem from Kapsia with multiple horizons of fine sediments from past flood events intercalated with the calcite is used to develop a new, quick and non-destructive method for tracing flood events in speleothems by analyzing a thick section with an XRF core scanner.
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| 21. |
- Finné, Martin, et al.
(författare)
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Speleothem evidence for late Holocene climate variability and floods in Southern Greece
- 2014
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Ingår i: Quaternary Research. - : Cambridge University Press (CUP). - 0033-5894 .- 1096-0287. ; 81:2, s. 213-227
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Tidskriftsartikel (refereegranskat)abstract
- We present stable isotope data (delta O-18, delta C-13) from a detrital rich stalagmite from Kapsia Cave, the Peloponnese, Greece. The cave is rich in archeological remains and there are reasons to believe that flooding of the cave has directly affected humans using the cave. Using a combination of U-Th and C-14 dating to constrain a site-specific correction factor for (Th-232/U-238) detrital molar ratio, a linear age model was constructed. The age model shows that the stalagmite grew during the period from ca. 950 BC to ca. AD 830. The stable oxygen record from Kapsia indicates cyclical changes of close to 500 yr in precipitation amount, with rapid shifts towards wetter conditions followed by slowly developing aridity. Superimposed on this signal, wetter conditions are inferred around 850, 700, 500 and 400-100 BC, and around AD 160-300 and AD 770; and driest conditions are inferred to have occurred around 450 BC, AD 100-150 and AD 650. Detrital horizons in the stalagmite indicate that three major floods took place in the cave at 500 BC, 70 BC and AD 450. The stable carbon isotope record reflects changes in biological activity being a result of both climate and human activities. (c) 2014 University of Washington.
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| 22. |
- Forsare, Carina, et al.
(författare)
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Non-linear transformations of age at diagnosis, tumor size, and number of positive lymph nodes in prediction of clinical outcome in breast cancer
- 2018
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Ingår i: BMC Cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Prognostic factors in breast cancer are often measured on a continuous scale, but categorized for clinical decision-making. The primary aim of this study was to evaluate if accounting for continuous non-linear effects of the three factors age at diagnosis, tumor size, and number of positive lymph nodes improves prognostication. These factors will most likely be included in the management of breast cancer patients also in the future, after an expected implementation of gene expression profiling for adjuvant treatment decision-making. Methods: Four thousand four hundred forty seven and 1132 women with primary breast cancer constituted the derivation and validation set, respectively. Potential non-linear effects on the log hazard of distant recurrences of the three factors were evaluated during 10 years of follow-up. Cox-models of successively increasing complexity: dichotomized predictors, predictors categorized into three or four groups, and predictors transformed using fractional polynomials (FPs) or restricted cubic splines (RCS), were used. Predictive performance was evaluated by Harrell's C-index. Results: Using FP-transformations, non-linear effects were detected for tumor size and number of positive lymph nodes in univariable analyses. For age, non-linear transformations did, however, not improve the model fit significantly compared to the linear identity transformation. As expected, the C-index increased with increasing model complexity for multivariable models including the three factors. By allowing more than one cut-point per factor, the C-index increased from 0.628 to 0.674. The additional gain, as measured by the C-index, when using FP- or RCS-transformations was modest (0.695 and 0.696, respectively). The corresponding C-indices for these four models in the validation set, based on the same transformations and parameter estimates from the derivation set, were 0.675, 0.700, 0.706, and 0.701. Conclusions: Categorization of each factor into three to four groups was found to improve prognostication compared to dichotomization. The additional gain by allowing continuous non-linear effects modeled by FPs or RCS was modest. However, the continuous nature of these transformations has the advantage of making it possible to form risk groups of any size.
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| 23. |
- Gaines, Hans, et al.
(författare)
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Six-week follow-up after HIV-1 exposure: a position statement from the Public Health Agency of Sweden and the Swedish Reference Group for Antiviral Therapy
- 2016
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Ingår i: Infectious Diseases. - : Informa UK Limited. - 2374-4235 .- 2374-4243. ; 48:2, s. 93-98
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Forskningsöversikt (refereegranskat)abstract
- In 2014 the Public Health Agency of Sweden and the Swedish Reference Group for Antiviral Therapy (RAV) conducted a review and analysis of the state of knowledge on the duration of follow-up after exposure to human immunodeficiency virus (HIV). Up until then a follow-up of 12 weeks after exposure had been recommended, but improved tests and new information on early diagnosis motivated a re-evaluation of the national recommendations by experts representing infectious diseases and microbiology, county medical officers, the RAV, the Public Health Agency, and other national authorities. Based on the current state of knowledge the Public Health Agency of Sweden and the RAV recommend, starting in April 2015, a follow-up period of 6 weeks after possible HIV-1 exposure, if HIV testing is performed using laboratory-based combination tests detecting both HIV antibody and antigen. If point-of-care rapid HIV tests are used, a follow-up period of 8 weeks is recommended, because currently available rapid tests have insufficient sensitivity for detection of HIV-1 antigen. A follow-up period of 12 weeks is recommended after a possible exposure for HIV-2, since presently used assays do not include HIV-2 antigens and only limited information is available on the development of HIV antibodies during early HIV-2 infection. If pre- or post-exposure prophylaxis is administered, the follow-up period is recommended to begin after completion of prophylaxis. Even if infection cannot be reliably excluded before the end of the recommended follow-up period, HIV testing should be performed at first contact for persons who seek such testing.
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| 24. |
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| 25. |
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| 26. |
- Göransson, J., et al.
(författare)
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Performance of a System for Rapid Phenotypic Antimicrobial Susceptibility Testing of Gram-Negative Bacteria Directly from Positive Blood Culture Bottles
- 2023
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Ingår i: Journal of Clinical Microbiology. - : American Society for Microbiology. - 0095-1137 .- 1098-660X. ; 61:3
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Tidskriftsartikel (refereegranskat)abstract
- The rapid administration of optimal antimicrobial treatment is paramount for the treatment of bloodstream infections (BSIs), and rapid antimicrobial susceptibility testing (AST) results are essential. Q-linea has developed the ASTar system, a rapid phenotypic AST device. Here, we report the performance of the ASTar BC G- (Gram-negative) kit when assessed according to the ISO 20776-2:2007 standard for performance evaluation of in vitro diagnostic AST devices. The evaluated ASTar BC G- kit uses a broad panel of 23 antimicrobials for the treatment of BSIs caused by Gram-negative fastidious and nonfastidious bacteria across a range of 6 to 14 2-fold dilutions, including cefoxitin as a screening agent for AmpC-producing Enterobacterales. The ASTar system processes blood culture samples to generate data on MICs and susceptible, intermediate, or resistant (SIR) category. The automated protocol includes concentration determination and concentration adjustment to enable a controlled inoculum, followed by broth microdilution (BMD) and microscopy performed continuously to generate MIC values within approximately 6 h once the test is run on the ASTar system. The performance of the ASTar system was assessed against the ISO 20776-2:2007 standard BMD reference method. Testing was performed across three sites, with results from 412 contrived blood cultures and 74 fresh clinical blood cultures. The ASTar system was also tested for reproducibility, with triplicate testing of 11 strains. The accuracy study comprised 8,650 data points of bacterium-antimicrobial tests. The ASTar system demonstrated an overall essential agreement (EA) of 95.8% (8,283/8,650) and a categorical agreement (CA) of 97.6% (8,433/8,639) compared to the reference BMD method. The overall rate of major discrepancies (MDs) was 0.9% (62/6,845), and that of very major discrepancies (VMDs) was 2.4% (30/1,239). This study shows that the ASTar system delivers reproducible results with overall EA and CA of >95%.
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| 27. |
- Haars, Jonathan, et al.
(författare)
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Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023
- 2023
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Ingår i: Microorganisms. - : MDPI. - 2076-2607. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- Monoclonal antibodies (mAbs) are an important treatment option for COVID-19 caused by SARS-CoV-2, especially in immunosuppressed patients. However, this treatment option can become ineffective due to mutations in the SARS-CoV-2 genome, mainly in the receptor binding domain (RBD) of the spike (S) protein. In the present study, 7950 SARS-CoV-2 positive samples from the Uppsala and Örebro regions of central Sweden, collected between March 2022 and May 2023, were whole-genome sequenced using amplicon-based sequencing methods on Oxford Nanopore GridION, Illumina MiSeq, Illumina HiSeq, or MGI DNBSEQ-G400 instruments. Pango lineages were determined and all single nucleotide polymorphism (SNP) mutations that occurred in these samples were identified. We found that the dominant sublineages changed over time, and mutations conferring resistance to currently available mAbs became common. Notable ones are R346T and K444T mutations in the RBD that confer significant resistance against tixagevimab and cilgavimab mAbs. Further, mutations conferring a high-fold resistance to bebtelovimab, such as the K444T and V445P mutations, were also observed in the samples. This study highlights that resistance mutations have over time rendered currently available mAbs ineffective against SARS-CoV-2 in most patients. Therefore, there is a need for continued surveillance of resistance mutations and the development of new mAbs that target more conserved regions of the RBD.
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| 28. |
- Haglund, Sofie, 1975-, et al.
(författare)
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CXCL13 in laboratory diagnosis of Lyme neuroborreliosis-the performance of the recomBead and ReaScan CXCL13 assays in human cerebrospinal fluid samples
- 2022
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Ingår i: European Journal of Clinical Microbiology and Infectious Diseases. - : Springer. - 0934-9723 .- 1435-4373. ; 41:1, s. 175-179
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Tidskriftsartikel (refereegranskat)abstract
- The chemokine CXCL13 is used as complement to serology in the diagnostics of Lyme neuroborreliosis (LNB). We evaluated and compared the semi-quantitative, cassette-based ReaScan CXCL13 assay with the quantitative recomBead CXCL13 assay using a collection of 209 cerebrospinal fluid samples. The categorical agreement between results interpreted as negative, grey zone, and positive by the two methods was 87%. The diagnostic sensitivity was higher using the recomBead assay, whereas specificity was higher using ReaScan. Few manual steps, and a short turn-around time with no batching of samples makes the ReaScan CXCL13 assay an attractive complement to serology in the diagnostics of LNB.
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| 29. |
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| 30. |
- Hedin, Katarina, et al.
(författare)
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The aetiology of pharyngotonsillitis in adolescents and adults : Fusobacterium necrophorum is commonly found
- 2015
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Ingår i: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X .- 1469-0691. ; 21:3
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Tidskriftsartikel (refereegranskat)abstract
- Sore throat is common in primary healthcare. Aetiological studies have focused on the presence of a limited number of pathogens. The aim of the present study was to investigate the presence of a wide range of bacteria and viruses, including Fusobacterium necrophorum, in patients with pharyngotonsillitis and in asymptomatic controls. A prospective case control study was performed in primary healthcare in Kronoberg County, Sweden. Patients (n = 220) aged 15 to 45 years with a suspected acute pharyngotonsillitis, and controls (n = 128), were included. Nasopharyngeal and throat swabs were analysed for beta-hemolytic streptococci, F. necrophorum, Mycoplasma pneumoniae, and Chlamydophila pneumoniae, and 13 respiratory viruses. Serum samples were analysed for antibodies to Epstein-Barr virus. The patient history and symptoms, including Centor score, were analysed in relation to pathogens. In 155/220 (70.5%) of the patients, as compared to 26/128 (20.3%) of the controls (p < 0.001), at least one microorganism was found. Group A streptococci, F. necrophorum, and influenza B virus were the three most common findings, and all significantly more common in patients than in controls (p < 0.001, p 0.001, and p 0.002, respectively). Patients with F. necrophorum only (n = 14) displayed a lower Centor score than patients with Group A streptococcus only (n = 46), but a higher score than patients with influenza B, other viruses, or no potential pathogen (Kruskal-Wallis p < 0.001). A pathogen was detected in 70% of the patients, displaying a wide range of pathogens contributing to the aetiology of pharyngotonsillitis. This study supports F. necrophorum as one of the pathogens to be considered in the aetiology of pharyngotonsillitis. Clinical Microbiology and Infection (C) 2014 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. Open access under CC BY-NC-ND license.
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| 31. |
- Hendrikx, Tijn, et al.
(författare)
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Atrial fibrillation among patients under investigation for suspected obstructive sleep apnea
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:2
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Tidskriftsartikel (refereegranskat)abstract
- STUDY OBJECTIVES: Obstructive sleep apnea is common among patients with atrial fibrillation, but the prevalence and risk factors for atrial fibrillation among patients who are being investigated on suspicion of sleep apnea are not well known. The aim of the study was to estimate the prevalence of atrial fibrillation among patients investigated for suspected obstructive sleep apnea and to identify risk factors for atrial fibrillation among them.METHODS: The prevalence of atrial fibrillation was investigated among 201 patients referred for suspected obstructive sleep apnea. Patients without known atrial fibrillation were investigated with a standard 12-lead ECG at hospital and short intermittent handheld ECG recordings at home, during 14 days.RESULTS: Atrial fibrillation occurred in 13 of 201 subjects (6.5%), and in 12 of 61 men aged 60 years and older (20%). The prevalence of atrial fibrillation increased with sleep apnea severity (p = 0.038). All patients with atrial fibrillation were men and all had sleep apnea. Age 60 or older, the occurrence of central sleep apnea and diabetes mellitus were independent risk factors for atrial fibrillation after adjustments for body mass index, gender, sleep apnea and cardiovascular disease.CONCLUSIONS: Atrial fibrillation is common among subjects referred for sleep apnea investigation and the prevalence of atrial fibrillation increases with sleep apnea severity. Independent risk factors for atrial fibrillation among patients investigated for suspected obstructive sleep apnea include the occurrence of coexisting central sleep apnea, age 60 years or older and diabetes mellitus.
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| 32. |
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| 33. |
- Henning, Claes, et al.
(författare)
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Rekommenderade metoder Diagnostik av infektioner i blod orsakade av bakterier och svamp
- 2024
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- I detta dokument beskrivs rekommenderade metoder för blododling inkluderat fungemi(svampinfektion i blod) samt metodik för diagnostik av endokardit och misstanke om infektion relaterad till kärlkatetrar. Rekommendationerna är baserade på internationella riktlinjer och relevant vetenskaplig litteratur. Där det finns icke tillräcklig vetenskapligt stöd har arbetsgruppen antingen avstått från en rekommendation eller givit en rekommendation baserad på de ingående medlemmarnas erfarenhet och kunnande.
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| 34. |
- Hu, Xianfeng, et al.
(författare)
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Materials Properties and Liquid Flow in the Hearth of the Experimental Blast Furnace
- 2019
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Ingår i: Metals. - : MDPI. - 2075-4701. ; 9:5
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Tidskriftsartikel (refereegranskat)abstract
- The materials’ properties in the hearth of the blast furnace are very crucial for the hearthconditions. In this study, a number of coke, slag, metal, and aggregate samples were collected fromthe hearth of the LKAB’s experimental blast furnace (EBF). Subsequently, the coke, slag, and metalsamples were chemically analyzed by X-ray fluorescence (XRF) or optical emission spectrometer(OES); the aggregate samples were analyzed by scanning electron microscope combined withenergy-dispersive X-ray spectroscopy (SEM/EDS). The possible flow field of the liquid in the EBFhearth before quenching is depicted according to Cu tracers in the metal samples. Selected elementsin the coke, slag, and metal were mapped for two sampling layers in the hearth, as well as in one crosssection of the flow field. The results indicate that there exists an area beneath, and in front of, tuyere 3,where the flow resistance of the liquid was high. The high flow resistance contributed to the formationof a cold zone in the close-to-wall region and at the bottom of the EBF hearth. The temperaturedistribution in the EBF hearth has significant impacts on the chemical properties of the materials indierent positions of the EBF hearth, as well as on the radial and vertical distributions of certainelements/components.
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| 35. |
- Idelevich, E. A., et al.
(författare)
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Microbiological diagnostics of bloodstream infections in Europe-an ESGBIES survey
- 2019
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Ingår i: Clinical Microbiology and Infection. - : Elsevier. - 1198-743X .- 1469-0691. ; 25:11, s. 1399-1407
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: High-quality diagnosis of bloodstream infections (BSI) is important for successful patient management. As knowledge on current practices of microbiological BSI diagnostics is limited, this project aimed to assess its current state in European microbiological laboratories.Methods: We performed an online questionnaire-based cross-sectional survey comprising 34 questions on practices of microbiological BSI diagnostics. The ESCMID Study Group for Bloodstream Infections, Endocarditis and Sepsis (ESGBIES) was the primary platform to engage national coordinators who recruited laboratories within their countries.Results: Responses were received from 209 laboratories in 25 European countries. Although 32.5% (68/209) of laboratories only used the classical processing of positive blood cultures (BC), two-thirds applied rapid technologies. Of laboratories that provided data, 42.2% (78/185) were able to start incubating BC in automated BC incubators around-the-clock, and only 13% (25/192) had established a 24-h service to start immediate processing of positive BC. Only 4.7% (9/190) of laboratories validated and transmitted the results of identification and antimicrobial susceptibility testing (AST) of BC pathogens to clinicians 24 h/day. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry from briefly incubated sub-cultures on solid media was the most commonly used approach to rapid pathogen identification from positive BC, and direct disc diffusion was the most common rapid AST method from positive BC.Conclusions: Laboratories have started to implement novel technologies for rapid identification and AST for positive BC. However, progress is severely compromised by limited operating hours such that current practice of BC diagnostics in Europe complies only partly with the requirements for optimal BSI management.
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| 36. |
- Ingberg, Edvin, 1988-, et al.
(författare)
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16S metagenomics for bacterial identification versus cultures in acute pharyngotonsillitis patients and controls
- 2018
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Konferensbidrag (refereegranskat)abstract
- Background: Sore throat/pharyngotonsillitis is a very common condition. While most cases are viral, the primary bacterial pathogen is group A beta-hemolytic streptococcus (Streptococcus pyogenes). Further, Fusobacterium necrophorum has over the last decade attracted attention. rnrnSequence-based techniques continue to gain ground in medical microbiology. To describe the microbiota in a sample, either the whole genomes (metagenomics) or marker genes/genomic regions (metataxonomics), such as the 16S rRNA gene, can be sequenced. Some studies have investigated how findings from these methods correspond to conventional microbiological methods for infectious diseases, such as cultures. However, no previous study has approached the condition acute pharyngotonsillitis this way.Methods: Throat samples from patients with acute sore throat (n=129) and controls (n=86), both groups aged 15-45, were collected. DNA was extracted and the V3-V4 regions of the 16S rRNA genes were amplified using PCR. After normalization based on fragment analysis, and size selection with Ampure beads and PCR against adapter sequences coupled to the V3-V4 fragments, clonal amplifiction was performed with isothermal PCR. Finally, sequencing was performed on the Ion Torrent S5 XL. The SILVA database was used for taxonomic classification and the results were compared to culture findings for S. pyogenes and F. necrophorum, using Mann Whitney U tests.Results: Among the 215 samples, 46 patients and 1 of the controls were culture-positive for S. pyogenes. For F. necrophorum, 20 patients and 3 controls were culture-positive. Seven of the samples were culture-positive for both S. pyogenes and F. necrophorum. rnrnIn the metataxonomic analysis, S. pyogenes were significantly more abundant among patients than controls (p=0.0046), and in samples culture-positive for S. pyogenes, compared to culture-negative (p<0.0001).The percent of reads representing F. necrophorum were significantly higher in patients compared to controls (p<0.001), as well as in culture-positive samples compared to culture-negative (p<0.0001). rnrnAlthough significant differences between culture-positive and culture-negative samples were seen, even among culture-positive samples the abundance of S. pyogenes or F. necrophorum were on average low (2,1% and 10,6%, respectively) and with large variation (0-49,8% and 0-76,1%, respectively).Conclusions: Findings from a metataxonomic 16S rRNA gene analysis differed regarding species of interest between groups based on symptoms of a sore throat or culture findings. However, the results were heterogeneous and difficult to interpret for a single sample.
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| 37. |
- Ingberg, Edvin, 1988-, et al.
(författare)
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RT-PCR cycle threshold value in combination with visual scoring of chest computed tomography at hospital admission predicts outcome in COVID-19
- 2022
-
Ingår i: Infectious Diseases. - : Taylor & Francis. - 2374-4235 .- 2374-4243. ; 54:6, s. 431-440
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: COVID-19 has a most variable prognosis. Several risk factors for an unfavourable outcome have been identified including extensive lung involvement on chest CT and high viral load estimated by RT-PCR cycle threshold (Ct) values. We investigated Ct value for outcome prediction, relation between Ct value and extent of lung involvement on chest CT and the combination of Ct value and chest CT lung involvement to predict outcome in COVID-19.METHODS: Population-based retrospective study on all patients (n = 286) hospitalised for COVID-19 in Örebro Region, Sweden, between 1 March and 31 August 2020. Nasopharyngeal samples and chest CT at hospital admission were evaluated in relation to outcome of COVID-19.RESULTS: Both Ct value and chest CT lung involvement were independently associated with risk for ICU admission or death. Lung involvement was superior as a single parameter, but addition of Ct value increased the prediction performance. Ct value was especially useful to identify patients with high risk for severe disease despite limited lung involvement.CONCLUSIONS: The addition of RT-PCR Ct value to the assessment of lung involvement on chest CT adds valuable prognostic information in COVID-19. We believe that this information can be used to support clinical decision-making when managing COVID-19 patients.
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| 38. |
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| 39. |
- Johansson, Åsa, et al.
(författare)
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The detection and verification of carbapenemases using ertapenem and Matrix Assisted Laser Desorption Ionization-Time of Flight
- 2014
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Ingår i: BMC Microbiology. - : BioMed Central. - 1471-2180. ; 14
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The increase in carbapenemase producing Enterobacteriaceae and Pseudomonas aeruginosa is a significant threat to modern medicine. A rapid detection of carbapenemase production in Klebsiella pneumoniae and Pseudomonas aeruginosa is of importance for the institution of correct antibiotic treatment and infection control measures.Results: Standardised inoculums of K. pneumoniae or P. aeruginosa were incubated at 37 degrees C with ertapenem in 15 and 120 min followed by centrifugation. The supernatant was applied on a steel target plate, covered with HCCA matrix and analysed using a Microflex(TM) (Bruker Daltonics) in the mass range of 4-600 Da. The assay detected and separated KPC from other carbapenemases in K. pneumoniae after only 15 min incubation. In P. aeruginosa, however, only 8/14 isolates of VIM-producing P. aeruginosa were detected. None of the tested carbapenemase negative isolates displayed a pattern of hydrolysis of ertapenem.Conclusions: This assay allows for a very rapid detection and verification of KPC (45 min including the preparation steps) and MBL production (150 min) in K. pneumoniae and can be performed using standard matrix. However, the study revealed the need for optimization of the substrate/species combination in assays for the detection of carbapenemases in P. aeruginosa using MALDI-TOF.
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| 40. |
- Jonsson, Jonas, et al.
(författare)
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Instrumentation and vehicle platform of a miniaturized submersible for exploration of terrestrial and extraterrestrial aqueous environments
- 2012
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Ingår i: Acta Astronautica. - : Elsevier BV. - 0094-5765 .- 1879-2030. ; 79, s. 203-211
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Tidskriftsartikel (refereegranskat)abstract
- An example of an extraterrestrial environment likely to support life is the vast liquid body believed to hide underneath the frozen crust of Jupiter's moon Europa. The hypothetical exploration of this, as well as the more accessible subglacial lakes on Earth, has been used as model applications for the development of a heavily miniaturized, yet qualified, submersible with the potential to be deployable either in itself through a long and narrow borehole or as the daughter craft of an ice-penetrating cryobot.Onboard the submersible, which is only 20 cm in length and 5 cm in diameter, accommodation of a versatile set of sensors and instruments capable of characterizing and imaging the surroundings, and even collecting water samples with microorganisms for return, is facilitated through the use of miniaturization technologies. For instance, together with a small camera, a laser-based, microoptic device enables the 3-D reconstruction of imaged objects for topographical measurements. As a complement, when the water is turbid or a longer range is wanted, the world's smallest side-scanning sonar, exhibiting centimeter resolution and a range of over 30 m, has been developed. The work on miniaturizing a CTD, which is a widely employed oceanographic instrument used to measure and correlate conductivity, temperature, and depth, has commenced. Furthermore, a device employing acoustics to trap microscopic particles and organisms, and, by this, enrich water samples, is under development. To ensure that the gathered samples are pristine until analyzed at the end of a mission, the device is equipped with high-pressure, latchable valves.Remote operation and transfer of measurement data and images, or even live streaming of video, is made possible through a kilometer-long fiber optic cable being reeled out from the vehicle underway and tethering it to a terminal. To extend the missions, the same fiber shall also be capable of charging the onboard batteries.In this paper, the vehicle and its subsystems are summarized. Subsystems essential for the vehicle's operation, e.g., hull structure, communication and power management, are treated separately from those of more mission-specific nature, like the instruments mentioned above.
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| 41. |
- Jonsson, Jonas, et al.
(författare)
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Miniaturized submersible for exploration of aqueous environments on Earth and beyond
- 2011
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Konferensbidrag (refereegranskat)abstract
- Some of the most likely environments to support extraterrestrial life in our solar system are the ice-covered moons, suchas Europa, thought to harbor a liquid ocean underneath its frozen crust. Exploration, however, necessitates an ice-penetratingcryobot, or a long and narrow borehole, and the subsequent deployment of a small submersible, a hydrobot, with severe sizerestrictions imposed on its scientific payload. As a stepping stone for exploration of such environments, a small instrumentladenedsubmersible vehicle is currently under development.Employment of a large set of instruments capable of characterizing the aqueous environment, imaging the surroundingsand collecting microorganisms is essential for the determination of habitability. Despite the submersible being only 20 cm inlength and 5 cm in diameter, a high degree of functionality is facilitated here through the use of miniaturization technologies. Forinstance, a compact laser-illuminated diffractive optical element, paired with a high-resolution camera, enable photogrammetryand the reconstruction of objects’ shapes in 3-D space. Also for imaging, the world’s smallest side-scanning sonar has beendeveloped to acoustically image, either where water is too turbid for the camera, or where longer range is necessary. Currently,the sonar exhibits centimeter resolution and ranges over 30 meters. On the sensor side, a most vital oceanographic instrument, theCTD, used to measure the conductivity, temperature, and depth of water, has been heavily miniaturized and preliminaryevaluated. Additionally, a water sampler combining integrated selection and enriching capabilities to filter out and accommodate,e.g., microbes in the size range of 1-10 μm, is under development. Among other parts, its high-pressure valves and microfluidicacoustic traps have already been realized.For remote operation and upload of measurement data or images, or even live streaming of video, the submersible will betethered with a bi-directionally transmitting fiber optic cable, also capable of charging the onboard batteries for long missions.The one kilometer long fiber will be fitted within the hull, and by reeling out the fiber from the submersible, drag will be reduced.Herein, test results and images of the vehicle and its complete, and continuously developed, subsystems are presented.The vehicle, and its subsystems as stand-alone instruments, will enable the exploration of previously unreachable analogenvironments on Earth, vital to the field of astrobiology, and act as a forerunner to a submersible hydrobot that can explore icecoveredoceans elsewhere in our solar system.
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| 42. |
- Jonsson, Jonas, et al.
(författare)
-
Miniaturized submersible for exploration of small aqueous environments
- 2011
-
Ingår i: Oceans’11 MTS/IEEE Kona, Hilton Waikoloa Village, Kona, Hawai‘i September 19-22, 2011.
-
Konferensbidrag (refereegranskat)abstract
- Remotely operated vehicles (ROVs) are commonlyused for sub-surface exploration. However, multi-functionalROVs tend to be fairly large, while preferred small and compactROVs suffer from limited functionality. The Deeper Access,Deeper Understanding (DADU) project aims to develop a smallsubmersible concept using miniaturization technologies to enablea high functionality. An operator is able to maneuver the vehiclewith five degrees of freedom using eight small thrusters, while aset of accelerometers and gyros monitor the orientation of thesubmersible. A single fiber optic cable will connect thesubmersible to a control station and enable simultaneous dataand command transfers. Rechargeable battery packs providepower to the submersibles subsystems during operation. Thesewill be rechargeable through the fiber connection. A forwardlooking camera is aided by a laser topography measurementsystem, where distances, sizes and shapes of objects in view canbe determined to within 0.5 cm. For murkier environments, orwhen a more extensive mapping of the surroundings is needed,the small high-frequency side-scanning sonar can be used.Salinity calculations of the water will be available throughmeasurements of the conductivity, temperature and depth.Samples of water and particles within it will be enabled through awater sampler with an enriching capability. Flow sensors will beable to measure the water movement around the submersible’shull. The submersible and its subsystems are under continuousdevelopment. The vehicle itself, and its subsystems as stand-aloneinstruments, will enable the exploration of previouslyunreachable submerged environments, such as the sub-glaciallakes found in Iceland and Antarctica, or other submerged smallenvironments, such as pipe and cave systems.
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| 43. |
- Karah, Nabil, et al.
(författare)
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Plasmid-mediated quinolone resistance determinants qnr and aac(6')-Ib-cr in Escherichia coli and Klebsiella spp. from Norway and Sweden
- 2010
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Ingår i: Diagnostic microbiology and infectious disease. - : Elsevier BV. - 0732-8893 .- 1879-0070. ; 66:4, s. 425-431
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Tidskriftsartikel (refereegranskat)abstract
- The prevalence of the plasmid-mediated quinolone resistance genes qnr and aac(6')-Ib-cr was investigated among clinical isolates of Escherichia coli and Klebsiella spp. selected from 2 collections of consecutive isolates collected in 2004 to 2005 in Norway (n = 2479) and Sweden (n = 2980) and 1 group of extended-spectrum beta-lactamase (ESBL)-producing isolates collected in 2003 in Norway (n = 71). A total of 414 isolates was selected for screening based on resistance to nalidixic acid and/or reduced susceptibility/resistance to ciprofloxacin. The prevalence of both qnr and aac(6')-Ib-cr was higher among the ESBL producers (9.1% and 52.3%, respectively) than in the consecutive isolates (1.1% and 3.2%, respectively). qnrS1 was detected in 6 isolates, whereas qnrB1 and qnrB7 were detected in 2 isolates. The genetic structure surrounding qnrS1 was similar to previously described structures. In 2 isolates, qnrS1 was located on conjugative IncN-type plasmids of approximately 140 kb.
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| 44. |
- Koskela, Anita, 1979-, et al.
(författare)
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Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization
- 2023
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) worldwide pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14–30 were run using three different protocols: the Twist Bioscience SARS‑CoV‑2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS‑CoV‑2 sequencing and guidance in selecting suitable methods for various purposes.
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| 45. |
- Lamy, Brigitte, et al.
(författare)
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Bloodstream infections - Standard and progress in pathogen diagnostics
- 2020
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Ingår i: Clinical Microbiology and Infection. - : Elsevier. - 1198-743X .- 1469-0691. ; 26:2, s. 142-150
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Forskningsöversikt (refereegranskat)abstract
- Background: Bloodstream infection (BSI) is a major public health burden worldwide, with high mortality. Patient outcome is critically influenced by delayed therapy, and fast and accurate pathogen diagnostics decisively improves the care of patients. During the past two decades major improvements have been made in the diagnostic performance of blood culture diagnostics through actions on pre-analysis and time to result.Aims: To review and discuss the literature for standard procedures and the progress in BSI pathogen diagnostics, and to propose a new mindset to reach an improved diagnostic workflow.Sources: Scientific articles and reviews available through NCBI/Pubmed.Content: Blood culture performance relies largely on the quality of its pre-analytical phase that is improved with educational actions monitored by using key performance indicators, and external quality assessment. Advanced blood culture systems now provide tools for an automated estimation of bottle filling. These proved efficient to facilitate effective training for improving blood collection. On analytic aspects, rapid methods for pathogen identification, among which matrix-assisted laser desorption/ ionization time of flight mass spectrometry dominates, and rapid antimicrobial susceptibility testing are reviewed. These technical developments call for improvements in all other steps, especially in pre- and post-analytic logistics to give the full reciprocation of these techniques on patient management. This aspect is summarized by the term 'microbiologistics', which covers all possible improvements in the logistic chain from sampling to report.
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| 46. |
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| 47. |
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| 48. |
- Liljedahl Prytz, Karolina, 1976-, et al.
(författare)
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Antibiotic treatment with one single dose of gentamicin at admittance in addition to a beta-lactam antibiotic in the treatment of community-acquired bloodstream infection with sepsis
- 2020
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 15:7
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Tidskriftsartikel (refereegranskat)abstract
- Background: Combination therapy in the treatment of sepsis, especially the value of combining a beta-Lactam antibiotic with an aminoglycoside, has been discussed. This retrospective cohort study including patients with sepsis or septic shock aimed to investigate whether one single dose of gentamicin at admittance (SGA) added to beta-Lactam antibiotic could result in a lower risk of mortality than beta-Lactam monotherapy, without exposing the patient to the risk of nephrotoxicity.Methods and findings: All patients with positive blood cultures were evaluated for participation (n = 1318). After retrospective medical chart review, a group of patients with community-acquired sepsis with positive blood cultures who received beta-Lactam antibiotic with or without the addition of SGA (n = 399) were included for the analysis. Mean age was 74.6 yrs. (range 19-98) with 216 (54%) males. Sequential Organ Failure Assessment score (SOFA score) median was 3 (interquartile range [IQR] 2-5) and the median Charlson Comorbidity Index for the whole group was 2 (IQR 1-3). Sixty-seven (67) patients (17%) had septic shock. The 28-day mortality in the combination therapy group was 10% (20 of 197) and in the monotherapy group 22% (45 of 202), adjusted HR 3.5 (95% CI (1.9-6.2),p= < 0.001. No significant difference in incidence of acute kidney injury (AKI) was detected.Conclusion: This retrospective observational study including patients with community-acquired sepsis or septic shock and positive blood cultures, who meet Sepsis-3 criteria, shows that the addition of one single dose of gentamicin to beta-lactam treatment at admittance was associated with a decreased risk of mortality and was not associated with AKI. This antibiotic regime may be an alternative to broad-spectrum antibiotic treatment of community-acquired sepsis. Further prospective studies are warranted to confirm these results.
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| 49. |
- Lind, Alexander, et al.
(författare)
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Anxiety, depression and quality of life in relation to SARS-CoV-2 antibodies in individuals living with diabetes during the second wave of COVID-19
- 2024
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Ingår i: Diabetes epidemiology and management. - : Elsevier. - 2666-9706. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Aims: The objective was to compare anxiety, depression, and quality of life (QoL) in individuals living with type 1 (T1D) and type 2 (T2D) diabetes with matched controls during the second wave of the COVID-19 pandemic.Methods: Via randomization, individuals living with diabetes T1D (n = 203) and T2D (n = 413), were identified during February-July 2021 through health-care registers. Population controls (n = 282) were matched for age, gender, and residential area. Questionnaires included self-assessment of anxiety, depression, QoL, and demographics in relation to SARS-CoV-2 exposure. Blood was collected through home-capillary sampling, and SARS-CoV-2 Nucleocapsid (NCP) and Spike antibodies (SC2_S1) were determined by multiplex Antibody Detection by Agglutination-PCR (ADAP) assays.Results: Younger age and health issues were related to anxiety, depression, and QoL, with no differences between the study groups. Female gender was associated with anxiety, while obesity was associated with lower QoL. The SARS-CoV-2 NCP seroprevalence was higher in T1D (8.9 %) compared to T2D (3.9 %) and controls (4.0 %), while the SARS-CoV-2 SC2_S1 seroprevalence was higher for controls (25.5 %) compared to T1D (16.8 %) and T2D (14.0 %).Conclusions: A higher SARS-CoV-2 infection rate in T1D may be explained by younger age and higher employment rate, and the associated increased risk for viral exposure.
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