| 1. |
- Segerman, Bo, et al.
(författare)
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The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content
- 2022
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing (WGS) is becoming the new standard for bacterial high-resolution typing and the performance of laboratories is being evaluated in interlaboratory comparisons. The use of the Illumina Nextera XT library preparation kit has been found to be associated with poorer performance due to a GC-content-dependent coverage bias. The bias is especially strong when sequencing low GC-content species. Here, we have made an in-depth analysis of the Nextera XT coverage bias problem using data from a proficiency test of the low GC-content species Campylobacter jejuni. We have compared Nextera XT with Nextera Flex/DNA Prep and examined the consequences on downstream WGS analysis when using different quantities of raw data. We have also analyzed how the coverage bias relates to differential usage of tagmentation cleavage sites. We found that the tagmentation site was characterized by a symmetrical motif with a central AT-rich region surrounded by Gs and Cs. The Gs and Cs appeared to be the main determinant for cleavage efficiency and the genomic regions that were associated with low coverage only contained low-efficiency cleavage sites. This explains why low GC-content genomes and regions are more subjected to coverage bias. We furthermore extended our analysis to other datasets representing other bacterial species. We visualized how the coverage bias was large in low GC-content species such as C. jejuni, C. coli, Staphylococcus aureus, and Listeria monocytogenes, whereas species with neutral GC-content such as Salmonella enterica and Escherichia coli were only affected in certain regions. Species with high GC-content such as Mycobacterium tuberculosis and Pseudomonas aeruginosa were hardly affected at all. The coverage bias associated with Nextera XT was not found when Nextera Flex/DNA Prep had been used.
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| 2. |
- Allard, Christina, et al.
(författare)
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Rasbiologiskt språkbruk i statens rättsprocess mot sameby : DN Debatt 2015-06-11
- 2015
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Annan publikation (populärvet., debatt m.m.)abstract
- Statens hantering av forskningsresultat i rättsprocessen med Girjas sameby utgör ett hot mot Sverige som rättsstat och kunskapsnation. Åratal av svensk och internationell forskning underkänns och man använder ett språkbruk som skulle kunna vara hämtat från rasbiologins tid. Nu måste staten ta sitt ansvar och börja agera som en demokratisk rättsstat, skriver 59 forskare.
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| 3. |
- Anniballi, F., et al.
(författare)
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Management of animal botulism outbreaks : From clinical suspicion to practical countermeasures to prevent or minimize outbreaks
- 2013
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Ingår i: Biosecurity and bioterrorism. - : Mary Ann Liebert Inc. - 1538-7135 .- 1557-850X. ; 11:SUPPL. 1, s. S191-S199
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Tidskriftsartikel (refereegranskat)abstract
- Botulism is a severe neuroparalytic disease that affects humans, all warm-blooded animals, and some fishes. The disease is caused by exposure to toxins produced by Clostridium botulinum and other botulinum toxin-producing clostridia. Botulism in animals represents a severe environmental and economic concern because of its high mortality rate. Moreover, meat or other products from affected animals entering the food chain may result in a public health problem. To this end, early diagnosis is crucial to define and apply appropriate veterinary public health measures. Clinical diagnosis is based on clinical findings eliminating other causes of neuromuscular disorders and on the absence of internal lesions observed during postmortem examination. Since clinical signs alone are often insufficient to make a definitive diagnosis, laboratory confirmation is required. Botulinum antitoxin administration and supportive therapies are used to treat sick animals. Once the diagnosis has been made, euthanasia is frequently advisable. Vaccine administration is subject to health authorities' permission, and it is restricted to a small number of animal species. Several measures can be adopted to prevent or minimize outbreaks. In this article we outline all phases of management of animal botulism outbreaks occurring in wet wild birds, poultry, cattle, horses, and fur farm animals. © 2013, Mary Ann Liebert, Inc.
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| 4. |
- Johansson, Håkan, 1972-, et al.
(författare)
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Characterization of Campylobacter spp. isolated from wild birds in the Antarctic and Sub-Antarctic
- 2018
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 13:11
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Tidskriftsartikel (refereegranskat)abstract
- A lack of knowledge of naturally occurring pathogens is limiting our ability to use the Antarctic to study the impact human-mediated introduction of infectious microorganisms have on this relatively uncontaminated environment. As no large-scale coordinated effort to remedy this lack of knowledge has taken place, we rely on smaller targeted efforts to both study present microorganisms and monitor the environment for introductions. In one such effort, we isolated Campylobacter species from fecal samples collected from wild birds in the Antarctic Peninsula and the sub-Antarctic island of South Georgia. Indeed, in South Georgia, we found Campylobacter lari and the closely related Campylobacter peloridis, but also distantly related human-associated multilocus sequence types of Campylobacter jejuni. In contrast, in the Antarctic Peninsula, we found C. tart and two closely related species, Campylobacter subantarcticus and Campylobacter volucris, but no signs of human introduction. In fact, our finding of human-associated sequence types of C. jejuni in South Georgia, but not in the Antarctic Peninsula, suggests that efforts to limit the spread of infectious microorganisms to the Antarctic have so far been successful in preventing the introduction of C. jejuni. However, we do not know how it came to South Georgia and whether the same mode of introduction could spread it from there to the Antarctic Peninsula.
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| 5. |
- Klint, Markus, et al.
(författare)
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High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis
- 2007
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Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 45:5, s. 1410-1414
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Tidskriftsartikel (refereegranskat)abstract
- Genotyping of Chlamydia trachomatis is limited by the low sequence variation in the genome, and no adequatemethod is available for analysis of the spread of chlamydial infections in the community. We have developeda multilocus sequence typing (MLST) system based on five target regions and compared it with analysis ofompA, the single gene most extensively used for genotyping. Sequence determination of 16 reference strains,comprising all major serotypes, serotypes A to L3, showed that the number of genetic variants in the fiveseparate target regions ranged from 8 to 16. The genetic variation in 47 clinical C. trachomatis isolates ofrepresentative serotypes (14 serotype D, 12 serotype E, 11 serotype G, and 10 serotype K strains) was analyzed;and the MLST system detected 32 variants, whereas 12 variants were detected by using ompA analysis.Specimens of the predominant serotype, serotype E, were differentiated into seven genotypes by MLST but intoonly two by ompA analysis. The MLST system was applied to C. trachomatis specimens from a population ofmen who have sex with men and was able to differentiate 10 specimens of one predominant ompA genotype Gvariant into four distinct MLST variants. To conclude, our MLST system can be used to discriminate C.trachomatis strains and can be applied to high-resolution molecular epidemiology.
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| 6. |
- Ringqvist, Emma, et al.
(författare)
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Release of metabolic enzymes by Giardia in response to interaction with intestinal epithelial cells
- 2008
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Ingår i: Molecular and biochemical parasitology (Print). - : Elsevier BV. - 0166-6851 .- 1872-9428. ; 159:2, s. 85-91
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Tidskriftsartikel (refereegranskat)abstract
- Giardia lamblia, an important cause of diarrheal disease, resides in the small intestinal lumen in close apposition to epithelial cells. Since the disease mechanisms underlying giardiasis are poorly understood, elucidating the specific interactions of the parasite with the host epithelium is likely to provide clues to understanding the pathogenesis. Here we tested the hypothesis that contact of Giardia lamblia with intestinal epithelial cells might lead to release of specific proteins. Using established co-culture models, intestinal ligated loops and a proteomics approach, we identified three G. lamblia proteins (arginine deiminase, ornithine carbamoyl transferase and enolase), previously recognized as immunodominant antigens during acute giardiasis. Release was stimulated by cell-cell interactions, since only small amounts of arginine deiminase and enolase were detected in the medium after culturing of G. lamblia alone. The secreted G. lamblia proteins were localized to the cytoplasm and the inside of the plasma membrane of trophozoites. Furthermore, in vitro studies with recombinant arginine deiminase showed that the secreted Giardia proteins can disable host innate immune factors such as nitric oxide production. These results indicate that contact of Giardia with epithelial cells triggers metabolic enzyme release, which might facilitate effective colonization of the human small intestine.
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| 7. |
- Skarin, Hanna
(författare)
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Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements
- 2011
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Conclusions: The completion of the genome of C. botulinum group III has revealed it to be a genome with dual identity. It belongs to the pathogenic species C. botulinum, but as a genotypic species it should also include C. novyi and C. haemolyticum. The genotypic species share a conserved chromosomal core that can be transformed into various pathogenic variants by modulation of the highly plastic plasmidome.
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| 8. |
- Skarin, Hanna, et al.
(författare)
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Elongation factor 1-alpha is released into the culture medium during growth of Giardia intestinalis trophozoites
- 2011
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Ingår i: Experimental parasitology. - : Elsevier BV. - 0014-4894 .- 1090-2449. ; 127:4, s. 804-810
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Tidskriftsartikel (refereegranskat)abstract
- The molecular pathogenesis of the intestinal parasite Giardia intestinalis is still not fully understood but excretory-secretory products have been suggested to be important during host-parasite interactions. Here we used SOS-PAGE gels and MALDI-TOF analysis to identify proteins released by Giardia trophozoites during in vitro growth. Serum proteins (mainly bovine serum albumin) in the growth medium, bind to the parasite surface and they are continuously released, which interfere with parasite secretome characterization. However, we identified two released Giardia proteins: elongation factor-1 alpha (EF-1 alpha) and a 58 kDa protein, identified as arginine deiminase (ADI). This is the first description of EF-1 alpha as a released/secreted Giardia protein, whereas ADI has been identified in an earlier secretome study. Two genes encoding EF-1 alpha were detected in the Giardia WB genome 35 kbp apart with almost identical coding sequences but with different promoter and 3' regions. Promoter luciferase-fusions showed that both genes are transcribed in trophozoites. The EF-1 alpha protein localizes to the nuclear region in trophozoites but it relocalizes to the cytoplasm during host-cell interaction. Recombinant EF-1 alpha is recognized by serum from giardiasis patients. Our results suggest that released EF-1 alpha protein can be important during Giardia infections.
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| 9. |
- Skarin, Hanna
(författare)
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Genomic organization and diversity of Clostridium botulinum group III : the bug behind animal botulism
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Botulism is caused by botulinum neurotoxins (BoNTs) produced by the spore forming strictly anaerobic bacterium Clostridium botulinum. Seven different types of BoNTs (type A-F) have so far been established on the basis of neutralization with different antibodies. Botulism affects both humans and animals, and there are occasionally large-scale outbreaks of high mortality in animals. Especially large outbreaks of avian botulism have been reported from various countries, including Sweden. Other animals relatively commonly affected are cattle, horses, sheep and farmed fur animals. C. botulinum is a diverged species and can be organized into four groups, which reflect their genetic and physiological differences. C. botulinum group III strains producing BoNT types C, D and chimers C/D and D/C, are mainly connected to animal botulism. The gene encoding BoNT in C. botulinum group III strains is located on an unstable plasmid-like phage. In this thesis, strains of the previously relatively uncharacterised C. botulinum group III were isolated and genotyped with pulsed-field gel electrophoresis. Several pulsotypes were formed, but the majority clustered closely together and represented most of the chimeric strains. Strains representing different pulsotypes and different animal and geographical origin, were selected for whole genome sequencing and the resulting genomes could be divided into four genomic lineages. Comparisons against genomes of Clostridium novyi and Clostridium haemolyticum revealed that they could be organized into the same genomic lineages (lineages II-IV), which resulted in the suggested collective term C. novyi sensu lato. The organization of all sequenced genomes was analysed. It revealed a relatively conserved chromosome and an abundance of highly dynamic plasmids. The plasmids, lineages and species were entwined because plasmids and toxin genes had moved across the lineage boundaries. Of the four lineages, only lineage I was C. botulinum specific, and this lineage includes strains of the most common pulsotype. One genome of lineage I was assembled into completion. It was smaller than C. botulinum group I and II genomes, but contained as much as five plasmids. Most of the identified putative toxin genes were found on these plasmids. Strains of lineage I may be more virulent than other C. botulinum group III strains, which is reflected by their domination in animal botulism cases today.
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| 10. |
- Skarin, Hanna, 1980-, et al.
(författare)
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Giardia intestinalis Elongation Factor 1-alpha is released during host cell interaction
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Annan publikation (refereegranskat)abstract
- Giardia intestinalis is an intestinal diarrhea-causing parasite but the disease mechanism is not fully understood. Here we used SDS-PAGE gels and MALDI-TOF analysis to identify proteins released by Giardia trophozoites during axenic growth with and without host cells. We detected serum proteins that bind strongly to the parasite surface but also two Giardia proteins: elongation factor-1 alpha (EF-1α) and a 58kDa protein identified as arginine deiminase (ADI). Two genes encoding EF-1α were detected in the Giardia WB genome 35kbp apart. The coding sequences are identical but the promoter and 3’ regions differ. Promoter luciferase-fusions showed that both genes are transcribed in trophozoites. The EF-1α protein localizes to the ER region but it relocalizes to the plasma membrane and is secreted during host cell interaction. Recombinant EF-1α is recognized by serum from giardiasis patients. Our results suggest that EF-1α is important during Giardia infections and that ADI can be the earlier identified 58kDa enterotoxin.
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