| 1. |
- Berglund, Björn, et al.
(författare)
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Insertion sequence transpositions and point mutations in mgrB causing colistin resistance in a clinical strain of carbapenem-resistant Klebsiella pneumoniae from Vietnam
- 2018
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Ingår i: International Journal of Antimicrobial Agents. - : ELSEVIER SCIENCE BV. - 0924-8579 .- 1872-7913. ; 51:5, s. 789-793
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Tidskriftsartikel (refereegranskat)abstract
- Resistance among Klebsiella pneumoniae to the last-resort antibiotics carbapenems and colistin is increasing worldwide. In this study, whole-genome sequencing was used to determine the colistin resistance mechanisms in clinical isolates of carbapenem-and colistin-resistant K. pneumoniae from Vietnam. Alterations in the regulatory gene mgrB, via mutations and insertion sequence transpositions, were found in 30 of 31 isolates, emphasising the importance of this resistance mechanism in colistin-resistant K. pneumoniae. (c) 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.
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| 2. |
- Ehlersson, Gustaf, et al.
(författare)
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Phenotypic characterisation of coagulase-negative staphylococci isolated from blood cultures in newborn infants, with a special focus on Staphylococcus capitis
- 2017
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Ingår i: Acta Paediatrica. - : John Wiley & Sons. - 0803-5253 .- 1651-2227. ; 106:10, s. 1576-1582
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Tidskriftsartikel (refereegranskat)abstract
- AIM: This Swedish study determined which species of coagulase-negative staphylococci (CoNS) were found in neonatal blood cultures and whether they included Staphylococcus capitis clones with decreased susceptibility to vancomycin.METHODS: CoNS isolates (n = 332) from neonatal blood cultures collected at Örebro University Hospital during 1987-2014 were identified to species level with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). The antibiotic susceptibility pattern of S. capitis isolates was determined by the disc diffusion test and Etest, and the presence of heterogeneous glycopeptide-intermediate S. capitis (hGISC) was evaluated.RESULTS: Staphylococcus epidermidis (67.4%), Staphylococcus haemolyticus (10.5%) and S. capitis (9.6%) were the most common CoNS species. Of the S. capitis isolates, 75% were methicillin-resistant and 44% were multidrug-resistant. No isolate showed decreased susceptibility to vancomycin, but at least 59% displayed the hGISC phenotype. Staphylococcus capitis isolates related to the strain CR01 displaying pulsotype NRCS-A were found.CONCLUSION: Staphylococcus epidermidis, S. haemolyticus and S. capitis were the predominant species detected in neonatal blood cultures by MALDI-TOF MS. The number of episodes caused by S. capitis increased during the study period, but no isolates with decreased susceptibility to vancomycin were identified. However, S. capitis isolates related to the strain CR01 displaying pulsotype NRCS-A were found.
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| 3. |
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| 4. |
- Karlsson, Frida, et al.
(författare)
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Occurrence of Treponema spp. in porcine skin ulcers and gingiva
- 2013
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Ingår i: Veterinary Microbiology. - : Elsevier BV. - 0378-1135 .- 1873-2542. ; 165, s. 402-409
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Tidskriftsartikel (refereegranskat)abstract
- Porcine shoulder ulcers and ear necrosis are a significant animal welfare concern and impair efficient livestock production. Although spirochetes have been detected in both types of lesions the potential role of these bacteria in lesion propagation has received little attention. The objective of this study was to investigate the occurrence of spirochetes of the genus Treponema in shoulder ulcers or ear necrosis in pigs and compare these with treponemes from porcine gingiva. Samples were collected from gingiva and necrotic ulcers in 169 pigs. Presence of spirochetes was observed in silver stained histological sections and by phase contrast microscopy in scrapings from the necrotic lesions. Additionally, PCR of the 16SrRNA-tRNA(Ile) intergenic spacer region (ISR2) was used to detect Treponema spp. in all samples. Combined analysis showed that 73% of the shoulder ulcers and 53% of the ear necroses were positive for spirochetes. Treponema spp. were detected in 9.7% of the gingival samples. Comparative DNA sequence analysis of the ISR2 sequences revealed the presence of three distinct genetic phylotypes of Treponema spp. corresponding to Treponema pedis, and as yet two unnamed phylotypes represented by GenBank sequences C1UD1 (Acc. No. AY342041) and C1BT2-8 (Acc. No. AY342046). Detection of identical ISR2 sequences from gingiva and ulcer samples indicates that oral Treponema spp. are spread from mouth to ulcer. We conclude that Treponema spp. frequently occur in shoulder ulcers and ear necrosis in pigs, and suggest a possible infection route through biting and licking. (c) 2013 Elsevier B.V. All rights reserved.
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| 5. |
- Reichenbach, Tom, et al.
(författare)
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Structural and biochemical characterization of the Cutibacterium acnes exo-β-1,4-mannosidase that targets the N-glycan core of host glycoproteins.
- 2018
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 13:9
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Tidskriftsartikel (refereegranskat)abstract
- Commensal and pathogenic bacteria have evolved efficient enzymatic pathways to feed on host carbohydrates, including protein-linked glycans. Most proteins of the human innate and adaptive immune system are glycoproteins where the glycan is critical for structural and functional integrity. Besides enabling nutrition, the degradation of host N-glycans serves as a means for bacteria to modulate the host's immune system by for instance removing N-glycans on immunoglobulin G. The commensal bacterium Cutibacterium acnes is a gram-positive natural bacterial species of the human skin microbiota. Under certain circumstances, C. acnes can cause pathogenic conditions, acne vulgaris, which typically affects 80% of adolescents, and can become critical for immunosuppressed transplant patients. Others have shown that C. acnes can degrade certain host O-glycans, however, no degradation pathway for host N-glycans has been proposed. To investigate this, we scanned the C. acnes genome and were able to identify a set of gene candidates consistent with a cytoplasmic N-glycan-degradation pathway of the canonical eukaryotic N-glycan core. We also found additional gene sequences containing secretion signals that are possible candidates for initial trimming on the extracellular side. Furthermore, one of the identified gene products of the cytoplasmic pathway, AEE72695, was produced and characterized, and found to be a functional, dimeric exo-β-1,4-mannosidase with activity on the β-1,4 glycosidic bond between the second N-acetylglucosamine and the first mannose residue in the canonical eukaryotic N-glycan core. These findings corroborate our model of the cytoplasmic part of a C. acnes N-glycan degradation pathway.
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| 6. |
- Svartström, Olov, et al.
(författare)
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Characterization of Treponema spp. isolates from pigs with ear necrosis and shoulder ulcers
- 2013
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Ingår i: Veterinary Microbiology. - : Elsevier BV. - 0378-1135 .- 1873-2542. ; 166, s. 617-623
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Tidskriftsartikel (refereegranskat)abstract
- Ear necrosis and shoulder ulcers in pigs are animal welfare problems and ethical issues that can cause economic losses for producers. Spirochetes have been observed microscopically in scrapings from pig ulcers since the early 1900s, but have until recently not been cultured and therefore not characterized. In this study, 12 Treponema spp. isolates were acquired from porcine ear necrosis, shoulder ulcers and gingiva. DNA analysis of the 16S rRNA-tRNA(Ile) intergenic spacer region (ISR2) or the 16S rRNA gene revealed relatedness to oral treponemes found in dogs and humans. All isolates except one aligned into two clusters, Treponema pedis and Treponema sp. OMZ 840-like. The 16S rRNA gene of the remaining isolate shared 99% nucleotide identity with Treponema parvum. Genetic fingerprinting of the isolates was performed through random amplification of polymorphic DNA (RAPD). In addition, the isolates were characterized by biochemical tests, including api (R) ZYM, tryptophanase and hippuricase activity, and by testing the antimicrobial susceptibility to tiamulin, valnemulin, tylosin, tylvalosin, lincomycin and doxycycline using broth dilution. All isolates except two showed unique RAPD fingerprints, whereas metabolic activity tests could not differentiate between the isolates. The MICs of all antimicrobial agents tested were low. (C) 2013 Elsevier B.V. All rights reserved.
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| 7. |
- Svartström, Olov, et al.
(författare)
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Genome-Wide Relatedness of Treponema pedis, from Gingiva and Necrotic Skin Lesions of Pigs, with the Human Oral Pathogen Treponema denticola
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Treponema pedis and T. denticola are two genetically related species with different origins of isolation. Treponema denticola is part of the human oral microbiota and is associated with periodontitis while T. pedis has been isolated from skin lesions in animals, e.g., digital dermatitis in cattle and necrotic ulcers in pigs. Although multiple Treponema phylotypes may exist in ulcerative lesions in pigs, T. pedis appears to be a predominant spirochete in these lesions. Treponema pedis can also be present in pig gingiva. In this study, we determined the complete genome sequence of T. pedis strain T A4, isolated from a porcine necrotic ear lesion, and compared its genome with that of T. denticola. Most genes in T. pedis were homologous to those in T. denticola and the two species were similar in general genomic features such as size, G+C content, and number of genes. In addition, many homologues of specific virulence-related genes in T. denticola were found in T. pedis. Comparing a selected pair of strains will usually not give a complete picture of the relatedness between two species. We therefore complemented the analysis with draft genomes from six T. pedis isolates, originating from gingiva and necrotic ulcers in pigs, and from twelve T. denticola strains. Each strain carried a considerable amount of accessory genetic material, of which a large part was strain specific. There was also extensive sequence variability in putative virulence-related genes between strains belonging to the same species. Signs of lateral gene-transfer events from bacteria known to colonize oral environments were found. This suggests that the oral cavity is an important habitat for T. pedis. In summary, we found extensive genomic similarities between T. pedis and T. denticola but also large variability within each species.
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| 8. |
- Svartström, Olov, et al.
(författare)
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Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation
- 2017
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Ingår i: The ISME Journal. - : Nature Publishing Group. - 1751-7362 .- 1751-7370. ; 11:11, s. 2538-2551
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Tidskriftsartikel (refereegranskat)abstract
- The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
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| 9. |
- Svartström, Olov
(författare)
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Treponema spp. in necrotic skin ulcers in pigs : phenotypic and genetic features
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Treponema belongs to the phylum Spirochaetes consisting of bacteria distinguishable by a unique cell architecture that enables corkscrew-like motility. In two case studies, treponemes were isolated from ear necrosis and shoulder ulcers, two types of skin lesions that have impact on animal welfare and may cause economic losses. This doctoral thesis focuses on a hypothesis that Treponema spp. have a pathogenic role in the progression of ear necrosis and shoulder ulcers in pigs and, as Treponema spp. are present in gingiva of pigs, that transmission to skin is mediated by biting or licking. The thesis describes their occurrence, phenotypic and genetic features. We sampled 109 pigs with lesions and 60 apparently healthy piglets. Spirochetes were present in 73% of the shoulder ulcers, in 53% of the ear necroses and in 9.7% of the gingivae. Many identified phylotypes were similar to Treponema spp. considered as pathogens in bovine digital dermatitis, a claw disease in cattle. Similar phylotypes were present both in gingiva and ulcers. There were indications of transmission between gingiva and ulcers. Twelve isolates were acquired and identified as T. pedis, T. parvum and T. sp. OMZ840-like. Metabolic patterns were similar to those of other treponemes and were not discriminatory between isolates. All except two gingival isolates showed unique DNA fingerprints. Treponema sp. OMZ840-like and T. pedis isolates were hemolytic, T. parvum was not. The isolates were generally susceptible to the tested antimicrobials. The genome sequence of T. pedis strain T A4 from ear necrosis was de novo assembled and analyzed. The genome was most similar to that of T. denticola, a species strongly associated with human periodontitis. Several of the predicted genes in T. pedis were homologous to virulence related genes in T. denticola, including those encoding the major surface sheath protein, dentilisin and dentipain. In T. denticola, IdeT is a protein that includes the oligopeptidase domain dentipain. An IdeT-homologue in T. pedis strain T A4, TPE0673, was recombinantly expressed in Escherichia coli and purified for in vitro testing. TPE0673 did not display protease activity towards immunoglobulin G (IgG) or insulin as its homologues. However, western blot analysis showed that IgG in serum from sows with shoulder ulcers bound to purified TPE0673, suggesting an immunogenic property of this gene. In conclusion, this thesis describes an association between Treponema spp. with ear necrosis and shoulder ulcers. The treponemes present in pig ulcers were phylogenetically similar to those of oral origin and transmission between gingiva and ulcer was indicated. Finally, analysis of the genome of T. pedis revealed the presence of several putative virulence genes indicating a pathogenic potential for this species.
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