| 1. |
- Zamora, L, et al.
(författare)
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Chryseobacterium oncorhynchi sp. nov., isolated from rainbow trout (Oncorhynchus mykiss).
- 2012
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Ingår i: Systematic and applied microbiology. - : Elsevier BV. - 1618-0984 .- 0723-2020. ; 35:1, s. 24-9
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Tidskriftsartikel (refereegranskat)abstract
- Genotypic and phenotypic analyses were performed on five Gram-negative, catalase and oxidase-positive, rod-shaped bacteria isolated from the gill and liver of four rainbow trout. Studies based on comparative 16S rRNA gene sequence analysis showed that the five new isolates shared 99.8-100% sequence similarity and that they belong to the genus Chryseobacterium. The nearest phylogenetic neighbours of the strain 701B-08(T) were Chryseobacterium ureilyticum F-Fue-04IIIaaaa(T) (99.1% 16S rRNA gene sequence similarity) and Chryseobacterium joosteii LMG 18212(T) (98.6%). DNA-DNA hybridization values between the five isolates were 91-99% and ranged from 2 to 53% between strain 701B-08(T) and the type strains of phylogenetically closely related species of Chryseobacterium. Strain 701B-08(T) had a DNA G+C content of 36.3 mol%, the major fatty acids were iso-C(15:0), iso-C(17:1)ω9c, C(16:1)ω6c and iso-C(17:0) 3-OH and the predominant respiratory quinone was MK-6. The novel isolates were distinguished from related Chryseobacterium species by physiological and biochemical tests. The genotypic and phenotypic properties of the isolates from rainbow trout suggest their classification as representatives of a novel species of the genus Chryseobacterium, for which the name Chryseobacterium oncorhynchi sp. nov. is proposed. The type strain is 701B-08(T) (=CECT 7794(T)=CCUG 60105(T)).
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| 2. |
- Svensson, Liselott A, et al.
(författare)
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New genotypic and phenotypic analyses of clinically-relevant Gram-negative, non-fermenting bacteria: MALDI-TOF MS as a rapid, high-resolution method for identifying and typing microorganisms
- 2010
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Ingår i: 20th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna, Austria.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Objectives. Identification of Gram-negative, non-fermenting bacilli, using phenotypic characterization is problematic. Many of the species of this group are frequent nosocomial infectious agents and are ubiquitous in the environment. The aims of this study were to assess the resolving capacities of “house-keeping” gene sequences, including 16S rRNA, atpD, gyrB, recA, rpoB and rpoD, and to compare a multi-locus sequence analysis (MLSA) with matrix-assisted laser desorption time-of-flight (MALDI-TOF) mass spectrometry analyses for identifying and typing strains of Achromobacter, Bordetella, Burkholderia, Pseudomonas, and Stenotrophomonas species. Methods. Genotypic analyses. Type strains of the focus genera and species-complexes, other well-characterised reference strains and selected clinically-relevant strains representing a range of phenotypic and genotypic similarities were included in this study. Partial genes, 16S rRNA, atpD, recA, gyrB and rpoD recA were amplified by PCR and sequenced. DNA-DNA hybridisation analyses were carried out on selected strains for confirmation of species designations. MALDI-TOF analysis. Bacterial biomass were prepared from cultures on agar medium and analysed by MALDI-TOF MS, in the positive mode, using the SARAMIS software for analysis (1) Results. MLSA, using the respective house keeping genes were able to differentiate and identify the most closely related species of the analysed taxa and cluster analyses showed similarities of branching order between species that correlated well between different genes. However, different genes were not equally effective in differentiating species of the different genera. The MALDI-TOF analyses were effective in differentiating the most closely related species of the respective genera. Good correlation was observed between the results of MALDI-TOF MS and MLSA data. Conclusion. In most cases, clinically-relevant isolates and strains of Gram negative, non-fermenting bacilli exhibited good agreement between the methods of this study. In some cases, strains previously defined as given species were observed to be genotypically more similar to other species, as well as some strains with highly aberrant phenotypes were almost genotypically identical to the type strain. MALDI-TOF identification was very well correlated to the MLSA results, and is a much less expensive and effectively able to reduce identification times by 24-48 hours. (1) Vanlaere E et al. J. Microbiol. Meth. 75: 279-286 (2008).
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| 3. |
- Zamora, L, et al.
(författare)
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Flavobacterium oncorhynchi sp. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss).
- 2012
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Ingår i: Systematic and applied microbiology. - : Elsevier BV. - 1618-0984 .- 0723-2020. ; 35:2, s. 86-91
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Tidskriftsartikel (refereegranskat)abstract
- Eighteen isolates of a Gram-negative, catalase and oxidase-positive, rod-shaped bacterium, recovered from diseased rainbow trout (Oncorhynchus mykiss), were characterized, using a polyphasic taxonomic approach. Studies based on comparative 16S rRNA gene sequence analysis showed that that the eighteen new isolates shared 99.2-100% sequence similarities. Phylogenetic analysis revealed that isolates from trout belonged to the genus Flavobacterium, showing the highest sequence similarities to F. chungangense (98.6%), F. frigidimaris (98.1%), F. hercynium (97.9%) and F. aquidurense (97.8%). DNA-DNA reassociation values between the trout isolates (exemplified by strain 631-08(T)) and five type strains of the most closely related Flavobacterium species exhibited less than 27% similarity. The G+C content of the genomic DNA was 33.0 mol%. The major respiratory quinone was observed to be menaquinone 6 (MK-6) and iso-C(15:0), C(15:0) and C(16:1) ω7c the predominant fatty acids. The polar lipid profile of strain 631-08(T) consisted of phosphatidylethanolamine, unknown aminolipids AL1 and AL3, lipids L1, L2, L3 and L4 and phospholipid PL1. The novel isolates were differentiated from related Flavobacterium species by physiological and biochemical tests. On the basis of the evidence from this polyphasic study, it is proposed that the isolates from rainbow trout be classified as a new species of the genus Flavobacterium, Flavobacterium oncorhynchi sp. nov. The type strain is 631-08(T) (= CECT 7678(T) = CCUG 59446(T)).
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| 4. |
- Svensson, Liselott A
(författare)
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Applications of MALDI-SARAMIS at CCUG
- 2010
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Ingår i: AnagnosTec MALDI-TOF MS Expert Meeting, Potsdam, Germany.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Svensson-Stadler, Liselott, 1971, et al.
(författare)
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Stenotrophomonas interspecies differentiation and identification by gyrB sequence analysis.
- 2012
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Ingår i: FEMS microbiology letters. - : Oxford University Press (OUP). - 1574-6968 .- 0378-1097. ; 327:1, s. 15-24
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Tidskriftsartikel (refereegranskat)abstract
- Stenotrophomonas species are found commonly in environmental and clinical samples; Stenotrophomonas maltophilia is an important opportunistic pathogen of humans. Traditional phenotyping protocols, as well as genotyping by 16S rRNA gene sequence analysis, do not reliably distinguish the species of Stenotrophomonas. Sequence analyses of two targeted PCR-amplified regions of the gyrB gene, which encodes the β-subunit of DNA gyrase, enabled resolution and identification of these species. Most type strains of the different species of Stenotrophomonas exhibited more than 7% dissimilarity in the gyrB gene sequences. Among these, strains identified as the same species exhibited sequence dissimilarities up to 4.6% and 5.9% for the two regions, respectively. Strains identified as S. maltophilia, with 16S rRNA gene sequence similarities > 99.0%, were grouped within a 'S. maltophilia complex'; these organisms exhibited gyrB similarities as low as 93%. Many of these strains possessed genomic DNA similarities with the type strain of S. maltophilia CCUG 5866(T) below 70%. These data, including gyrB sequence comparisons, indicate that strains identified as S. maltophilia may comprise distinct, new species.
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| 6. |
- Vaz-Moreira, Ivone, et al.
(författare)
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Shinella fusca sp. nov., isolated from domestic waste compost
- 2010
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 60:1, s. 144-148
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Tidskriftsartikel (refereegranskat)abstract
- A bacterium, designated strain DC-196(T), isolated from kitchen refuse compost was analysed by using a polyphasic approach. Strain DC-196(T) was characterized as a Gram-negative short rod that was catalase- and oxidase-positive, and able to grow at 10-40 degrees C, pH 6-9 and in NaCl concentrations as high as 3 %. Chemotaxonomically, C(18 : 1) was observed to be the predominant cellular fatty acid and ubiquinone 10 (Q10) was the predominant respiratory quinone. The G+C content of the genomic DNA was determined to be 66 mol%. On the basis of the genotypic, phenotypic and chemotaxonomic characteristics, strain DC-196(T) was assigned to the genus Shinella, although with distinctive features. At the time of writing, 16S rRNA gene sequence similarities of 97.6-96.8 % and the low DNA-DNA hybridization values of 38.2-32.2 % with the type strains of the three recognized Shinella species confirmed that strain DC-196(T) represents a novel species of the genus, for which the name Shinella fusca sp. nov. is proposed (type strain DC-196(T)=CCUG 55808(T)=LMG 24714(T)).
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