| 1. |
- Cotta, M. A., et al.
(author)
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Two novel species Enterococcus lemanii sp nov and Enterococcus eurekensis sp nov., isolated from a swine-manure storage pit
- 2013
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In: Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology. - : Springer Science and Business Media LLC. - 0003-6072. ; 103:1, s. 89-98
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Journal article (peer-reviewed)abstract
- A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular genetic methods was performed on six strains of unknown Gram-positive, nonspore-forming, facultative anaerobic coccus-shaped bacteria isolated from a swine-manure storage pit. On the basis of the 16S rRNA, RNA polymerase alpha-subunit (rpoA) and 60 kDa chaperonin (cpn60) gene sequence analyses, it was shown that all the isolates were enterococci but formed two separate lines of descent. Pairwise 16S rRNA gene sequence comparisons demonstrated that the two novel organisms were most closely related to each other (97.9 %) and to Enterococcus aquimarinus (97.8 %). Both organisms contained major amounts of C-16:0, C-16:1 omega 7c, C-16:1 omega 7c, and C-18:1 omega 7c/12t/9t as the major cellular fatty acids. Based on biochemical, chemotaxonomic and phylogenetic evidence, the names Enterococcus lemanii sp. nov. (type strain PC32(T) = CCUG 61260(T) = NRRL B-59661(T)) and Enterococcus eurekensis sp. nov. (type strain PC4B(T) = CCUG 61259(T) = NRRL B-59662(T)) are proposed for these hitherto undescribed species.
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| 2. |
- Cuadrado, Virginia, et al.
(author)
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Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil
- 2010
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 60:11, s. 2606-2612
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Journal article (peer-reviewed)abstract
- A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6(T), the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6(T) did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5-4.5% NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5%; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA-DNA hybridization data revealed low levels of genomic DNA similarity (less than 30%) between strain CPDB6(T) and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16:1ω7c) and hexadecanoic (16:0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6(T) was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6(T) (=CCUG 55948(T)=CCM-A-29:1289(T)) as the type strain.
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| 3. |
- Gomila, Margarita, et al.
(author)
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Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol contaminated soil.
- 2011
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 61:9, s. 2231-2237
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Journal article (peer-reviewed)abstract
- A polyphasic taxonomic approach was applied for the study of a Gram negative bacterium (B2(T)) isolated from soil by selective enrichment with pentachlorophenol. The 16S rRNA gene sequence analysis of strain B2(T) showed that this strain belongs to the genus Achromobacter, within the Betaproteobacteria. The 16S rRNA gene sequence possessing more than 99% similarity to the sequences of the type strains of all species in Achromobacter, with the highest sequence similarities to those of A. spanius CCM 7183(T) and A. piechaudii CCM 2986(T) (99.8 %). On the basis of phylogenetic analysis, genomic DNA-DNA similarities and phenotypic characteristics, including chemotaxonomic (cell fatty acid profile) analysis, a novel species is proposed, Achromobacter marplatensis sp. nov., with the type strain B2(T) (= CCM 7608(T) = CCUG 56371(T) = CECT 7342(T)).
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| 4. |
- Gomila, Margarita, et al.
(author)
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Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae.
- 2010
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 60:4, s. 809-814
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Journal article (peer-reviewed)abstract
- A strictly aerobic, Gram-negative bacterium, strain KIN192(T), isolated from fresh water from Lake Kinneret, Israel, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA and gyrB genes and ITS1 revealed close relationships to species of the genera Pelomonas, Mitsuaria and Roseateles, in the Rubrivivax branch of the family Comamonadaceae of the Betaproteobacteria. Physiological and biochemical tests, cellular fatty acid analysis and DNA-DNA hybridizations indicated that this strain should be assigned to a new genus and species in the Rubrivivax phylogenetic branch, for which the name Kinneretia asaccharophila gen. nov., sp. nov., is proposed. The type strain of Kinneretia asaccharophila is strain KIN192(T) (=CCUG 53117(T) =CECT 7319(T)).
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| 5. |
- Hedberg, Maria E, et al.
(author)
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Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae: characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prevot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov.
- 2012
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 62:Pt 11, s. 2685-90
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Journal article (peer-reviewed)abstract
- Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3:22(T) and N1(T)) are described. Strain CD3:22(T) was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1(T) from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H(2)S, NH(3), butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98% sequence similarity) between the two isolates, as well as the type strain of Eubacterium saburreum and four other Lachnospiraceae bacterium-/E. saburreum-like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family Lachnospiraceae. While Eubacterium species are reported to be non-spore-forming, reanalysis of E. saburreum CCUG 28089(T) confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3:22(T) and N1(T) represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family Lachnospiraceae [within the order Clostridiales, class Clostridia, phylum Firmicutes]. Strain CD3:22(T) (=CCUG 58757(T) =DSM 23576(T)) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1(T) (=CCUG 60305(T)=DSM 24553(T)) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089(T) =ATCC 33271(T) =CIP 105341(T) =DSM 3986(T) =JCM 11021(T) =VPI 11763(T)).
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| 6. |
- Hedberg, Maria E., et al.
(author)
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Prevotella jejuni sp. nov., isolated from the small intestine of a child with celiac disease.
- 2013
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 63:11, s. 4218-4223
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Journal article (peer-reviewed)abstract
- Five obligately anaerobic, Gram-negative, saccharolytic and proteolytic, non-spore-forming bacilli (CD3:27, CD3:28T, CD3:33, CD3:32 and CD3:34) are described. All five strains were isolated from the small intestine of a female child with celiac disease. The cells of the five strains were observed to be short rods or coccoid cells with longer filamentous forms seen sporadically. The organisms produced acetic acid and succinic acid as major metabolic end products. Phylogenetic analysis, based on comparative 16S rRNA gene sequence analysis revealed close relationships between CD3:27, CD3:28T and CD3:33 on one hand, between CD3:32 and P. histicola CCUG 55407T and between CD3:34 and P. melaninogenica CCUG 4944BT on the other. The strains CD3:27, CD3:28T and CD3:33 were clearly different from any other species within the genus Prevotella and most closely related to but distinct from P. melaninogenica. Based on 16S rRNA gene, RNA polymerase β-subunit gene and 60-kDa chaperonin protein subunit gene sequencing, phenotypic, chemical and biochemical properties strains CD3:27, CD3:28T and CD3:33 have been determined to represent a novel species within the genus Prevotella, named Prevotella jejuni sp. nov. Strain CD3:28T (CCUG 60371T = DSM 26989T) is the type strain of the proposed new species. All five strains were able to form homologous aggregates, in which tube-like structures were connecting individual bacteria cells. The five strains were able to bind to human intestinal carcinoma cell lines at 37 °C.
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| 7. |
- Helldal, Lisa, et al.
(author)
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Shift of CTX-M genotypes has determined the increased prevalence of extended-spectrum beta-lactamase-producing Escherichia coli in south-western Sweden
- 2013
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In: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X .- 1469-0691. ; 19:2
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Journal article (peer-reviewed)abstract
- The prevalence of Escherichia coli producing extended-spectrum β-lactamases (ESBLs) markedly increased during 2004-2008 in south-western Sweden, with a greater increase in urinary isolates in hospitals (0.2-2.5%) than in the community (0.2-1.6%). ESBLs of genotype CTX-M predominated, with a significant (p<0.02) shift from the CTX-M-9 to CTX-M-1 phylogroup occurring among urinary ESBL-producing E.coli isolated early (n=41) as compared with late (n=221) in the study period. The increase in ESBL-producing E.coli was polyclonal, and only partly attributable to an increase (0-24%) in the number of O25b-ST131 isolates carrying CTX-M-15. The increase was prominent in men and in elderly patients, and warrants continued surveillance.
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| 8. |
- Helldal, Lisa, et al.
(author)
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Shifts in Extended-Spectrum Beta-Lactamase types with increasing prevalence of Escherichia coli producing ESBL
- 2010
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In: 20th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna, Austria.
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Conference paper (other academic/artistic)abstract
- Objectives: Contrary to other multidrug-resistant pathogens, the prevalence of bacteria producing extended-spectrum beta-lactamase (ESBL) is increasing rapidly in Sweden. In Europe, ESBL of CTX-M-, TEM-, OXA- and SHV-types are generally associated with E. coli infections, CTX-M being the most predominant. We have investigated how the prevalence of these types has changed during the last five years in the low endemic setting of western Sweden. Methods: Yearly resistance in urinary (approximately 10,000 isolates/year) and blood (approximately 250 isolates/year) E. coli during 2004-2008 were determined. Cephalosporin-resistant isolates were screened for ESBL, using a double-disk assay with clavulanic acid as the inhibitory agent. All ESBL-E. coli isolated in the region during the periods Sept 2003-April 2005 (n=46) and April 2008-March 2009 (n=256) were typed by multiplex-PCR, detecting CTX-M, TEM, OXA and SHV. CTX-M-positive isolates were sub-typed by real time Q-PCR for CTX-M-1, CTX-M-2 and CTXM-9 groups. Results: During 2004-2008, ESBL-producing E. coli strains increased from 0.3-1.5% in urinary and 0-1.4% in blood isolates. Resistance to quinolones and trimethoprim was observed in 60-80% of strains, as compared to less than 8% in non-ESBL-producing E. coli. The majority of the ESBL-E. coli strains possessed the CTX-M gene-type, increasing from 78% (36/46) in 2003-2005 to 93% (238/256) in 2008-2009. Between these time-periods, a marked shift occurred in the distribution of CTX-M types, in that strains with the CTX-M-9 group decreased from 42% (15/36) of isolates to 21% (51/238, p=0.01) and, simultaneously, strains with the CTX-M-1 group increased from 58% (21/36) to 78% (185/238, p= 0.02). Furthermore, strains of CTX-M-type exhibiting also TEM- and/or OXA increased to comprise 86% of cases, as compared to 75% previously. Similar trends were seen for community and hospital detected isolates and with no differences associated with age in affected patients. Conclusion: A steady increase in multidrug-resistant ESBL-E. coli, possessing the genes for multiple ESBL-types, was observed in western Sweden, contrary to the patterns of other multidrug-resistant bacteria. As ESBL has increased during the five-year study period, we detected a shift in the prevalence of ESBL-types, currently dominated by the CTX-M-1 group. These observations suggest that a novel ESBL-producing E. coli clone may have emerged in the area, which will be further investigated and presented.
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| 9. |
- Hinse, D, et al.
(author)
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Differentiation of species of the Streptococcus bovis/equinus-complex by MALDI-TOF Mass Spectrometry in comparison to sodA sequence analyses
- 2011
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In: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 34:1, s. 52-57
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Journal article (peer-reviewed)abstract
- The Streptococcus bovis/equinus complex is a heterogeneous group within the group D streptococci with important clinical relevance regarding infective endocarditis, sepsis and colon carcinoma. The taxonomic identification of species and sub-species of this complex, by the standard methods remains difficult. In the present study, we compared the cluster analysis of 88 strains of species of the S. bovis/equinus complex by sequence analysis of the manganese-dependent superoxide dismutase gene (sodA) and by Matrix Assisted Laser Desorption/Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS). We observed a high congruence of strain grouping by MALDI-TOF MS in comparison with sodA sequence analyses, demonstrating the accuracy and reliability of MALDI-TOF MS in comparison to DNA sequencebased method. By generating mass spectra for each species and sub-species, we were able to discriminate all members of the S. bovis/equinus complex. Furthermore,wedemonstrated reliable identifications to the species level by MALDI-TOF MS, independently of cultivation conditions.
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| 10. |
- Janzon, Anders, 1978, et al.
(author)
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Exploring the microbial resistome in river sediments exposed to extraordinary high levels of antibiotics
- 2010
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In: 35th FEBS Congress: Molecules of Life.
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Conference paper (other academic/artistic)abstract
- The rapid development and propagation of antibiotic resistance in pathogenic and opportunistic bacteria is a major threat to public health worldwide. The phenomenon has been widely studied in the clinical setting, but comparatively little is known about the prevalence and diversity of antibiotic resistance in communities of environmental bacteria, often referred to as the environmental resistome. As the external environment may function as a reservoir of resistance genes to human pathogens, we are interested in how environmental bacteria are affected by antibiotic pollution. We have previously isolated microbial DNA from river sediments taken up- and downstream from a water treatment plant that processes waste water from several pharmaceutical plants producing antibiotics. In a previous study, we used deep sequencing to identify unprecedented frequencies of known resistance genes to several classes of antibiotics in these samples. In this study, we aim to functionally characterize the resistome in a more open and exploratory way by screening genomic DNA libraries transformed into sensitive hosts. To generate the libraries, several experimental strategies were explored, including mechanical shearing and enzymatic digestion of the isolated DNA followed by blunt- or sticky end cloning into different plasmids, subsequently transformed into sensitive E. coli. Pros and cons of the different strategies will be discussed along with preliminary results of the screening against selected antibiotics.
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